Enterobacter

What was studied?

This randomized, double-blind, placebo-controlled trial tested whether daily supplementation with two specific probiotic strains, Bifidobacterium animalis subsp. lactis XLTG11 and Lactiplantibacillus plantarum CCFM8661, could reduce recurrent respiratory tract infections (RRTIs) in children. Over 180 days, the study tracked infection frequency and duration alongside changes in gut microbiota composition, functional metabolic pathways, and immune biomarkers. The design allowed the researchers to link clinical respiratory outcomes to underlying shifts in the gut microbial community and immune regulation.

Who was studied?

The study enrolled 120 children who had been diagnosed with recurrent respiratory tract infections. Participants were randomly assigned to receive either the probiotic combination or a matched placebo daily for 180 days. The abstract does not provide further demographic details such as age range or sex distribution.

What were the most important findings?

Children receiving the probiotics had significantly reduced duration and frequency of fever, cough, upper respiratory tract infections, trachea or bronchitis, pneumonia, and overall RRTI recurrence compared with placebo (all p < 0.05). Gut microbiota profiling at day 180 showed clear community differences between groups, with the probiotic group showing greater abundance of beneficial commensal taxa and the placebo group showing more opportunistic genera. Functional pathway analysis pointed to enhanced metabolic stability in the probiotic recipients, and immune biomarker patterns showed comparatively stable IgG, IgM, and complement C3 levels, suggesting a more regulated humoral immune response. Growth trajectories remained normal in both groups.

What are the greatest implications of this study?

These findings support strain-defined probiotic supplementation as a viable adjunct strategy for reducing the burden of recurrent respiratory infections in children. The parallel shifts in gut microbial composition, metabolic function, and humoral immune stability suggest the respiratory benefit may be mediated through gut-immune axis modulation rather than a direct respiratory-tract effect. Because growth remained normal, the intervention appears well tolerated over a six-month period, supporting its potential for longer-term pediatric preventive use pending further confirmatory trials.

What was studied?

Helminth infections are consistently associated with reduced cardiovascular disease (CVD) risk, yet the biological mechanisms underlying this relationship remain unclear. The gut microbiome and metabolome are key regulators of cardiometabolic health and may mediate infection-associated effects on host physiology. Here we show that Schistosoma mansoni infection associates with distinct gut microbial and metabolic profiles linked to CVD risk in people living in Uganda. In a cross-sectional study of 209 individuals living in communities with contrasting S. mansoni endemicity, we profile the gut microbiome using 16S rRNA gene sequencing and the faecal metabolome using liquid chromatography-mass spectrometry. S. mansoni infection associates with increased gut microbial diversity and distinct taxonomic signatures, including enrichment of taxa such as Treponema and depletion of Prevotella and Streptococcus. Several infection-associated microbial taxa statistically mediate the relationships between S. mansoni infection and cardiovascular disease risk. Faecal metabolomic profiling identifies infection-associated metabolites, and integrative analyses showed linked microbe-metabolite networks associated with cardiovascular risk.These findings identify gut microbiome and metabolome signatures associated with S. mansoni infection and cardiovascular disease risk in Uganda. Although causality cannot be inferred, this work provides insight into host-parasite-microbiome interactions and highlights microbial and metabolic pathways relevant to cardiometabolic health.

What was studied?

Extranodal natural killer/T-cell lymphoma (ENKTL) predominantly manifests in East Asia and Latin America. Despite shared intrinsic factors, such as ethnic and genetic backgrounds, the progression of ENKTL can be influenced by extrinsic factors related to changing lifestyle patterns.

Who was studied?

This study collected stool samples from newly diagnosed (ND)-ENKTL patients (n=40) and conducted whole genome shotgun sequencing.

What were the most important findings?

ND-ENKTL revealed reduced alpha diversity in ND-ENKTL compared to healthy controls (HCs) (p=0.008), with Enterobacteriaceae abundance significantly contributing to the beta diversity difference between ENKTL and HCs (p < 0.001). Functional analysis indicated upregulated aerobic metabolism and degradation of aromatic compounds in ND-ENKTL. Enterobacteriaceae were associated not only with clinical data explaining disease status (serum C-reactive protein, stage, prognosis index of natural killer cell lymphoma [PINK], and PINK-E) but also with clinical outcomes (early relapse and short progression-free survival). The relative abundance of Enterobacteriaceae at the family level was similar between ENKTL and diffuse large B-cell lymphoma (DLBCL) (p=0.140). However, the ENKTL exhibited a higher abundance of Escherichia, in contrast to the prevalence of Enterobacter and Citrobacter in DLBCL. Linear regression analysis demonstrated a significant association between Escherichia abundance and programmed cell death-ligand-1 (PD-L1) levels in tissue samples (p=0.025), whereas no correlation with PD-L1 was observed for Enterobacteriaceae at the family level (p=0.571).

What are the greatest implications of this study?

ND-ENKTL exhibited an abundance of Enterobacteriaceae and a dominant presence of Escherichia. These microbial characteristics correlated with disease status, treatment outcomes, and PD-L1 expression, suggesting the potential of the ENKTL microbiome as a biomarker and cause of lymphomagenesis, which warrants further exploration.

What was studied?

With the improvement of living standards, alcoholic liver disease caused by long-term drinking has been a common multiple disease. Probiotic interventions may help mitigate liver damage caused by alcohol intake, but the mechanisms need more investigation.

Who was studied?

This study involved 70 long-term alcohol drinkers (18-65 years old, alcohol consumption ≥20 g/day, lasting for more than one year) who were randomly assigned to either the BC99 group or the placebo group. Two groups were given BC99 (3 g/day, 1 × 1010 CFU) or placebo (3 g/day) for 60 days, respectively. Before and after the intervention, blood routine indicators, liver function, renal function, inflammatory factors and intestinal flora were evaluated.

What were the most important findings?

The results showed that intervention with Weizmannia coagulans BC99 reduced the levels of alanine aminotransferase, aspartate aminotransferase, glutamyl transpeptidase, serum total bilirubin, blood urea nitrogen, uric acid and 'blood urea nitrogen/creatinine'. Weizmannia coagulans BC99 also reduced the levels of pro-inflammatory factors TNF-α and IL-6 and increased the levels of anti-inflammatory factor IL-10. The results of intestinal flora analysis showed that Weizmannia coagulans BC99 regulated the imbalance of intestinal flora, increased the beneficial bacteria abundance (Prevotella, Faecalibacterium and Roseburia) and reduced the conditionally pathogenic bacteria abundance (Escherichia-Shigella and Klebsiella). Both LEfSe analysis and random forest analysis indicated that the increase in the abundance of Muribaculaceae induced by BC99 was a key factor in alleviating alcohol-induced liver damage.

What are the greatest implications of this study?

These findings demonstrate that Weizmannia coagulans BC99 has the potential to alleviate alcoholic liver injury and provide an effective strategy for liver protection in long-term drinkers.

What was studied?

Acute respiratory infections (ARI) with multiple types of viruses are common in infants and children. This study was conducted to assess the difference of oropharyngeal microbiome during acute respiratory viral infection using whole-genome shotgun metagenomic sequencing. The overall taxonomic alpha diversity did not differ by the types of infected virus. The beta diversity differed by disease severity, disease-related symptoms, and types of infected virus. Nine species had significantly higher abundance in outpatients than in inpatients, with five of them in the genus Achromobacter. Three microbial community types were identified. The prevalence of community type (CT) 1 was higher among patients with influenza virus, enterovirus, and human adenvirus; CT2 was higher among patients with human metapneumovirus; and CT3 was higher among patients with respiratory syncytial virus and human adenvirus infections. Our results suggest that the oropharyngeal microbiome is associated with ARI disease severity, disease-related symptoms, and the types of infected virus.

What was studied?

This study investigated whether alterations in the gut microbiome are associated with allograft rejection in kidney transplant (KT) recipients. Researchers used 16S rRNA gene amplicon sequencing to characterize gut microbiome composition and function over time. They tracked how the microbiome changed from the pre-transplant, chronic kidney disease (CKD) state through recovery, and examined shifts occurring before and after rejection events. Functional analysis focused on the microbiome's capacity to produce short-chain fatty acids, including propionate and butyrate.

Who was studied?

The study analyzed 562 samples collected from 245 individuals as part of a multicenter prospective study. Of these participants, 217 had received a kidney transplant. This design allowed comparison of microbiome trajectories across the CKD-to-post-transplant recovery period and around the time of graft rejection events.

What were the most important findings?

Overall, gut microbiome composition gradually recovered after transplantation, mirroring the CKD-to-health transition, as shown by increasing Shannon diversity. However, prior to graft rejection, microbial diversity decreased along with a reduction in short-chain fatty acid-producing taxa. Functional analysis confirmed a decreased potential for short-chain fatty acid production before rejection, and this was validated using quantitative PCR targeting propionate and butyrate production potential. After rejection, these microbiome features normalized again, and the alterations preceding rejection partially overlapped with microbiome signatures previously reported in CKD patients.

What are the greatest implications of this study?

The findings suggest that gut microbiome changes, particularly loss of diversity and short-chain fatty acid-producing taxa, may precede and potentially help predict graft rejection in kidney transplant recipients. This raises the possibility that monitoring microbiome composition and short-chain fatty acid production capacity could serve as an early warning signal for clinicians. Because these pre-rejection alterations partially resemble CKD-associated microbiome signatures, they may reflect a shared pathway of microbial dysfunction linked to immune dysregulation. This work supports further exploration of the gut microbiome as a noninvasive biomarker source and a potential target for interventions to support graft survival.

What was studied?

Accumulating evidence indicates that antibiotic exposure may lead to impaired vaccine responses1-4; however, the mechanisms underlying this association remain poorly understood. Here we prospectively followed 191 healthy, vaginally born, term infants from birth to 15 months, using a systems vaccinology approach to assess the effects of antibiotic exposure on immune responses to vaccination. Exposure to direct neonatal but not intrapartum antibiotics was associated with significantly lower antibody titres against various polysaccharides in the 13-valent pneumococcal conjugate vaccine and the Haemophilus influenzae type b polyribosylribitol phosphate and diphtheria toxoid antigens in the combined 6-in-1 Infanrix Hexa vaccine at 7 months of age. Blood from infants exposed to neonatal antibiotics had an inflammatory transcriptional profile before vaccination; in addition, faecal metagenomics showed reduced abundance of Bifidobacterium species in these infants at the time of vaccination, which was correlated with reduced vaccine antibody titres 6 months later. In preclinical models, responses to the 13-valent pneumococcal conjugate vaccine were strongly dependent on an intact microbiota but could be restored in germ-free mice by administering a consortium of Bifidobacterium species or a probiotic already widely used in neonatal units. Our data suggest that microbiota-targeted interventions could mitigate the detrimental effects of early-life antibiotics on vaccine immunogenicity.

What was studied?

The colonization and evolution of gut microbiota early in life play a vital role in shaping a healthy, robust immune system for infant health, whether in combating short-term illness or improving long-term health outcomes. Early-life clinical practices may interrupt or disrupt the normal colonization process of the infant gut microbiota, thereby increasing disease susceptibility. In this prospective cohort study, we analyzed the gut microbiota of 46 term and 23 preterm infants using 16S rRNA gene metagenomic sequencing. Fecal samples were collected at six timepoints during the first three months of life. Notably, gestational age was the main factor contributing to differences in the meconium microbial composition. Intriguingly, our study unveiled a more homogeneous microbial composition in preterm infants with more abundant Bifidobacterium from the postnatal age (PNA) of one month. Concurrently, the beneficial bacteria Bifidobacterium and Lactobacillus gradually increased, and the potentially pathogenic bacteria Clostridium, Enterobacter, Enterococcus, Klebsiella, and Pseudomonas gradually decreased. Furthermore, our study underscored a link between decreased microbial diversity of preterm infants and exclusive breastfeeding and antibiotic exposure. Moreover, preterm infants with patent ductus arteriosus (PDA) exhibited reduced microbial diversity but higher abundances of Streptococcus oralis and Streptococcus mitis.

What was studied?

This study investigated the gut microbiota of older adults with sarcopenic obesity (SO) and sarcopenia without obesity (Sar), compared with age-matched controls. Researchers used 16S rRNA gene sequencing targeting the V3-V4 regions to characterize microbial composition and diversity. The goal was to determine whether gut dysbiosis is associated with the development and progression of sarcopenia and sarcopenic obesity, a link previously suspected but not well documented.

Who was studied?

The sample was drawn from a community-based cohort of 1558 older adults (age 65 and older) in Shanghai, China, who underwent sarcopenia screening with the SARC-F questionnaire. Of these, 351 completed further assessment, and 60 participants were ultimately categorized using the Asian Working Group for Sarcopenia 2019 criteria and World Health Organization obesity criteria. The final groups were sarcopenic obesity (n=20), sarcopenia without obesity (n=18), and controls (n=22).

What were the most important findings?

Gut microbiota diversity and composition differed significantly between the sarcopenic obesity, sarcopenia, and control groups. Alpha diversity, measured by the Chao1 and ACE indices, was reduced specifically in the sarcopenic obesity group. Beta diversity, assessed by unweighted UniFrac PCoA, also differed significantly among the three groups, and LEfSe analysis identified 39 taxa with differential abundance across groups.

What are the greatest implications of this study?

The findings support the idea that gut microbiota alterations are distinctly linked to sarcopenic obesity rather than sarcopenia alone, with reduced diversity marking the combined obesity and muscle-loss phenotype. This suggests the gut microbiome could serve as a distinguishing biomarker between these related but distinct conditions in older adults. Identifying these taxa-level differences may help guide future microbiome-targeted approaches for prevention or management of sarcopenic obesity in aging populations.

What was studied?

This case-control study characterized the gut microbiome in older adults with Alzheimer disease (AD) and mild cognitive impairment (MCI), comparing them to cognitively normal controls. Researchers extracted DNA from fecal samples and sequenced PCR products using Nanopore technology. They applied diversity indices, principal coordinate analysis, PERMANOVA, and LEfSe to identify microbial differences among the three groups. The study aimed to determine whether gut microbiome composition and diversity differ across the cognitive spectrum from healthy aging to dementia.

Who was studied?

The study recruited 104 participants aged 60 years and older from urban and rural populations in Uganda. Participants were categorized into AD, MCI, and control groups based on Montreal Cognitive Assessment (MoCA) scores and ICD-11/DSM-V diagnostic criteria. This design allowed comparison of gut microbiome features across a spectrum of cognitive status within an African population, a group underrepresented in prior microbiome-dementia research.

What were the most important findings?

Gut microbiome diversity, measured by the Chao1 and Shannon indices, was significantly reduced in patients with AD compared to the other groups. This reduced diversity aligns with prior findings that AD is associated with altered abundance of specific microbial taxa. The abstract text provided ends before detailing which specific taxa were enriched or depleted in the AD group, so those specifics cannot be reported here.

What are the greatest implications of this study?

The findings support the idea that reduced gut microbial diversity is linked to Alzheimer disease and may reflect disruption of the gut-brain axis, including increased intestinal permeability, systemic inflammation, and oxidative stress. Because this research was conducted in Uganda, it extends microbiome-dementia evidence to an African population, broadening the generalizability of prior findings from other regions. These results reinforce the potential of gut microbiome diversity as a marker of neurodegenerative risk and support further investigation into the microbiome as a target for aging-related cognitive health interventions.

What was studied?

Introduction. Alterations in ocular surface microbiota (OSM) have been noted in both dry eye disease (DED) and glaucoma. However, the combined effects of these conditions on OSM have not been explored.Hypothesis. We hypothesized that patients with both glaucoma and dry eye would exhibit distinct changes in OSM composition and diversity compared to those with only glaucoma, only dry eye or healthy individuals.Aim. We employed amplicon sequencing to investigate OSM profiles in patients with glaucoma and/or dry eye disease.Methods. Swab samples from the conjunctiva of both eyes were collected from 28 glaucomatous patients [13 without dry eye syndrome (G-only) and 15 with dry eye syndrome (G-DED)], 13 DED patients without glaucoma (DED-only) and 31 age-matched healthy controls (HCs). After V3-V4 16S rRNA sequencing, MOTHUR tools and R language were used to elucidate and compare OSM composition and diversity between groups.Results. Our data revealed very diverse bacterial communities with 28 phyla and 785 genera. All the groups shared the three most abundant phyla, Actinobacteria (67.47%), Firmicutes (17.14%) and Proteobacteria (13.73%). Corynebacterium (54.75%), Staphylococcus (10.71%), Cutibacterium (8.77%) and Streptococcus (3.20%) were the most abundant genera. Only the G-DED group showed higher alpha diversity than the HC group (P<0.05). However, significant differences in beta diversity were observed between all three patient groups and the HC group. The Differential Expression for Sequencing 2 (DESeq2) analysis unveiled an increased presence of opportunistic bacteria across all pathological groups, with the G-DED group demonstrating the most pronounced alterations.Conclusions. Our findings confirm the predominance of Gram-positive bacteria in normal OSM and the rise of opportunistic Gram-negative bacteria in glaucoma and dry eye disease. This is the first study to characterize OSM in glaucoma patients with DED.

What was studied?

Recent studies have revealed associations between gut microbiota and glioma. However, the underlying mechanisms remain poorly understood. This study primarily aims to elucidate the impact of altered gut microbiota on tumor progression in glioma-bearing mice.

Who was studied?

Fecal samples were collected from glioma patients and healthy controls to compare the effects of human-derived gut microbiota on glioma development in mice. We also analyzed the associations between these microbiota profiles and plasma metabolites.

What were the most important findings?

Significant differences were observed in both the composition and diversity of the gut microbiota between glioma patients and healthy controls. Mice transplanted with gut microbiota from high-grade glioma patients (HGG-FMT) exhibited accelerated glioma progression compared to those transplanted with microbiota from healthy individuals (HC-FMT). Specifically, Eisenbergiella, Mailhella, and Merdimonas were significantly enriched in HGG-FMT mice, while Limosilactobacillus and Anaerospora increased in HC-FMT mice. Furthermore, Merdimonas showed a positive correlation with sphingosine, sphingosine 1-phosphate, and D-sphingosine in HGG-FMT mice. Conversely, Limosilactobacillus was positively correlated with stearidonic acid and eicosapentaenoic acid in HC-FMT mice.

What are the greatest implications of this study?

Our findings demonstrate that gut microbiota from high-grade glioma patients can promote glioma progression in mice, potentially through mechanisms involving sphingosine 1-phosphate. This metabolite may enter the bloodstream and accelerate glioma growth, offering novel insights into glioma pathogenesis and potential treatment options.

What was studied?

Preterm infants (<37 weeks' gestation) are commonly given broad-spectrum antibiotics due to their risk of severe conditions like necrotising enterocolitis and sepsis. However, antibiotics can disrupt early-life gut microbiota development, potentially impairing gut immunity and colonisation resistance. Probiotics (e.g., certain Bifidobacterium strains) may help restore a healthy gut microbiota. In this study, we investigated the effects of probiotics and antibiotics on the gut microbiome and resistome in two unique cohorts of 34 very-low-birth-weight, human-milk-fed preterm infants - one of which received probiotics. Within each group, some infants received antibiotics (benzylpenicillin and/or gentamicin), while others did not. Using shotgun metagenomic sequencing on 92 longitudinal faecal samples, we reconstructed >300 metagenome-assembled genomes and obtained ~90 isolate genomes via targeted culturomics, allowing strain-level analysis. We also assessed ex vivo horizontal gene transfer (HGT) capacity of multidrug-resistant (MDR) Enterococcus using neonatal gut models. Here we show that probiotic supplementation significantly reduced antibiotic resistance gene prevalence, MDR pathogen load, and restored typical early-life microbiota profile. However, persistent MDR pathogens like Enterococcus, with high HGT potential, underscore the need for continued surveillance. Our findings underscore the complex interplay between antibiotics, probiotics, and HGT in shaping the neonatal microbiome and support further research into probiotics for antimicrobial stewardship in preterm populations.

What was studied?

This study examined cocoa (Theobroma cacao L.) bean fermentation, the spontaneous process that shapes the final flavour of chocolate. The researchers investigated how abiotic factors (pH and temperature) and biotic factors (bacterial and fungal microbiota) interact to produce key flavour attributes in premium chocolate. They used genome-resolved metagenomics to identify the metabolic traits within the fermentation microbial community responsible for flavour development. They then tested whether a defined microbial consortium could reproduce those fine flavour attributes under controlled conditions.

Who was studied?

The study drew on cocoa bean fermentation samples collected from farms in Colombia. From these samples, the researchers characterized the natural bacterial and fungal community and used genome-resolved metagenomics to build a picture of the metabolic capacities present. They then assembled a separate, defined and metabolically competent microbial consortium, rather than studying a human or animal cohort, to test controlled fermentation. A trained tasting panel was also used to evaluate the resulting chocolate.

What were the most important findings?

The pH, temperature, and combined bacterial and fungal microbiota composition of the fermentation samples all influenced key flavour attributes of the resulting premium chocolate. Genome-resolved metagenomics showed that the metabolic traits needed for flavour development were redundantly encoded across multiple members of the fermentation community, not confined to a single organism. Using a defined microbial consortium built from this information, the researchers replicated fine flavour attributes of chocolate under controlled conditions. This was confirmed through omics analyses, metabolic network modeling, and evaluation by a trained tasting panel.

What are the greatest implications of this study?

These findings show that the flavour-relevant functions of spontaneous cocoa fermentation can be captured in a defined, reproducible microbial consortium rather than relying on uncontrolled natural fermentation. This provides a basis for designing standardized fermentation starters that can reliably reproduce fine chocolate flavour characteristics. Such starters could help cocoa producers achieve consistent premium quality across batches and locations. The approach also demonstrates a model for linking metagenomic and metabolic data to sensory outcomes in food fermentation more broadly.

What was studied?

This study examined seasonal changes in gut microbiota composition and function across four bear species: giant pandas, Asian black bears, brown bears, and polar bears. Researchers combined comparative seasonal microbiome analysis with fecal microbiota transplantation (FMT) experiments in mice to test whether bear gut microbiota actively drives host energy metabolism. The core question was whether giant pandas, long considered metabolically unique due to their specialized herbivorous diet and low metabolic rate, actually rely on a distinct microbial regulatory mechanism compared to other bears.

Who was studied?

The subjects were four Ursidae species: giant pandas (Ailuropoda melanoleuca), Asian black bears (Ursus thibetanus), brown bears (Ursus arctos), and polar bears (Ursus maritimus), sampled across seasons to capture gut microbiota dynamics. The abstract does not specify exact animal counts or sampling sites. Recipient mice were also used as a secondary population in the fecal microbiota transplantation experiments to test the functional effects of bear gut microbiota on host metabolism and appetite.

What were the most important findings?

The gut microbial composition was similar across all four bear species, with Firmicutes and Proteobacteria as the dominant phyla. Firmicutes became enriched in winter, which enhanced lipid metabolism and helped the bears adapt to seasonal dietary differences, pointing to a convergent microbial functional strategy shared across the Ursidae family rather than a panda-specific mechanism. In FMT experiments, winter bear gut microbiota transferred stronger capacity to regulate host energy metabolism and appetite in mice, increasing energy intake, demonstrating that these microbial shifts causally promote seasonal metabolic adaptation.

What are the greatest implications of this study?

By showing convergent, shared microbial functional strategies across giant pandas, black bears, brown bears, and polar bears, the findings challenge the long-standing view that giant panda gut microbiota is metabolically unique among bears. This reframes seasonal energy adaptation in Ursidae as a family-wide, diet-responsive microbiome trait rather than an evolutionary novelty confined to pandas. The FMT results also suggest that bear-derived winter microbiota could serve as a model system for studying microbiome-driven regulation of energy intake and appetite in mammals more broadly.

What was studied?

This study examined whether rifaximin, a gut-specific non-absorbable antibiotic, could reduce gut-derived systemic inflammation in severe acute pancreatitis (SAP). The researchers combined murine experimental models with a single-center, open-label randomized controlled trial (ChiCTR2100049794). They assessed pancreatic injury, systemic inflammatory markers, and gut microbiota composition, and tested whether rifaximin's effects depended on modulating the microbiota by using antibiotic-treated and germ-free mice.

Who was studied?

The animal component used murine models of severe acute pancreatitis, including antibiotic-treated and germ-free mice used to probe the mechanism. The clinical component enrolled 60 patients with predicted severe acute pancreatitis, randomized to receive rifaximin or standard control treatment. No further demographic details are given in the abstract.

What were the most important findings?

In mice, rifaximin reduced pancreatic injury and systemic inflammation and decreased mucin-degrading gut genera such as Akkermansia, but its protective effects persisted even in antibiotic-treated and germ-free mice, indicating mechanisms beyond microbiota modulation. In patients, rifaximin significantly lowered systemic inflammation, with white blood cell count falling from a median of 11.50 x10^9/L to 8.49 x10^9/L and TNF-alpha falling from 15.05 pg/mL to 11.00 pg/mL. However, the rate of culture-confirmed infection was identical between rifaximin and control groups (13.3% vs 13.3%), and adverse events were comparable between groups.

What are the greatest implications of this study?

The findings suggest rifaximin can dampen systemic inflammation in severe acute pancreatitis through mechanisms that are not solely dependent on reshaping the gut microbiota, pointing to a possible direct anti-inflammatory or barrier-protective effect. Because inflammation markers improved without any change in infection risk, rifaximin may offer a safe adjunct for controlling inflammatory injury in SAP without added infectious risk. This supports further investigation of rifaximin as a therapeutic strategy for gut-derived inflammation in acute pancreatitis, alongside continued study of its non-microbiota-dependent mechanisms.

What was studied?

The maternal microbiome during pregnancy and the peripartum period plays a critical role in maternal health outcomes and establishing the neonatal gut microbiome, with long-term implications for offspring health. However, a healthy microbiome during these key periods has not been definitively characterized. This longitudinal study examines maternal and neonatal microbiomes using 16S rRNA amplicon sequencing in a Japanese cohort throughout pregnancy and the postpartum period. Forty-two mothers and their forty-five offspring participate in the study. The maternal vaginal microbiome remains relatively stable during pregnancy but significantly changes in the postpartum period. Among Lactobacillus species, the Lactobacillus crispatus group is predominant. A higher abundance of Lactobacillus early in pregnancy is associated with a favorable gestational period. The maternal gut microbiome is associated with the vaginal microbiome throughout pregnancy. The neonatal gut microbiome substantially changes in early life, with bacterial composition influenced by delivery mode. Over time, bacteria shared with the maternal gut microbiome become dominant in the neonatal gut. This study provides insights into microbiome dynamics in Japanese mothers and their offspring during pregnancy and the postpartum period. Identification of common patterns across diverse populations may help define keystone microbes essential for human health and inform the development of microbiome-based interventions.

What was studied?

UNLABELLED: Kimjang kimchi is traditionally made in Korea in autumn to preserve vegetables during colder winter times after the harvest. Kimjang is an important societal tradition in which families and communities come together to process vegetables, such as cabbage, into kimchi. The origin of the microorganisms that contribute to the flavor and safety during fermentation is still unclear. Although bacteria present on the raw ingredients are considered to be important colonizers of the fermentation, in Korean culture, the term "Sonmat" is often used, which literally translates into "hand flavor," suggesting a role for hand microbiota in the kimchi fermentation. In this citizen-science project, we investigate the impact of the hand microbiome on kimchi fermentation during the Sonmat festival organized in Belgium. The kimchi fermentations contained mainly lactic acid bacteria belonging to the genera Leuconostoc, Weissella, and Latilactobacillus. The hand microbiota was characterized by the presence of Staphylococcus, Corynebacterium, Micrococcus, and Enhydrobacter. Associations were found between the relative abundance of Staphylococcus on the hand and the relative abundance of Latilactobacillus and Leuconostoc found in kimchi, despite limited overlap between the hand and the kimchi microbiome. In addition, different microbiota were found to dominate the kimchi made following the traditional group Kimjang practices compared with individually prepared kimchi. These findings pave the way for future research into how traditional practices and the skin microbiome influence the unique qualities of kimchi, offering exciting possibilities for enhancing fermentation processes and cultural food heritage through citizen science. IMPORTANCE: Vegetable fermentation has been a staple of human culture for centuries, with deeply rooted traditions behind it. However, the effects of these traditional practices on the microbes in the final fermented product, and their origin, are often not understood. By using participatory citizen-science approaches, it is possible to study these important foods while preserving the authenticity and integrity of the traditional fermentation practices that define them. The results obtained from our citizen-science case study support the importance of exploring traditional fermentation practices and their effect on microbial and sensory properties of fermented foods. Additionally, our case study found associations between microbiota present on the hand and microbiota important in the early successional stage of kimchi fermentation.

What was studied?

This study examined the early development of the human gut microbiome by comparing infants to their mothers and grandmothers within the same family lines. Researchers used a multi-omics approach combining metagenomics (16S rRNA gene and shotgun sequencing) with two independent metabolomics platforms, gas chromatography and capillary electrophoresis coupled to mass spectrometry. The goal was to characterize differences in microbial populations, function, and metabolite output across three generations.

Who was studied?

Fecal samples were collected from 200 individuals spanning three generations of the same families. This included infants aged 0 to 12 months (55% female, 45% male) along with their respective mothers and grandmothers. The design allowed direct comparison of gut microbiota and metabolome across a shared generational line.

What were the most important findings?

Infants showed markedly less diverse gut microbiota than their mothers and grandmothers, along with distinct microbial population and functional profiles. The infant metabolome also differed substantially from the adults, particularly in short- and branched-chain fatty acids. These metabolite shifts were linked to corresponding differences in bacterial populations between infants and elders.

What are the greatest implications of this study?

The findings offer biochemical insight into how the gut microbiome is shaped during infancy within a single family lineage. Because dysregulation of the gut microbiome at this early stage may contribute to disease later in life, understanding these generational differences could inform strategies to support healthy microbiome development in infants. The authors suggest this multi-omics approach could ultimately help improve childhood health outcomes.

What was studied?

This pilot prospective cohort study examined whether ethnicity influences gut microbiome dysbiosis in pregnancies complicated by gestational diabetes mellitus (GDM). The researchers also investigated whether diet and lifestyle modifications made after a GDM diagnosis could modulate the gut microbiome. Fecal samples were collected at two time points, 24 to 28 weeks and 36 to 40 weeks of gestation, and analyzed using targeted 16S rRNA gene-based amplicon sequencing. Statistical comparisons between groups used PERMANOVA, differential abundance testing used DeSeq2, and functional predictions were generated with PICRUSt2.

Who was studied?

The cohort included 53 women with GDM and 16 women without GDM, all residing in Singapore. Participants belonged to three Asian ethnic groups: Chinese, Malay, and Indian. This design allowed comparison of gut dysbiosis patterns both across GDM status and across ethnic background within the same population.

What were the most important findings?

Among women with GDM, gut microbiomes from the different ethnic groups shared common features rather than diverging by ethnicity. This suggests that GDM-related dysbiosis is a relatively consistent phenomenon across the Chinese, Malay, and Indian groups studied. The abstract indicates that ethnicity was not a major driver of the microbiome differences observed in these GDM pregnancies.

What are the greatest implications of this study?

If GDM-associated gut dysbiosis is largely independent of Asian ethnic background, microbiome-targeted strategies for GDM may generalize across these ethnic groups rather than needing ethnicity-specific approaches. This supports the idea that dietary and lifestyle interventions after a GDM diagnosis could be evaluated and applied similarly across diverse populations. As a pilot study, these findings point to the need for larger cohorts to confirm whether microbiome-based interventions can be standardized across ethnicities.

What was studied?

This study examined whether the traditional Chinese medicine formula Shenling Baizhu San (SLBZS) could prevent or treat non-alcoholic fatty liver disease (NAFLD) at the preclinical level. Researchers induced NAFLD using a western diet combined with CCl4 injection, then treated mice with SLBZS for six weeks. They measured body weight, energy intake, liver enzymes, pro-inflammatory factors, and hepatic steatosis. They also tracked gut microbiota and metabolite changes using 16S rRNA gene sequencing and untargeted metabolomics, alongside serotonin-pathway markers TPH1, 5-HT, HTR2A, and HTR2B.

Who was studied?

The study used male C57BL/6J mice, a standard inbred laboratory mouse strain, divided into three groups. One group received a normal diet, a second received a western diet plus CCl4 injection to induce NAFLD, and a third received the same NAFLD-inducing regimen plus SLBZS intervention. No human subjects were studied; this was an animal model investigation.

What were the most important findings?

SLBZS intervention for six weeks reduced serum and liver lipid levels, blood glucose, and pro-inflammatory factors, while improving insulin resistance and liver function indexes, effectively alleviating NAFLD in the mice. The treatment also produced significant changes in intestinal TPH-1, 5-HT, liver 5-HT, and the related receptors HTR2A and HTR2B. Gut microbiota analysis via 16S rRNA sequencing showed SLBZS altered the composition of the gut microbiota, linking these microbial shifts to the observed metabolic and serotonergic changes.

What are the greatest implications of this study?

The findings suggest SLBZS may offer a multi-target approach to NAFLD prevention and treatment by simultaneously improving liver function, metabolic markers, gut microbiota composition, and gut-liver serotonin signaling. This supports further investigation of traditional Chinese medicine formulas as adjunct or alternative therapies for NAFLD. Because this work was conducted in mice, human clinical studies are needed before drawing conclusions about efficacy in people.

What was studied?

Polycystic ovary syndrome (PCOS) is an endocrinopathy in childbearing-age females which can cause many complications, such as diabetes, obesity, and dyslipidemia. The metabolic disorders in patients with PCOS were linked to gut microbial dysbiosis. However, the correlation between the gut microbial community and dyslipidemia in PCOS remains unillustrated. Our study elucidated the different gut microbiota in patients with PCOS and dyslipidemia (PCOS.D) compared to those with only PCOS and healthy women.

What were the most important findings?

In total, 18 patients with PCOS, 16 healthy females, and 18 patients with PCOS.D were enrolled. The 16 S rRNA sequencing in V3-V4 region was utilized for identifying the gut microbiota, which analyzes species annotation, community diversity, and community functions. Our results showed that the β diversity of gut microbiota did not differ significantly among the three groups. Regarding gut microbiota dysbiosis, patients with PCOS showed a decreased abundance of Proteobacteria, and patients with PCOS.D showed an increased abundance of Bacteroidota compared to other groups. With respect to the gut microbial imbalance at genus level, the PCOS.D group showed a higher abundance of Clostridium_sensu_stricto_1 compared to other two groups. Furthermore, the abundances of Faecalibacterium and Holdemanella were lower in the PCOS.D than those in the PCOS group. Several genera, including Faecalibacterium and Holdemanella, were negatively correlated with the lipid profiles. Pseudomonas was negatively correlated with luteinizing hormone levels. Using PICRUSt analysis, the gut microbiota community functions suggested that certain metabolic pathways (e.g., amino acids, glycolysis, and lipid) were altered in PCOS.D patients as compared to those in PCOS patients.

What are the greatest implications of this study?

The gut microbiota characterizations in patients with PCOS.D differ from those in patients with PCOS and controls, and those might also be related to clinical parameters. This may have the potential to become an alternative therapy to regulate the clinical lipid levels of patients with PCOS in the future.

What was studied?

This study used shotgun metagenomics to compare the microbial composition and function of normal rectal mucosa against matched fecal samples. The researchers analyzed both microbial taxonomic classification and KEGG Orthology (KO) functional annotations for each sample type. They then examined how the mucosal microbiota related to host factors including age, gender, BMI, and colonic polyp risk level.

Who was studied?

The study included 20 patients with colonic polyps, each contributing a paired sample of normal rectal mucosa and feces. This matched within-person design let the researchers directly compare the two sample types from the same individuals. No further demographic breakdown is given in the abstract beyond age, gender, and BMI being used as variables of interest.

What were the most important findings?

The mucosal and fecal microbiomes were clearly distinct from one another, with the mucosal microbiome containing fewer genera overall. Burkholderia was identified as the single most discriminating genus separating feces from mucosa, indicating a notably strong mucosal presence. The team also identified novel taxonomic biomarkers linked to host factors, such as Clostridium ramosum and Enterobacter cloacae in association with age. Functionally, the mucosal microbiota was enriched for KO pathways involved in sugar transport and short-chain fatty acid metabolism.

What are the greatest implications of this study?

The findings show that fecal samples alone do not capture the distinct microbial community living at the rectal mucosal surface, a gap most gut microbiome research has overlooked. Because the mucosal niche appears compositionally and functionally distinct, with its own host-associated biomarkers and short-chain fatty acid-related activity, mucosal sampling may add diagnostic or mechanistic information that feces cannot provide. This supports incorporating mucosal microbiome analysis alongside fecal analysis in future studies of colonic polyps and related conditions.

What was studied?

This study examined the composition and function of the gut microbiota in people with schizophrenia. Researchers used both 16S rRNA gene sequencing and whole-genome shotgun metagenomic sequencing to characterize microbial diversity, taxonomic composition, and functional gene content. The aim was to explore how gut microbes, acting through the gut-brain axis, might relate to this severe and complex psychiatric disorder.

Who was studied?

The study included 29 patients diagnosed with schizophrenia and 30 age-matched normal controls. This is a relatively small clinical cohort, and the abstract does not specify additional demographic details such as sex distribution, geographic location, or illness duration. Both 16S rRNA and metagenomic sequencing were performed on samples from these same participants.

What were the most important findings?

Patients with schizophrenia had higher abundances of the bacterial genera Clostridium and Megasphaera compared to controls. Functional analysis linked schizophrenia to alterations in sphingolipid metabolism, phosphonate and phosphinate metabolism, and glutamine metabolism. These findings were consistent across both the 16S rRNA and metagenomic sequencing approaches. The abstract does not mention Desulfovibrio, sulfate-reducing bacteria, hydrogen sulfide, or sulfur metabolism.

What are the greatest implications of this study?

The findings support the idea that the gut microbiota has a measurable effect on schizophrenia, reinforcing the relevance of the gut-brain axis to this disorder. Specific taxa such as Clostridium and Megasphaera, along with the identified metabolic pathways, may serve as leads for future mechanistic or biomarker research. These results provide a foundation for further investigation into microbiome-based understanding or management of schizophrenia.

What was studied?

This study examined whether dietary inulin, a prebiotic fiber, could improve intestinal flora composition and metabolism-related indicators in obese patients with polycystic ovary syndrome (PCOS). PCOS is a common endocrine disorder in women of reproductive age that is closely tied to chronic low-grade inflammation and metabolic disturbance. Because inulin had already shown benefits for gut flora and inflammation in PCOS mouse models, the researchers set out to test whether the same effects would hold in a clinical human population. Patients were followed over three months of inulin treatment, with intestinal flora and metabolic markers measured before and after.

Who was studied?

The study population consisted of obese women with polycystic ovary syndrome compared against healthy controls. The abstract does not give an exact number of participants, so the precise sample size cannot be stated. What can be said honestly is that this was a clinical (human) comparison of PCOS patients versus controls, rather than an animal model, following three months of inulin intervention in the PCOS group.

What were the most important findings?

Dietary inulin improved sex hormone disorders and reduced both BMI and waist-hip ratio (WHR) in obese women with PCOS. The intervention also lowered plasma inflammatory markers, including TNF-alpha, IL-1beta, IL-6, and MCP-1. Gut flora shifted favorably: Actinobacteria, Fusobacteria, Lachnospira, and Bifidobacterium increased, while the Firmicutes/Bacteroidetes ratio and the abundance of Proteobacteria, Sutterella, and Enterobacter decreased. Correlation analyses linked these microbial shifts to changes in plasma inflammatory factors and sex steroid hormones, suggesting the three systems move together.

What are the greatest implications of this study?

The findings suggest that a simple dietary prebiotic, inulin, may offer a low-risk way to address the combined metabolic, hormonal, and inflammatory disturbances seen in obese PCOS patients. Because gut flora changes correlated with both inflammatory and hormonal shifts, the intestinal microbiome may be a mechanistic link connecting diet to PCOS symptoms rather than an incidental bystander. This supports further clinical investigation of inulin or similar fibers as an adjunct therapy for obese women with PCOS, particularly for managing BMI, WHR, and systemic inflammation.

What was studied?

Systemic inflammatory response syndrome (SIRS) is a severe inflammatory response that can lead to organ dysfunction and death. Modulating the gut microbiome is a promising therapeutic approach for managing SIRS. This study assesses the therapeutic potential of the Xuanfei Baidu (XFBD) formula in treating SIRS. The results showed that XFBD administration effectively reduced mortality rates and inflammation in SIRS mice. Using 16S rRNA sequencing and fecal microbiota transplantation (FMT), we substantiated that the therapeutic effects of XFBD are partly attributed to gut microbiota modulation. We conducted in vitro experiments to accurately assess the gut microbiome remodeling effects of 51 compounds isolated from XFBD. These compounds exhibited varying abilities to induce a microbial structure that closely resembles that of the healthy control group. By quantifying their impact on microbial structure and clustering their regulatory patterns, we devised multiple gut microbiome remodeling compound (GMRC) cocktails. GMRC cocktail C, comprising aucubin, gentiopicroside, syringic acid, gallic acid, p-hydroxybenzaldehyde, para-hydroxybenzoic acid, and isoimperatorin, demonstrated superior efficacy in treating SIRS compared to a single compound or to other cocktails. Finally, in vitro experiments showcased that GMRC cocktail C effectively rebalanced bacteria composition in SIRS patients. This study underscores XFBD's therapeutic potential in SIRS and highlights the importance of innovative treatment approaches for this disease by targeting the gut microbiota.IMPORTANCEDeveloping effective treatment strategies for systemic inflammatory response syndrome (SIRS) is crucial due to its severe and often life-threatening nature. While traditional treatments like dexamethasone have shown efficacy, they also come with significant side effects and limitations. This study makes significant strides by demonstrating that the Xuanfei Baidu (XFBD) formula can substantially reduce mortality rates and inflammation in SIRS mice through effective modulation of the gut microbiota. By quantitatively assessing the impact of 51 compounds derived from XFBD on the gut microbiome, we developed a potent gut microbiome remodeling compound cocktail. This cocktail outperformed individual compounds and other mixtures in efficacy against SIRS. These findings highlight the potential of XFBD as a therapeutic solution for SIRS and underscore the critical role of innovative strategies targeting the gut microbiota in addressing this severe inflammatory condition.

What was studied?

The gut microbiota of infants in low- to middle-income countries is underrepresented in microbiome research. This study explored the faecal microbiota composition and faecal cytokine profiles in a cohort of infants in a rural province of Cambodia and investigated the impact of sample storage conditions and infant environment on microbiota composition. Faecal samples collected at three time points from 32 infants were analysed for microbiota composition using 16S rRNA amplicon sequencing and concentrations of faecal cytokines. Faecal bacterial isolates were subjected to whole genome sequencing and genomic analysis. We compared the effects of two sample collection methods due to the challenges of faecal sample collection in a rural location. Storage of faecal samples in a DNA preservation solution preserved Bacteroides abundance. Microbiota analysis of preserved samples showed that Bifidobacterium was the most abundant genus with Bifidobacterium longum the most abundant species, with higher abundance in breast-fed infants. Most infants had detectable pathogenic taxa, with Shigella and Klebsiella more abundant in infants with recent diarrhoeal illness. Neither antibiotics nor infant growth were associated with gut microbiota composition. Genomic analysis of isolates showed gene clusters encoding the ability to digest human milk oligosaccharides in B. longum and B. breve isolates. Antibiotic-resistant genes were present in both potentially pathogenic species and in Bifidobacterium. Faecal concentrations of Interlukin-1alpha and vascular endothelial growth factor were higher in breast-fed infants. This study provides insights into an underrepresented population of rural Cambodian infants, showing pathogen exposure and breastfeeding impact gut microbiota composition and faecal immune profiles.

What was studied?

This study examined how the gut microbiome and serum metabolome differ between people with lactose intolerance (LI) and those without it. The researchers combined a paired-sample analysis of American Gut Project (AGP) data with metagenomic and untargeted metabolomic analyses in a separate cohort. They also performed fecal microbiota transplantation (FMT) experiments to test whether the LI-associated gut microbiome could influence inflammatory outcomes. The goal was to characterize the interaction between gut microbiota and circulating metabolites in LI.

Who was studied?

The study drew on two data sources: paired samples from the American Gut Project (AGP), a large public microbiome dataset, and a Chinese cohort in which metagenomic and metabolomic profiling was performed. The abstract does not give exact sample sizes for either group. FMT experiments were also conducted, implying an animal model component, though further details are not specified in the abstract.

What were the most important findings?

Fourteen microbial genera differed significantly between LI and control individuals in the AGP data. In the Chinese cohort, a machine learning approach identified seven bacterial species and nine metabolites that could distinguish the two groups. Notably, increased Escherichia coli in the LI group was negatively correlated with several metabolites, including PC (22:6/0:0), indole, and Lyso PC, while reduced levels of Faecalibacterium prausnitzii and Eubacterium rectale were positively associated with other metabolic changes.

What are the greatest implications of this study?

The findings suggest that lactose intolerance is accompanied by a distinct gut microbial and metabolic signature, not just a lactase enzyme deficiency. The rise in Escherichia coli alongside depletion of beneficial short-chain-fatty-acid producers like Faecalibacterium prausnitzii and Eubacterium rectale points to a shift toward a more pro-inflammatory microbial community. This raises the possibility that microbiome-targeted interventions could help manage LI-related gastrointestinal symptoms, and the FMT experiments support a causal link between this altered microbiome and inflammatory outcomes.

What was studied?

This study characterized gastrointestinal microbial communities involved in gastric carcinogenesis by pooling 16S rRNA sequencing data across 11 independent published and open datasets. The researchers compared both intratumoral (gastric biopsy) and fecal microbiota between gastric cancer patients and non-cancer individuals. They used tools including VSEARCH, QIIME, and R packages such as vegan, phyloseq, cooccur, and random forest for diversity analysis, network analysis, and biomarker identification, with PICRUSt used to predict functional pathways.

Who was studied?

The analysis drew on 1,642 gastric biopsy samples and 394 stool samples aggregated across 11 independent studies. The abstract does not give demographic details such as age, sex, or geographic origin of the underlying cohorts. This was a meta-analysis of existing sequencing data rather than a newly recruited single-site cohort.

What were the most important findings?

Alpha-diversity of the intratumoral microbiota differed significantly between gastric cancer patients and non-cancer patients, while fecal microbiota diversity showed no significant difference between groups. Network analysis revealed that positive correlations among gastric cancer-enriched bacteria increased, while positive correlations among gastric cancer-depleted bacteria decreased, compared to healthy individuals. Functional prediction analyses pointed to alterations in pathways related to carbohydrate metabolism, though the abstract text describing these functional results was truncated.

What are the greatest implications of this study?

The findings suggest that local, tumor-site microbial signatures may be more informative for gastric cancer detection than stool-based sampling, since diversity differences were seen intratumorally but not fecally. The shifting co-occurrence network structure around cancer-enriched and cancer-depleted bacteria points to microbial community reorganization as a feature of gastric carcinogenesis. By pooling data across 11 studies, this work moves toward identifying more reproducible microbial markers for early gastric cancer detection across populations.

What was studied?

This study examined whether iron overload in thalassemia patients is linked to gut dysbiosis and cognitive impairment through the gut-brain axis. Researchers assessed iron burden, cognitive function, and both gut and blood microbiome composition across different blood-transfusion regimens. The goal was to determine whether specific microbial shifts track with iron accumulation and cognitive status in this population.

Who was studied?

Sixty participants were recruited, comprising healthy controls, transfusion-dependent thalassemia (TDT) patients, and non-transfusion-dependent thalassemia (NTDT) patients. TDT patients receive more frequent blood transfusions and, consistent with this, showed greater iron overload than NTDT patients. This design allowed comparisons of gut and blood microbiota across a spectrum of iron-overload severity within the same disease population.

What were the most important findings?

Most thalassemia patients developed gut dysbiosis, and about 25% developed minor cognitive impairment. Both TDT and NTDT groups showed increased Fusobacteriota and Verrucomicrobiota with decreased Fibrobacterota, and TDT patients had more abundant Verrucomicrobia, described as beneficial bacteria. Iron overload correlated with cognitive impairment, and increased Butyricimonas with decreased Paraclostridium was associated with higher cognitive function. No blood microbiota was detected, and blood bacterial profiles did not differ significantly between thalassemia patients and controls.

What are the greatest implications of this study?

The findings suggest that iron overload in thalassemia is associated with gut microbial imbalance that may relate to cognitive outcomes through the gut-brain axis. Specific gut taxa such as Butyricimonas and Paraclostridium emerge as candidate markers linked to cognitive function, while the blood compartment appears not to harbor a distinct microbiome signal in this context. This points to the gut, rather than blood, as the more relevant site for future investigation of microbiome-cognition relationships in iron-overloaded thalassemia patients.

What was studied?

This study tested whether a healthy low-carbohydrate diet (HLCD) and time-restricted eating (TRE), alone or combined, affect body weight and the gut microbiome beyond what caloric restriction alone produces. It used a 12-week two-by-two factorial randomized controlled feeding trial with a 28-week follow-up period. The design let researchers isolate the added effects of carbohydrate restriction and eating-window timing on top of isocaloric-restricted feeding.

Who was studied?

The trial enrolled 96 participants with overweight or obesity. Participants were assigned across the two-by-two factorial design to receive isocaloric-restricted feeding with or without HLCD and with or without TRE. The abstract does not give further demographic detail such as age or sex distribution.

What were the most important findings?

Isocaloric-restricted feeding produced significant weight loss ranging from 2.57 to 4.11 kg across groups, and both HLCD and TRE produced additional reductions in body mass index beyond caloric restriction alone. HLCD led to additional fat mass loss, while TRE led to more lean mass loss, showing the two strategies affect body composition differently. HLCD also decreased fecal branched-chain amino acids, and TRE tended to increase the abundance of probiotic species that synthesize short-chain fatty acids. The fat-mass-reducing effect of HLCD persisted through the post-intervention follow-up period.

What are the greatest implications of this study?

The findings suggest that dietary carbohydrate composition and meal timing each add measurable value to weight management beyond simple calorie counting. HLCD and TRE produce distinct effects on body composition (fat versus lean mass) and distinct, profound alterations to the gut microbiome and metabolome. The persistence of HLCD's fat-loss effect after the intervention ended points to potential durability of low-carbohydrate approaches. These results support tailoring weight-management strategies to specific metabolic and microbiome-related goals rather than treating all caloric-restriction approaches as equivalent.

What was studied?

Vitiligo is an autoimmune disease characterized by loss of pigmentation in the skin. It affects 0.4 to 2% of the global population, but the factors that trigger autoimmunity remain elusive. Previous work on several immune-mediated dermatological disorders has illuminated the substantial roles of the gut microbiome in disease pathogenesis. Here, we examined the gut microbiome composition in a cohort of vitiligo patients and healthy controls from India, including patients with a family history of the disease.

What were the most important findings?

Our results show significant alterations in the gut microbiome of vitiligo patients compared to healthy controls, affecting taxonomic and functional profiles as well as community structure. We observed a reduction in the abundance of several bacterial taxa commonly associated with a healthy gut microbiome and noted a decrease in the abundance of SCFA (Short Chain Fatty Acids) producing taxa in the vitiligo group. Observation of a higher abundance of genes linked to bacteria-mediated degradation of intestinal mucus suggested a potential compromise of the gut mucus barrier in vitiligo. Functional analysis also revealed a higher abundance of fatty acid and lipid metabolism-related genes in the vitiligo group. Combined analysis with data from a French cohort of vitiligo also led to the identification of common genera differentiating healthy and gut microbiome across populations.

What are the greatest implications of this study?

Our observations, together with available data, strengthen the role of gut microbiome dysbiosis in symptom exacerbation and possibly pathogenesis in vitiligo. The reported microbiome changes also showed similarities with other autoimmune disorders, suggesting common gut microbiome-mediated mechanisms in autoimmune diseases. Further investigation can lead to the exploration of dietary interventions and probiotics for the management of these conditions.

What was studied?

Constipation is a common symptom in maintenance hemodialysis patients and greatly affects the quality of survival of hemodialysis patients. Fecal microbiota transplantation and probiotics are feasible treatments for functional constipation, but there is still a gap in the research on the characteristics of gut flora in patients with maintenance hemodialysis combined with constipation. The aim of this study is to clarify the characteristics of the intestinal flora and its changes in maintenance hemodialysis patients with constipation.

Who was studied?

Fecal samples were collected from 45 participants, containing 15 in the maintenance hemodialysis constipation group,15 in the maintenance hemodialysis non-constipation group and 15 in the healthy control group. These samples were analyzed using 16S rRNA gene sequencing. The feature of the intestinal microbiome of maintenance hemodialysis constipation group and the microbiome differences among the three groups were elucidated by species annotation analysis, α-diversity analysis, β-diversity analysis, species difference analysis, and predictive functional analysis.

What were the most important findings?

The alpha diversity analysis indicated that maintenance hemodialysis constipation group was less diverse and homogeneous than maintenance hemodialysis non-constipation group and healthy control group. At the genus level, the top ten dominant genera in maintenance hemodialysis constipation group patients were Enterococcus, Escherichia-Shigella, Bacteroides, Streptococcus, Bifidobacterium, Ruminococcus_gnavus_group, Lachnospiraceae_unclassified, Faecalibacterium, Akkermansia and UCG-002. Compared with non-constipation group, the Enterococcus, Rhizobiales_unclassified, Filomicrobium, Eggerthella, Allobaculum, Prevotella_7, Gordonibacter, Mitochondria_unclassified, Lachnoanaerobaculum were significantly higher in constipation group (p<0.05). Compared with non-constipation group, the Kineothrix, Rhodopirellula, Weissella were significantly lower in constipation group (p<0.05). The predictive functional analysis revealed that compared with non-constipation group, constipation group was significantly enriched in pathways associated with pyruate metabolism, flavonoid biosynthesis.

What are the greatest implications of this study?

This study describes for the first time the intestinal microbiome characteristics of maintenance hemodialysis patients with constipation. The results of this study suggest that there is a difference in the intestinal flora between maintenance hemodialysis patients with constipation and maintenance hemodialysis patients without constipation.

What was studied?

This study aimed to investigate the dynamic changes in the microbiome of patients with locally advanced rectal cancer (LARC) undergoing neoadjuvant chemoradiotherapy (nCRT), focusing on the relationship between the microbiome and response to nCRT.

Who was studied?

We conducted a longitudinal study involving 103 samples from 26 patients with LARC. Samples were collected from both the tumor and normal rectal tissues before and after nCRT. Diversity, taxonomic, and network analyses were performed to compare the microbiome profiles across different tissue types, pre- and post-nCRT time-points, and nCRT responses.

What were the most important findings?

Between the tumor and normal tissue samples, no differences in microbial diversity and composition were observed. However, when pre- and post-nCRT samples were compared, there was a significant decrease in diversity, along with notable changes in composition. Non-responders exhibited more extensive changes in their microbiome composition during nCRT, characterized by an increase in pathogenic microbes. Meanwhile, responders had relatively stable microbiome communities with more enriched butyrate-producing bacteria. Network analysis revealed distinct patterns of microbial interactions between responders and non-responders, where butyrate-producing bacteria formed strong networks in responders, while opportunistic pathogens formed strong networks in non-responders. A Bayesian network model for predicting the nCRT response was established, with butyrate-producing bacteria playing a major predictive role.

What are the greatest implications of this study?

Our study demonstrated a significant association between the microbiome and nCRT response in LARC patients, leading to the development of a microbiome-based response prediction model. These findings suggest potential applications of microbiome signatures for predicting and optimizing nCRT treatment in LARC patients.

What was studied?

This study examined whether gut microbiome composition differs in people with nontreated plaque psoriasis compared with people without the condition. The researchers used metagenomic gene sequencing of fecal samples to compare microbial taxa and functional gene pathways across groups. They also compared psoriasis patients directly against their own healthy spouses, a design meant to control for shared household and dietary exposures. Gene functional analysis was performed to see whether specific microbial pathways were altered alongside compositional shifts.

Who was studied?

The study included 32 nontreated plaque psoriasis patients, 15 unrelated healthy controls, and 17 healthy spouses of the patients (healthy couples). Fecal samples from these three cohorts were analyzed by metagenomic sequencing. The abstract does not specify age, sex distribution, or geographic origin of participants.

What were the most important findings?

The relative abundance of intestinal microbiota in the psoriasis group differed from both healthy controls and the patients' own healthy partners, though overall microbial diversity was similar across all three groups. At the phylum level, the relative abundances of Firmicutes and Bacteroidetes were reversed in psoriasis patients, and Escherichia coli was significantly enriched compared with both comparison groups. Functional gene analysis showed ribosome pathway genes upregulated, while flagellar assembly and bacterial chemotaxis pathways were downregulated in the psoriasis cohort. Additionally, microbiota composition differed between patients with severe psoriasis and those with milder disease, suggesting a relationship between gut dysbiosis and disease severity.

What are the greatest implications of this study?

These findings strengthen the case for a link between intestinal flora and psoriasis, including a possible relationship between microbial dysbiosis and disease severity. Using patients' own healthy spouses as a comparison group helps address some of the conflicting results in prior psoriasis microbiome research. The authors note that further, more meaningful experiments are needed to clarify the mechanisms underlying this association.

What was studied?

This study examined the bacterial tear film microbiome in aqueous-deficient dry eye, comparing Sjogren's syndrome (SS) and non-Sjogren's syndrome (NSS) dry eye to healthy eyes. Researchers sequenced the V3-V4 region of the 16S rRNA gene from tear film DNA samples using the Illumina HiSeq2500 platform. Taxa were assigned using the QIIME pipeline, and alpha and beta diversity were assessed statistically in R. Differences between groups were further characterized using principal coordinate analysis (PCoA), differential abundance testing, and network analysis.

Who was studied?

The study included tear film samples from 33 healthy individuals, 17 individuals with Sjogren's syndrome dry eye, and 28 individuals with non-Sjogren's syndrome dry eye, for a total of 78 participants. The abstract does not provide further demographic details such as age, sex, or geographic location of the cohorts.

What were the most important findings?

The phyla Actinobacteria, Firmicutes, and Bacteroidetes showed significant changes in both SS and NSS dry eye compared to healthy eyes, while Lactobacillus and Bacillus were the predominant genera across all three groups. PCoA and heat map analyses revealed that SS and NSS samples formed distinct clusters separate from the healthy cohort. Several genera, including Prevotella, Coriobacteriaceae UCG-003, Enterococcus, Streptomyces, Rhodobacter, Ezakiella, and Microbacterium, were significantly increased in the disease groups relative to healthy eyes.

What are the greatest implications of this study?

These findings suggest that aqueous-deficient dry eye, whether associated with Sjogren's syndrome or not, is accompanied by a distinct shift in the ocular surface microbiome rather than a uniform or random change. The clear separation between disease and healthy clusters indicates the tear microbiome could potentially serve as a biomarker to help distinguish dry eye subtypes. This work supports further investigation into whether these microbial shifts contribute to, or result from, the inflammatory processes seen in aqueous-deficient dry eye.

What was studied?

This study examined the gut microbiome and serum metabolome in patients with functional constipation (FC), a common gastrointestinal disorder that significantly affects physical and mental health. The researchers used 16S rRNA microbial genomics to profile gut microbiota composition and non-target metabolomics based on liquid chromatography-mass spectrometry to characterize serum metabolic profiles. The study was designed to address inconsistent prior findings on the gut microbiome and FC, and to better link microbiome changes to host metabolites.

Who was studied?

The study included 30 patients with functional constipation and 28 healthy individuals as a comparison group. Fecal samples were used for 16S rRNA gut microbiota analysis and serum samples were used for metabolomic profiling in these participants. The abstract does not specify additional demographic details such as age or sex distribution.

What were the most important findings?

FC patients had distinct gut microbiota structures and serum metabolic profiles compared to healthy individuals. Patients with FC showed increased levels of Bacteroides and of several butyrate-producing bacteria, including Roseburia, Faecalibacterium, and Butyricicoccus. Serum levels of upstream products of host arginine biosynthesis, specifically 2-oxoglutaric acid, L-glutamic acid, N-acetylornithine, and L-ornithine, were significantly reduced in FC patients.

What are the greatest implications of this study?

The findings suggest that functional constipation may be associated with an altered gut microbiota, including increased Bacteroidetes, alongside downregulation of host arginine biosynthesis intermediates. This points to a potential link between specific gut bacteria and disrupted host amino acid metabolism in FC. The pairing of microbiome and metabolome data offers a more integrated view of FC pathophysiology than microbiome data alone, which could inform future mechanistic or therapeutic research.

What was studied?

Atrial fibrillation (AF) is an important heart rhythm disorder in aging populations. The gut microbiome composition has been previously related to cardiovascular disease risk factors. Whether the gut microbial profile is also associated with the risk of AF remains unknown.

Who was studied?

We examined the associations of prevalent and incident AF with gut microbiota in the FINRISK 2002 study, a random population sample of 6763 individuals. We replicated our findings in an independent case-control cohort of 138 individuals in Hamburg, Germany.

What were the most important findings?

Multivariable-adjusted regression models revealed that prevalent AF (N = 116) was associated with nine microbial genera. Incident AF (N = 539) over a median follow-up of 15 years was associated with eight microbial genera with false discovery rate (FDR)-corrected P < 0.05. Both prevalent and incident AF were associated with the genera Enorma and Bifidobacterium (FDR-corrected P < 0.001). AF was not significantly associated with bacterial diversity measures. Seventy-five percent of top genera (Enorma, Paraprevotella, Odoribacter, Collinsella, Barnesiella, Alistipes) in Cox regression analyses showed a consistent direction of shifted abundance in an independent AF case-control cohort that was used for replication.

What are the greatest implications of this study?

Our findings establish the basis for the use of microbiome profiles in AF risk prediction. However, extensive research is still warranted before microbiome sequencing can be used for prevention and targeted treatment of AF.

What was studied?

Polycystic ovary syndrome (PCOS) is an endocrine and metabolic disorder characterized by chronic low-grade inflammation. Previous studies have demonstrated that the gut microbiome can affect the host tissue cells' mRNA N6-methyladenosine (m6A) modifications. This study aimed to understand the role of intestinal flora in ovarian cells inflammation by regulating mRNA m6A modification particularly the inflammatory state in PCOS. The gut microbiome composition of PCOS and Control groups was analyzed by 16S rRNA sequencing, and the short chain fatty acids were detected in patients' serum by mass spectrometry methods. The level of butyric acid was found to be decreased in the serum of the obese PCOS group (FAT) compared to other groups, and this was correlated with increased Streptococcaceae and decreased Rikenellaceae based on the Spearman's rank test. Additionally, we identified FOSL2 as a potential METTL3 target using RNA-seq and MeRIP-seq methodologies. Cellular experiments demonstrated that the addition of butyric acid led to a decrease in FOSL2 m6A methylation levels and mRNA expression by suppressing the expression of METTL3, an m6A methyltransferase. Additionally, NLRP3 protein expression and the expression of inflammatory cytokines (IL-6 and TNF-α) were downregulated in KGN cells. Butyric acid supplementation in obese PCOS mice improved ovarian function and decreased the expression of local inflammatory factors in the ovary. Taken together, the correlation between the gut microbiome and PCOS may unveil crucial mechanisms for the role of specific gut microbiota in the pathogenesis of PCOS. Furthermore, butyric acid may present new prospects for future PCOS treatments.

What was studied?

This study examined whether the gut microbiota is associated with the development of Graves' disease (GD), an autoimmune thyroid condition. Researchers profiled gut microbiota composition using 16S rRNA sequencing, comparing samples taken before and after treatment in GD patients. They also measured interleukin-17 levels to explore a possible immune link, and used a random forest model to see whether specific bacterial genera could distinguish GD patients from healthy individuals.

Who was studied?

The study included 65 patients newly diagnosed with Graves' disease, sampled both before and after treatment. A comparison group of 33 physical examination personnel (presumed healthy individuals) was also profiled. All participants underwent gut microbiota analysis via 16S rRNA sequencing.

What were the most important findings?

Gut microbiota composition differed significantly between GD patients and the comparison group, with differences spanning 1 class, 1 order, 5 families, and 14 genera. After treatment, bacterial taxa that had been enriched in GD patients decreased, while taxa that had been depleted increased, alongside a significant decrease in interleukin-17 levels. A random forest analysis identified 12 genera capable of distinguishing GD patients from healthy controls. The abstract does not mention Desulfovibrio, sulfate-reducing bacteria, hydrogen sulfide, sulfide, or sulfur metabolism.

What are the greatest implications of this study?

The findings suggest that gut microbiota alterations in Graves' disease are linked to immune imbalance, given the parallel changes in microbiota composition and interleukin-17 levels after treatment. The identification of 12 discriminating genera raises the possibility that gut microbiota profiling could help distinguish GD patients from healthy individuals. The partial normalization of microbiota after treatment suggests gut microbiota may be a dynamic marker worth monitoring alongside thyroid disease activity.

What was studied?

This study examined the oral (saliva) microbiome composition of diverse human populations from southwestern Angola and Zimbabwe. It used the non-human sequencing reads recovered from an expanded exome capture approach, repurposing genomic data to characterize salivary bacterial communities. The aim was to add southern African, non-industrialized populations to the global picture of oral microbiome composition and diversity, which remains poorly understood on a broad scale.

Who was studied?

The sample comprised 52 individuals drawn from eight ethnolinguistically diverse southern African populations. These included the Kuvale, Kwepe, Himba, Tjimba, Kwisi, Twa, and !Xun from Angola, and the Tshwa from Zimbabwe. The groups represented a range of subsistence strategies, including foragers, food-producers, and peripatetic communities that provide services to dominant neighboring groups.

What were the most important findings?

Neisseria, Streptococcus, Prevotella, Rothia, and Porphyromonas were the five most frequent genera across all southern African groups, consistent with patterns reported in other human populations worldwide. Neither host genetics nor livelihood strategy appeared to shape the overall oral microbiome profile, pointing to a broadly homogeneous core community. However, some individuals from the Tshwa and Twa forager groups showed an enrichment of pathogenic genera belonging to the Enterobacteriaceae family, a family that includes Salmonella and other clinically relevant organisms.

What are the greatest implications of this study?

The findings suggest that the human oral microbiome maintains a stable, homogeneous core composition across ethnolinguistically and subsistence-diverse populations, independent of genetic ancestry or lifestyle. This supports the idea that core oral genera are a conserved feature of human biology rather than a product of industrialization or diet alone. The localized enrichment of pathogenic Enterobacteriaceae in specific forager subgroups also highlights that certain communities may carry distinct risks worth further investigation in relation to oral and systemic health.

What was studied?

Gut microbiota and their secreted metabolites have an influence on the initiation and progression of colon cancer. Probiotics are extensively perceived as a potential microbiota-modulation strategy to promote the health of the host, while the effectiveness of preventing colon cancer based on microbiota therapy has not been confirmed, and antitumor mechanisms influenced by microbiota and their metabolites with the intervention of probiotics remain to be further investigated. In vitro, Lactobacillus (JY300-8 and JMR-01) significantly inhibited the proliferation of CT26, HT29, and HCT116 cells. Moreover, we studied the prevention and therapy efficiency of Lactobacillus and its underlying antitumor mechanism through the alteration of gut microbiota and their metabolites regulated by Lactobacillus in colon cancer models in mice. We demonstrated that the pre-administration of Lactobacillus (JY300-8 and JMR-01) for 20 days before establishing tumor models resulted in an 86.21% reduction in tumor formation rate compared to tumor control group. Subsequently, continuous oral administration of living Lactobacillus significantly suppresses tumor growth, and tumor volumes decrease by 65.2%. Microbiome and metabolome analyses reveal that Lactobacillus suppresses colonic tumorigenesis and progression through the modulation of gut microbiota homeostasis and metabolites, including the down-regulation of secondary bile acids, sphingosine 1-phosphate (S1P), and pyrimidine metabolism, as well as the production of anticarcinogenic compounds in tumor-bearing mice. Additionally, metabolome analyses of Lactobacillus (JY300-8 and JMR-01) indicate that living Lactobacillus could reduce the relative abundance of alanine and L-serine to suppress tumor progression by regulating the tumor microenvironment, including down-regulation of pyrimidine metabolism and S1P signaling in cancer. These findings provide a potential prevention strategy and therapeutic target for colon cancer through the intervention of dietary Lactobacillus. IMPORTANCE The modulation of gut microbiota and metabolites has a significant influence on the progression of colon cancer. Our research indicated that the intervention of probiotics is a potentially feasible strategy for preventing colon cancer. We have also revealed the underlying antitumor mechanism through the alteration of gut microbiota and their metabolites, which could lead to broader biomedical impacts on the prevention and therapy of colon cancer with microbiota-based therapy regulated by probiotics.

What was studied?

Microbiome changes on the ocular surface may cause dry eyes. A metagenome assay was used to compare the microbiome composition and function of the ocular surface between diabetic children and adolescents with dry eye, diabetic children and adolescents without dry eye, and normal children.

Who was studied?

Twenty children and adolescents aged 8 to 16 with diabetes were selected from the Shanghai Children and Adolescent Diabetes Eye Study. Ten healthy children and adolescents belonging to the same age group were selected from the outpatient clinic during the same period. The participants were classified into the dry eye group (DM-DE group, n = 10), the non-dry eye group (DM-NDE group, n = 10) and the normal group (NDM group, n = 10). A conjunctival sac swab was collected for metagenomic sequencing, and the relationship between the microbiome composition and functional gene differences on the ocular surface with dry eye was studied.

What were the most important findings?

The classification composition and metabolic function of the microorganisms on the ocular surface of children in the 3 groups were analyzed. It was found that children's ocular microbiota was composed of bacteria, viruses and fungi. There were significant differences in α diversity and β diversity of microbial composition of ocular surface between DM-DE group and NDM group(P<0.05). There were significant differences in α and β diversity of metabolic pathways between the two groups(P<0.05). The functional pathways of ocular surface microorganisms in diabetic children with dry eyes were mainly derived from human disease, antibiotic resistance genes, carbohydrate, coenzyme and lipid transport and metabolism-related functional genes; In normal children, the functional pathways were mainly derived from replication, recombination, repair, signal transduction and defense-related functional genes.

What are the greatest implications of this study?

The DM-DE group have unique microbial composition and functional metabolic pathways. The dominant species and unique metabolic pathways of the ocular surface in the DM-DE group may be involved in the pathogenesis of dry eye in diabetic children.

What was studied?

Like its human counterpart, canine atopic dermatitis (cAD) is a chronic relapsing condition; thus, most cAD-affected dogs will require lifelong treatment to maintain an acceptable quality of life. A potential intervention is modulation of the composition of gut microbiota, and in fact, probiotic treatment has been proposed and tried in human atopic dermatitis (AD) patients. Since dogs are currently receiving intensive medical care, this will be the same option for dogs, while evidence of gut dysbiosis in cAD is still missing, although skin microbial profiling in cAD has been conducted in several studies. Therefore, we conducted a comprehensive analysis of both gut and skin microbiota in cAD in one specific cAD-predisposed breed, Shiba Inu. Additionally, we evaluated the impact of commonly used medical management on cAD (Janus kinase; JAK inhibitor, oclacitinib) on the gut and skin microbiota. Furthermore, we genotyped the Shiba Inu dogs according to the mitochondrial DNA haplogroup and assessed its association with the composition of the gut microbiota.

What were the most important findings?

Staphylococcus was the most predominant bacterial genus observed in the skin; Escherichia/Shigella and Clostridium sensu stricto were highly abundant in the gut of cAD-affected dogs. In the gut microbiota, Fusobacteria and Megamonas were highly abundant in healthy dogs but significantly reduced in cAD-affected dogs. The abundance of these bacterial taxa was positively correlated with the effect of the treatment and state of the disease. Oclacitinib treatment on cAD-affected dogs shifted the composition of microbiota towards that in healthy dogs, and the latter brought it much closer to healthy microbiota, particularly in the gut. Additionally, even within the same dog breed, the mtDNA haplogroup varied, and there was an association between the mtDNA haplogroup and microbial composition in the gut and skin.

What are the greatest implications of this study?

Dysbiosis of both the skin and the gut was observed in cAD in Shiba Inu dogs. Our findings provide a basis for the potential treatment of cAD by manipulating the gut microbiota as well as the skin microbiota. Video Abstract.

What was studied?

The most common toxic side effect after chemotherapy, one of the main treatments for colorectal cancer (CRC), is myelosuppression. To analyze the correlation between gut microbiota and leukopenia after chemotherapy in CRC patients.

Who was studied?

Stool samples were collected from 56 healthy individuals and 55 CRC patients. According to the leukocytes levels in peripheral blood, the CRC patients were divided into hypoleukocytes group (n = 13) and normal leukocytes group (n = 42). Shannon index, Simpson index, Ace index, Chao index and Coverage index were used to analyze the diversity of gut microbiota. LDA and Student's t-test(St test) were used for analysis of differences. Six machine learning algorithms, including logistic regression (LR) algorithm, random forest (RF) algorithm, neural network (NN) algorithm, support vector machine (SVM) algorithm, catboost algorithm and gradient boosting tree algorithm, were used to construct the prediction model of gut microbiota with leukopenia after chemotherapy for CRC.

What were the most important findings?

Compared with healthy group, the microbiota alpha diversity of CRC patients was significantly decreased (p < 0.05). After analyzing the gut microbiota differences of the two groups, 15 differential bacteria, such as Bacteroides, Faecalibacterium and Streptococcus, were screened. RF prediction model had the highest accuracy, and the gut microbiota with the highest predictive value were Peptostreptococcus, Faecalibacterium, and norank_f__Ruminococcaceae, respectively. Compared with normal leukocytes group, the microbiota alpha diversity of hypoleukocytes group was significantly decreased (p < 0.05). The proportion of Escherichia-Shigella was significantly decreased in the hypoleukocytes group. After analyzing the gut microbiota differences of the two groups, 9 differential bacteria, such as Escherichia-Shigella, Fusicatenibacter and Cetobacterium, were screened. RF prediction model had the highest accuracy, and the gut microbiota with the highest predictive value were Fusicatenibacte, Cetobacterium, and Paraeggerthella.

What are the greatest implications of this study?

Gut microbiota is related to leukopenia after chemotherapy. The gut microbiota may provide a novel method for predicting myelosuppression after chemotherapy in CRC patients.

What was studied?

Grade C (previously aggressive) periodontitis (GCP) in adolescents is prevalent in certain parts of Africa where it is associated with JP2 genotype, a highly virulent strain of Aggregatibacter actinomycetemcomitans. The aim of this study was to characterize the subgingival bacteriome in Moroccan subjects with GCP positive to A. actinomycetemcomitans JP2 genotype.

Who was studied?

Subgingival plaque samples were collected from shallow and deep pockets of 8 subjects with GCP (17.2 ± 1.5 years) and from gingival sulci of 13 controls with no periodontitis (14.6 ± 1.1 years). Identification and genotyping of A. actinomycetemcomitans was performed using PCR analysis of the ltx operon, while bacteriome profiling was done by 16S rRNA gene sequencing (V1-V3 region). Groups were compared in terms of microbial diversity, abundances, and dysbiosis.

What were the most important findings?

The shallow and deep pocket sites from GCP cases had a significantly altered microbial composition compared to controls. Species associated with health included Haemophilus parainfluenzae, Lautropia mirabilis, Streptococcus spp., Gemella spp., and Rothia spp. While known periodontal pathogens, including Porphyromonas gingivalis, Tannerella forsythia, Treponema spp. and Fretibacterium spp., were significantly enriched in GCP, non-conventional taxa, including Pseudomonas oral taxon C61 and Enterobacter cloacae were more abundant and showed stronger association with the disease. Less significant differences in abundances of individual taxa were observed between shallow and deep pockets. Overall dysbiosis measured in terms of Subgingival Microbial Dysbiosis Index (SMDI) differentiated between GCP and no-periodontitis with 95% accuracy.

What are the greatest implications of this study?

The results suggest that several periodontal pathogens involved in the adult-type periodontitis also play a role in JP2 genotype-associated GCP. The potential role of non-conventional taxa in the pathogenesis of GCP warrants further investigation.

What was studied?

Orthokeratology (OK) lens wear increases the risk of bacterial infection, but little is known about the microbiota of the conjunctival sac in myopic children wearing OK lenses. This study aimed to investigate the changes of conjunctival microbiota in children after treatment with OK lenses using 16 S rDNA sequencing.

Who was studied?

Twenty-eight myopic children who had been continuously wearing OK lenses for 12 to 13 months were enrolled in this prospective study. Twenty-two gender- and age-matched myopic children who had not worn OK lenses or discontinued OK lens wear at least 1 year ago were recruited as controls. Conjunctival swabs from each participant were collected for exploration of the microbiota profiles, targeting the V3-V4 regions of the 16 S rRNA gene by MiSeq sequencing. The differences in the microbial community structure and diversity were also compared between groups.

What were the most important findings?

The bacterial alpha diversity indices in the OK lens group were not different from those in the non-wearer group (P > 0.05, Wilcoxon test), while beta diversity examined using principle coordinate analysis of unweighted UniFrac divided the two groups into different clusters. Proteobacteria, Bacteroidetes, and Firmicutes were the abundant phyla in the conjunctival sac microbiota in both groups (P < 0.05, Mann-Whitney U test). Among children in the OK lens group, the Linear discriminant analysis Effect Size identified the compositional changes in OK lens-associated bacteria. Key functional genera such as Blautia, Parasutterella, and Muribaculum were enriched, whereas Brevundimonas, Acinetobacter, Proteus, and Agathobacter decreased significantly (P < 0.05, Mann-Whitney U test). Phylogenetic investigation of communities by reconstruction of unobserved states also showed altered bacterial metabolic pathways in OK lens-associated microbiota. Moreover, using receiver operating characteristic curves, Brevundimonas, Acinetobacter, Proteus, and Agathobacter alone (the area under the curve was all > 0.7500) or in combination (the area under the curve was 0.9058) were revealed to discriminate OK lens wearers from controls.

What are the greatest implications of this study?

The relative abundance of the microbial community in the conjunctival sac of myopic children can alter after OK lens wear. Brevundimonas, Acinetobacter, Proteus, and Agathobacter may be candidate biomarkers to distinguish between OK lens wearers and non-wearers.

What was studied?

Preterm birth is associated with the development of acute and chronic disease, potentially, through the disruption of normal gut microbiome development. Probiotics may correct for microbial imbalances and mitigate disease risk. Here, we used amplicon sequencing to characterise the gut microbiome of probiotic-treated premature infants. We aimed to identify and understand variation in bacterial gut flora from admission to discharge and in association with clinical variables.

Who was studied?

Infants born <32 weeks gestation and <1500 g, and who received probiotic treatment, were recruited in North Queensland Australia. Meconium and faecal samples were collected at admission and discharge. All samples underwent 16S rRNA short amplicon sequencing, and subsequently, a combination of univariate and multivariate analyses.

What were the most important findings?

71 admission and 63 discharge samples were collected. Univariate analyses showed significant changes in the gut flora from admission to discharge. Mixed-effects modelling showed significantly lower alpha diversity in infants diagnosed with either sepsis or retinopathy of prematurity (ROP) and those fed formula. In addition, chorioamnionitis, preeclampsia, sepsis, necrotising enterocolitis and ROP were also all associated with the differential abundance of several taxa.

What are the greatest implications of this study?

The lower microbial diversity seen in infants with diagnosed disorders or formula-fed, as well as differing abundances of several taxa across multiple variables, highlights the role of the microbiome in the development of health and disease. This study supports the need for promoting healthy microbiome development in preterm neonates.

What was studied?

This study examined whether dysbiosis of the skin microbiome and the gut microbiome is associated with melanoma growth and progression. The researchers used the MeLiM porcine model, which spontaneously develops melanoma that can progress or regress, to study this relationship. They performed parallel analysis of cutaneous (skin) microbiota and faecal microbiota from the same animals, comparing melanoma tissue to healthy skin and comparing MeLiM piglets to control piglets. Bacterial composition was profiled using high throughput sequencing of the V4-V5 region of the 16S rRNA gene.

Who was studied?

The subjects were MeLiM piglets aged 8 to 12 weeks, a porcine model of melanoma progression and spontaneous regression. Skin swabs from melanoma tissue and healthy skin, along with faecal samples, were collected from the same individual animals. A control group of piglets without melanoma was also included for comparison of the faecal microbiome. The abstract does not specify the exact number of animals sampled.

What were the most important findings?

There was a significant difference in microbiome diversity and richness between melanoma tissue and healthy skin, and between the faecal microbiome of MeLiM piglets and control piglets. Principal Coordinate Analysis and Non-metric multidimensional scaling both showed clear dissimilarities between these different bacterial communities. Linear discriminant analysis was used to identify specific bacterial taxa distinguishing the groups, though the abstract text is cut off before naming these taxa. Overall, the findings indicate that melanoma progression is accompanied by detectable shifts in both cutaneous and gut bacterial community composition.

What are the greatest implications of this study?

The findings support the idea that skin microbiome alterations, not just gut microbiome alterations, may be relevant to the tumor microenvironment in melanoma. This suggests a potential link between local skin dysbiosis and systemic gut dysbiosis during melanoma progression, an area the authors note had not been previously investigated. Because the gut microbiome has already been shown to modulate response to melanoma immunotherapy, these results raise the possibility that skin microbiota could also influence tumor behavior or serve as an additional biomarker. This porcine model may offer a useful system for further mechanistic study of microbiome-melanoma interactions relevant to human disease.

What was studied?

This study examined how delivery mode shapes the early gut microbiota of newborns using high-resolution shotgun sequencing. Researchers tracked the composition and dynamics of the neonatal gut microbiome over the first month of life. The design specifically compared elective cesarean section against vaginal delivery to sidestep the confounding effect of emergency cesareans, which can muddy conclusions about delivery mode's true influence.

Who was studied?

The cohort consisted of Tunisian newborns, with stool samples collected from 5 infants born by elective cesarean section and 5 born vaginally. Samples were taken longitudinally at Day 0, Day 15, and Day 30 after birth. This is a small, delivery-mode-stratified newborn cohort rather than a large population sample.

What were the most important findings?

Bacterial richness and diversity were similar between the elective cesarean and vaginally delivered groups, and both showed a shift in microbiota community composition during the first two weeks regardless of delivery mode. Both groups were dominated by Proteobacteria, Actinobacteria, and Firmicutes. However, starting from the second week, cesarean-delivered infants showed an underrepresentation of Bacteroides alongside an enrichment of opportunistic pathogenic species belonging to the ESKAPE group.

What are the greatest implications of this study?

The findings suggest that even elective, non-emergency cesarean delivery is associated with a distinct early gut microbiota signature marked by Bacteroides depletion and ESKAPE pathogen enrichment, not merely overall diversity differences. This points to delivery mode as an independent driver of neonatal microbiome composition beyond confounding clinical circumstances. The emergence of opportunistic ESKAPE species by two weeks of age raises questions about potential vulnerability to opportunistic infection in cesarean-born infants that merit further, larger-scale investigation.

What was studied?

The microbial population of the intestinal tract and its relationship to specific diseases has been extensively studied during the past decade. However, reports characterizing the bile microbiota are rare. This study aims to investigate the microbiota composition in patients with pancreaticobiliary cancers and benign diseases by 16S rRNA gene amplicon sequencing and to evaluate its potential value as a biomarker for the cancer of the bile duct, pancreas, and gallbladder.

What were the most important findings?

We enrolled patients who were diagnosed with cancer, cystic lesions, and inflammation of the pancreaticobiliary tract. The study cohort comprised 244 patients. We extracted microbiome-derived DNA from the bile juice in surgically resected gallbladders. The microbiome composition was not significantly different according to lesion position and cancer type in terms of alpha and beta diversity. We found a significant difference in the relative abundance of Campylobacter, Citrobacter, Leptotrichia, Enterobacter, Hungatella, Mycolicibacterium, Phyllobacterium and Sphingomonas between patients without and with lymph node metastasis.

What are the greatest implications of this study?

There was a significant association between the relative abundance of certain microbes and overall survival prognosis. These microbes showed association with good prognosis in cholangiocarcinoma, but with poor prognosis in pancreatic adenocarcinoma, and vice versa. Our findings suggest that pancreaticobiliary tract cancer patients have an altered microbiome composition, which might be a biomarker for distinguishing malignancy.

What was studied?

HIV-exposed uninfected infants (HEU) have abnormal immunologic functions and increased infectious morbidity in the first 6 months of life, which gradually decreases thereafter. The mechanisms underlying HEU immune dysfunctions are unknown. We hypothesized that unique characteristics of the HEU gut microbiota associated with maternal HIV status may underlie the HEU immunologic dysfunctions. We characterized the infant gut, maternal gut, and breast milk microbiomes of mother-infant pairs, including 123 with HEU and 117 with HIV-uninfected infants (HUU), from South Africa. Pan-bacterial 16S rRNA gene sequencing was performed on (i) infant stool at 6, 28, and 62 weeks; (ii) maternal stool at delivery and 62 weeks; and (iii) breast milk at 6 weeks. Infant gut alpha and beta diversities were similar between groups. Microbial composition significantly differed, including 12 genera, 5 families and 1 phylum at 6 weeks; 12 genera and 2 families at 28 weeks; and 2 genera and 2 families at 62 weeks of life. Maternal gut microbiomes significantly differed in beta diversity and microbial composition, and breast milk microbiomes differed in microbial composition only. Infant gut microbiotas extensively overlapped with maternal gut and minimally with breast milk microbiotas. Nevertheless, exclusively breastfed HEU and HUU had less divergent microbiomes than nonexclusively breastfed infants. Feeding pattern and maternal gut microbiome imprint the HEU gut microbiome. Compared to HUU, the HEU gut microbiome prominently differs in early infancy, including increased abundance of taxa previously observed to be present in excess in adults with HIV. The HEU and HUU gut microbiome compositions converge over time, mirroring the kinetics of HEU infectious morbidity risk. IMPORTANCE HIV-exposed uninfected infants (HEU) are highly vulnerable to infections in the first 6 months of life, and this vulnerability decreases to the age of 24 months. Because the microbiome plays a critical role in the education of the infant immune system, which protects them against infections, we characterized the gut microbiomes of HEU and HIV-unexposed infants (HUU) in the first year of life. The HEU and HUU gut microbiomes showed prominent differences at 6 and 28 weeks of life but converged at 62 weeks of life, mirroring the time course of the HEU excess infectious morbidity and suggesting a potential association between the infant gut microbiome structure and susceptibility to infections. Infant gut microbiotas extensively overlapped with maternal gut and minimally with breast milk microbiotas. Moreover, exclusively breastfed HEU and HUU had less divergent microbiomes at 6 and 28 weeks than nonexclusively breastfed HEU and HUU. The factors that affect the HEU gut microbiome, maternal gut microbiome and exclusive breastfeeding, may be targeted by interventions.

What was studied?

Viral infections are known to modulate the upper respiratory tract microbiome, but few studies have addressed differences in the nasopharyngeal microbiome following SARS-CoV-2 infection. Using nasopharyngeal swab medical waste samples from 79 confirmed SARS-CoV-2 positive and 20 SARS-CoV-2 negative patients, we assessed microbiome composition with metagenomic sequencing. COVID-19 status and breathing assistive device use was associated with differences in beta diversity, principal component analyses, community composition and abundance of several species. Serratia more frequently appeared in COVID-19 patient samples compared to negative patient samples, and Serratia, Streptococcus, Enterobacter, Veillonella, Prevotella, and Rothia appeared more frequently in samples of those who used breathing assistive devices. Smoking and age were associated with differences in alpha diversity. Cross-sectional differences in the microbiome were apparent with SARS-CoV-2 infection, but longitudinal studies are needed to understand the dynamics of viral and breathing treatment modulation of microbes.

What was studied?

This study examined the effect of antiparkinsonian medication, specifically levodopa (LD) and levodopa-carbidopa intestinal gel (LCIG), on the gut microbiota and fecal metabolome in Parkinson disease (PD). Fecal DNA was analyzed using next-generation sequencing of the V3 and V4 regions of the 16S rRNA gene. Fecal metabolic extracts were also evaluated using gas chromatography mass spectrometry to characterize metabolome differences across treatment groups.

Who was studied?

The study included 107 patients with a clinical diagnosis of Parkinson disease. Patients were divided into three groups: an LCIG group (n = 38) receiving levodopa-carbidopa intrajejunal gel, an LD group (n = 46) receiving oral levodopa, and a Naive group (n = 23) not taking any antiparkinsonian medications. This design allowed comparison of gut microbiota composition across different treatment exposures within a PD population.

What were the most important findings?

Multivariate analysis showed that the LCIG group had a significantly higher abundance of Enterobacteriaceae, Escherichia, and Serratia compared to the LD group. Compared to the Naive group, the LD group showed a reduction of Blautia and Lachnospirae. The LCIG group additionally showed an increase in Proteobacteria and Enterobacteriaceae alongside a reduction in Firmicutes, Lachnospiraceae, and Blautia relative to the Naive group.

What are the greatest implications of this study?

The findings suggest that the route and form of levodopa therapy, oral versus intrajejunal gel, are associated with distinct gut microbiota profiles in Parkinson disease. The reduction of Blautia and Lachnospiraceae, taxa associated with short-chain fatty acid production, alongside enrichment of Enterobacteriaceae in LCIG-treated patients points to a treatment-related shift toward a less favorable microbial composition. These distinctive features may warrant further investigation into how PD medication choice shapes gut microbial and metabolic health over the course of treatment.

What was studied?

Although gut microbiota dysbiosis has been reported in HIV infected individuals recently, the relationship between the gut microbiota and immune activation in patients with different immune responses to highly active antiretroviral therapy (HAART) is still not well understood. Gut microbiota and immune activation were studied in 36 non-HIV-infected subjects (healthy controls) and 58 HIV-infected individuals, including 28 immunological responders (IR) and 30 immunological non-responders (INR) (≥500 and < 200 CD4+ T-cell counts/μl after 2 years of HIV-1 viral suppression respectively) without comorbidities.

What were the most important findings?

Metagenome sequencing revealed that HIV-infected immunological responders and immunological non-responders could not recover completely from the gut microbiota dysbiosis. At a 97% similarity level, the relative abundances of Fusobacterium, Ruminococcus gnavus and Megamonas were greater, whereas Faecalibacterium, Alistipes, Bifidobacterium, Eubacterium rectale and Roseburia were more depleted in the IR and INR groups than those in the healthy controls. Ruminococcaceae and Alistipes were positively correlated with nadir and current CD4+ T-cell counts, but negatively correlated with CD8 + CD57+ T-cell counts. Inflammation markers and translocation biomarkers (LPS) levels were positively correlated with the abundances of genera Ruminococcus and Fusobacterium but were negatively correlated with the genus Faecalibacterium. The relative abundances of Escherichia-Shigella and Blautia were significantly higher in the IR than those in the INR group. Escherichia-Shigella were negatively correlated with the CD4/CD8 ratio but positively correlated with the amount of CD8 + CD57+ T-cells. Roseburia and Blautia were negatively associated with nadir CD4+ T-cell and positively associated with CD8 + CD57+ T-cell counts.

What are the greatest implications of this study?

Gut microbiota dysbiosis may be one of the factors contributing to different immune responses and treatment outcomes to HAART.

What was studied?

This study examined whether gut bacterial microbiome dysbiosis, already reported in type 2 diabetes mellitus (T2DM), also links to diabetic retinopathy (DR). Fecal samples were analyzed using 16S rRNA gene sequencing, with community composition assessed using QIIME and R software. The researchers compared gut bacterial diversity and abundance at the phyla and genera level across groups.

Who was studied?

The study compared healthy controls (HC) with people who had T2DM without DR and people who had T2DM with DR. Exact sample sizes are not given in the abstract, but the design involved three human fecal-sample groups defined by diabetes and retinopathy status. This is described as the first report of its kind comparing gut microbiome dysbiosis specifically in people with DR against healthy controls.

What were the most important findings?

Gut microbiome dysbiosis at the phyla and genera level was observed in both T2DM and T2DM-with-DR groups compared to healthy controls. People with DR showed greater discrimination from healthy controls than people with T2DM alone, and the microbiomes of the T2DM and DR groups were also significantly different from each other. Both diabetes and DR were associated with a decrease in anti-inflammatory, probiotic, and other beneficial bacteria relative to healthy controls, alongside an increase in potentially pathogenic bacteria, with this shift being more pronounced in people with DR.

What are the greatest implications of this study?

This is the first report demonstrating gut microbiome dysbiosis specifically associated with diabetic retinopathy, distinct from T2DM alone. The findings suggest the gut microbiome could serve as a marker to distinguish DR from T2DM without retinal complications. The authors note this work could help inform the development of novel, targeted therapies aimed at improving treatment of diabetic retinopathy.

What was studied?

This study examined whether the gut microbiome carries a detectable signature of prediabetes, a stage preceding type 2 diabetes mellitus (T2D). Researchers sequenced the V1-V5 variable regions of the 16S rRNA gene to profile gut microbiota composition. They also measured fasting serum inflammatory biomarkers in the same participants. The goal was to identify robust microbial signatures that could aid early diagnosis and prevention of T2D.

Who was studied?

The study analyzed two cohorts, one from India and one from Denmark, combining prediabetic and normoglycemic individuals. In total, 262 prediabetic subjects were compared against 275 normoglycemic subjects. This trans-ethnic design allowed the researchers to correct for a strong country-specific cohort effect and look for microbial patterns shared across both populations.

What were the most important findings?

After correcting for cohort effects, 16 operational taxonomic units (OTUs) were enriched in normoglycemic subjects relative to those with prediabetes, including members of Prevotella9, Phascolarctobacterium, Barnesiella, Flavonifractor, Tyzzerella_4, Bacteroides, Faecalibacterium, and Agathobacter. Faecalibacterium, a genus that includes the anti-inflammatory, butyrate-producing species Faecalibacterium prausnitzii, was among the taxa depleted in prediabetic subjects. Conversely, 144 OTUs were found enriched in the prediabetic subjects, indicating a broader shift in community composition alongside the loss of these beneficial commensals.

What are the greatest implications of this study?

The depletion of Faecalibacterium and other short-chain-fatty-acid-associated genera in prediabetes, observed consistently across two ethnically distinct cohorts, supports gut microbiota as a candidate early marker of metabolic disease risk. Because these signatures held after correcting for country-specific effects, they suggest a trans-ethnic microbial pattern rather than a population-specific artifact. This strengthens the rationale for using microbiome profiling in early prediabetes screening and for exploring interventions that restore anti-inflammatory, butyrate-producing commensals before progression to overt T2D.

What was studied?

This study examined the nasal and oropharyngeal (NOP) microbial community using 16S rRNA gene sequencing. Researchers compared the microbiota composition and diversity across groups differing in COVID-19 status and severity. The goal was to characterize how SARS-CoV-2 infection alters the local respiratory microbiome, since no reliable markers exist to predict disease prognosis in these patients.

Who was studied?

The cohort included 21 patients affected by COVID-19, some paucisymptomatic and others admitted to the Intensive Care Unit (ICU). They were compared against 10 controls who tested negative for COVID-19, as well as 8 patients infected with other human coronaviruses (HKU1, NL63, and OC43). All samples were drawn from nasal/oropharyngeal swabs analyzed by 16S rRNA sequencing.

What were the most important findings?

Chao1 index, a measure of microbial richness, was significantly lower in ICU COVID-19 patients compared to paucisymptomatic patients. Chao1 was also decreased across ICU, paucisymptomatic, and other-coronavirus groups relative to controls. Shannon diversity index, which accounts for both richness and evenness, was significantly reduced only in ICU patients compared to controls and paucisymptomatic patients. At the phylum level, Deinococcus-Thermus was detected only in controls and was absent in SARS-CoV-2 and other-coronavirus patient groups.

What are the greatest implications of this study?

The progressive loss of microbial diversity in the nasal/oropharyngeal tract, most pronounced in ICU patients, suggests that upper respiratory microbiome disruption tracks with COVID-19 severity. These findings raise the possibility that 16S rRNA-based diversity indices, such as Chao1 and Shannon, could serve as candidate biomarkers to help stratify disease severity. Further research could clarify whether restoring microbial diversity or targeting specific taxa like Deinococcus-Thermus has prognostic or therapeutic relevance in COVID-19 management.

What was studied?

This study examined the relationship between the intestinal microbiota and SARS-CoV-2 infection in a United States hospital cohort. Researchers collected fecal samples and used 16S rRNA sequencing plus qPCR analysis to compare microbial composition across infection states. They compared actively infected patients, recovered patients, and uninfected controls seen for unrelated respiratory conditions, and also tested for fecal viral shedding.

Who was studied?

The cohort included 50 patients actively infected with SARS-CoV-2, 9 patients who had recovered from SARS-CoV-2 infection, and 34 uninfected control subjects seen at the hospital for unrelated respiratory medical conditions. The study is described as a United States, majority African American and minority-dominated cohort. Fecal DNA and RNA were collected prospectively from all three groups for microbiota analysis.

What were the most important findings?

Fecal microbial composition differed significantly between SARS-CoV-2 patients and controls, independent of antibiotic exposure, with Peptoniphilus, Corynebacterium, and Campylobacter enriched in COVID-19 patients. Actively infected patients also had a distinct gut microbiota compared to recovered patients, with Campylobacter most enriched during active infection and Agathobacter and Faecalibacterium enriched after recovery. Notably, recovered patients showed no difference in microbial community structure or alpha diversity compared to uninfected controls. Nearly half of the COVID-19 patients (24 of 50, 48%) tested positive by RT-qPCR for fecal viral material.

What are the greatest implications of this study?

The findings suggest that SARS-CoV-2 infection is associated with a transient disruption of gut microbial composition that resolves as patients recover, rather than causing lasting dysbiosis. This return to an uninfected-like microbiome state in recovered patients supports the gut as a site of active but reversible interaction with the virus. The high rate of fecal viral detection also reinforces concern about potential fecal-oral transmission during active infection.

What was studied?

The disease severity, ranging from being asymptomatic to having acute illness, and associated inflammatory responses has suggested that alterations in the gut microbiota may play a crucial role in the development of chronic disorders due to COVID-19 infection. This study describes gut microbiota dysbiosis in COVID-19 patients and its implications relating to the disease.

Who was studied?

A cross sectional prospective study was performed on thirty RT-PCR-confirmed COVID-19 patients admitted to the All India Institute of Medical Sciences, Bhopal, India, between September 10 and 20, 2020. Ten healthy volunteers were recruited as the control group. IFN, TNF, and IL-21 profiling was conducted using plasma samples, and gut bacterial analysis was performed after obtaining the metagenomics data of stool samples.

What were the most important findings?

Patients with a variable COVID-19 severity showed distinct gut microflora and peripheral interleukin-21 levels. A low Firmicute/Bacteroidetes ratio, caused by the depletion of the fibre-utilizing bacteria, F. prausnitzii, B. Plebius, and Prevotella, and an increase in Bacteroidetes has associated gut microbiota dysbiosis with COVID-19 disease severity.

What are the greatest implications of this study?

The loss of the functional attributes of signature commensals in the gut, due to dysbiosis, is a predisposing factor of COVID-19 pathophysiology.

What was studied?

Chronic inflammation is a hallmark of human immunodeficiency virus (HIV) infection and a risk factor for the development and progression of age-related comorbidities. Although HIV-associated gut dysbiosis has been suggested to be involved in sustained chronic inflammation, there remains a limited understanding of the association between gut dysbiosis and chronic inflammation during HIV infection. Here, we investigated compositional changes in the gut microbiome and its role in chronic inflammation in patients infected with HIV. We observed that the gut microbiomes of patients with low CD4 counts had reduced alpha diversity compared to those in uninfected controls. Following CD4 recovery, alpha diversity was restored, but intergroup dissimilarity of bacterial composition remained unchanged between patients and uninfected controls. Patients with HIV had higher abundance of the classes Negativicutes, Bacilli, and Coriobacteriia, as well as depletion of the class Clostridia. These relative abundances positively correlated with inflammatory cytokines and negatively correlated with anti-inflammatory cytokines. We found that gut dysbiosis accompanying HIV infection was characterized by a depletion of obligate anaerobic Clostridia and enrichment of facultative anaerobic bacteria, reflecting increased intestinal oxygen levels and intestinal permeability. Furthermore, it is likely that HIV-associated dysbiosis shifts the immunological balance toward inflammatory Th1 responses and encourages proinflammatory cytokine production. Our results suggest that gut dysbiosis contributes to sustaining chronic inflammation in patients with HIV infection despite effective antiretroviral therapy and that correcting gut dysbiosis will be effective in improving long-term outcomes in patients. IMPORTANCE Chronic inflammation is a hallmark of HIV infection and is associated with the development and progression of age-related comorbidities. Although the gastrointestinal tract is a major site of HIV replication and CD4+ T-cell depletion, the role of HIV-associated imbalance of gut microbiome in chronic inflammation is unclear. Here, we aimed to understand the causal relationship between abnormalities in the gut microbiome and chronic inflammation in patients with HIV. Our results suggest HIV-associated gut dysbiosis presents a more aerobic environment than that of healthy individuals, despite prolonged viral suppression. This dysbiosis likely results from a sustained increase in intestinal permeability, which supports sustained bacterial translocation in HIV patients, despite effective therapy. Additionally, we observed that several bacterial taxa enriched in HIV patients were associated with increased expression of inflammatory cytokines. Collectively, these results suggest that gut dysbiosis plays an important role in chronic inflammation in HIV patients.

What was studied?

This prospective observational study evaluated whether gut microbiome composition is associated with stroke-associated pneumonia (SAP) in patients with acute ischemic stroke. Researchers collected fecal and serum samples at admission and used 16S rRNA V4 tag sequencing, analyzed with QIIME and LEfSe, to characterize gut microbiota. They also measured fecal short-chain fatty acids and serum markers of gut barrier integrity, including D-lactate, intestinal fatty acid-binding protein, and lipopolysaccharide binding protein.

Who was studied?

The training cohort included 188 patients with acute ischemic stroke, of whom 52 (27.7%) developed stroke-associated pneumonia. Findings were validated in an independent cohort of 144 patients, 28 of whom (19.4%) developed SAP. Disease severity scores were recorded by specialized physicians alongside the microbiome and biomarker data.

What were the most important findings?

Gut microbiome composition differed significantly between patients who developed SAP and those who did not. Patients with SAP showed depletion of Roseburia along with enrichment of opportunistic pathogens, a pattern confirmed in the independent validation cohort. Multivariate analysis identified Roseburia as a protective factor against SAP in both the training and validation cohorts, supporting gut dysbiosis as an independent risk factor for this complication.

What are the greatest implications of this study?

These findings suggest gut microbiota, particularly Roseburia abundance, could serve as an early biomarker to identify stroke patients at higher risk of pneumonia. Because Roseburia acted as a protective factor across two independent cohorts, restoring or supporting this taxon may represent a potential avenue for reducing SAP risk. The results also point toward gut-lung axis mechanisms as a relevant target for future preventive strategies in acute ischemic stroke care.

What was studied?

This study examined the gut microbiota of breast cancer patients according to menopausal status, focusing specifically on premenopausal breast cancer, which has been understudied compared to postmenopausal disease. The researchers assessed overall microbial diversity, community composition, and functional pathways. They also evaluated whether specific gut microbial markers could distinguish breast cancer patients by menopausal status and whether these markers had diagnostic value.

Who was studied?

The study analyzed 267 breast cancer patients with different menopausal statuses (premenopausal and postmenopausal) along with age-matched female controls. The abstract notes that premenopausal breast cancer is a growing concern in Asian countries, where younger patients make up an increasing share of cases, in contrast to Western countries where breast cancer more often occurs in older postmenopausal women. Beyond the total cohort size, no further demographic or geographic details are given in the abstract.

What were the most important findings?

Alpha-diversity of the gut microbiota was significantly reduced in premenopausal breast cancer patients, and beta-diversity differed significantly between breast cancer patients and controls. Through multiple analyses and classification approaches, the researchers identified 14 microbial markers that differed according to menopausal status in breast cancer. Notably, Bacteroides fragilis was specifically found in younger, premenopausal patients, while Klebsiella pneumoniae was specifically found in older, postmenopausal patients.

What are the greatest implications of this study?

The findings suggest that gut microbial profiles in breast cancer are menopausal-status specific, meaning premenopausal and postmenopausal disease may involve distinct microbial signatures rather than a single uniform pattern. The identification of menopausal-specific microbial markers, such as Bacteroides fragilis in premenopausal patients, points toward potential diagnostic applications tailored to age and menopausal status. This underscores the need for future breast cancer microbiome research to separately account for premenopausal patients rather than focusing predominantly on postmenopausal disease.

What was studied?

Slow transit constipation (STC) is one of the most frequent gastrointestinal diagnoses. In this study, we conducted a quantitative metagenomics study in 118 Chinese individuals. These participants were divided into the discovery cohort of 50 patients with STC and 40 healthy controls as well as a validation cohort of 16 patients and 12 healthy controls. We found that the intestinal microbiome of patients with STC was significantly different from that of healthy individuals at the phylum, genus, and species level. Patients with STC had markedly higher levels of Alistipes and Eubacterium and lower abundance of multiple species belonging to the Roseburia genus. Patients with STC gene expression levels and the Kyoto Encyclopedia of Genes and Genomes (KEGG) orthology pathway (such as fatty acid biosynthesis, butanoate metabolism, and methane metabolism pathways) enrichment were also substantially different from those of healthy controls. These microbiome and metabolite differences may be valuable biomarkers for STC. Our findings suggest that alteration of the microbiome may lead to constipation by changing the levels of microbial-derived metabolites in the gut. Above findings may help us in the development of microbial drugs.

What was studied?

Next-generation sequencing has revolutionized our perspective on the gut microbiome composition, revealing the true extent of the adverse effects of antibiotics. The impact of antibiotic treatment on gut microbiota must be considered and researched to provide grounds for establishing new treatment strategies that are less devastating on commensal bacteria. This study investigates the impact on gut microbiome when a commonly used antibiotic, azithromycin is administered, as well as uncovers the benefits induced when it is used in combination with lactulose, a prebiotic known to enhance the proliferation of commensal microbes.

Who was studied?

16S rRNA gene sequencing analysis of stool samples obtained from 87 children treated with azithromycin in combination with or without lactulose have been determined. Children's gut microbial profile was established at the pre- and post-treatment stage.

What were the most important findings?

Azithromycin caused an increase in the relative abundance of opportunistic pathogens such as Streptococcus that was evident 60 days after treatment. While few days after treatment, children who also received lactulose started to show a higher relative abundance of saccharolytic bacteria such as Lactobacillus, Enterococcus, Anaerostipes, Blautia and Roseburia, providing a protective role against opportunistic pathogens. In addition, azithromycin-prebiotic combination was able to provide a phylogenetic profile more similar to the pre-treatment stage.

What are the greatest implications of this study?

It is suggested that during azithromycin treatment, lactulose is able to reinstate the microbiome equilibrium much faster as it promotes saccharolytic microbes and provides a homeostatic effect that minimizes the opportunistic pathogen colonization.

What was studied?

The roles of gut microbiota on the natural course of atopic dermatitis (AD) are not yet fully understood. We investigated whether the composition and function of gut microbiota and short-chain fatty acids (SCFAs) at 6 months of age could affect the natural course of AD up to 24 months in early childhood.

Who was studied?

Fecal samples from 132 infants were analyzed using pyrosequencing, including 84 healthy controls, 22 transient AD and 26 persistent AD subjects from the Cohort for Childhood Origin of Asthma and Allergic Diseases (COCOA) birth cohort. The functional profile of the gut microbiome was analyzed by whole-metagenome sequencing. SCFAs were measured using gas chromatography-mass spectrometry.

What were the most important findings?

Low levels of Streptococcus and high amounts of Akkermansia were evident in transient AD cases, and low Clostridium, Akkermansia and high Streptococcus were found in children with persistent AD. The relative abundance of Streptococcus positively correlated with scoring of AD (SCORAD) score, whereas that of Clostridium negatively correlated with SCORAD score. The persistent AD group showed decreased gut microbial functional genes related to oxidative phosphorylation compared with healthy controls. Butyrate and valerate levels were lower in transient AD infants compared with healthy and persistent AD infants.

What are the greatest implications of this study?

Compositions, functions and metabolites of the early gut microbiome are related to natural courses of AD in infants.

What was studied?

This study examined whether gut microbiota composition in young children and their mothers is associated with different environmental exposures in a low-income, rural setting. Researchers analyzed faecal samples using 16S rRNA sequencing to characterize bacterial OTU and genus abundances, microbiota maturity, diversity, and UniFrac distances. Environmental exposure variables considered included socio-economic status, water source, sanitary facility, presence of domestic animals, maternal characteristics, season, antibiotic use, and delivery mode. The guiding hypothesis was that more adverse environmental exposures would correspond to lower microbiota maturity and diversity.

Who was studied?

The study drew on faecal samples from up to 631 children and their mothers participating in a nutrition intervention trial in rural Malawi. Children were sampled longitudinally at 1, 6, 12, 18, and 30 months of age, while mothers were sampled at 1 month after their child's birth. This is a population from a low-income setting where childhood malnutrition is common, a context the authors note has been understudied for microbiota-environment relationships.

What were the most important findings?

The abstract text describing the results is truncated, so specific quantitative findings on microbiota maturity and diversity in children cannot be reported here. What is stated is that measures of microbiota maturity and diversity in children were examined in relation to the listed environmental exposures using comparisons of OTU and genus abundances and UniFrac distances. No mention of Faecalibacterium prausnitzii, butyrate, or specific anti-inflammatory commensals appears in the provided abstract text.

What are the greatest implications of this study?

By linking specific environmental exposures, such as water source, sanitation, domestic animal contact, and antibiotic use, to gut microbiota development in early childhood, this work supports the idea that environmental conditions shape microbiota maturation in low-income settings. Because childhood malnutrition is common in this population, understanding these environment-microbiota relationships could inform strategies to support healthier microbiota development during a critical early-life window. The longitudinal, multi-timepoint design in both children and mothers also provides a framework for tracking how exposures and microbiota composition evolve together over the first years of life.

What was studied?

The meconium microbiome may provide insight into intrauterine and peripartum exposures and the very earliest intestinal pioneering microbes. Prenatal antibiotics have been associated with later obesity in children, which is thought to be driven by microbiome dependent mechanisms. However, there is little data regarding associations of prenatal or peripartum antibiotic exposure, with or without cesarean section (CS), with the features of the meconium microbiome. In this study, 16S ribosomal RNA gene sequencing was performed on bacterial DNA of meconium samples from 105 infants in a birth cohort study. After multivariable adjustment, delivery mode (p = 0.044), prenatal antibiotic use (p = 0.005) and peripartum antibiotic use (p < 0.001) were associated with beta diversity of the infant meconium microbiome. CS (vs. vaginal delivery) and peripartum antibiotics were also associated with greater alpha diversity of the meconium microbiome (Shannon and Simpson, p < 0.05). Meconium from infants born by CS (vs. vaginal delivery) had lower relative abundance of the genus Escherichia (p < 0.001). Prenatal antibiotic use and peripartum antibiotic use (both in the overall analytic sample and when restricting to vaginally delivered infants) were associated with differential abundance of several bacterial taxa in the meconium. Bacterial taxa in the meconium microbiome were also differentially associated with infant excess weight at 12 months of age, however, sample size was limited for this comparison. In conclusion, prenatal and peripartum antibiotic use along with CS delivery were associated with differences in the diversity and composition of the meconium microbiome. Whether or not these differences in the meconium microbiome portend risk for long-term health outcomes warrants further exploration.

What was studied?

Aim: To identify intestinal microbiota compositions in elderly functional constipation (FC) patients. Materials and methods: Fecal samples from 61 FC patients and 48 healthy age-matched volunteers were analyzed through 16S rRNA gene sequencing. Results: The intestinal microbiota compositions of FC patients were significantly different from healthy controls. Additionally, the species diversity of healthy controls was greater than that of FC patients. Indeed, the abundance of Firmicutes and Proteobacteria was significantly decreased, whereas that of Bacteroides, Prevotella, Lactococcus, Ruminococcus and Butyricimonas was remarkably increased in FC patients. Conclusion: Elderly FC patients appear to have a unique intestinal microbiota profile. Our findings should provide insight regarding the pathogenic mechanism of FC and evidence for exploring new therapeutic strategies in elderly FC patients.

What was studied?

This cross-sectional study used shotgun metagenomic sequencing of fecal samples to identify gut microbial species associated with polycystic ovary syndrome (PCOS). Researchers compared the gut microbiota composition of women with PCOS to that of women without the condition. They also collected clinical parameters, including body mass index, endocrine hormone levels, and glycemia, to test for correlations with the microbial findings.

Who was studied?

The study included 14 reproductive-aged women diagnosed with PCOS and 14 control women, all recruited from an academic Centre for Reproductive Medicine. Fecal samples from these 28 participants underwent shotgun metagenomic sequencing. Clinical and metabolic data were gathered from the same women for correlation analysis.

What were the most important findings?

Several microbial strains were significantly more abundant in the PCOS group, including Parabacteroides merdae, Bacteroides fragilis, and strains of Escherichia and Shigella, while Faecalibacterium prausnitzii was enriched in controls. Metagenomic species analysis showed that the microbial profiles of the PCOS group were negatively correlated with those of the control group. Microbial species associated with PCOS were positively correlated with endocrine disturbances, including higher body mass index and elevated serum testosterone levels.

What are the greatest implications of this study?

The findings support a pathological association between gut dysbiosis and PCOS, linking specific bacterial taxa to hormonal and metabolic disturbances seen in the condition. The enrichment of Escherichia and Shigella strains alongside depletion of the beneficial species Faecalibacterium prausnitzii suggests a shift toward a more pro-inflammatory gut environment in PCOS. These results point to the gut microbiome as a potential target for understanding or managing the endocrine and metabolic features of PCOS, though further work is needed to establish causality.

What was studied?

General chronic periodontitis (GCP) is a bacterial inflammatory disease with complex pathology. Despite extensive studies published on the variation in the oral microbiota and metabolic profiles of GCP patients, information is lacking regarding the correlation between host-bacterial interactions and biochemical metabolism. This study aimed to analyze the oral microbiome, the oral metabolome, and the link between them and to identify potential molecules as useful biomarkers for predictive, preventive, and personalized medicine (PPPM) in GCP.

Who was studied?

In this study, gingival crevicular fluid (GCF) samples were collected from patients with GCP (n = 30) and healthy controls (n = 28). The abundance of oral microbiota constituents was obtained by Illumina sequencing, and the relative level of metabolites was measured by gas chromatography-mass spectrometry. Full-mouth probing depth, clinical attachment loss, and bleeding on probing were recorded as indices of periodontal disease.

What were the most important findings?

The relative abundances of 7 phyla and 82 genera differed significantly between the GCP and healthy groups. Seventeen differential metabolites involved in different metabolism pathways were selected based on variable influence on projection values (VIP > 1) and P values (P < 0.05). Through Spearman's correlation analysis, microorganisms, metabolites in GCF, and clinical data together showed a clear trend, and clinical data regarding periodontitis can be reflected in the shift of the oral microbial community and the change in metabolites in GCF. A combination of citramalic acid and N-carbamylglutamate yielded satisfactory accuracy (AUC = 0.876) for the predictive diagnosis of GCP.

What are the greatest implications of this study?

Dysbiosis in the polymicrobial community structure and changes in metabolism could be mechanisms underlying periodontitis. The differential microorganisms and metabolites in GCF between periodontitis patients and healthy individuals are possibly biomarkers, pointing to a potential strategy for the prediction, diagnosis, prognosis, and management of personalized periodontal therapy.

What was studied?

Identification of the gut microbiome compositions associated with disease has become a research focus worldwide. Emerging evidence has revealed the presence of gut microbiota dysbiosis in Parkinson's disease. In this study, we aimed to identify the gut microbiome associated with Parkinson's disease and subsequently to screen and to validate potential diagnostic biomarkers of Parkinson's disease. This case-control study investigated gut microbial genes in faeces from 40 volunteer Chinese patients with Parkinson's disease and their healthy spouses using shotgun metagenomic sequencing. Furthermore, the identified specific gut microbial gene markers were validated with real-time PCR in an independent Chinese cohort of 78 Parkinson's disease patients, 75 control subjects, 40 patients with multiple system atrophy and 25 patients with Alzheimer's disease. We developed the first gut microbial gene catalogue associated with Parkinson's disease. Twenty-five gene markers were identified that distinguished Parkinson's disease patients from healthy control subjects, achieving an area under the receiver operating characteristic curve (AUC) of 0.896 (95% confidence interval: 83.1-96.1%). A highly accurate Parkinson's disease index, which was not influenced by disease severity or Parkinson's disease medications, was created. Testing these gene markers using quantitative PCR distinguished Parkinson's disease patients from healthy controls not only in the 40 couples (AUC = 0.922, 95% confidence interval: 86.4-98.0%), but also in an independent group of 78 patients with Parkinson's disease and 75 healthy control subjects (AUC = 0.905, 95% confidence interval: 86.0-95.1%). This classifier also performed a differential diagnosis power in discriminating these 78 patients with Parkinson's disease from a cohort of 40 patients with multiple system atrophy and 25 patients with Alzheimer's disease based on the panel of 25 biomarkers. Based on our results, the identified Parkinson's disease index based on the gene set from the gut microbiome may be a potential diagnostic biomarker of Parkinson's disease.

What was studied?

This study examined gut microbiota composition and fecal metabolite profiles in people with Parkinson's disease compared to controls. Researchers used next-generation sequencing to characterize bacterial taxa and gas chromatography-mass spectrometry to measure fecal metabolites. The goal was to identify microbiome and metabolome alterations associated with Parkinson's disease, a neurodegenerative disorder marked by misfolded alpha-synuclein aggregates along the cerebral axis. The abstract notes that a cause-effect relationship between intestinal dysbiosis and Parkinson's disease has not yet been established.

Who was studied?

The study included 64 Italian patients with Parkinson's disease and 51 controls. Both groups underwent gut microbiota sequencing and fecal metabolite analysis. No further demographic details, such as age or sex distribution, are given in the abstract.

What were the most important findings?

Parkinson's disease patients showed reduced levels of bacterial taxa linked to anti-inflammatory and neuroprotective effects, particularly within the Lachnospiraceae family, including Butyrivibrio, Pseudobutyrivibrio, Coprococcus, and Blautia. Fecal metabolite analysis revealed changes across several compound classes. These included lipids such as linoleic acid, oleic acid, succinic acid, and sebacic acid, vitamins such as pantothenic acid and nicotinic acid, amino acids such as isoleucine, leucine, phenylalanine, glutamic acid, and pyroglutamic acid, and other organic compounds such as cadaverine, ethanolamine, and hydroxy propionic acid. The abstract does not mention Desulfovibrio, sulfate-reducing bacteria, or hydrogen sulfide.

What are the greatest implications of this study?

The findings reinforce that Parkinson's disease is accompanied by a distinct pattern of gut dysbiosis and metabolic disturbance, with depletion of beneficial, anti-inflammatory Lachnospiraceae members standing out as a key feature. The combined microbiota and metabolome approach suggests that fecal biomarkers could eventually help characterize or monitor the disease. Because the abstract states that causality remains unestablished, these results should be viewed as associative rather than proof that gut changes drive Parkinson's disease pathology.

What was studied?

Intestinal microbial dysbiosis is evident in chronic HIV-infected individuals and may underlie inflammation that persists even during antiretroviral therapy (ART). It remains unclear, however, how early after HIV infection gut dysbiosis emerges and how it is affected by early ART.

Who was studied?

Fecal microbiota were studied by 16s rDNA sequencing in 52 Thai men who have sex with men (MSM), at diagnosis of acute HIV infection (AHI), Fiebig Stages 1-5 (F1-5), and after 6 months of ART initiation, and in 7 Thai MSM HIV-uninfected controls. Dysbiotic bacterial taxa were associated with relevant inflammatory markers.

What were the most important findings?

Fecal microbiota profiling of AHI pre-ART vs HIV-uninfected controls showed a mild dysbiosis. Transition from F1-3 of acute infection was characterized by enrichment in pro-inflammatory bacteria. Lower proportions of Bacteroidetes and higher frequencies of Proteobacteria and Fusobacteria members were observed post-ART compared with pre-ART. Fusobacteria members were positively correlated with levels of soluble CD14 in AHI post-ART.

What are the greatest implications of this study?

Evidence of gut dysbiosis was observed during early acute HIV infection and was partially restored upon early ART initiation. The association of dysbiotic bacterial taxa with inflammatory markers suggests that a potential relationship between altered gut microbiota and systemic inflammation may also be established during AHI.

What was studied?

Gut tryptophan (Trp) metabolites are produced by microbiota and/or host metabolism. Some of them have been proven to promote or inhibit colorectal cancer (CRC) in vitro and animal models. We hypothesized that there is an alteration of gut Trp metabolism mediated by microbiota and that it might be involved in the pathogenesis of cancer in patients with CRC. To investigate the features of Trp metabolism in CRC and the correlation between fecal Trp metabolites and gut microbiota.

Who was studied?

Seventy-nine patients with colorectal neoplastic lesions (33 with colon adenoma and 46 with sporadic CRC) and 38 healthy controls (HCs) meeting the inclusion and exclusion criteria were included in the study. Their demographic and clinical features were collected. Fecal Trp, kynurenine (KYN), and indoles (metabolites of Trp metabolized by gut microbiota) were examined by ultraperformance liquid chromatography coupled to tandem mass spectrometry. Gut barrier marker and indoleamine 2,3-dioxygenase 1 (IDO1) mRNA were analyzed by quantitative real-time polymerase chain reaction. Zonula occludens-1 (ZO-1) protein expression was analyzed by immunohistochemistry. The gut microbiota was detected by 16S ribosomal RNA gene sequencing. Correlations between fecal metabolites and other parameters were examined in all patients.

What were the most important findings?

The absolute concentration of KYN [1.51 (0.70, 3.46) nmol/g vs 0.81 (0.64, 1.57) nmol/g, P = 0.036] and the ratio of KYN to Trp [7.39 (4.12, 11.72) × 10-3 vs 5.23 (1.86, 7.99) × 10-3, P = 0.032] were increased in the feces of patients with CRC compared to HCs, while the indoles to Trp ratio was decreased [1.34 (0.70, 2.63) vs 2.46 (1.25, 4.10), P = 0.029]. The relative ZO-1 mRNA levels in patients with CRC (0.27 ± 0.24) were significantly lower than those in HCs (1.00 ± 0.31) (P < 0.001), and the relative IDO1 mRNA levels in patients with CRC [1.65 (0.47-2.46)] were increased (P = 0.035). IDO1 mRNA levels were positively associated with the KYN/Trp ratio (r = 0.327, P = 0.003). ZO-1 mRNA and protein levels were positively correlated with the indoles/Trp ratio (P = 0.035 and P = 0.009, respectively). In addition, the genera Asaccharobacter (Actinobacteria) and Parabacteroides (Bacteroidetes), and members of the phylum Firmicutes (Clostridium XlVb, Fusicatenibacter, Anaerofilum, and Anaerostipes) decreased in CRC and exhibited a positive correlation with indoles in all subjects.

What are the greatest implications of this study?

Alteration of fecal Trp metabolism mediated by microbiota is associated with intestinal barrier function and tissue Trp metabolism, and may be involved in the pathogenesis of CRC.

What was studied?

This cross-sectional study examined whether the gut microbiota is associated with extraintestinal joint inflammation in patients with inflammatory bowel disease (IBD). Stool samples were collected and DNA was sequenced on the Illumina platform, with reads quality-controlled using SHI7 and processed with SHOGUN. Microbial abundance and diversity were assessed with QIIME, and compositional biomarkers distinguishing groups were identified using LEfSe. The study also evaluated microbial functional pathways, including tyrosine degradation, and examined history of bowel surgery as a possible source of variability.

Who was studied?

One hundred eighty patients were included in the analysis, divided into four groups: those with IBD-associated arthropathy (IBD-A), IBD without arthropathy (IBD-N), rheumatoid arthritis (RA), and non-IBD, nonarthritis controls. The abstract does not give a numeric breakdown of how many patients fell into each of the four groups. This design allowed direct comparison of gut microbial composition across intestinal and joint-related inflammatory phenotypes.

What were the most important findings?

IBD-A was associated with an increased abundance of microbial tyrosine degradation pathways compared with IBD-N (P = 0.02). IBD-A and RA patients both showed an increased abundance of Clostridiaceae compared with controls (P = 0.045), suggesting a shared microbial signature across two distinct arthritis-associated conditions. History of bowel surgery was also identified as a significant source of variability among IBD patients (P = 0.001) and was linked to decreased alpha diversity.

What are the greatest implications of this study?

The shared enrichment of Clostridiaceae in both IBD-associated arthritis and rheumatoid arthritis suggests a common gut microbial feature may underlie joint inflammation across different autoimmune and inflammatory contexts. Altered tyrosine degradation pathways in IBD-A point to a possible metabolic mechanism linking gut microbes to extraintestinal disease manifestations. The findings also highlight bowel surgery history as an important confounder to account for in future microbiome studies of IBD patients. Together, these results support further investigation of Clostridiaceae and related microbial pathways as potential targets or biomarkers for arthritis in IBD.

Who was studied?

Healthy subjects of Chinese (n = 12), Malay (n = 12) and Indian (n = 10) ancestry, aged 21-37 years, were enrolled. They provided a baseline stool sample (Day 1) and were then given a course of omeprazole at therapeutic dose (20 mg daily) for seven days. Stool samples were collected again on Day 7 and 14 (one week after stopping omeprazole). Microbial DNA was extracted from the stool samples, followed by polymerase chain reaction, library construction, 16S rRNA sequencing using Illumina MiSeq, and statistical and bioinformatics analyses.

What were the most important findings?

The findings showed an increase in species richness (p = 0.018) after omeprazole consumption on Day 7, which reverted to baseline on Day 14. There were significant increases in the relative abundance of Streptococcus vestibularis (p = 0.0001) and Veillonella dispar (p = 0.0001) on Day 7, which diminished on Day 14. Faecalibacterium prausnitzii, Sutterella stercoricanis and Bacteroides denticanum were characteristic of Chinese, Malays and Indians, respectively. Lactobacillaceae and Bacteroides xylanisolvens were the signature taxa of male and female subjects, respectively.

What are the greatest implications of this study?

The study demonstrated alterations in the gut microbiome following omeprazole treatment. This may explain the underlying pathology of increased risk of Clostridium difficile infections associated with omeprazole therapy.

What was studied?

This study examined the relationship between gut microbiome composition and childhood eczema using 16S rRNA gene sequencing. Researchers compared microbial profiles between healthy children and children with eczema, stratifying samples into four age groups (0-0.5, 0.5-1, 1-2, and 2-3 years) to account for developmental and environmental influences on the gut microbiome. Findings from sequencing were further verified using quantitative polymerase chain reaction targeting Bifidobacterium and Bacteroides.

Who was studied?

The cohort included 172 subjects under age three, divided into a healthy group of 123 children and an eczema group of 49 children. Samples were further split across four narrower age brackets to examine how the microbiome-eczema relationship changed over early development. No further demographic or geographic details were given in the abstract.

What were the most important findings?

Lower relative abundance of Bifidobacterium was associated with childhood eczema, though this difference was not significant in infants younger than six months old. From 0.5 to 3 years of age, decreased Bifidobacterium was a major and consistent finding in the eczema group compared to age-matched healthy controls. Decreased microbial diversity was also observed in eczema samples across all age groups, most significantly in children aged 2-3 years. Bifidobacterium operational taxonomic units showed strong predictive power for eczema status, with a Random Forest model achieving an AUC of 0.83 in ROC analysis.

What are the greatest implications of this study?

The findings suggest that reduced Bifidobacterium levels in the gut, emerging after the first six months of life, may be linked to the development of childhood eczema. Because Bifidobacterium abundance showed high predictive accuracy for eczema status, it may serve as a candidate microbial marker for risk assessment in early childhood. The age-stratified design also indicates that timing matters: the microbiome-eczema association strengthens as children move past infancy, pointing to a developmental window relevant to future preventive or diagnostic strategies.

What was studied?

Recently, gut microbiota have been studied extensively for health promotion, disease prevention, disease treatment, and exercise performance. It is recommended that athletes avoid dietary fiber and resistant starch to promote gastric emptying and reduce gastrointestinal distress during exercise, but this diet may reduce microbial diversity and compromise the health of the athlete's gut microbiota. This study compared fecal microbiota characteristics using high-throughput sequencing among healthy sedentary men (as controls), bodybuilders, and distance runners, as well as the relationships between microbiota characteristics, body composition, and nutritional status.

Who was studied?

Body composition was measured using DXA, and physical activity level was assessed using IPAQ. Dietary intake was analyzed with the computerized nutritional evaluation program. The DNA of fecal samples was extracted and it was sequenced for the analysis of gut microbial diversity through bioinformatics cloud platform.

What were the most important findings?

We showed that exercise type was associated with athlete diet patterns (bodybuilders: high protein, high fat, low carbohydrate, and low dietary fiber diet; distance runners: low carbohydrate and low dietary fiber diet). However, athlete type did not differ in regard to gut microbiota alpha and beta diversity. Athlete type was significantly associated with the relative abundance of gut microbiota at the genus and species level: Faecalibacterium, Sutterella, Clostridium, Haemophilus, and Eisenbergiella were the highest (p < 0.05) in bodybuilders, while Bifidobacterium and Parasutterella were the lowest (p < 0.05). At the species level, intestinal beneficial bacteria widely used as probiotics (Bifidobacterium adolescentis group, Bifidobacterium longum group, Lactobacillus sakei group) and those producing short chain fatty acids (Blautia wexlerae, Eubacterium hallii) were the lowest in bodybuilders and the highest in controls. In addition, aerobic or resistance exercise training with an unbalanced intake of macronutrients and low intake of dietary fiber led to similar diversity of gut microbiota. Specifically, daily protein intake was negatively correlated with operation taxonomic unit (r = - 0.53, p < 0.05), ACE (r = - 0.51, p < 0.05), and Shannon index (r = - 0.64, p < 0.01) in distance runners..

What are the greatest implications of this study?

Results suggest that high-protein diets may have a negative impact on gut microbiota diversity for athletes, while athletes in resistance sports that carry out the high protein low carbohydrates diet demonstrate a decrease in short chain fatty acid-producing commensal bacteria.

What was studied?

This study used next-generation 16S ribosomal RNA gene sequencing to characterize the salivary (oral) microbiota associated with throat cancer. Researchers compared microbial community diversity and composition among throat cancer patients, vocal cord polyp patients, and healthy controls. They also built a diagnostic model based on constituent bacteria and verified select findings with real-time quantitative PCR.

Who was studied?

The study analyzed 70 oral (salivary) samples collected from three groups: 32 patients with throat cancer, nine patients with a vocal cord polyp, and 29 healthy individuals serving as normal controls. All participants were drawn from a clinical setting where throat cancer and vocal cord polyp diagnoses had been made, alongside disease-free comparison subjects.

What were the most important findings?

The salivary microbiota of throat cancer patients was significantly different from that of polyp patients and healthy individuals, with beta diversity clearly divergent in the cancer group. Alpha diversity was significantly reduced in cancer patients, as shown by the Chao1 estimator (P = 8.1e-05), Simpson index (P = 0.0045), and Shannon index (P = 0.0071). The genera Aggregatibacter, Pseudomonas, Bacteroides, and Ruminiclostridium were significantly enriched in throat cancer patients compared with the other two groups, a result confirmed by qPCR. A diagnostic model built from these bacterial constituents achieved 87.5% accuracy in distinguishing cancer patients from the other groups.

What are the greatest implications of this study?

These findings suggest that reduced salivary microbial diversity and enrichment of specific bacterial genera may serve as biological indicators associated with throat cancer. The strong diagnostic accuracy of the bacteria-based model points to the potential for salivary microbiota profiling as a non-invasive tool to help distinguish throat cancer from benign vocal cord polyps and healthy states. Because this is an association-based study, further research is needed to determine whether these microbial shifts are causal, secondary to tumor presence, or influenced by other factors before clinical application.

What was studied?

This study characterized the gut (fecal) and blood microbiota of patients with Alzheimer's disease (AD) and mild cognitive impairment (MCI) compared with normal controls, testing the hypothesis that dysbiosis begins in the MCI predementia stage. The goal was to determine whether microbiota changes could serve as early diagnostic biomarkers before the onset of dementia.

Who was studied?

The study enrolled patients with AD, patients with MCI, and normal controls, with diagnoses based on symptoms and neuroimaging (AD biomarkers were not used). Fecal and blood samples were profiled using 16S rRNA gene sequencing, and a diagnostic model was applied to a set of 30 MCI patients.

What were the most important findings?

Patients with AD and MCI had decreased microbial diversity, and 11 genera in feces and 11 genera in blood differed between AD and controls, while no genus-level differences were detected between AD and MCI. Escherichia was increased at the genus level in both fecal and blood samples from AD and MCI patients, and a fecal diagnostic model using all differing genera correctly identified 93% (28 of 30) of MCI patients.

What are the greatest implications of this study?

The authors conclude that gut microbiota alterations occur before AD onset and are already detectable in MCI, offering potential diagnostic biomarkers for early detection of dementia. Because this is an observational study, the findings represent association rather than causation, and the authors note that diagnoses lacked AD biomarker confirmation and that longitudinal prospective studies are needed to link microbiota changes to dementia progression.

What was studied?

This study characterized the gut microbiome of women with locally advanced cervical cancer using 16S rDNA sequencing of fecal samples. Researchers measured alpha diversity (within-sample diversity, via the Shannon diversity index) and beta diversity (between-sample diversity, via unweighted Unifrac distances and principal coordinate analysis). They then compared relative abundance of microbial taxa between groups using LEfSe (Linear Discriminant Analysis Effect Size), adjusting for age and race.

Who was studied?

The study included 42 women with locally advanced cervical cancer and 46 healthy female controls. Fecal samples from these two groups were profiled and compared directly. The abstract does not provide further demographic detail beyond the age- and race-adjusted analysis used in the statistical comparisons.

What were the most important findings?

Alpha diversity was significantly higher in cervical cancer patients than in controls, though this difference was driven mainly by older women (over 50 years). Notably, alpha diversity correlated positively with age in cancer patients but inversely with age in controls, suggesting opposite age-related diversity trends between the two groups. Beta diversity also differed significantly between cervical cancer patients and controls, and age- and race-adjusted LEfSe analysis identified multiple taxa that differed between groups, including Prevotella and Porphyromonas.

What are the greatest implications of this study?

The findings suggest that cervical cancer is associated with detectable, age-dependent shifts in gut microbial community structure and composition. The identification of specific differentially abundant genera, such as Prevotella and Porphyromonas, points to candidate taxa that could be further investigated for mechanistic links to cervical cancer. These results support continued investigation of the gut microbiome as a potential factor in cervical cancer biology, though the abstract does not describe causal mechanisms or clinical applications.

What was studied?

This study examined whether gut microbiome composition differs in people with kidney stones (nephrolithiasis) compared to healthy people. Researchers used 16S ribosomal RNA (rRNA) gene sequencing to characterize the gut microbiota of both groups. They assessed diversity, overall community structure, and genus-level abundance differences, and examined correlations between specific bacterial genera and blood trace-element concentrations.

Who was studied?

The study included 13 patients with multiple kidney stones and 13 matched healthy controls. This is a small, case-control cohort rather than a large population sample. Matching between the two groups was used to help isolate microbiome differences associated with nephrolithiasis.

What were the most important findings?

Beta diversity analysis showed a clear separation in gut microbial community structure between nephrolithiasis patients and healthy controls. Twenty genera differed significantly in relative abundance between the two groups. Among these, Phascolarctobacterium, Parasutterella, Ruminiclostridium_5, Erysipelatoclostridium, Fusicatenibacter, and Dorea were correlated with blood concentrations of trace elements including potassium, sodium, calcium, and chlorinum. A decreasing trend in observed species richness was seen in patients, though it did not reach statistical significance (p = 0.086).

What are the greatest implications of this study?

These findings suggest a distinct gut microbiome signature is associated with nephrolithiasis and may link to blood trace-element balance. This raises the possibility that specific gut genera could serve as biomarkers or contribute mechanistically to kidney stone risk. Given the small sample size, larger studies are needed to confirm these associations and clarify causality.

What was studied?

This study examined how the human gut microbiome changes during infection with soil-transmitted helminths (STHs), intestinal parasites that infect roughly 1.5 billion people worldwide. Researchers used a cross-sectional analysis to compare microbial signatures across two countries, Liberia and Indonesia, and also analyzed longitudinal samples from a double-blind randomized deworming trial. The goal was to characterize cross-kingdom interactions between STHs and gut bacteria and to see how the microbiome responds to treatment.

Who was studied?

The abstract describes cohorts from two countries, Liberia and Indonesia, that were compared in a cross-sectional design. A subset of participants was also followed longitudinally as part of a double-blind randomized trial of deworming treatment. Exact sample sizes are not given in the abstract, so no specific participant count can be stated.

What were the most important findings?

Conserved microbial signatures were positively or negatively associated with STH infection across both Liberia and Indonesia, including 12 bacterial taxa significant in both countries and one taxon, Lachnospiraceae, negatively associated with infection in both settings. Olsenella, a taxon associated with reduced gut inflammation, was also significantly reduced in abundance after infection clearance. Individuals who self-cleared their infection had more similar microbiome assemblages to one another than those who remained infected, and deworming altered microbial community gene abundances, including functional categories such as arachidonic acid metabolism, without fully shifting the microbiome back to an uninfected-like state.

What are the greatest implications of this study?

The findings suggest that STH infection leaves a reproducible, cross-population signature on the gut microbiome rather than a country-specific one, pointing to shared host-parasite-microbe biology. The persistence of an altered microbiome state even after deworming implies that treatment alone may not restore a pre-infection microbial community, which could have consequences for recovery and reinfection risk. Identifying taxa like Olsenella and functional pathways such as arachidonic acid metabolism offers potential leads for understanding inflammation and immune modulation during STH infection and clearance.

What was studied?

As urinary tract infection (UTI) pathogens originate from the gut, we hypothesized that the gut environment reflected by intestinal microbiome influences the risk of UTI. Our prospective case-control study compared the intestinal microbiomes of 37 children with a febrile UTI with those of 69 healthy children. We sequenced the regions of the bacterial 16S rRNA gene and used the LefSe algorithm to calculate the size of the linear discriminant analysis (LDA) effect. We measured fecal lactoferrin and iron concentrations and quantitative PCR for Escherichia coli. At the phylum level, there were no significant differences. At the genus level, Enterobacter was more abundant in UTI patients with an LDA score > 3 (log 10), while Peptostreptococcaceae were more abundant in healthy subjects with an LDA score > 3 (log 10). In total, 20 OTUs with significantly different abundances were observed. Previous use of antimicrobials did not associate with intestinal microbiome. The relative abundance of E. coli was 1.9% in UTI patients and 0.5% in controls (95% CI of the difference-0.8 to 3.6%). The mean concentration of E.coli in quantitative PCR was 0.14 ng/μl in the patients and 0.08 ng/μl in the controls (95% CI of the difference-0.04 to 0.16). Fecal iron and lactoferrin concentrations were similar between the groups. At the family and genus level, we noted several differences in the intestinal microbiome between children with UTI and healthy children, which may imply that the gut environment is linked with the risk of UTI in children.

What was studied?

Type 1 diabetes is associated with compositional differences in gut microbiota. To date, no microbiome studies have been performed in maturity-onset diabetes of the young 2 (MODY2), a monogenic cause of diabetes. Gut microbiota of type 1 diabetes, MODY2, and healthy control subjects was compared.

Who was studied?

This was a case-control study in 15 children with type 1 diabetes, 15 children with MODY2, and 13 healthy children. Metabolic control and potential factors modifying gut microbiota were controlled. Microbiome composition was determined by 16S rRNA pyrosequencing.

What were the most important findings?

Compared with healthy control subjects, type 1 diabetes was associated with a significantly lower microbiota diversity, a significantly higher relative abundance of Bacteroides, Ruminococcus, Veillonella, Blautia, and Streptococcus genera, and a lower relative abundance of Bifidobacterium, Roseburia, Faecalibacterium, and Lachnospira. Children with MODY2 showed a significantly higher Prevotella abundance and a lower Ruminococcus and Bacteroides abundance. Proinflammatory cytokines and lipopolysaccharides were increased in type 1 diabetes, and gut permeability (determined by zonulin levels) was significantly increased in type 1 diabetes and MODY2. The PICRUSt analysis found an increment of genes related to lipid and amino acid metabolism, ABC transport, lipopolysaccharide biosynthesis, arachidonic acid metabolism, antigen processing and presentation, and chemokine signaling pathways in type 1 diabetes.

What are the greatest implications of this study?

Gut microbiota in type 1 diabetes differs at taxonomic and functional levels not only in comparison with healthy subjects but fundamentally with regard to a model of nonautoimmune diabetes. Future longitudinal studies should be aimed at evaluating if the modulation of gut microbiota in patients with a high risk of type 1 diabetes could modify the natural history of this autoimmune disease.

What was studied?

Emerging evidence suggests the microbiome may affect a number of diseases, including lung cancer. However, the direct relationship between gut bacteria and lung cancer remains uncharacterized. In this study, we directly sequenced the hypervariable V1-V2 regions of the 16S rRNA gene in fecal samples from patients with lung cancer and healthy volunteers. Unweighted principal coordinate analysis (PCoA) revealed a clear difference in the bacterial community membership between the lung cancer group and the healthy control group. The lung cancer group had remarkably higher levels of Bacteroidetes, Fusobacteria, Cyanobacteria, Spirochaetes, and Lentisphaerae but dramatically lower levels of Firmicutes and Verrucomicrobia than the healthy control group (P < 0.05). Despite significant interindividual variation, eight predominant genera were significantly different between the two groups. The lung cancer group had higher levels of Bacteroides, Veillonella, and Fusobacterium but lower levels of Escherichia-Shigella, Kluyvera, Fecalibacterium, Enterobacter, and Dialister than the healthy control group (P < 0.05). Most notably, correlations between certain specific bacteria and serum inflammatory biomarkers were identified. Our findings demonstrated an altered bacterial community in patients with lung cancer, providing a significant step in understanding the relationship between gut bacteria and lung cancer. To our knowledge, this is the first study to evaluate the correlations between certain specific bacteria and inflammatory indicators. To better understand this relationship, further studies should investigate the underlying mechanisms of gut bacteria in lung cancer animal models.

What was studied?

Recent studies break with traditional opinion that the lower respiratory tract is sterile, and increasingly focus on the lung microbiome and disease. Smoking, as an important etiology of inflammatory lung disease, was considered as a factor influencing lung microbiome variations in our study, and we aimed to study the effect of smoking on inflammation and microbial diversity and community.

Who was studied?

Forty male mice were selected and randomly divided into a smoking and a non-smoking group. Mice in the smoking group were exposed to smoke smog for 2 h/day for 90 days. Blood and lung tissues were obtained after the experiment, and ELISA was used to measure interleukin-6 and C reactive protein concentrations. 16S rRNA gene quantification and sequencing technology were used to compare microbial diversity and community between the two groups. SAS 9.1 and R software were used to analyze the data.

What were the most important findings?

Thirty-six mice survived, and the weight of the smoking group increased more slowly than that of the non-smoking group. Denser inflammation and congestion were observed in the lungs of the smoking mice compared with the non-smoking group Higher microbial diversity was observed in the smoking group, and Enterobacter, Acidimicrobiales_norank, and Caulobacteraceae_Unclassified genus were significantly more abundant in the non-smoking group (P < 0.001).

What are the greatest implications of this study?

Smoking altered microbial diversities and communities in the lower respiratory tract of mice. Microbial variation should be considered in future studies focusing on smoking-induced inflammatory disease.

What was studied?

Perturbations to the colonization process of the human gastrointestinal tract have been suggested to result in adverse health effects later in life. Although much research has been performed on bacterial colonization and succession, much less is known about the other two domains of life, archaea, and eukaryotes. Here we describe colonization and succession by bacteria, archaea and microeukaryotes during the first year of life (samples collected around days 1, 3, 5, 28, 150, and 365) within the gastrointestinal tract of infants delivered either vaginally or by cesarean section and using a combination of quantitative real-time PCR as well as 16S and 18S rRNA gene amplicon sequencing. Sequences from organisms belonging to all three domains of life were detectable in all of the collected meconium samples. The microeukaryotic community composition fluctuated strongly over time and early diversification was delayed in infants receiving formula milk. Cesarean section-delivered (CSD) infants experienced a delay in colonization and succession, which was observed for all three domains of life. Shifts in prokaryotic succession in CSD infants compared to vaginally delivered (VD) infants were apparent as early as days 3 and 5, which were characterized by increased relative abundances of the genera Streptococcus and Staphylococcus, and a decrease in relative abundance for the genera Bifidobacterium and Bacteroides. Generally, a depletion in Bacteroidetes was detected as early as day 5 postpartum in CSD infants, causing a significantly increased Firmicutes/Bacteroidetes ratio between days 5 and 150 when compared to VD infants. Although the delivery mode appeared to have the strongest influence on differences between the infants, other factors such as a younger gestational age or maternal antibiotics intake likely contributed to the observed patterns as well. Our findings complement previous observations of a delay in colonization and succession of CSD infants, which affects not only bacteria but also archaea and microeukaryotes. This further highlights the need for resolving bacterial, archaeal, and microeukaryotic dynamics in future longitudinal studies of microbial colonization and succession within the neonatal gastrointestinal tract.

What was studied?

The assessment and characterization of the gut microbiome has become a focus of research in the area of human autoimmune diseases. Ankylosing spondylitis is an inflammatory autoimmune disease and evidence showed that ankylosing spondylitis may be a microbiome-driven disease.

What were the most important findings?

To investigate the relationship between the gut microbiome and ankylosing spondylitis, a quantitative metagenomics study based on deep shotgun sequencing was performed, using gut microbial DNA from 211 Chinese individuals. A total of 23,709 genes and 12 metagenomic species were shown to be differentially abundant between ankylosing spondylitis patients and healthy controls. Patients were characterized by a form of gut microbial dysbiosis that is more prominent than previously reported cases with inflammatory bowel disease. Specifically, the ankylosing spondylitis patients demonstrated increases in the abundance of Prevotella melaninogenica, Prevotella copri, and Prevotella sp. C561 and decreases in Bacteroides spp. It is noteworthy that the Bifidobacterium genus, which is commonly used in probiotics, accumulated in the ankylosing spondylitis patients. Diagnostic algorithms were established using a subset of these gut microbial biomarkers.

What are the greatest implications of this study?

Alterations of the gut microbiome are associated with development of ankylosing spondylitis. Our data suggest biomarkers identified in this study might participate in the pathogenesis or development process of ankylosing spondylitis, providing new leads for the development of new diagnostic tools and potential treatments.

What was studied?

Human schistosomiasis is a highly prevalent neglected tropical disease (NTD) caused by Schistosoma species. Research on the molecular mechanisms influencing the outcomes of bladder infection by Schistosoma haematobium is urgently needed to develop new diagnostics, therapeutics and infection prevention strategies. The objective of the research study was to determine the microbiome features and changes in urine during urogenital schistosomiasis and induced bladder pathologies.

Who was studied?

Seventy participants from Eggua, southwestern Nigeria provided morning urine samples and were screened for urogenital schistosomiasis infection and bladder pathologies in a cross-sectional study. Highthroughput NGS sequencing was carried out, targeting the 16S V3 region. Filtered reads were processed and analyzed in a bioinformatics pipeline.

What were the most important findings?

The study participants (36 males and 34 females, between ages 15 and 65) were categorized into four groups according to status of schistosomiasis infection and bladder pathology. Data analytics of the next-generation sequencing reads revealed that Proteobacteria and Firmicutes dominated and had influence on microbiome structure of both non-infected persons and persons with urogenital schistosomiasis. Furthermore, gender and age influenced taxa abundance independent of infection or bladder pathology. Several taxa distinguished urogenital schistosomiasis induced bladder pathologies from urogenital schistosomiasis infection alone and from healthy persons, including known immune-stimulatory taxa such as Fusobacterium, Sphingobacterium and Enterococcus. Some of these significant taxa, especially Sphingobacterium were projected as markers of infection, while several genera including potentially beneficial taxa such as Trabulsiella and Weissella, were markers of the non-infected. Finally, expected changes in protein functional categories were observed to relate to cellular maintenance and lipid metabolism.

What are the greatest implications of this study?

The urinary microbiome is a factor to be considered in developing biomarkers, diagnostic tools, and new treatment for urogenital schistosomiasis and induced bladder pathologies.

What was studied?

Pancreatic carcinoma (PC) is a lethal cancer. Gut microbiota is associated with some risk factors of PC, e.g. obesity and types II diabetes. However, the specific gut microbial profile in clinical PC in China has never been reported. This prospective study collected 85 PC and 57 matched healthy controls (HC) to analyze microbial characteristics by MiSeq sequencing. The results showed that gut microbial diversity was decreased in PC with an unique microbial profile, which partly attributed to its decrease of alpha diversity. Microbial alterations in PC featured by the increase of certain pathogens and lipopolysaccharides-producing bacteria, and the decrease of probiotics and butyrate-producing bacteria. Microbial community in obstruction cases was separated from the un-obstructed cases. Streptococcus was associated with the bile. Furthermore, 23 microbial functions e.g. Leucine and LPS biosynthesis were enriched, while 13 functions were reduced in PC. Importantly, based on 40 genera associated with PC, microbial markers achieves a high classification power with AUC of 0.842. In conclusion, gut microbial profile was unique in PC, providing a microbial marker for non-invasive PC diagnosis.

What was studied?

This study compared the colonic microbial composition of patients with systemic sclerosis (SSc) to that of healthy controls. Researchers used 16S ribosomal RNA sequencing on mucosal lavage samples collected from the cecum and sigmoid colon during colonoscopy. They also examined whether specific bacterial genera were associated with the presence and severity of gastrointestinal tract symptoms in the SSc patients.

Who was studied?

The study included 17 adult patients with systemic sclerosis, 88 percent of whom were female, with a median age of 52.1 years. Healthy controls were matched to the SSc patients by age and sex on a one-to-one basis. Gastrointestinal symptom burden in the SSc group was assessed with the GI Tract 2.0 score, which averaged 0.7 with a standard deviation of 0.6.

What were the most important findings?

Principal coordinate analysis showed significant differences in microbial community structure between SSc patients and healthy controls in both the cecum and sigmoid regions. Patients with SSc had decreased levels of commensal bacteria such as Faecalibacterium and Clostridium, a pattern similar to that seen in other inflammatory disease states. The abstract text provided is cut off before detailing which genera were increased in SSc patients or which specific genera correlated with GI symptoms, so those findings cannot be reported here.

What are the greatest implications of this study?

The findings suggest that systemic sclerosis is associated with a distinct colonic microbial consortium that departs from that of healthy individuals, marked by loss of beneficial commensal genera. Because this shift parallels patterns observed in other inflammatory conditions, it raises the possibility that the gut microbiome contributes to or reflects the inflammatory processes underlying SSc. This supports further investigation into the colonic microbiota as a potential factor in SSc-related gastrointestinal symptoms and as a possible target for future research or intervention.

What was studied?

This study examined whether early-life gut microbiota composition is associated with the natural resolution of cow's milk allergy over time. Fecal samples were profiled using 16s rRNA sequencing, with functional prediction performed via QIIME, PICRUSt, and STAMP. Children were followed longitudinally from infancy through age 8 years with clinical evaluation, milk-specific IgE levels, and milk skin prick testing.

Who was studied?

The cohort included 226 children with milk allergy enrolled in infancy through the Consortium of Food Allergy observational study of food allergy. Fecal samples were collected at age 3 to 16 months. Participants underwent repeated clinical follow-up at enrollment, 6 months, 12 months, and yearly thereafter until age 8 years.

What were the most important findings?

Milk allergy resolved by age 8 years in 128 of the 226 children, or 56.6 percent. Gut microbiome composition at age 3 to 6 months was significantly associated with milk allergy resolution by age 8 years. Children whose milk allergy later resolved showed enrichment of Clostridia and Firmicutes in their infant gut microbiome, and metagenome functional prediction supported a link between this early microbial composition and allergy outcome.

What are the greatest implications of this study?

The findings suggest that specific early-life gut microbiota, particularly Clostridia and Firmicutes enrichment, may promote or mark the developmental path toward outgrowing cow's milk allergy. This raises the possibility of using early infant microbiome composition as a biomarker to predict which children are more likely to resolve their milk allergy. It also points toward gut microbiota as a potential target for interventions aimed at promoting tolerance to cow's milk.

What was studied?

The available evidence suggests that alterations in gut microbiota may be tightly linked to the increase in microbial translocation and systemic inflammation in patients with human immunodeficiency virus 1 (HIV-1) infection. We profiled the fecal microbiota as a proxy of gut microbiota by parallel barcoded 454-pyrosequencing in 67 HIV-1-infected patients (32 receiving highly active antiretroviral therapy [HAART] and 35 HAART naïve) and 16 healthy controls from a Chinese population. We showed that α-diversity indices did not differ significantly between the healthy control and HIV-1-infected patients. The ratio of Firmicutes/Bacteroidetes increased significantly in HIV-1-infected patients. Several key bacterial phylotypes, including Prevotella, were prevalent in HIV-1-infected patients; whereas Phascolarctobacterium, Clostridium XIVb, Dialister and Megamonas were significantly correlated with systemic inflammatory cytokines. After short-term, effective HAART, the viral loads of HIV-1 were reduced; however, the diversity and composition of the fecal microbiota were not completely restored. and the dysbiosis remained among HIV-1-infected subjects undergoing HAART. Our detailed analysis demonstrated that dysbiosis of fecal microbiota might play an active role in HIV-1 infection. Thus, new insights may be provided into therapeutics that target the microbiota to attenuate the progression of HIV disease and to reduce the risk of gut-linked disease in HIV-1-infected patients.

What was studied?

This study examined whether the composition of the gut microbiota in infants differs between those with eczema and those without. Researchers used high-throughput sequencing of the V3-V4 hypervariable regions of the 16S rRNA gene to profile bacterial communities in fecal samples. The analysis identified 12,386 operational taxonomic units (OTUs) at 97% similarity and compared taxa abundance and composition between groups.

Who was studied?

The study was a case-control comparison of 50 infants with eczema (cases) and 51 healthy infants without eczema (controls). Fecal samples from these 101 infants were the source material for the 16S rRNA sequencing analysis. No further demographic details are given in the abstract.

What were the most important findings?

Gut microbiota differed between groups in taxa abundance, though not in overall taxonomic composition. Healthy infants showed enrichment of Bifidobacterium, Megasphaera, Haemophilus and Streptococcus. Infants with eczema showed enrichment of Escherichia/Shigella, Veillonella, Faecalibacterium, Lachnospiraceae incertae sedis and Clostridium XlVa, with Faecalibacterium prausnitzii and Ruminococcus gnavus, taxa associated with atopy or inflammation, significantly enriched in the eczema group. Higher abundance of Akkermansia muciniphila in eczematous infants was also noted and may relate to reduced intestinal barrier integrity.

What are the greatest implications of this study?

The findings support a link between altered gut bacterial abundance and eczema in infancy, pointing to specific genera and species as candidate markers of the atopic gut. The enrichment of Faecalibacterium prausnitzii alongside other inflammation-associated taxa in eczema cases suggests that microbiota composition changes may accompany, or contribute to, atopic disease processes rather than protect against them in this context. These results could inform future research into microbiota-targeted approaches for eczema risk assessment or intervention in infants.

What was studied?

Insulin-dependent or type 1 diabetes is a prototypic autoimmune disease whose incidence steadily increased over the past decades in industrialized countries. Recent evidence suggests the importance of the gut microbiota to explain this trend. Here, non-obese diabetic (NOD) mice that spontaneously develop autoimmune type 1 diabetes were treated with different antibiotics to explore the influence of a targeted intestinal dysbiosis in the progression of the disease. A mixture of wide spectrum antibiotics (i.e. streptomycin, colistin and ampicillin) or vancomycin alone were administered orally from the moment of conception, treating breeding pairs, and during the postnatal and adult life until the end of follow-up at 40 weeks. Diabetes incidence significantly and similarly increased in male mice following treatment with these two antibiotic regimens. In NOD females a slight yet not significant trend towards an increase in disease incidence was observed. Changes in gut microbiota composition were assessed by sequencing the V3 region of bacterial 16S rRNA genes. Administration of the antibiotic mixture resulted in near complete ablation of the gut microbiota. Vancomycin treatment led to increased Escherichia, Lactobacillus and Sutterella genera and decreased members of the Clostridiales order and Lachnospiraceae, Prevotellaceae and Rikenellaceae families, as compared to control mice. Massive elimination of IL-17-producing cells, both CD4+TCRαβ+ and TCRγδ+ T cells was observed in the lamina propria of the ileum and the colon of vancomycin-treated mice. These results show that a directed even partial ablation of the gut microbiota, as induced by vancomycin, significantly increases type 1 diabetes incidence in male NOD mice thus prompting for caution in the use of antibiotics in pregnant women and newborns.

What was studied?

Preterm birth is the second leading cause of death in children under the age of five years worldwide, but the etiology of many cases remains enigmatic. The dogma that the fetus resides in a sterile environment is being challenged by recent findings and the question has arisen whether microbes that colonize the fetus may be related to preterm birth. It has been posited that meconium reflects the in-utero microbial environment. In this study, correlations between fetal intestinal bacteria from meconium and gestational age were examined in order to suggest underlying mechanisms that may contribute to preterm birth.

Who was studied?

Meconium from 52 infants ranging in gestational age from 23 to 41 weeks was collected, the DNA extracted, and 16S rRNA analysis performed. Resulting taxa of microbes were correlated to clinical variables and also compared to previous studies of amniotic fluid and other human microbiome niches.

What were the most important findings?

Increased detection of bacterial 16S rRNA in meconium of infants of <33 weeks gestational age was observed. Approximately 61·1% of reads sequenced were classified to genera that have been reported in amniotic fluid. Gestational age had the largest influence on microbial community structure (R = 0·161; p = 0·029), while mode of delivery (C-section versus vaginal delivery) had an effect as well (R = 0·100; p = 0·044). Enterobacter, Enterococcus, Lactobacillus, Photorhabdus, and Tannerella, were negatively correlated with gestational age and have been reported to incite inflammatory responses, suggesting a causative role in premature birth.

What are the greatest implications of this study?

This provides the first evidence to support the hypothesis that the fetal intestinal microbiome derived from swallowed amniotic fluid may be involved in the inflammatory response that leads to premature birth.

What was studied?

Eighty-one stool samples from Taiwanese were collected for analysis of the association between the gut flora and obesity. The supervised analysis showed that the most, abundant genera of bacteria in normal samples (from people with a body mass index (BMI) ≤ 24) were Bacteroides (27.7%), Prevotella (19.4%), Escherichia (12%), Phascolarctobacterium (3.9%), and Eubacterium (3.5%). The most abundant genera of bacteria in case samples (with a BMI ≥ 27) were Bacteroides (29%), Prevotella (21%), Escherichia (7.4%), Megamonas (5.1%), and Phascolarctobacterium (3.8%). A principal coordinate analysis (PCoA) demonstrated that normal samples were clustered more compactly than case samples. An unsupervised analysis demonstrated that bacterial communities in the gut were clustered into two main groups: N-like and OB-like groups. Remarkably, most normal samples (78%) were clustered in the N-like group, and most case samples (81%) were clustered in the OB-like group (Fisher's P  value = 1.61E - 07). The results showed that bacterial communities in the gut were highly associated with obesity. This is the first study in Taiwan to investigate the association between human gut flora and obesity, and the results provide new insights into the correlation of bacteria with the rising trend in obesity.

What was studied?

The study characterized the microbiota of colorectal carcinoma to assess whether specific microbial community changes are associated with the tumor microenvironment. It used a genomics-first approach, profiling tumor tissue against matched normal tissue and validating candidate organisms with independent molecular methods.

Who was studied?

The discovery set consisted of whole genome sequences from nine colorectal tumor/normal tissue pairs. Findings were then validated in 95 carcinoma/normal DNA pairs using quantitative PCR and 16S rDNA sequence analysis, with additional in situ confirmation by fluorescence in situ hybridization (FISH).

What were the most important findings?

Fusobacterium sequences were enriched in carcinomas relative to matched normal tissue, a result confirmed by quantitative PCR and 16S rDNA sequencing, whereas the Bacteroidetes and Firmicutes phyla were depleted in tumors. Fusobacteria were also directly visualized within colorectal tumors by FISH, supporting their physical presence in the tumor tissue.

What are the greatest implications of this study?

The authors conclude that colorectal cancer is associated with distinct alterations in the tumor microbiota, notably Fusobacterium enrichment. Because this is an observational, association-based analysis, causation is not established, and the authors state that the precise role of Fusobacteria in colorectal carcinoma pathogenesis requires further investigation.

What was studied?

This study examined whether human intestinal microbes play a role in the autoimmunity that often leads to type 1 diabetes (T1D), building on prior murine and rat models linking gut bacteria to diabetes onset. Researchers used high-throughput, culture-independent sequencing approaches to profile gut bacterial communities over time. They tracked how bacterial composition and diversity changed as autoimmunity developed, comparing children who progressed to T1D-associated autoimmunity with those who did not.

Who was studied?

The subjects were young children at high genetic risk for type 1 diabetes. Autoimmune cases were compared over time against age-matched, genotype-matched, nonautoimmune control children. The abstract does not give an exact sample size, but the design followed this at-risk pediatric cohort longitudinally as they moved from infancy toward the toddler stage.

What were the most important findings?

Bacterial diversity diminished over time in children who developed autoimmunity, relative to matched nonautoimmune controls. A single species, Bacteroides ovatus, accounted for nearly 24% of the total increase in the phylum Bacteroidetes in autoimmune cases compared with controls. Conversely, a human Firmicute strain (CO19) represented nearly 20% of the increase in Firmicutes seen in controls over the same period, a pattern opposite to what was seen in cases.

What are the greatest implications of this study?

The findings support the idea that healthy infants develop increasingly stable, more diverse microbiomes as they approach toddlerhood, while children destined for autoimmunity show a different, less stable trajectory. This suggests specific microbial shifts, including loss of certain Firmicutes and expansion of Bacteroides ovatus, may be linked to the immune processes preceding type 1 diabetes. The results point toward the gut microbiome as a potential early marker or contributor to autoimmune risk in genetically susceptible children, warranting further work to define an autoimmune-associated microbiome signature.

What was studied?

The mosquito gut represents an ecosystem that accommodates a complex, intimately associated microbiome. It is increasingly clear that the gut microbiome influences a wide variety of host traits, such as fitness and immunity. Understanding the microbial community structure and its dynamics across mosquito life is a prerequisite for comprehending the symbiotic relationship between the mosquito and its gut microbial residents. Here we characterized gut bacterial communities across larvae, pupae and adults of Anopheles gambiae reared in semi-natural habitats in Kenya by pyrosequencing bacterial 16S rRNA fragments. Immatures and adults showed distinctive gut community structures. Photosynthetic Cyanobacteria were predominant in the larval and pupal guts while Proteobacteria and Bacteroidetes dominated the adult guts, with core taxa of Enterobacteriaceae and Flavobacteriaceae. At the adult stage, diet regime (sugar meal and blood meal) significantly affects the microbial structure. Intriguingly, blood meals drastically reduced the community diversity and favored enteric bacteria. Comparative genomic analysis revealed that the enriched enteric bacteria possess large genetic redox capacity of coping with oxidative and nitrosative stresses that are associated with the catabolism of blood meal, suggesting a beneficial role in maintaining gut redox homeostasis. Interestingly, gut community structure was similar in the adult stage between the field and laboratory mosquitoes, indicating that mosquito gut is a selective eco-environment for its microbiome. This comprehensive gut metatgenomic profile suggests a concerted symbiotic genetic association between gut inhabitants and host.

What was studied?

This study examined how diet shapes gut microbial composition by comparing the fecal microbiota of children eating different diets. Researchers used high-throughput 16S rDNA sequencing together with biochemical analyses to characterize bacterial community composition and short-chain fatty acid output. The design set a fiber-rich, agrarian-style diet against a modern European diet to test whether microbiota differ along with dietary pattern.

Who was studied?

The study compared fecal samples from European children (EU) with those from children living in a rural African village in Burkina Faso (BF). The BF children's diet was high in fiber content and described as similar to the diet of early human settlements around the birth of agriculture. Exact sample sizes are not given in the abstract, but the comparison was structured as two defined pediatric cohorts, one European and one rural Burkinabe.

What were the most important findings?

BF children showed significant enrichment in Bacteroidetes and depletion in Firmicutes compared to EU children (P < 0.001). BF children also had a unique abundance of Prevotella and Xylanibacter, genera known to carry genes for cellulose and xylan hydrolysis, which were completely absent in EU children. BF children produced significantly more short-chain fatty acids than EU children (P < 0.001). Enterobacteriaceae, specifically Shigella and Escherichia, were significantly underrepresented in BF children relative to EU children (P < 0.05).

What are the greatest implications of this study?

The findings support the idea that gut microbiota coevolved with a polysaccharide-rich diet, helping BF children extract more energy from fiber through bacterial fermentation to short-chain fatty acids. The reduced abundance of Enterobacteriaceae, including Shigella and Escherichia, in the high-fiber BF group suggests diet may also influence the balance between beneficial fiber-degrading bacteria and potentially pathogenic Enterobacteriaceae. Together these results indicate that dietary pattern is a major driver of gut microbial ecology in children, with possible downstream effects on metabolic energy harvest and gut colonization resistance.