Saccharomyces

What was studied?

COVID-19 has had a profound impact on public health globally. However, most studies have focused on patients with long COVID or those in the acute phase of infection, with limited research on the health of individuals who have recovered from mild COVID-19. This study investigates the long-term changes in bacterial and fungal communities in individuals recovering from mild COVID-19 and their clinical relevance.

Who was studied?

Healthy individuals from Hainan Province were enrolled before the COVID-19 outbreak, along with individuals recovering from COVID-19 at 3 months and 6 months post-recovery. Stool, blood samples, and metadata were collected. Metagenomic sequencing and Internal Transcribed Spacer (ITS) analysis characterized bacterial and fungal communities, while bacterial-fungal co-occurrence networks were constructed. A random forest model evaluated the predictive capacity of key taxa.

What were the most important findings?

The gut microbiota of COVID-19 recoverees differed significantly from that of healthy individuals. At 3 months post-recovery, probiotics (e.g., Blautia massiliensis and Kluyveromyces spp.) were enriched, linked to improved metabolism, while at 6 months, partial recovery of probiotics (e.g., Acidaminococcus massiliensis and Asterotremella spp.) was observed alongside persistent pathogens (e.g., Streptococcus equinus and Gibberella spp.). Dynamic changes were observed, with Acidaminococcus massiliensis enriched at both baseline and 6 months but absent at 3 months. Co-occurrence network analysis revealed synergies between bacterial (Rothia spp.) and fungal (Coprinopsis spp.) taxa, suggesting their potential roles in gut restoration. The bacterial random forest model (10 taxa) outperformed the fungal model (8 taxa) in predicting recovery status (AUC = 0.99 vs. 0.80).

What are the greatest implications of this study?

These findings highlight the significant long-term impacts of mild COVID-19 recovery on gut microbiota, with key taxa influencing metabolism and immune regulation, supporting microbiome-based strategies for recovery management.

What was studied?

This cross-sectional study examined how chronic psychological stress relates to gut microbiota composition and microbiota-derived metabolites in adolescents. Researchers used validated stress instruments to stratify participants by stress level, then profiled fecal microbiota using 16S rRNA gene sequencing across the full sample. A subset also underwent deeper metagenomic sequencing and untargeted metabolomics to characterize functional and metabolic differences tied to stress. The aim was to clarify a multi-omics gut-stress relationship that remains understudied in adolescent populations.

Who was studied?

The study population was 124 adolescents aged 12 to 16 years, assessed with the Adolescent Life Events Scale and the Study Stress Scale. Participants were divided into low stress (n=42), medium stress (n=41), and high stress (n=41) groups based on these measures. A smaller subset of 30 high-stress and 29 low-stress adolescents was selected for the additional metagenomic and metabolomic analyses. All participants provided fecal samples for microbiota testing.

What were the most important findings?

Adolescents with high chronic stress showed lower gut microbial alpha diversity, distinct beta diversity, and a more complex microbial co-occurrence network compared to lower-stress peers. Statistical testing identified five bacterial genera reduced in abundance among high-stress adolescents, including Faecalibacterium, Bacteroides, Akkermansia, and an unclassified Lachnospiraceae genus. These genera are commonly associated with short-chain fatty acid production and gut barrier support, suggesting stress corresponds with a less favorable, lower-diversity microbial community. The abstract text was truncated before metabolomic results could be fully detailed.

What are the greatest implications of this study?

The findings support a link between chronic psychological stress and a disrupted, less diverse gut microbiota in adolescents, a population where this multi-omics relationship has been little studied. Depletion of genera like Faecalibacterium, Bacteroides, and Akkermansia points toward reduced capacity for beneficial microbial functions under high stress. This raises the possibility that gut microbiota profiles could serve as biomarkers of chronic stress exposure or as targets for intervention in stressed youth. Further work integrating the metabolomic data would help clarify the mechanistic pathways connecting stress, microbiota, and adolescent health.

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 analyzed a newly built resource called curatedMetagenomicData (cMD) 3, a uniformly processed collection of over 22,000 human microbiome samples with manually curated metadata. The researchers combined data across 94 studies and 42 countries to make large-scale meta-analysis possible, something that had been difficult due to a lack of standardization across public datasets. Using this resource, they searched for microbial species and functions associated with host traits and disease status. They also developed a new metric, the oral enrichment score (OES), based on the relative abundance in the gut of bacteria that are typically found in the oral cavity rather than the gut.

Who was studied?

The analysis drew on more than 22,000 human microbiome samples aggregated from 94 separate studies conducted across 42 countries. This is a public, pooled metagenomic dataset rather than a single original cohort recruited for this study. The abstract does not give specific demographic breakdowns beyond noting that sex, age, body mass index, and disease status were among the host variables examined across this large, internationally diverse sample collection.

What were the most important findings?

The meta-analysis identified hundreds of microbial species and thousands of microbial functions that were significantly associated with a person's sex, age, body mass index, and disease status. The team catalogued these associations as a reference resource for the field. Most notably, they found that a higher oral enrichment score (OES), meaning greater relative abundance of oral-type bacteria in the gut, was a consistent feature of individuals with disease. The overall patterns identified across the dataset were described as modest but widely shared across the many studies pooled together.

What are the greatest implications of this study?

The findings suggest that OES can serve as a simple, quantifiable signal of altered gut microbiome health, since oral bacteria showing up in the gut appears to track with disease status across many different conditions and populations. Because cMD 3 is described as reproducible and readily updatable, it offers an ongoing reference dataset that other researchers can use to validate microbiome-disease associations. This kind of large, standardized meta-analysis approach could help establish more generalizable, cross-study biomarkers of microbiome health rather than relying on findings from single, smaller cohorts.

What was studied?

The association between the gut mycobiome and its potential influence on host metabolism in the Thai Cohort was assessed. Two distinct predominant enterotypes, Saccharomyces (Sa) and Aspergillus/Penicillium (Ap/Pe) showed differences in gut mycobiota diversity and composition. Notably, the Sa enterotype exhibited lower evenness and richness, likely due to the prevalence of Saccharomyces, while both enterotypes displayed unique metabolic behaviors related to nutrient metabolism and body composition. Fiber consumption was positively correlated with adverse body composition and fasting glucose levels in individuals with the Sa enterotype, whereas in the Ap/Pe enterotype it was positively correlated with fat and protein intake. The metabolic functional analysis revealed the Sa enterotype associated with carbohydrate metabolism, while the Ap/Pe enterotype involved in lipid metabolism. Very interestingly, the genes involved in the pentose and glucuronate interconversion pathway, such as polygalacturonase and L-arabinose-isomerase, were enriched in the Sa enterotype signifying a metabolic capacity for complex carbohydrate degradation and utilization of less common sugars as energy sources. These findings highlight the interplay between gut mycobiome composition, dietary habits, and metabolic outcomes within the Thai cohort studies.

What was studied?

Recent studies have more focused on gut microbial alteration in tuberculosis (TB) patients. However, no detailed study on gut fungi modification has been reported till now. So, current research explores the characteristics of gut microbiota (bacteria)- and mycobiota (fungi)-dysbiosis in TB patients and also assesses the correlation between the gut microbiome and serum cytokines. It may help to screen the potential diagnostic biomarker for TB.

What were the most important findings?

The results show that the alpha diversity of the gut microbiome (including bacteria and fungi) decreased and altered the gut microbiome composition of TB patients. The bacterial genera Bacteroides and Prevotella were significantly increased, and Blautia and Bifidobacterium decreased in the TB patients group. The fungi genus Saccharomyces was increased while decreased levels of Aspergillus in TB patients. It indicates that gut microbial equilibrium between bacteria and fungi has been altered in TB patients. The fungal-to-bacterial species ratio was significantly decreased, and the bacterial-fungal trans-kingdom interactions have been reduced in TB patients. A set model including Bacteroides, Blautia, Eubacterium_hallii_group, Apiotrichum, Penicillium, and Saccharomyces may provide a better TB diagnostics option than using single bacterial or fungi sets. Also, gut microbial dysbiosis has a strong correlation with the alteration of IL-17 and IFN-γ.

What are the greatest implications of this study?

Our results demonstrate that TB patients exhibit the gut bacterial and fungal dysbiosis. In the clinics, some gut microbes may be considered as potential biomarkers for auxiliary TB diagnosis.

What was studied?

This cross-sectional study examined the oral fungal microbiota (mycobiome) in patients with schizophrenia compared to healthy controls. Researchers sampled tongue coating and used internal transcribed spacer 1 (ITS1) amplicon sequencing to characterize fungal communities. They also measured host immune markers with multiplex immunoassays to see whether fungal changes tracked with systemic inflammation.

Who was studied?

The study enrolled 118 Chinese patients with schizophrenia and 97 age-matched healthy controls. Fungal profiling was based on tongue coating samples from these participants. The abstract does not report additional demographic details such as sex distribution or illness duration.

What were the most important findings?

Schizophrenia patients had reduced oral fungal richness and significant differences in overall fungal community composition (beta-diversity) compared to healthy controls. Within the fungal community, two mycotypes emerged: a Candida-dominant type and a Malassezia-dominant type, with schizophrenia patients showing increased Malassezia and decreased Candida relative to controls. Patients also showed immune dysfunction, with elevated pro-inflammatory cytokines (IL-6, TNF-alpha) and chemokines (MIP-1alpha, MCP-1); the Malassezia mycotype correlated positively with these inflammatory markers, while the Candida mycotype correlated negatively with them.

What are the greatest implications of this study?

The findings suggest oral fungal dysbiosis, marked by a shift away from Candida toward Malassezia, may be linked to the systemic immune dysregulation seen in schizophrenia. Because these mycotypes tracked oppositely with inflammatory cytokines, oral fungal profiling could serve as a non-invasive diagnostic biomarker candidate for schizophrenia. The results also point toward the oral mycobiome as a potential axis connecting microbial dysbiosis to neuroimmune dysfunction, warranting further mechanistic and longitudinal study.

What was studied?

This study characterized the oral fungal microbiota, or mycobiome, in patients with COVID-19 and in recovered patients. Researchers used internal transcribed spacer (ITS) sequencing on tongue coating specimens to profile fungal communities. They compared fungal richness, diversity, and composition across COVID-19 patients, suspected cases, recovered patients, and controls, and examined correlations between distinct fungi and bacteria.

Who was studied?

The cohort included 71 COVID-19 patients, 36 suspected cases (SCs), 22 recovered COVID-19 patients, 36 SCs who recovered, and 132 controls, all from Henan. Tongue coating specimens were collected from each group for fungal sequencing. The study also used training, testing, and independent cohorts to validate a diagnostic classifier built from the sequencing data.

What were the most important findings?

Oral fungal richness was increased in COVID-19 patients compared to controls, and beta diversity analysis showed distinct fungal community structures between the two groups. The ratio of Ascomycota to Basidiomycota was higher in COVID-19 patients, and opportunistic genera including Candida, Saccharomyces, and Simplicillium were increased. A classifier built from two fungal biomarkers distinguished COVID-19 patients from controls across training, testing, and independent cohorts, and correctly identified SCs with positive SARS-CoV-2 IgG antibodies as COVID-19 patients.

What are the greatest implications of this study?

The findings suggest the oral mycobiome, including enrichment of opportunistic fungi such as Candida, may play a role in COVID-19 pathophysiology. Fungal biomarkers from tongue coating samples show potential as a noninvasive diagnostic tool for identifying COVID-19 cases, including those missed by other testing approaches. The documented correlations between oral fungi and bacteria point to cross-kingdom microbial interactions that merit further investigation in respiratory viral infection.

What was studied?

Polycystic ovary syndrome (PCOS) is a serious disease characterized by high androgen, insulin resistance (IR), hyperglycemia, and obesity, leading to infertility. The gut mycobiota has been reported to evolve in metabolic diseases including obesity, hyperglycemia, and fatty liver. However, little is known about the gut mycobiota and PCOS. In the current study, we recruited 17 PCOS patients and 17 age-matched healthy controls for community structure and functional analysis of the gut mycobiota. The results showed that PCOS patients have reduced diversity and richness of the gut microbiota compared with healthy controls. β-Diversity analysis showed that the community structure of the gut microbiota of patients with PCOS was significantly different from healthy controls. At the phylum level, PCOS patients have reduced Basidiomycota and increased Ascomycota compared with healthy controls. At the family level, the higher relative abundance of Saccharomycetaceae and lower Trichosporonaceae and Ascomycota_unclassified were detected in PCOS patients than in healthy controls. At the genus level, different microbial compositions were also observed between PCOS patients and healthy controls. In addition, PICRUSt2 showed that patients with PCOS have different microbial functions in the gut compared with healthy controls. LEfSe indicated that Saccharomyces and Lentinula were enriched in the fecal samples of PCOS patients, while Aspergillus was depleted compared with healthy controls. Our finding indicates that PCOS patients have different community structures and functions of the gut mycobiota, which provides new insight into PCOS pathogenesis and intervention. IMPORTANCE It was found that intestinal fungi as well as serum metabolites in PCOS patients were significantly different from those in healthy subjects. However, no studies have been done to show exactly which fungus interacts with which bacteria in humans or which fungus acts alone. As fungal research progresses, it will be possible to fill this gap.

What was studied?

Amphibian skin harbors microorganisms that are associated with the fungal pathogen Batrachochytrium dendrobatidis (Bd), which causes chytridiomycosis, one of the most significant wildlife diseases known. This pathogen originated in Asia, where diverse Bd lineages exist; hence, native amphibian hosts have co-existed with Bd over long time periods. Determining the nuances of this co-existence is crucial for understanding the prevalence and spread of Bd from a microbial context. However, associations of Bd with the natural skin microbiome remain poorly understood for Asian hosts, especially in relation to skin-associated fungi. We used 16 S rRNA and fungal internal transcribed spacer (ITS) gene sequencing to characterize the skin microbiome of four native Asian amphibian species and examined the relationships between Bd infection and their skin bacterial and fungal communities; we also analyzed the correlates of the putative anti-Bd bacteria. We show that both skin bacterial and fungal community structure and composition had significant associations with infection status (Bd presence/absence) and infection intensity (frequency of Bd sequence reads). We also found that the putative anti-Bd bacterial richness was correlated with Bd infection status and infection intensity, and observed that the relative abundance of anti-Bd bacteria roughly correspond with changes in both Bd prevalence and mean infection intensity in populations. Additionally, the microbial co-occurrence network of infected frogs was significantly different from that of uninfected frogs that were characterized by more keystone nodes (connectors) and larger proportions in correlations between bacteria, suggesting stronger inter-module bacterial interactions. These results indicate that the mutual effects between Bd and skin-associated microbiome, including the interplay between bacteria and fungi, might vary with Bd infection in susceptible amphibian species. This knowledge will help in understanding the dynamics of Bd from a microbial perspective, potentially contributing to mitigate chytridiomycosis in other regions of the world.

What was studied?

The studies on microbiome in the human digestive tract indicate that fungi could also be one of the external factors affecting development of diabetes. The aim of this study was to evaluate the quantitative and qualitative mycobiome composition in the colon of the adults with type 1 (T1D), n = 26 and type 2 (T2D) diabetes, n = 24 compared to the control group, n = 26. The gut mycobiome was characterized in the stool samples using the analysis of the whole internal transcribed spacer (ITS) region of the fungal rDNA gene cluster by next-generation sequencing (NGS) with increased sensitivity. At the L2 (phylum) level, Basidiomycota fungi were predominant in all 3 study groups. Group T1D presented significantly lower number of Ascomycota compared to the T2D group, and at the L6 (genus) level, the T1D group presented significantly lower number of Saccharomyces genus compared to control and T2D groups. In the T1D group, a significant positive correlation between total cholesterol and low-density lipoprotein cholesterol (LDL-C) levels and fungi of the genus Saccharomyces, and in the T2D group, a negative correlation between the total cholesterol level and Malassezia genus was found. The obtained results seem to be a good foundation to extend the analysis of the relationship between individual genera and species of fungi and the parameters determining the metabolism of carbohydrates and lipids in the human body.

What was studied?

This study examined whether gut microbiota composition is associated with fever in patients with moderate COVID-19. Researchers compared clinical features and laboratory results between patients with and without fever, and identified inflammatory markers linked to fever. They then conducted a gut metagenome-wide association study to characterize the microbes and microbial epitopes potentially involved in fever and hyperinflammation.

Who was studied?

The cohort included 187 patients with moderate COVID-19, of whom 127 (67.9 percent) presented with fever and the remainder did not. A subset of 31 individuals from this group underwent gut metagenome-wide association analysis to identify microbial features linked to fever and hyperinflammation. The abstract does not provide further demographic details such as age or sex distribution.

What were the most important findings?

Patients with fever showed significantly reduced lymphocytes, CD3+ T cells, CD4+ T cells, and CD4+ to CD8+ T cell ratios, alongside significantly elevated AST, LDH, CRP, IL-6, and IL-10. Gut microbiome composition differed significantly between patients with fever and those without. Opportunistic pathogens, including Enterococcus faecalis and Saccharomyces cerevisiae, were enriched in patients with fever, and E. faecalis abundance was positively correlated with LDH and D-dimer levels.

What are the greatest implications of this study?

These findings suggest that gut microbiota dysbiosis, particularly enrichment of opportunistic pathogens such as Enterococcus faecalis, may be linked to the abnormal immune responses and inflammation seen in febrile moderate COVID-19 patients. This raises the possibility that gut microbes or their components contribute to fever and hyperinflammation in this population. The results point to gut microbiota as a potential area of interest for understanding COVID-19 severity and prognosis in moderate cases.

What was studied?

Seborrheic dermatitis (SD) is a recurrent common inflammatory skin disease that affects all ethnic groups in all regions worldwide. However, no specific treatment or preventive measure is yet available. Identifying effective treatments with acceptable safety and tolerability is desirable. In this study, scalp microbiota alterations were measured in SD, showing significantly greater abundance of Malassezia and Staphylococcus and diminished fungal and bacterial diversity compared with healthy controls. We investigated the benefit of a 4-week treatment with 0.5 mg ml-1 recombinant human thymosin β4 (rhTβ4) gel or 2% ketoconazole lotion on the scalp condition of 71 patients with SD compared with 21 healthy individuals. Clinical assessment (Adherent Scalp Flaking Score, and the Maximum Erythema Area) and physiological conditions (transepidermal water loss, hydration, and sebum secretion) were evaluated. The rhTβ4 treatment provided significantly greater efficacy than ketoconazole and a sustained effect in the treatment of scalp SD. More importantly, rhTβ4 dramatically improved the microbiome homeostasis and prompted a shift of scalp microflora towards healthy composition, helping symptoms and ameliorating physiological conditions more effectively and durably than ketoconazole. Our research demonstrated the scalp microbe dysbiosis of SD and highlighted rhTβ4 as a promising therapeutic strategy in the prevention and treatment of SD.

What was studied?

The human cervicovaginal microbiota resides at an interface between the host and the environment and may affect susceptibility to disease. Puerto Rican women have high human papillomavirus (HPV) infection and cervical cancer rates. We hypothesized that the population structure of the cervicovaginal bacterial and fungal biota changed with cervical squamous intraepithelial lesions and HPV infections. DNA was extracted from cervix, introitus, and anal sites of 62 patients attending high-risk San Juan clinics. The 16S rRNA V4 region and ITS-2 fungal regions were amplified and sequenced using Illumina technology. HPV genotyping was determined by reverse hybridization with the HPV SPF10-LiPA25 kit. HPV prevalence was 84% of which ∼44% subjects were infected with high-risk HPV, ∼35% were co-infected with as many as 9 HPV types and ∼5% were infected with exclusively low-risk HPV types. HPV diversity did not change with cervical dysplasia. Cervical bacteria were more diverse in patients with CIN3 pre-cancerous lesions. We found enrichment of Atopobium vaginae and Gardnerella vaginalis in patients with CIN3 lesions. We found no significant bacterial biomarkers associated with HPV infections. Fungal diversity was significantly higher in cervical samples with high-risk HPV and introitus samples of patients with Atypical Squamous Cells of Undetermined Significance (ASCUS). Fungal biomarker signatures for vagina and cervix include Sporidiobolaceae and Sacharomyces for ASCUS, and Malassezia for high-risk HPV infections. Our combined data suggests that specific cervicovaginal bacterial and fungal populations are related to the host epithelial microenvironment, and could play roles in cervical dysplasia.