Association between clinical and environmental factors and the gut microbiota profiles in young South African childrenOriginal paper
Karen Pendergrass is a microbiome researcher specializing in microbiome-targeted interventions (MBTIs). She systematically analyzes scientific literature to identify microbial patterns, develop hypotheses, and validate interventions. As the founder of the Microbiome Signatures Database, she bridges microbiome research with clinical practice. In 2012, based on her own investigative research, she became the first documented case of FMT for Celiac Disease, four years before the first published case study.
Read MoreWhat was studied?
This study described the baseline gut bacterial microbiota of urban South African children under 5 years old. It tested how demographic, clinical, and environmental factors shape those profiles. Researchers collected one stool sample per child and sequenced the 16S rRNA gene V4 region on the Illumina MiSeq platform. They compared bacterial richness, evenness, and community structure across age groups and exposures. Diversity was assessed with Shannon and Faith indices, and differential taxa were found using ANCOM.
Who was studied?
The cohort was 115 children under 5 years old from urban Cape Town communities, analyzed after one sample failed purity checks. The median age was 32 months, and 60 (52.2%) were boys. All children were household contacts of an adult with multidrug-resistant tuberculosis, nested in the TB-CHAMP trial. Only one child was HIV-positive. Children were grouped by age: group A (0 to 1 year, n=24), group B (over 1 to 2 years, n=25), and group C (over 2 to 5 years, n=66).
What were the most important findings?
Age was the main driver of microbiota differences, with richness and evenness rising through the first 3 years then stabilizing. After infancy the gut bacteria were dominated by Firmicutes and Bacteroidota. Children under 1 year had more Proteobacteria (16.6%) and Actinobacteriota (9.8%) than those over 2 years (4.6% and 2.9%). Children aged 2 to 5 years were dominated by Firmicutes (45.1%) and Bacteroidota (44.9%). Antibiotics within 2 weeks lowered diversity (p=0.005), as did indoor wood or paraffin cooking fires (p=0.004). Deworming (p=0.029) and living with pets (p=0.03) raised diversity.
What are the greatest implications of this study?
These profiles give a rare baseline for relatively healthy children in an under-studied urban African setting. The abundance of taxa linked to good health suggests low overall dysbiosis in this population. Recent antibiotics and indoor cooking fires marked the children at greatest risk for diversity loss. This supports continued microbial surveillance where such exposures are common. Because diet was not recorded and age-stratified subgroups were small, associations are observational and cannot establish cause.