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The Baby Biome Study is currently the largest genomic analysis of infant microbiomes. A collaborative effort by team of UK researchers from the Wellcome Sanger Institute, University of College London, and the University of Birmingham, this project aims to “understand how interactions between microorganisms, the immune system, and clinical, social, and behavioral factors during pregnancy and early life influence later health and disease.” Established in 2014, the Baby Biome Study has since recruited thousands of mother-infant pairs and collected stool samples, vaginal swabs, and umbilical cord blood for microbial analytics with the hope of longitudinal follow up to assess trends over time.

“…those delivered vaginally were found to have more healthy or ‘commensal’ gut bacteria…”

In an initial study published in Nature in 2019, Dr. Yan Shao and colleagues shared their findings that birth method impacted babies’ gut microbiomes: those delivered vaginally were found to have more healthy or “commensal” gut bacteria (Bifidobacterium and Bacterioides species) than those delivered via caesarean section. The latter also had a higher prevalence of hospital acquired potentially disease causing or “opportunistic” microbes including species of Enterococcus, Enterobacter, and Klebsiella.

Building upon their prior work, the authors published new research earlier this month (Sept 2024) in Nature Microbiology revealing that neonatal gut microbiota can be divided into three primary communities dominated by a single microbial species. They assessed a dataset including 2,387 gut microbiota samples from 1,288 healthy UK neonates (< 1 month old) and identified three main bacterial species: Bifidobacterium longum, Bifidobacterium breve, and Enterococcus faecalis as predominant or “driver” species in each respective community state.

“Infant sex, maternal ethnicity, age, and number of prior births also impacted predominant bacterial community states.”

To assess factors influencing community states, researchers performed epidemiological analyses of clinical and sociodemographic variables to find that Enterococcus faecalis was associated with caesarian section birth, maternal administration of antibiotics during labor. Infant sex, maternal ethnicity, age, and number of prior births also impacted predominant bacterial community states. Most vaginally delivered infants with Bifidobacterium predominant community states during week 1 after birth, retained these states when resampled in week 3 (reflecting microbial stability) as opposed to those with Enterococcus predominant community. This dominance of Bifidobacterium extended into infancy when resampled at 6-12 months.

“…potentially related to differences in composition of breast milk.”

Bifidobacterium longum species predominance seemed linked to factors such as vaginal delivery and absence of maternal antibiotic use, whereas Bifidobacterium breve predominance seemed associated with maternal ethnicity, potentially related to differences in composition of breast milk. A Enterococcus faecalis predominant community state seemed related to higher pathogen colonization into infancy.

While there is much more research needed to better elucidate the above findings, this impressive work is beginning to lay the foundation for practical clinical applications. This may include use of probiotics targeted to supplement neonate or infant microbiomes and potentially improve pathogen resistance during this vulnerable stage of life.