Early Gut Bacteria Differ Between Vaginal and C-Section Births, Study Finds

A new study published today, November 4, 2025, reveals significant differences in the gut microbiome of babies born vaginally versus those delivered via Cesarean section, with potential implications for early health and immune development.

Researchers found that by day seven, vaginally-born babies typically hosted either B. longum or B. brevae in their digestive tracts, while babies born via C-section were more likely colonized by E. faecalis. The study also confirmed that bacteria are primarily transferred from a mother’s gut to her baby, not her vagina, resulting in vaginally-born babies having gut microbiomes more closely resembling their mothers’. Conversely, C-section babies showed a greater presence of bacteria commonly found in hospital environments.

“E. faecalis is a bacteria that’s associated with opportunistic infection. So if your immune system is not working very well, it can cause disease,” explained researcher Field. While these differences largely evened out by a baby’s first birthday, the study tracked over 1,000 infants and found a correlation between early gut bacteria and health outcomes. Specifically, babies with B. longum dominance were approximately half as likely to be hospitalized for respiratory tract infections within their first two years of life. Understanding the importance of infection control is crucial in these early stages.

These findings suggest that the absence of beneficial gut bacteria like B. longum could potentially contribute to the slightly elevated risk of inflammatory conditions – such as asthma, allergies, autoimmune disorders, and obesity – sometimes seen in babies born via C-section, though further research is needed to establish a definitive link. This research builds on growing understanding of the human microbiome and its impact on overall health.

Researchers will continue to monitor the long-term health trajectories of the study participants to further investigate the lasting effects of early gut microbiome composition.