Infant Gut Microbiota Development and Influencing Factors

The establishment of the gut microbiota during infancy is a finely tuned ecological process that begins at birth and evolves rapidly over the first months of life. Initial community assembly is shaped by maternal microbial transmission, the mode of delivery and early feeding practices, which set the stage for a succession of dominant taxa. Vaginal birth typically seeds the infant gut with maternal bifidobacteria and Bacteroidota, while caesarean delivery often delays colonisation by these beneficial groups and permits transient overgrowth of skin‐associated or environmental taxa. Breastfeeding further reinforces the dominance of infant‐adapted bifidobacteria through human milk oligosaccharides, whereas formula feeding and early antibiotic exposure can shift community trajectories towards increased Proteobacteria and a more diverse resistome. Beyond these perinatal factors, household environment, sibling contact and geographic setting contribute to ongoing microbial influx, leading to maturation of a more complex ecosystem by the end of the first year. This developmental choreography influences immune education, metabolic programming and resistance to pathogen colonisation, with deviations from the normal succession pattern linked to later risk of allergic, metabolic and inflammatory disorders.

Research from Nature Portfolio

Recent studies have delineated the critical role of primary colonisers in directing neonatal microbiota assembly. Longitudinal metagenomic analysis of over a thousand neonates identified three distinct community states dominated by single species, with Bifidobacterium longum and B. breve pioneers driving stable succession and robust colonisation resistance to pathogens. In contrast, communities led by Enterococcus faecalis exhibited stochastic assembly and persistent high pathogen loads. Experimental models confirmed strain-specific priority effects of B. breve in conferring pathogen resistance, underlining the importance of early bifidobacterial dominance. Complementary work employing dual culture-based and metagenomic approaches clarified maternal–infant strain transfer, revealing that nearly half of mother–infant dyads share bifidobacterial strains. Vaginal delivery, spontaneous rupture of membranes and avoidance of intrapartum antibiotics were key facilitators of transfer. The study further demonstrated that cultivation and metagenomics capture complementary aspects of strain transmission, emphasising the need for combined methodologies to map early microbial inheritance accurately.

Infant Gut Microbiota Development and Influencing Factors publication trend

The graph below shows the total number of articles in infant gut microbiota development and influencing factors across all publications each year (not limited to Nature Index journals).

Technical terms

Gut microbiota: The collection of microorganisms, including bacteria, archaea and fungi, inhabiting the intestinal tract.

Primary succession: The initial colonisation and sequential establishment of microbial communities in a previously uncolonised environment.

Priority effects: The influence that early‐arriving species exert on the assembly and function of an ecological community.

Resistome: The repertoire of antimicrobial resistance genes present within a microbial community.

Colonisation resistance: The ability of a resident microbial community to prevent pathogen establishment through competition and inhibitory mechanisms.

Metagenomics: The study of genetic material recovered directly from environmental or host‐associated microbiota without prior culturing.

References

1. Infant age inversely correlates with gut carriage of resistance genes, reflecting modifications in microbial carbohydrate metabolism during early life. iMeta (2024).
2. Primary succession of Bifidobacteria drives pathogen resistance in neonatal microbiota assembly. Nature Microbiology (2024).
3. Detailed mapping of Bifidobacterium strain transmission from mother to infant via a dual culture-based and metagenomic approach. Nature Communications (2023).
4. Mother-to-Infant Microbial Transmission from Different Body Sites Shapes the Developing Infant Gut Microbiome. Cell Host & Microbe (2018).
5. Early-Life Events, Including Mode of Delivery and Type of Feeding, Siblings and Gender, Shape the Developing Gut Microbiota. PLOS ONE (2016).
6. Impact of delivery mode-associated gut microbiota dynamics on health in the first year of life. Nature Communications (2019).
7. Selective maternal seeding and environment shape the human gut microbiome. Genome Research (2018).
8. Developmental trajectory of the healthy human gut microbiota during the first 5 years of life. Cell Host & Microbe (2021).
9. Temporal development of the infant gut microbiome. Open Biology (2019).