Why the early gut microbiome matters
The gut microbiome begins forming at birth and evolves rapidly during infancy, shaping the infant’s digestion, immunity, and even brain development. Early microbial colonization is influenced by factors such as the mode of delivery method, feeding practices, the use of antimicrobials, and environmental exposures.
Early colonizers like Bifidobacteria thrive on breast milk, while later microbes help process solid foods. Disruptions in this process have been linked to allergies, metabolic disorders, and neurodevelopmental conditions later in life, making it essential to understand how a healthy microbiome matures.
Common patterns across the globe
Until now, most studies have focused on small, localized cohorts, leaving gaps in our understanding of global patterns. In a recent study, scientists analyzed over 3,000 stool samples from infants 2-18 months of age across 12 countries in Africa, Europe, Asia, and America, providing a comprehensive view of early microbiome development.
The study found that despite differences in diet and environment, infants worldwide show similar microbial succession trends. Bifidobacterium spp. dominate early infancy but decline as Faecalibacterium prausnitzii and Lachnospiraceae bacteria increase—a shift tied to dietary changes like weaning. Microbial alpha diversity also increases with age, reflecting a more complex gut community despite significant socioeconomic and geographical differences.
Notably, these patterns were consistent across continents, including high- and low-income settings, suggesting universal developmental milestones. Functional analysis revealed that microbial genes involved in carbohydrate metabolism change predictably, aligning with transitions from milk to solid foods. For instance, shifts toward the intake of complex carbohydrates drive key age-related patterns in the infant gut microbiome, reflected by the rise of glycolytic and pentose-phosphate pathway enzymes. This consistency highlights the robustness of these microbial “blueprints” for healthy gut maturation.
Complementary findings from other research groups have found an association between GABA concentrations in infant stool and specific behavioral traits during early infancy. Considering this and given the observed variation in the levels of a Bifidobacterium enzyme linked to GABA production -a key neurotransmitter-, scientists proposed that further exploration of the role of Bifidobacterium in modulating GABA levels in infant stool might help to understand the influence of early gut microbiota on brain development.
Limitations and future directions
While the study provides a global perspective, it didn’t account for factors like delivery mode, breastfeeding duration, or antibiotic use, which can influence microbiome development.
Importantly, understanding the functions of the gut microbiome is still limited because many microbial species, especially the understudied ones, are not yet fully mapped or characterized at the genome level. Additionally, this study focused solely on bacterial communities, without exploring the role of other gut inhabitants like viruses, fungi, or parasites in early-life gut microbiome development.
Future research could integrate these variables to refine age-prediction models and explore how deviations from normative patterns affect health. Such tools might one day guide personalized nutrition or early interventions for at-risk infants, turning microbiome science into actionable health strategies.
Conclusions
This study lays the groundwork for detecting disruptions that could signal future health issues by identifying universal patterns of early microbiome development. Future research could focus on strategies to support optimal gut microbiota development, such as probiotic supplementation, targeted nutrition, and microbiome-friendly medical practices. As research continues, these insights may lead to microbiome-based guidelines for nurturing infant health—proving that even the smallest microbes can have a big impact on lifelong well-being.
References:
Fahur Bottino G, Bonham KS, Patel F, et al. Early life microbial succession in the gut follows common patterns in humans across the globe. Nature Communications. 2025;16(1). doi: 10.1038/s41467-025-56072-w.
Mullaney JA, Roy NC, Halliday C, et al. Effects of early postnatal life nutritional interventions on immune-microbiome interactions in the gastrointestinal tract and implications for brain development and function. Frontiers in Microbiology. 2022;13. doi: 10.3389/fmicb.2022.960492.
Beller L, Deboutte W, Falony G, et al. Successional Stages in Infant Gut Microbiota Maturation. Huffnagle GB, ed. mBio. 2021;12(6). doi: 10.1128/mbio.01857-21.
Dogra S, Chung C, Wang D, et al. Nurturing the Early Life Gut Microbiome and Immune Maturation for Long Term Health. Microorganisms. 2021;9(10):2110. doi:10.3390/microorganisms9102110.
Zuffa S, Schimmel P, Gonzalez-Santana A, et al. Early-life differences in the gut microbiota composition and functionality of infants at elevated likelihood of developing autism spectrum disorder. Transl Psychiatry. 2023 Jul 13;13(1):257. doi: 10.1038/s41398-023-02556-6
Laue, H.E., Korrick, S.A., Baker, E.R. et al. Prospective associations of the infant gut microbiome and microbial function with social behaviors related to autism at age 3 years. Sci Rep 10, 15515 (2020). doi: 10.1038/s41598-020-72386-9