Ecological insights into the assembly of bifidobacterial communities in the infant gut

Abstract

The initial community assembly of the gut microbiome during infancy significantly influences its development over time. Strains of the genus Bifidobacterium are some of the early colonizers in the infant gut and a commonly used probiotic taxon, but their colonization success varies significantly by situation. This review explores the importance of ecological processes underlying the community establishment of Bifidobacterium strains in the gut by focusing on the potential roles of dispersal, drift, selection, and diversification. We highlight the role of maternal sources in microbial dispersal at birth and discuss the possible consequences of random changes to relative abundances caused by ecological drift. Selective pressures exerted by dietary components, particularly human milk oligosaccharides (HMOs) in breastmilk, can also influence community structure. Diversification enhances genetic variability and enables bifidobacteria to adapt to selective pressures. However, these processes interact with each other, and predicting the colonization success of bifidobacteria is challenging. Here, we propose that considering the balance between stochastic and deterministic processes can help refine strategies for promoting bifidobacterial colonization. When stochastic processes dominate during the initial stages of community assembly, early arrival can help bifidobacteria occupy open niches. On the other hand, once the gut microbiome reaches stability during the later stages of community assembly, deterministic factors become more prominent. In such cases, adding appropriate prebiotics may be necessary to provide a selective advantage. By integrating this framework, we suggest that future research consider how ecological processes affect the colonization success and abundance patterns of Bifidobacterium strains in the infant gut.