The early-life gut microbiome plays a critical role in shaping lifelong health, dynamically developing in both conjunction and response to environmental exposures during infancy. Among these, human milk oligosaccharides (HMOs) are key dietary substrates that drive early microbial assembly by selectively enriching taxa specialized in their utilization, particularly Bifidobacterium spp. Although multiple species, including Bifidobacterium longum subsp. infantis and Bifidobacterium bifidum, share the capacity to metabolize HMOs, the ecological relationships governing their coexistence and dominance across populations remain poorly understood. Here, we leverage cutting-edge metagenomic profiling to perform a cross-cohort, species-level analysis of Bifidobacterium community structure in over 1,500 infants from geographically and culturally diverse settings across the Americas, Europe, and Africa. Focusing on dominant HMO-utilizing species, we systematically evaluate patterns of co-occurrence and exclusion across cohorts.
Across studied populations, we observe a pattern of mutual exclusion between B. infantis and B. breve, indicating these species rarely co-dominate within the same microbial community. Contrasting ecological distributions – with B. infantis enriched in lower-diversity community states and B. breve and related taxa spanning a broader range of contexts – suggest a spectrum of niche exclusivity within HMO-utilizing Bifidobacterium taxa. These relationships persist across geographic contexts despite variability in feeding practices and overall Bifidobacterium composition, suggesting these configurations represent a conserved feature of early-life gut ecology. These findings provide a foundation for understanding how key microbial taxa organize within early-life communities and establish a framework for future work investigating determinants and consequences of species-level dominance in the developing gut microbiome.