Abundance of Bifidobacterium species in the infant gut microbiota and associations with maternal-infant characteristics in Dhaka, Bangladesh

The early infant gut microbiota is generally dominated by bifidobacteria, but there is substantial variation at the (sub)species level. Patterns of postnatal Bifidobacterium subspecies colonization in low- or middle-income countries have not been widely studied. We used (sub)species-specific qPCR to quantify B. infantis (n = 1132), B. longum (n = 364), and B. breve (n = 399) in stool samples from infants (0-6 months of age) in urban Dhaka, Bangladesh. B. infantis absolute abundance started low at birth but increased in the first two months, whereas B. longum and B. breve abundances remained comparatively low. B. infantis emerged earlier in infants delivered by C-section, but by ~2 months of age, infants delivered by C-section or vaginally had similar B. infantis absolute abundances. Infant antibiotic exposure (ever vs. never), human milk feeding patterns (exclusive, predominant, and partial), and detection of maternal stool B. infantis were not associated with infant B. infantis. In settings where B. infantis is widespread, its patterns of postnatal colonization can be used to inform the design of targeted microbiota-modifying interventions in infancy.IMPORTANCEBifidobacteria are considered to be an important member of the early infant gut microbiota, but several factors may influence the timing of their emergence and overall abundance. Moreover, bifidobacteria abundance varies considerably between different species and subspecies, underscoring the importance of techniques that enable sub-speciation. B. longum subspecies infantis (B. infantis) is thought to have several health-promoting properties, and despite growing interest in the use of B. infantis to promote health (e.g., probiotics), relatively few studies have explored its natural patterns of colonization, particularly in low- and middle-income countries. By applying (sub)species-specific qPCR, we precisely tracked the timing of emergence, longitudinal abundance patterns, and ecological dynamics of B. infantis, B. longum, and B. breve in the postnatal period, which provided new insights to inform the design of targeted microbiota-modifying interventions in early infancy.