Succession of Bifidobacterium longum Strains in Response to a Changing Early Life Nutritional Environment Reveals Dietary Substrate Adaptations

Abstract

Summary Diet-microbe interactions play a crucial role in modulation of the early life microbiota and infant health. Bifidobacterium dominates the breast-fed infant gut and may persist in individuals during transition from a milk-based to a more diversified diet. Here, we investigated adaptation of Bifidobacterium longum to the changing nutritional environment. Genomic characterization of 75 strains isolated from nine either exclusively breast- or formula-fed (pre-weaning) infants in their first 18 months revealed subspecies- and strain-specific intra-individual genomic diversity with respect to carbohydrate metabolism, which corresponded to different dietary stages. Complementary phenotypic studies indicated strain-specific differences in utilization of human milk oligosaccharides and plant carbohydrates, whereas proteomic profiling identified gene clusters involved in metabolism of selected carbohydrates. Our results indicate a strong link between infant diet and B . longum diversity and provide additional insights into possible competitive advantage mechanisms of this Bifidobacterium species and its persistence in a single host.

Dispersal strategies shape persistence and evolution of human gut bacteria

“…This was also true when separating persistence by phyla: Bacteroidota were more persistent than other phyla, especially in infants. Actinobacteriota (including Bifidobacterium ) had low strain persistence, particularly in infants, possibly related to weaning ( Kujawska et al., 2020 ). While taxonomic composition varied between infants and adults, the microbiome was gradually enriched for “persistent” species until the age of 10 years, a pattern that was observed in different phyla ( Figures S2 E and S2F).…”

A Comparison of the In Vitro Effects of 2’Fucosyllactose and Lactose on the Composition and Activity of Gut Microbiota from Infants and Toddlers

“…In fact, variation between human individuals is reported to be greater among children (0-3 years of age) than adults [7]. This can be explained by a multitude of factors such as vaginal versus cesarean section delivery, breast milk versus formula feeding, or the use of antibiotics, all factors that can impact the early colonization and subsequent development of the gut ecosystem [43]. As these factors result in different microbial community composition, they can thus also affect the utilization of dietary glycans [44,45].…”

Phylogenomic disentangling of the Bifidobacterium longum subsp. infantis taxon

“…Our data therefore suggest that B. longum subsp. longum plays an ecological role in the metabolism of dietary, plant-derived carbohydrates during weaning and postweaning phases when infants are gradually introduced to a solid diet containing such complex carbohydrates [80][81][82]). Accordingly, the identified fermentation capabilities may provide an explanation as to how B. longum subsp.…”