13 Diet-microbe interactions play a crucial role in infant development and modulation of the early-life 14 microbiota. The genus Bifidobacterium dominates the breast-fed infant gut, with strains of B. 15 longum subsp. longum (B. longum) and B. longum subsp. infantis (B. infantis) particularly prevalent. 16Although transition from milk to a more diversified diet later in infancy initiates a shift to a more 17 complex microbiome, specific strains of B. longum may persist in individual hosts for prolonged 18 periods of time. Here, we sought to investigate the adaptation of B. longum to the changing infant 19 diet. Genomic characterisation of 75 strains isolated from nine either exclusively breast-or formula-20 fed (pre-weaning) infants in their first 18 months revealed subspecies-and strain-specific intra-21 individual genomic diversity with respect to glycosyl hydrolase families and enzymes, which 22 2 persistence in a single host and may contribute to rational development of new dietary therapies for 31 this important developmental window. 32 33 35 particularly the ones involved in the degradation of breast milk-associated human milk 52 oligosaccharides (HMOs) (8). The presence of these genes is often species-and indeed strain-53 specific, and has been described in B. breve, B. bifidum, B. longum, B. infantis, and more rarely in B. 54 pseudocatenulatum (8,(25)(26)(27). However, previous studies have indicated co-existence of 55Bifidobacterium species and strains in individual hosts, resulting in interaction and metabolic co-56 operation within a single (HMO-associated) ecosystem (1, 28). 57Transition from breastfeeding to a more diversified diet and the introduction of solid foods has been 58 considered to initiate the development of a functionally more complex adult-like microbiome with 59 genes responsible for degradation of plant-derived complex carbohydrates, starches, and 60 xenobiotics, as well as production of vitamins (29, 30). Non-digestible complex carbohydrates such 61 as inulin-type fructans (ITF), arabino-xylans (AX) or arabinoxylo-oligosaccharides (AXOS) in 62 3 complementary foods have been proposed to potentially exert beneficial health effects through 63 their bifidogenic and prebiotic properties and resulting modulation of the intestinal microbiota and 64 metabolic end-products (31)(32)(33)(34). 65Despite the shift in microbiota composition during weaning, specific strains of Bifidobacterium, and 66 B. longum in particular, have previously been shown to persist in individuals over time (35, 36). B. 67 longum is currently recognised as four subspecies: longum and infantis (characteristic of the human 68 gut microbiota), and suis and suillum (from animal hosts) (37, 38). It is considered the most common 69 and prevalent species found in the human gut, with B. longum subsp. infantis detected in infants, 70 and B. longum subsp. longum widely distributed in both infants and adults (39, 40). The differences 71 in prevalence between the two subspecies, and the ability of infant, adult and elderly host t...