Genomic diversity and distribution of Bifidobacterium longum subsp. longum across the human lifespan

Abstract

Bifidobacterium longum subsp. longum represents one of the most prevalent bifidobacterial species in the infant, adult and elderly (human) gut. In the current study, we performed a comparative genome analysis involving 145 B. longum representatives, including 113 B. longum subsp. longum strains obtained from healthy Japanese subjects aged between 0 and 98 years. Although MCL clustering did not reveal any correlation between isolated strains and subject age, certain characteristics appear to be more prevalent among strains corresponding to specific host ages, such as genes involved in carbohydrate metabolism and environmental response. Remarkably, a substantial number of strains appeared to have been transmitted across family members, a phenomenon that was shown not to be confined to mother-infant pairs. This suggests that the ubiquitous distribution of B. longum subsp. longum across the human lifespan is at least partly due to extensive transmission between relatives. Our findings form a foundation for future research aimed at unraveling the mechanisms that allow B. longum strains to successfully transfer between human hosts, where they then colonize and persist in the gut environment throughout the host’s lifespan.

Succession ofBifidobacterium longumstrains in response to the changing early-life nutritional environment reveals specific adaptations to distinct dietary substrates

“…Bifidobacterium counts were not detectable nor was any Bifidobacterium -specific PCR product for DGGE obtained from this infant during the antibiotic administration; however, both were obtained for the sample collected one week after antibiotic treatment completed ( 44 ). Furthermore, the presence of clonal strains in both babies suggests vertical transmission of B. longum from mother to both infants, or potential horizontal transmission between babies, consistent with previous reports ( 42, 47-49 ). B. infantis strains isolated from infant BF2 showed the highest strain diversity, with the mean pairwise SNP distance of 9030.9±8036.6 SNPs.…”

“…Our comparative genomic analysis indicates that clonal strains of B. longum sp. can persist in individuals through infancy, for at least 18 months, despite significant changes in diet during weaning, which is consistent with previous reports ( 35, 42 ). Concurrently, new strains (that display different genomic content and potential carbohydrate metabolism capabilities) can be acquired, possibly in response to the changing diet.…”

“…High abundance of Bifidobacterium in early infancy is strongly linked to availability of nutrients, with dominance in breast-fed infants correlated with enrichment of genes required for the degradation of HMOs present in breast milk, while the transition to solid foods during weaning has been linked to genes involved in degradation of complex plant-derived carbohydrates ( 3, 29, 64 ). Bifidobacterium longum species appear to be widely distributed in individuals at different life stages, which may correlate with the abundance of genes responsible for carbohydrate metabolism ( 35, 42 ). In this study, we aimed to investigate the adaptations of B. longum to the changing infant diet during the early-life developmental window.…”

“…Initial vertical acquisition of Bifidobacterium from mother to newborn babies has been well documented ( 48, 49, 73 ); however, details of strain transmission events in later life are currently unclear. Work of Odamaki et al ( 42 ) identified person-to-person horizontal transmission of a particular B. longum strain between members of the same family, and suggested direct transfer, common dietary sources or environmental reservoirs, such as family homes ( 74 ), as potential vehicles and routes for strain transmission. Our results showed the presence of clonal strains in identical twins BF3 and BF4, which may have resulted from maternal transfer.…”

“…longum widely distributed in both infants and adults ( 39, 40 ). The differences in prevalence between the two subspecies, and the ability of infant, adult and elderly host to acquire new B. longum strains during a lifetime have been attributed to distinct bacterial carbohydrate utilisation capabilities and the overall composition of the resident microbiota ( 41, 42 ). However, longitudinal assessments of this species in single hosts over the course of changing dietary patterns are limited, and therefore further detailed studies are required.…”