Abstract
Members of the Bifidobacterium longum species have been shown to possess adaptive abilities to allow colonization of different mammalian hosts, including humans, primates and domesticated mammalian species, such as dogs, horses, cattle and pigs. To date, three subspecies have formally been recognized to belong to this bifidobacterial taxon, i.e. B. longum subsp. longum, B. longum subsp. infantis and B. longum subsp. suis. Although B. longum subsp. longum is widely distributed in the human gut irrespective of host age, B. longum subsp. infantis appears to play a significant role as a prominent member of the gut microbiota of breast-fed infants. Nevertheless, despite the considerable scientific relevance of these taxa and the vast body of genomic data now available, an accurate dissection of the genetic features that comprehensively characterize the B. longum species and its subspecies is still missing. In the current study, we employed 261 publicly available B. longum genome sequences, combined with those of 11 new isolates, to investigate genomic diversity of this taxon through comparative genomic and phylogenomic approaches. These analyses allowed us to highlight a remarkable intra-species genetic and physiological diversity. Notably, characterization of the genome content of members of B. longum subsp. infantis subspecies suggested that this taxon may have acquired genetic features for increased competitiveness in the gut environment of suckling hosts. Furthermore, specific B. longum subsp. infantis genomic features appear to be responsible for enhanced horizontal gene transfer (HGT) occurrences, underpinning an intriguing dedication toward acquisition of foreign DNA by HGT events.
Highlights
The human gut harbours at least 100 trillion (1014) microbial cells [1], collectively organized in a complex and dynamic microbial community that plays a fundamental role in defining the human health status [2]
We investigated the genome diversity of B. longum species and its subspecies B. longum subsp. longum, B. longum subsp. infantis and B. longum subsp. suis through comparative genomic analyses and phylogenomic reconstruction of 261 publicly available and high-q uality genomes, along with 11 novel strains sequenced as part of this study
These analyses revealed that members of B. longum subsp. infantis appear to contain a more extensive genetic repertoire than the other B. longum strains, highlighting how the former was shaped over the course of evolution through the acquisition of new genetic features
Summary
The human gut harbours at least 100 trillion (1014) microbial cells [1], collectively organized in a complex and dynamic microbial community that plays a fundamental role in defining the human health status [2]. It is well known that members of the gut microbiota engage in complex microbe– microbe and microbe–host interactions, with physiological consequences, including participation in metabolic activities such as (sometimes syntrophic) degradation of non- digestible carbohydrates, with consequent production of. HMOs constitute complex milk glycans known to elicit prebiotic activity by allowing the above-m entioned bifidobacterial species to establish and persist in the infant gut, thereby representing a clear example of host-m icrobe co-e volution in humans [16,17,18,19,20]
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