Comparative genomics of Bifidobacterium dentium reveals host adaptation and 2’/3-FL utilisation cluster in this species

Bifidobacteria are beneficial commensals of the human gastrointestinal tract and their presence in the gut has been associated with positive health effects on the host. They account for a vast proportion of the infant gut microbiota, when the infant is fed on a milk-based diet, with their number progressively decreasing in adult and elderly. In contrast to other bifidobacteria, B. dentium was initially considered an opportunistic pathogen as its presence in the oral cavity was associated with the development of dental caries. While B. dentium has been frequently isolated from the oral cavity of children with caries, recent microbiome investigations and preliminary genomic analyses have suggested that this species is also adapted to colonise the gastrointestinal tract, where could exert potential beneficial effects for the host. To gain a better understanding of B. dentium genomic diversity and metabolic potential, the current study presents analysis and characterisation of the genome sequence of 10 novel B. dentium isolates from human fecal samples, obtained by next-generation sequencing (NGS). Through an extensive comparative and pan-genome analysis we investigated the genomic diversity of genetic loci involved in host interaction and gut colonisation in this species. Through a combined genotypic and phenotypic characterisation in terms of its carbohydrate metabolism we were also able to identify a 2’/3FL utilization cluster in two representative strains, thus suggesting the adaptation of member of this species to survive in the gastrointestinal tract of infants.