Gene-trait matching among Bifidobacterium dentium strains reveals various glycan metabolism loci including a strain-specific fucosyllactose utilization cluster

Ortensia Catalano Gonzaga¹Stephen Mckenna²Ian O'Neill³Paul David Cotter⁴Fionnuala M McAuliffe⁵Aidan Coffey²Douwe Van Sinderen^3*Francesca Bottacini^2*

• ¹University College Cork, Cork, Ireland
• ²Department of Biological Sciences, Munster Technological University, CorK, Ireland
• ³APC Microbiome Ireland, University College Cork, Cork, Ireland
• ⁴Food Biosciences, Teagasc Food Research Centre Moorepark, Cork, Ireland
• ⁵UCD Perinatal Research Centre, School of Medicine, Dublin, Ireland

In contrast to other human-associated bifidobacteria, Bifidobacterium dentium is commonly classified as an opportunistic pathogen as its presence in the oral cavity has been associated with the development of dental caries. While B. dentium is 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 colonize the gastrointestinal tract. Understanding the genetic and metabolic adaptations that enable this flexible colonization ability is crucial to clarify its role in human health and disease. To assess B. dentium genomic diversity and metabolic potential, the current study presents analysis and characterization of 10 complete genome sequences from recently isolated B. dentium strains obtained from human fecal samples together with 48 publicly available genome sequences. We investigated genetic loci predicted to be involved in host interaction and gut colonization in this species by means of comparative and pangenome analyses. Employing a gene-trait matching approach on these newly isolated B. dentium strains, we gained insight into the species' carbohydrate fermentation capabilities. This analysis identified gene clusters involved in the utilization of plant-derived glycans and, for the first time, revealed B. dentium strains capable of utilizing human milk oligosaccharides (HMOs) through a fucosyllactose utilization cluster homologous to one found in several infant-derived bifidobacterial species. Moreover, investigating the genetic features of each B. dentium strain highlighted a taxon that is evolved to colonize multiple niches and to compete with other colonizers.