Characterization of <i>Bifidobacterium kashiwanohense</i> that utilizes both milk- and plant-derived oligosaccharides

Abstract

Bifidobacteria are prominent members of the human gut microbiota throughout life. The ability to utilize milk- and plant-derived carbohydrates is important for bifidobacterial colonization of the infant and adult gut. The <i>Bifidobacterium catenulatum</i> subspecies <i>kashiwanohense</i> (<i>B. kashiwanohense</i>) was originally isolated from infant feces. However, only a few strains have been described, and the characteristics of this subspecies have been poorly investigated. Here, we characterized genotypes and phenotypes of 23 <i>B. kashiwanohense</i>-associated strains, including 12 newly sequenced isolates. Genome-based analysis clarified the phylogenetic relationship between these strains, revealing that only 13 strains are genuine <i>B. kashiwanohense</i>. We defined specific marker sequences and investigated the worldwide prevalence of <i>B. kashiwanohense</i> based on metagenome data. This revealed that not only infants but also adults and weaning children harbor this subspecies in the gut. Most <i>B. kashiwanohense</i> strains utilize long-chain xylans and possess genes for extracellular xylanase (GH10), arabinofuranosidase and xylosidase (GH43), and ABC transporters that contribute to the utilization of xylan-derived oligosaccharides. We also confirmed that <i>B. kashiwanohense</i> strains utilize short- and long-chain human milk oligosaccharides and possess genes for fucosidase (GH95 and GH29) and specific ABC transporter substrate-binding proteins that contribute to the utilization of a wide range of human milk oligosaccharides. Collectively, we found that <i>B. kashiwanohense</i> strains utilize both plant- and milk-derived carbohydrates and identified key genetic factors that allow them to assimilate various carbohydrates.