Metabolic pathway analysis reveals hierarchical pentose sugar utilization and metabolic flexibility of Bifidobacterium longum.

Plant-derived pentose sugars represent a major nutrient source in the gut, yet their metabolism remains incompletely defined. Strains of the human gut commensal Bifidobacterium longum subsp. longum utilise arabinose- and xylose-containing glycans, which are found in the pectin and hemicellulose layers of plant cell walls. To gain insight into the metabolism of these two pentoses as well as ribose, a naturally occurring sugar and a component of RNA and ATP, we identified and analysed the genes responsible for their uptake and subsequent catabolism. Based on transcriptomic data and mutant phenotype analyses, we show that these three pentoses share a common, ABC-type uptake system encoded by penABCD. Furthermore, we identify a gene cluster, araBDA, and two genes, xylA and xylB, that are required for conversion of arabinose and xylose, respectively, into xylulose-5-phosphate, and rbsK, which converts ribose into ribose-5-phosphate. These intermediate metabolic products enter the bifid shunt, an energy-generating fermentative pathway typical of bifidobacteria. We also show that arabinose and xylose are co-metabolized, while xylose is preferentially utilised before ribose. This study provides molecular insights using a multi-omics approach, including comparative genomics and transcriptomics combined with mutational analysis, into how B. longum subsp. longum metabolizes pentose-containing plant glycans, common yet indigestible components of the adult human diet.