Transcriptional delineation of polysaccharide utilization loci in the human gut commensal DSM18205 and co-culture with exemplar species on dietary plant glycans.

UNLABELLED

There is growing interest in members of the genus (family ) as members of a well-balanced human gut microbiota (HGM). are particularly associated with the consumption of a diet rich in plant polysaccharides comprising dietary fiber. However, understanding of the molecular basis of complex carbohydrate utilization in species is currently incomplete. Here, we used RNA sequencing (RNA-seq) of the type strain DSM 18205 (previously CB7) to define precisely individual polysaccharide utilization loci (PULs) and associated carbohydrate-active enzymes (CAZymes) that are implicated in the catabolism of common fruit, vegetable, and grain polysaccharides (. mixed-linkage β-glucans, xyloglucans, xylans, pectins, and inulin). Although many commonalities were observed, several of these systems exhibited significant compositional and organizational differences homologs in the better-studied (sister family ), which predominate in post-industrial HGM. Growth on β-mannans, β(1, 3)-galactans, and microbial β(1, 3)-glucans was not observed, due to an apparent lack of cognate PULs. Most notably, is unable to grow on starch, due to an incomplete starch utilization system (Sus). Subsequent transcriptional profiling of bellwether Ton-B-dependent transporter-encoding genes revealed that PUL upregulation is rapid and general upon transfer from glucose to plant polysaccharides, reflective of de-repression enabling substrate sensing. Distinct from previous observations of species, we were unable to observe clearly delineated substrate prioritization on a polysaccharide mixture designed to mimic diverse plant cell wall digesta. Finally, co-culture experiments generally indicated stable co-existence and lack of exclusive competition between and representative HGM species ( and ) on individual polysaccharides, except in cases where corresponding PULs were obviously lacking.

IMPORTANCE

There is currently a great level of interest in improving the composition and function of the human gut microbiota (HGM) to improve health. The bacterium is prevalent in people who eat plant-rich diets and is therefore associated with a healthy lifestyle. On one hand, our study reveals the specific molecular systems that enable to proliferate on individual plant polysaccharides. On the other, a growing body of data suggests that the inability of to grow on starch and animal glycans, which dominate in post-industrial diets, as well as host mucin, contributes strongly to its displacement from the HGM by species, in the absence of direct antagonism.