The butyrate-producing Gram-positive human gut bacterium, Hoskinsella mucinilytica, selectively targets host mucin N-acetylhexosamines

The personalized microbial communities (micobiota) that inhabit the distal guts of humans have evolved to process a variety of complex carbohydrates. Many gut bacteria depolymerize and ferment dietary fiber polysaccharides, mutualistically providing short-chain fatty acids and other metabolites to their host. Some human gut bacteria have evolved to utilize components of host mucin glycoproteins-the major component of secreted mucus that protects the gut. Recent studies have implicated certain mucin-degrading bacteria in the development of intestinal inflammation, making the identification of new gut bacteria that possess the ability to degrade mucins an important goal. We used gastric mucin to isolate a novel bacterium, Hoskinsella mucinilytica, that is largely restricted to using the GlcNAc and GalNAc sugars found in the O-linked glycans appended to secreted mucin. This butyrate-producing bacterium accesses these sugars from both polymeric gastric mucin and chemically released oligosaccharides. It also has a genome with correspondingly restricted carbohydrate-active enzyme content, with only three demonstrated mucin-degrading glycoside hydrolase enzymes belonging to families GH31, 36, and 89. Surprisingly, strains with an identical 16S rRNA V4 region to this isolate appear to be rare in the now numerous sequence-based microbiota surveys, with only 30 of 7390 (0.41%) human subjects harboring detectable levels of this bacterium in their stool, with an overall relative abundance ranging from 0.0004% to 0.013% when it is detected. This combination of low prevalence and low abundance suggests that this species could occupy an unknown niche for which access to mucin is important but otherwise renders it difficult to detect in stool-based microbiota surveys.