Abstract
Commensal bacteria often have an especially rich source of glycan-degrading enzymes which allow them to utilize undigested carbohydrates from the food or the host. The species Ruminococcus gnavus is present in the digestive tract of ≥90% of humans and has been implicated in gut-related diseases such as inflammatory bowel diseases (IBD). Here we analysed the ability of two R. gnavus human strains, E1 and ATCC 29149, to utilize host glycans. We showed that although both strains could assimilate mucin monosaccharides, only R. gnavus ATCC 29149 was able to grow on mucin as a sole carbon source. Comparative genomic analysis of the two R. gnavus strains highlighted potential clusters and glycoside hydrolases (GHs) responsible for the breakdown and utilization of mucin-derived glycans. Transcriptomic and functional activity assays confirmed the importance of specific GH33 sialidase, and GH29 and GH95 fucosidases in the mucin utilisation pathway. Notably, we uncovered a novel pathway by which R. gnavus ATCC 29149 utilises sialic acid from sialylated substrates. Our results also demonstrated the ability of R. gnavus ATCC 29149 to produce propanol and propionate as the end products of metabolism when grown on mucin and fucosylated glycans. These new findings provide molecular insights into the strain-specificity of R. gnavus adaptation to the gut environment advancing our understanding of the role of gut commensals in health and disease.
Highlights
The human gastrointestinal (GI) tract contains a dynamic community of trillions of microorganisms leaving in a symbiotic relationship with the host [1]
Both strains possess similar number of GH13 enzymes while the E1 strain has a higher number of GH1, GH2 and GH3, together with a higher number of GH36 (a-galactosidase), GH78, GH43, GH29 and GH95 (a-fucosidases), and strain-specific GH63 (a-glucosidase), GH16 (b-glucanase), GH91, the E1 strain seems to be more adapted to the degradation of a diversified array of dietary carbohydratebased substrates [42]
The R. gnavus ATCC 29149 genome encodes less glycoside hydrolases (GHs) than E1 but with a higher proportion of enzymes putatively implicated in degradation of host-derived oligosaccharides, including predicted GH33 sialidase and GH98 endo-b-galactosidase, which are absent in the R. gnavus E1 genome, and both predicted to be extracellular
Summary
The human gastrointestinal (GI) tract contains a dynamic community of trillions of microorganisms leaving in a symbiotic relationship with the host [1]. Bacteroidetes and Firmicutes, dominate gut microbiota biodiversity [2], [3]. These symbionts have adapted to maximise metabolic access to a wide variety of dietary- and host-derived carbohydrates (mucin glycans), and competition for these nutrients is considered as a major factor shaping the structure-function of the microbiota [4]. The gut microbiota provides many crucial functions to the host including calorie extraction from the diet, generation of short-chain fatty acids (SCFAs), metabolism of xenobiotics, development of immune system and pathogen exclusion [5], [6]. Some changes in the microbial community are shared in CD and UC including reduced biodiversity (in particular Firmicutes), temporal instability and increased mucosa-associated bacteria [9], [10], [11]
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