Gut Microbiome of the Amazon Master of the Grasses Harbors Unprecedented Enzymatic Strategies for Plant Glycans Breakdown

Abstract

BackgroundPlant biomass is a promising feedstock to replace fossil-based products including fuels, chemicals and materials. However, the high resistance of plant biomass to either physicochemical or biological deconstruction has been hampering its broad industrial utilization and, consequently, the transition to a sustainable bioeconomy. The gut system from herbivores are formidable bioreactors in nature for lignocellulose breakdown and the diverse ecological niches where herbivores are found have led to the rise of a myriad of molecular strategies to cope with the sheer complexity of plant polysaccharides. This study illuminates how the unexplored microbiota of the largest living rodent, capybara, found in Pantanal wetlands and the Amazon basin, can efficiently depolymerize and utilize lignocellulosic biomass. ResultsHere, we have elucidated the gut microbial structure and composition of the semiaquatic herbivorous capybara through multi-omics approaches. Metabolic reconstruction of this microbiota showed that cellulose degradation is chiefly performed by Fibrobacter bacteria, whereas hemicelluloses and pectins are processed by a broad arsenal of Carbohydrate-Active enZymes (CAZymes) organized in polysaccharide utilization loci (PULs) identified in multiple metagenome-assembled genomes from the phylum Bacteroidetes. Furthermore, metabolomics analysis showed short chain fatty acids as major fermentation products, which are key markers of digestion performance of plant polysaccharides. Exploring the genomic dark matter of this gut microbial community, two novel CAZymes families were unveiled including a glycoside hydrolase family of β-galactosidases and a carbohydrate-binding module family involved in xylan binding that establishes an unprecedented three-dimensional fold among associated modules to CAZymes. ConclusionsOur results unveil how the capybara gut microbiota orchestrates the depolymerization and utilization of dietary plant polysaccharides, representing an untapped reservoir of new and intricate enzymatic strategies to overcome the recalcitrance of plant polysaccharides, a central challenge toward a circular and sustainable economy.

Taxonomic, genomic, and functional variation in the gut microbiomes of wild spotted hyenas across two decades of study

“…In captive sifakas (Propithecus coquereli), supplementing standard diets with diverse foliage blends versus with single plant species, was associated with greater concentrations of short-chain fatty acids (SCFAs) in the gut (123). At a larger scale across wild mammals, from rodents to carnivores and primates, several studies have found associations between specific microbial functions and diet type (herbivore, omnivore, piscivore, carnivore) (35,124,125).…”