A catalog of microbial genes from the bovine rumen unveils a specialized and diverse biomass-degrading environment

Abstract

BackgroundThe rumen microbiota provides essential services to its host and, through its role in ruminant production, contributes to human nutrition and food security. A thorough knowledge of the genetic potential of rumen microbes will provide opportunities for improving the sustainability of ruminant production systems. The availability of gene reference catalogs from gut microbiomes has advanced the understanding of the role of the microbiota in health and disease in humans and other mammals. In this work, we established a catalog of reference prokaryote genes from the bovine rumen. ResultsUsing deep metagenome sequencing we identified 13,825,880 non-redundant prokaryote genes from the bovine rumen. Compared to human, pig and mouse gut metagenome catalogs, the rumen is larger and richer in functions and microbial species associated with the degradation of plant cell wall material and production of methane. Genes encoding enzymes catalyzing the breakdown of plant polysaccharides showed a particularly high richness that is otherwise impossible to infer from available genomes or shallow metagenomics sequencing.The catalog expands by several folds the dataset of carbohydrate-degrading enzymes described in the rumen. Using an independent dataset from a group of 77 cattle fed 4 common dietary regimes, we found that only <0.1% of genes were shared by all animals, which contrast with a large overlap for functions, i.e. 63% for KEGG functions. Different diets induced differences in the relative abundance rather than the presence or absence of genes explaining the great adaptability of cattle to rapidly adjust to dietary changes. Conclusions

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

“…In capybara gut CAZymes arsenal, invertases from GH32 family were identi ed in a proportion of approx. 1.5%, which is similar to that reported for several gut microbiomes from ruminants to humans (30,31). It is worth to mention that in the sequenced genome of capybara itself there is no gene encoding GH32 invertases, which holds for all mammals sequenced to date.…”

“…These enzymes are often associated with the later steps in the degradation cascade of several plant polysaccharides such as cellulose, heteroxylans, mixed-linkage β-glucans and β-mannans. Moreover, it has already been reported that these families are highly abundant in several host-associated gut microbiomes such as human, mouse, swine, and cattle rumen (30), probably due to their broad functions.…”

Influence of Genetic Background and Dietary Oleic Acid on Gut Microbiota Composition in Duroc and Iberian Pigs.

“…36 and their abundance is highly related to high-fiber long-term diets 37,38 . Their presence in fecal microbiota is highly reported in human 39 and other animals such as ruminants, predominating in rumen microbiota [40][41][42] .…”

Communal living: glycan utilization by the human gut microbiota

“…gnPULs are generally identified in Bacteroidetes genomes by the presence of an adjacent susC and susD homologue pair (Terrapon et al, 2015;Wu et al, 2015;Svartström et al, 2017;Wong et al, 2017;Terrapon et al, 2018;Lapébie et al, 2019;Patnode et al, 2019;Li et al, 2020), which encodes a core TonB-dependent transporter (TBDT) and a tightly associated cell-surface glycan-binding protein (SGBP), respectively, to form an active transport complex (Cho and Salyers, 2001; Glenwright et al, 2017; Bolam and van den Berg, 2018) ( Fig. 1A).…”