Gene-centric metagenomics of the fiber-adherent bovine rumen microbiome reveals forage specific glycoside hydrolases

TLDR

The rumen microbiome is a dense, complex community that efficiently converts plant cell wall biomass into microbial protein, short‑chain fatty acids, and gases. The study aims to explore the rumen microbiome as a genetic resource for plant cell wall‑degrading enzymes that could aid biofuel production. The authors performed comparative metagenomic analysis of pyrosequencing data from three fiber‑adherent rumen microbiomes and one pooled liquid sample, using phylotype profiling and SEED subsystem annotations. The analysis revealed that, despite identical diets, the three rumen microbiomes differed markedly in community composition, phylotype distribution, and metabolic potential, with glycoside hydrolase repertoires indicating early colonizers target side chains of plant polysaccharides rather than cellulose, and distinct glycoside hydrolase profiles compared to the termite hindgut reflect diet‑driven differences.

Abstract

The complex microbiome of the rumen functions as an effective system for the conversion of plant cell wall biomass to microbial protein, short chain fatty acids, and gases. As such, it provides a unique genetic resource for plant cell wall degrading microbial enzymes that could be used in the production of biofuels. The rumen and gastrointestinal tract harbor a dense and complex microbiome. To gain a greater understanding of the ecology and metabolic potential of this microbiome, we used comparative metagenomics (phylotype analysis and SEED subsystems-based annotations) to examine randomly sampled pyrosequence data from 3 fiber-adherent microbiomes and 1 pooled liquid sample (a mixture of the liquid microbiome fractions from the same bovine rumens). Even though the 3 animals were fed the same diet, the community structure, predicted phylotype, and metabolic potentials in the rumen were markedly different with respect to nutrient utilization. A comparison of the glycoside hydrolase and cellulosome functional genes revealed that in the rumen microbiome, initial colonization of fiber appears to be by organisms possessing enzymes that attack the easily available side chains of complex plant polysaccharides and not the more recalcitrant main chains, especially cellulose. Furthermore, when compared with the termite hindgut microbiome, there are fundamental differences in the glycoside hydrolase content that appear to be diet driven for either the bovine rumen (forages and legumes) or the termite hindgut (wood).