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

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).

Fig. 1.

Comparison of taxonomic and functional variation in the rumen microbiome. (A) Phylogenetic composition of bacterial phyla from pyrosequence 16S rDNA sequences, 16S rDNA from full length clone libraries and EGTs from 4 pyrosequenced bovine rumen samples. The number of sequences in each of the bacterial phyla from the FA (bovines 8, 64, and 71) and PL rumen microbiomes is shown. (B) Multidimensional scaling plots comparing phylogenetic composition from pyrosequence and full-length 16S rRNA gene sequences. (C) Nonmetric multidimensional scaling plots comparing plant polysaccharide degrading components between Clostridium thermocellum genome and other metagenomic microbiomes. A hierarchal clustering analysis was conducted on the frequency distribution of sequences showing similarity to each gene within 3 gene groups using a χ² analysis (Table S3).