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).CAZymes ͉ cellulases ͉ plant cell wall ͉ pyrosequencing H erbivores carry out a foregut fermentation that digests plant cell wall materials by a complex and efficient microbial process. The microbiome inhabiting the rumen is characterized by its high population density, wide diversity, and complexity of interactions. Bacteria predominate the rumen, with a variety of anaerobic protozoa and fungi (1), and the associated occurrence of bacteriophage is well documented (2). The use of small subunit (SSU) rRNA sequence analysis has allowed for a more complete description of the rumen microbiome and these inventories have demonstrated that a large microbial component remains uncultured (3)(4)(5)(6)(7)(8)(9)(10)(11)(12) and that a high proportion of the fibrolytic population has not been thoroughly described (7,8,13,14). The rumen habitat contains a consortium of microbes that harbor the complex lignocellulosic degradation system for the microbial attachment and digestion of plant biomass. However, the complex chemical processes required to break down the plant cell wall are rarely carried out by a single species. Evidence also suggests that the most important organisms and gene sets involved in the most efficient hydrolysis of plant cell walls are associated with the fiber portion of the rumen digesta (15). Because we continue to investigate the community structure of the rumen, it is also clear that the system is not fully characterized with respect to the metabolic potential, especially as the system relates to plant...

Microbial biodiversity of the liquid fraction of rumen content from lactating cows

“…A further difference can be related to the higher sequencing depth and to the 16S region sequenced (V1-V3), which probably lead to a more complete and different description of the microbial phylogenic distribution. This is confirmed by Brulc et al (2009), who obtained a more accurate bacterial partitioning on the same samples by increasing the sequencing depth with the use of NGS. Brulc et al (2009) obtained, from samples collected in the same period (1 h after morning feeding) and 454 sequencing, a percentage of Firmicutes in the liquid fraction lower than the value reported in this study (62% v. 79%).…”

“…Mosoni et al, 2011). The advent of Next-Generation Sequencing (NGS) offers a breakthrough opportunity to go deeper into this knowledge (Woelders et al, 2011) and new rumen research in this field has recently been published (Brulc et al, 2009;Kong et al, 2010;Jami and Mizrahi, 2012;Ross et al, 2012). As a first attempt to depict the variation of the microbiome composition subsequent to yeast supplementation, NGS was applied to the rumen fluid fraction.…”

“…Bacteria account for more than 95% of the total number of rumen microorganisms (Brulc et al, 2009) and their metabolism has a significant effect on animal maintenance and performance. Although rumen bacterial populations have flexible metabolic capabilities, dietary composition and physical features of feedstuffs have a major influence on microbial diversity.…”

Metagenomic and metaproteomic insights into bacterial communities in leaf-cutter ant fungus gardens

“…Metagenomics and metaproteomics have previously been shown to be invaluable tools for analyzing microbial communities (Ram et al, 2005;Gill et al, 2006;Woyke et al, 2006;Kalyuzhnaya et al, 2008;Wilmes et al, 2008;Allgaier et al, 2009;Verberkmoes et al, 2009;Burnum et al, 2011), including those associated with herbivores (Warnecke et al, 2007;Brulc et al, 2009;Pope et al, 2010;Burnum et al, 2011). Here we use these techniques to provide insight into the fungus gardens of leaf-cutter ants.…”

Reducing the carbon footprint of Australian milk production by mitigation of enteric methane emissions

“…This requires a rumen metagenome reference sequence -a representation of DNA from all of the species likely to occur in the rumen. While Brulc et al (2009) and Hess et al (2011) have assembled rumen metagenome reference sequences, many species remain unknown, given the large number of species in the rumen.…”