Metagenomic Discovery of Biomass-Degrading Genes and Genomes from Cow Rumen

  title={Metagenomic Discovery of Biomass-Degrading Genes and Genomes from Cow Rumen},
  author={Matthias Hess and Alexander Sczyrba and Rob Egan and Tae-Wan Kim and Harshal A. Chokhawala and Gary P. Schroth and Shujun Luo and Douglas S. Clark and Feng Chen and Tao Zhang and Roderick Ian Mackie and Len A. Pennacchio and Susannah G. Tringe and Axel Visel and Tanja Woyke and Zhong Wang and Edward M. Rubin},
  pages={463 - 467}
Metagenomic sequencing of biomass-degrading microbes from cow rumen reveals new carbohydrate-active enzymes. The paucity of enzymes that efficiently deconstruct plant polysaccharides represents a major bottleneck for industrial-scale conversion of cellulosic biomass into biofuels. Cow rumen microbes specialize in degradation of cellulosic plant material, but most members of this complex community resist cultivation. To characterize biomass-degrading genes and genomes, we sequenced and analyzed… 

Metagenomic insights into the diversity of carbohydrate-degrading enzymes in the yak fecal microbial community

These findings shed light on a great diversity of carbohydrate-degrading enzymes in the yak gut microbial community and uncultured species, which provides a useful genetic resource for future studies on the discovery of novel enzymes for industrial applications.

Proteome specialization of anaerobic fungi during ruminal degradation of recalcitrant plant fiber

These findings elucidate the intricate networks of in situ recalcitrant fiber deconstruction, and suggests that the anaerobic rumen fungi contribute a specific set of CAZymes that complement the enzyme repertoire provided by the specialized plant cell wall degrading rumen bacteria.

Metagenomic Insights into the Carbohydrate-Active Enzymes Carried by the Microorganisms Adhering to Solid Digesta in the Rumen of Cows

Comparison with the large metagenomic datasets previously reported of other ruminant species (or cattle breeds) and wallabies showed that the rumen microbiome of Jersey cows might contain differing CAZymes, and future studies are needed to further explore how host genetics and diets affect the diversity and distribution ofCAZymes.

Unique pool of carbohydrate-degrading enzymes in novel bacteria assembled from cow and buffalo rumen metagenomes

The results strongly indicate that the rumen chamber harbors high numbers of deeply branched and as-yet uncultured microbes that encode novel CAZymes, candidates for prospective usage in plant biomass-hydrolyzing and biofuels industries.

Insights into rumen microbial biosynthetic gene cluster diversity through genome-resolved metagenomics

Recovering 2,809 microbial metagenome-assembled genomes from ruminants provides insight into the relationship between microbial populations and the production of secondary metabolites that may be important for manipulating rumen fermentation.

A catalog of microbial genes from the bovine rumen reveals the determinants of herbivory

Using deep metagenome sequencing, genes coding for enzymes that deconstruct plant polysaccharides showed a particularly high richness that is otherwise impossible to infer from available genomes or shallow metagenomics sequencing, bringing new insights on functions, enzymes and microbes of the rumen.

Metagenomic insights into the rumen microbial fibrolytic enzymes in Indian crossbred cattle fed finger millet straw

The results indicated that the cattle rumen microbiome and the CAZymes are highly complex, structurally similar but compositionally distinct from other ruminants.

Assembly of hundreds of microbial genomes from the cow rumen reveals novel microbial species encoding enzymes with roles in carbohydrate metabolism

220 high quality bacterial and archaeal genomes assembled directly from 768 gigabases of rumen metagenomic sequence data are presented, revealing that the majority of these represent previously unsequenced strains and species of bacteria and archaea.

Metatranscriptomic Analyses of Plant Cell Wall Polysaccharide Degradation by Microorganisms in the Cow Rumen

The results provide metatranscriptomic evidence in support of the notion that members of the genera Ruminococcus, Fibrobacter, and Prevotella are predominant PCWP degraders and point to the significant contribution of GH48 cellobiohydrolases and cellulosome-like structures to efficient PCWP degradation in the cow rumen.

Early-branching gut fungi possess a large, comprehensive array of biomass-degrading enzymes

A systems-level approach that integrates transcriptomic sequencing, proteomics, phenotype, and biochemical studies of relatively unexplored basal fungi is developed and identified several promising sequence-divergent enzyme candidates for lignocellulosic bioprocessing.



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

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.

Novel hydrolase diversity retrieved from a metagenome library of bovine rumen microflora.

The phylogenetic novelty of the hydrolases suggests that some of them may have potential for new applications in biocatalysis and the sequences and contexts of neighbouring genes suggested suggested tentative phylogenetic assignments of the rumen organisms producing the retrieved enzymes.

Metagenomic and functional analysis of hindgut microbiota of a wood-feeding higher termite

A metagenomic analysis of the bacterial community resident in the hindgut paunch of a wood-feeding ‘higher’ Nasutitermes species shows the presence of a large, diverse set of bacterial genes for cellulose and xylan hydrolysis, the first system-wide gene analysis of a microbial community specialized towards plant lignocellulose degradation.

Bioprospecting metagenomes: glycosyl hydrolases for converting biomass

This review compares function-based metagenome screening and sequence-based meetagenome data mining, discussing the advantages and limitations of both methods and describing the unusual enzymes discovered via metagenomics approaches.

Why don't ruminal bacteria digest cellulose faster?

  • P. Weimer
  • Biology, Medicine
    Journal of dairy science
  • 1996
In light of numerous proposals to improve microbial cellulose digestion in ruminants, it is instructive to examine the characteristics of these species that contribute to their superior cellulolytic capabilities and to identify the factors that prevent them from digesting cellulose even more rapidly.

The Glycobiome of the Rumen Bacterium Butyrivibrio proteoclasticus B316T Highlights Adaptation to a Polysaccharide-Rich Environment

Analysis of the B316 genome shows how one organism can contribute to the multi-organism complex that rapidly breaks down plant material in the rumen, and it can be concluded that B316, and similar organisms with broad polysaccharide-degrading capability, are well suited to being early colonizers and degraders of plantpolysaccharides in theRumen environment.

Adaptation to herbivory by the Tammar wallaby includes bacterial and glycoside hydrolase profiles different from other herbivores

Collective data demonstrate that Australian macropods not only harbor unique bacterial lineages underpinning plant biomass conversion, but their repertoire of glycoside hydrolases is distinct from those of the microbiomes of higher termites and the bovine rumen.

Assembling the Marine Metagenome, One Cell at a Time

The power of single cell DNA sequencing to generate reference genomes of uncultured taxa from a complex microbial community of marine bacterioplankton is demonstrated.

Matching phylogeny and metabolism in the uncultured marine bacteria, one cell at a time

The power of this approach lies in the ability to detect metabolic genes in uncultured microorganisms directly, even when the metabolic and phylogenetic markers are located far apart on the chromosome.