title: Metagenomic discovery of biomass-degrading genes and genomes from cow rumen.
abstract: 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 268 gigabases of metagenomic DNA from microbes adherent to plant fiber incubated in cow rumen. From these data, we identified 27,755 putative carbohydrate-active genes and expressed 90 candidate proteins, of which 57% were enzymatically active against cellulosic substrates. We also assembled 15 uncultured microbial genomes, which were validated by complementary methods including single-cell genome sequencing. These data sets provide a substantially expanded catalog of genes and genomes participating in the deconstruction of cellulosic biomass.
authors.affiliation: Department of Energy, Joint Genome Institute, Walnut Creek, CA 94598, USA.
authors.forename: Matthias
authors.initials: M
authors.lastname: Hess
authors.forename: Alexander
authors.initials: A
authors.lastname: Sczyrba
authors.forename: Rob
authors.initials: R
authors.lastname: Egan
authors.forename: Tae-Wan
authors.initials: TW
authors.lastname: Kim
authors.forename: Harshal
authors.initials: H
authors.lastname: Chokhawala
authors.forename: Gary
authors.initials: G
authors.lastname: Schroth
authors.forename: Shujun
authors.initials: S
authors.lastname: Luo
authors.forename: Douglas S
authors.initials: DS
authors.lastname: Clark
authors.forename: Feng
authors.initials: F
authors.lastname: Chen
authors.forename: Tao
authors.initials: T
authors.lastname: Zhang
authors.forename: Roderick I
authors.initials: RI
authors.lastname: Mackie
authors.forename: Len A
authors.initials: LA
authors.lastname: Pennacchio
authors.forename: Susannah G
authors.initials: SG
authors.lastname: Tringe
authors.forename: Axel
authors.initials: A
authors.lastname: Visel
authors.forename: Tanja
authors.initials: T
authors.lastname: Woyke
authors.forename: Zhong
authors.initials: Z
authors.lastname: Wang
authors.forename: Edward M
authors.initials: EM
authors.lastname: Rubin
mesh_terms: D000595:Amino Acid Sequence; D000818:Animals; D001419:Bacteria / Q000201:enzymology / Q000235:genetics* / Q000302:isolation & purification / Q000378:metabolism; D001426:Bacterial Proteins / Q000737:chemistry / Q000235:genetics / Q000378:metabolism; D018533:Biomass; D050260:Carbohydrate Metabolism; D002417:Cattle / Q000382:microbiology*; D002480:Cellulase / Q000235:genetics / Q000378:metabolism; D044602:Cellulases / Q000737:chemistry / Q000235:genetics* / Q000378:metabolism; D002482:Cellulose / Q000378:metabolism*; D043366:Cellulose 1,4-beta-Cellobiosidase / Q000235:genetics / Q000378:metabolism; D005798:Genes, Bacterial; D016680:Genome, Bacterial; D054892:Metagenome; D056186:Metagenomics / Q000379:methods; D058977:Molecular Sequence Annotation; D008969:Molecular Sequence Data; D006109:Poaceae / Q000382:microbiology; D012417:Rumen / Q000378:metabolism / Q000382:microbiology*; D017422:Sequence Analysis, DNA
chemical_list: D001426:Bacterial Proteins; D002482:Cellulose; D044602:Cellulases; D002480:Cellulase; D043366:Cellulose 1,4-beta-Cellobiosidase