title: Methane yield phenotypes linked to differential gene expression in the sheep rumen microbiome.
abstract: Ruminant livestock represent the single largest anthropogenic source of the potent greenhouse gas methane, which is generated by methanogenic archaea residing in ruminant digestive tracts. While differences between individual animals of the same breed in the amount of methane produced have been observed, the basis for this variation remains to be elucidated. To explore the mechanistic basis of this methane production, we measured methane yields from 22 sheep, which revealed that methane yields are a reproducible, quantitative trait. Deep metagenomic and metatranscriptomic sequencing demonstrated a similar abundance of methanogens and methanogenesis pathway genes in high and low methane emitters. However, transcription of methanogenesis pathway genes was substantially increased in sheep with high methane yields. These results identify a discrete set of rumen methanogens whose methanogenesis pathway transcription profiles correlate with methane yields and provide new targets for CH4 mitigation at the levels of microbiota composition and transcriptional regulation.
authors.affiliation: Department of Energy, Joint Genome Institute, Walnut Creek, California 94598, USA; Genomic Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, USA;
authors.forename: Weibing
authors.identifier: http://orcid.org/0000-0002-9291-8577
authors.initials: W
authors.lastname: Shi
authors.affiliation: AgResearch Limited, Grasslands Research Centre, Palmerston North 4442, New Zealand;
authors.forename: Christina D
authors.initials: CD
authors.lastname: Moon
authors.affiliation: AgResearch Limited, Grasslands Research Centre, Palmerston North 4442, New Zealand;
authors.forename: Sinead C
authors.initials: SC
authors.lastname: Leahy
authors.affiliation: Department of Energy, Joint Genome Institute, Walnut Creek, California 94598, USA; Genomic Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, USA;
authors.forename: Dongwan
authors.initials: D
authors.lastname: Kang
authors.affiliation: Department of Energy, Joint Genome Institute, Walnut Creek, California 94598, USA; Genomic Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, USA;
authors.forename: Jeff
authors.initials: J
authors.lastname: Froula
authors.affiliation: AgResearch Limited, Grasslands Research Centre, Palmerston North 4442, New Zealand;
authors.forename: Sandra
authors.initials: S
authors.lastname: Kittelmann
authors.affiliation: Department of Energy, Joint Genome Institute, Walnut Creek, California 94598, USA; Genomic Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, USA;
authors.forename: Christina
authors.initials: C
authors.lastname: Fan
authors.affiliation: Department of Energy, Joint Genome Institute, Walnut Creek, California 94598, USA; Genomic Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, USA;
authors.forename: Samuel
authors.initials: S
authors.lastname: Deutsch
authors.affiliation: AgResearch Limited, Grasslands Research Centre, Palmerston North 4442, New Zealand;
authors.forename: Dragana
authors.initials: D
authors.lastname: Gagic
authors.affiliation: AgResearch Limited, Grasslands Research Centre, Palmerston North 4442, New Zealand;
authors.forename: Henning
authors.initials: H
authors.lastname: Seedorf
authors.affiliation: AgResearch Limited, Grasslands Research Centre, Palmerston North 4442, New Zealand;
authors.forename: William J
authors.initials: WJ
authors.lastname: Kelly
authors.affiliation: AgResearch Limited, Grasslands Research Centre, Palmerston North 4442, New Zealand;
authors.forename: Renee
authors.initials: R
authors.lastname: Atua
authors.affiliation: AgResearch Limited, Grasslands Research Centre, Palmerston North 4442, New Zealand;
authors.forename: Carrie
authors.initials: C
authors.lastname: Sang
authors.affiliation: AgResearch Limited, Grasslands Research Centre, Palmerston North 4442, New Zealand;
authors.forename: Priya
authors.initials: P
authors.lastname: Soni
authors.affiliation: AgResearch Limited, Grasslands Research Centre, Palmerston North 4442, New Zealand;
authors.forename: Dong
authors.initials: D
authors.lastname: Li
authors.affiliation: AgResearch Limited, Grasslands Research Centre, Palmerston North 4442, New Zealand;
authors.forename: Cesar S
authors.initials: CS
authors.lastname: Pinares-Patiño
authors.affiliation: AgResearch Limited, Grasslands Research Centre, Palmerston North 4442, New Zealand;
authors.forename: John C
authors.initials: JC
authors.lastname: McEwan
authors.affiliation: AgResearch Limited, Grasslands Research Centre, Palmerston North 4442, New Zealand;
authors.forename: Peter H
authors.initials: PH
authors.lastname: Janssen
authors.affiliation: Department of Energy, Joint Genome Institute, Walnut Creek, California 94598, USA; Genomic Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, USA;
authors.forename: Feng
authors.initials: F
authors.lastname: Chen
authors.affiliation: Department of Energy, Joint Genome Institute, Walnut Creek, California 94598, USA; Genomic Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, USA; School of Natural Sciences, University of California, Merced, California 95343, USA.
authors.forename: Axel
authors.initials: A
authors.lastname: Visel
authors.affiliation: Department of Energy, Joint Genome Institute, Walnut Creek, California 94598, USA; Genomic Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, USA; School of Natural Sciences, University of California, Merced, California 95343, USA.
authors.forename: Zhong
authors.initials: Z
authors.lastname: Wang
authors.affiliation: AgResearch Limited, Grasslands Research Centre, Palmerston North 4442, New Zealand;
authors.forename: Graeme T
authors.initials: GT
authors.lastname: Attwood
authors.affiliation: Department of Energy, Joint Genome Institute, Walnut Creek, California 94598, USA; Genomic Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, USA; emrubin@lbl.gov.
authors.forename: Edward M
authors.initials: EM
authors.lastname: Rubin
mesh_terms: D000818:Animals; D001105:Archaea / Q000235:genetics / Q000378:metabolism; D019843:Archaeal Proteins / Q000235:genetics* / Q000378:metabolism; D001483:Base Sequence; D054892:Metagenome; D008697:Methane / Q000096:biosynthesis*; D064307:Microbiota; D008969:Molecular Sequence Data; D010641:Phenotype; D019655:Quantitative Trait, Heritable; D012417:Rumen / Q000378:metabolism / Q000382:microbiology*; D012756:Sheep / Q000378:metabolism / Q000382:microbiology*; D059467:Transcriptome
chemical_list: D019843:Archaeal Proteins; D008697:Methane