title: Rumen microbial community composition varies with diet and host, but a core microbiome is found across a wide geographical range.
abstract: Ruminant livestock are important sources of human food and global greenhouse gas emissions. Feed degradation and methane formation by ruminants rely on metabolic interactions between rumen microbes and affect ruminant productivity. Rumen and camelid foregut microbial community composition was determined in 742 samples from 32 animal species and 35 countries, to estimate if this was influenced by diet, host species, or geography. Similar bacteria and archaea dominated in nearly all samples, while protozoal communities were more variable. The dominant bacteria are poorly characterised, but the methanogenic archaea are better known and highly conserved across the world. This universality and limited diversity could make it possible to mitigate methane emissions by developing strategies that target the few dominant methanogens. Differences in microbial community compositions were predominantly attributable to diet, with the host being less influential. There were few strong co-occurrence patterns between microbes, suggesting that major metabolic interactions are non-selective rather than specific.
authors.affiliation: AgResearch Limited, Grasslands Research Centre, Palmerston North 4442, New Zealand.
authors.forename: Gemma
authors.initials: G
authors.lastname: Henderson
authors.affiliation: AgResearch Limited, Grasslands Research Centre, Palmerston North 4442, New Zealand.
authors.forename: Faith
authors.initials: F
authors.lastname: Cox
authors.affiliation: AgResearch Limited, Grasslands Research Centre, Palmerston North 4442, New Zealand.
authors.forename: Siva
authors.initials: S
authors.lastname: Ganesh
authors.affiliation: AgResearch Limited, Grasslands Research Centre, Palmerston North 4442, New Zealand.
authors.forename: Arjan
authors.initials: A
authors.lastname: Jonker
authors.affiliation: AgResearch Limited, Grasslands Research Centre, Palmerston North 4442, New Zealand.
authors.forename: Wayne
authors.initials: W
authors.lastname: Young
authors.affiliation: AgResearch Limited, Grasslands Research Centre, Palmerston North 4442, New Zealand.
authors.forename: Peter H
authors.initials: PH
authors.lastname: Janssen
mesh_terms: D000818:Animals; D001105:Archaea / Q000145:classification / Q000235:genetics / Q000502:physiology; D001419:Bacteria / Q000145:classification / Q000235:genetics / Q000254:growth & development; D058893:DNA Barcoding, Taxonomic / Q000379:methods; D019641:DNA, Archaeal / Q000737:chemistry / Q000235:genetics; D004269:DNA, Bacterial / Q000737:chemistry / Q000235:genetics; D016054:DNA, Protozoan / Q000737:chemistry / Q000235:genetics; D004032:Diet; D000069196:Gastrointestinal Microbiome / Q000235:genetics / Q000502:physiology*; D014644:Genetic Variation; D005843:Geography; D054884:Host-Pathogen Interactions; D010802:Phylogeny; D012417:Rumen / Q000382:microbiology* / Q000469:parasitology; D012418:Ruminants / Q000145:classification / Q000382:microbiology* / Q000469:parasitology; D017422:Sequence Analysis, DNA; D013045:Species Specificity
chemical_list: D019641:DNA, Archaeal; D004269:DNA, Bacterial; D016054:DNA, Protozoan