title: Illumina MiSeq Phylogenetic Amplicon Sequencing Shows a Large Reduction of an Uncharacterised Succinivibrionaceae and an Increase of the Methanobrevibacter gottschalkii Clade in Feed Restricted Cattle.
abstract: Periodic feed restriction is used in cattle production to reduce feed costs. When normal feed levels are resumed, cattle catch up to a normal weight by an acceleration of normal growth rate, known as compensatory growth, which is not yet fully understood. Illumina Miseq Phylogenetic marker amplicon sequencing of DNA extracted from rumen contents of 55 bulls showed that restriction of feed (70% concentrate, 30% grass silage) for 125 days, to levels that caused a 60% reduction of growth rate, resulted in a large increase of relative abundance of Methanobrevibacter gottschalkii clade (designated as OTU-M7), and a large reduction of an uncharacterised Succinivibrionaceae species (designated as OTU-S3004). There was a strong negative Spearman correlation (ρ = -0.72, P = <1x10(-20)) between relative abundances of OTU-3004 and OTU-M7 in the liquid rumen fraction. There was also a significant increase in acetate:propionate ratio (A:P) in feed restricted animals that showed a negative Spearman correlation (ρ = -0.69, P = <1x10(-20)) with the relative abundance of OTU-S3004 in the rumen liquid fraction but not the solid fraction, and a strong positive Spearman correlation with OTU-M7 in the rumen liquid (ρ = 0.74, P = <1x10(-20)) and solid (ρ = 0.69, P = <1x10(-20)) fractions. Reduced A:P ratios in the rumen are associated with increased feed efficiency and reduced production of methane which has a global warming potential (GWP 100 years) of 28. Succinivibrionaceae growth in the rumen was previously suggested to reduce methane emissions as some members of this family utilise hydrogen, which is also utilised by methanogens for methanogenesis, to generate succinate which is converted to propionate. Relative abundance of OTU-S3004 showed a positive Spearman correlation with propionate (ρ = 0.41, P = <0.01) but not acetate in the liquid rumen fraction.
authors.affiliation: Animal and Bioscience Research Department, Animal and Grassland Research and Innovation Centre, Teagasc, Grange, Dunsany, County Meath, Ireland.
authors.forename: Matthew Sean
authors.initials: MS
authors.lastname: McCabe
authors.affiliation: Animal and Bioscience Research Department, Animal and Grassland Research and Innovation Centre, Teagasc, Grange, Dunsany, County Meath, Ireland.
authors.forename: Paul
authors.initials: P
authors.lastname: Cormican
authors.affiliation: Animal and Bioscience Research Department, Animal and Grassland Research and Innovation Centre, Teagasc, Grange, Dunsany, County Meath, Ireland.
authors.forename: Kate
authors.initials: K
authors.lastname: Keogh
authors.affiliation: UCD School of Agriculture, Food Science and Veterinary Medicine, College of Life Sciences, University College Dublin, Belfield, Dublin, Ireland.
authors.forename: Aaron
authors.initials: A
authors.lastname: O'Connor
authors.affiliation: Animal and Bioscience Research Department, Animal and Grassland Research and Innovation Centre, Teagasc, Grange, Dunsany, County Meath, Ireland.
authors.forename: Eoin
authors.initials: E
authors.lastname: O'Hara
authors.affiliation: Department of Animal Production, University of Buenos Aires, Buenos Aires City, Argentina.
authors.forename: Rafael Alejandro
authors.initials: RA
authors.lastname: Palladino
authors.affiliation: Animal and Bioscience Research Department, Animal and Grassland Research and Innovation Centre, Teagasc, Grange, Dunsany, County Meath, Ireland.
authors.forename: David Anthony
authors.initials: DA
authors.lastname: Kenny
authors.affiliation: Animal and Bioscience Research Department, Animal and Grassland Research and Innovation Centre, Teagasc, Grange, Dunsany, County Meath, Ireland.
authors.forename: Sinéad Mary
authors.initials: SM
authors.lastname: Waters
mesh_terms: D000821:Animal Feed; D000818:Animals; D002417:Cattle / Q000254:growth & development / Q000382:microbiology* / Q000502:physiology; D019641:DNA, Archaeal / Q000235:genetics / Q000302:isolation & purification; D004269:DNA, Bacterial / Q000235:genetics / Q000302:isolation & purification; D005232:Fatty Acids, Volatile / Q000378:metabolism; D005508:Food Deprivation / Q000502:physiology; D000069196:Gastrointestinal Microbiome / Q000235:genetics; D008297:Male; D008697:Methane / Q000096:biosynthesis; D041581:Methanobrevibacter / Q000235:genetics* / Q000302:isolation & purification* / Q000378:metabolism; D023421:Models, Animal; D010802:Phylogeny; D012417:Rumen / Q000378:metabolism / Q000382:microbiology; D044063:Succinivibrionaceae / Q000235:genetics* / Q000302:isolation & purification* / Q000378:metabolism
chemical_list: D019641:DNA, Archaeal; D004269:DNA, Bacterial; D005232:Fatty Acids, Volatile; D008697:Methane