title: Influence of periparturient and postpartum diets on rumen methanogen communities in three breeds of primiparous dairy cows.
abstract: BACKGROUND
  Enteric methane from rumen methanogens is responsible for 25.9 % of total methane emissions in the United States. Rumen methanogens also contribute to decreased animal feed efficiency. For methane mitigation strategies to be successful, it is important to establish which factors influence the rumen methanogen community and rumen volatile fatty acids (VFA). In the present study, we used next-generation sequencing to determine if dairy breed and/or days in milk (DIM) (high-fiber periparturient versus high-starch postpartum diets) affect the rumen environment and methanogen community of primiparous Holstein, Jersey, and Holstein-Jersey crossbreeds.
  
  
  RESULTS
  When the 16S rRNA gene sequences were processed and assigned to operational taxonomic units (OTU), a core methanogen community was identified, consisting of Methanobrevibacter (Mbr.) smithii, Mbr. thaueri, Mbr. ruminantium, and Mbr. millerae. The 16S rRNA gene sequence reads clustered at 3 DIM, but not by breed. At 3 DIM, the mean % abundance of Mbr. thaueri was lower in Jerseys (26.9 %) and higher in Holsteins (30.7 %) and Holstein-Jersey crossbreeds (30.3 %) (P < 0.001). The molar concentrations of total VFA were higher at 3 DIM than at 93, 183, and 273 DIM, whereas the molar proportions of propionate were increased at 3 and 93 DIM, relative to 183 and 273 DIM. Rumen methanogen densities, distributions of the Mbr. species, and VFA molar proportions did not differ by breed.
  
  
  CONCLUSIONS
  The data from the present study suggest that a core methanogen community is present among dairy breeds, through out a lactation. Furthermore, the methanogen communities were more influenced by DIM and the breed by DIM interactions than breed differences.
authors.affiliation: Department of Animal and Veterinary Sciences, The University of Vermont, 570 Main Street, Burlington, Vermont, 05405, USA. laura.cersosimo@uvm.edu.
authors.forename: Laura M
authors.initials: LM
authors.lastname: Cersosimo
authors.affiliation: Department of Animal and Veterinary Sciences, The University of Vermont, 570 Main Street, Burlington, Vermont, 05405, USA.
authors.forename: Melissa L
authors.initials: ML
authors.lastname: Bainbridge
authors.affiliation: Department of Animal and Veterinary Sciences, The University of Vermont, 570 Main Street, Burlington, Vermont, 05405, USA.
authors.forename: Jana
authors.initials: J
authors.lastname: Kraft
authors.affiliation: Department of Animal and Veterinary Sciences, The University of Vermont, 570 Main Street, Burlington, Vermont, 05405, USA.|Present Address: School of Animal and Comparative Biomedical Sciences, The University of Arizona, 1117 East Lowell Street, Tucson, AZ, 85721, USA.
authors.forename: André-Denis G
authors.initials: AD
authors.lastname: Wright
mesh_terms: D000821:Animal Feed; D000818:Animals; D002417:Cattle; D016000:Cluster Analysis; D004269:DNA, Bacterial / Q000235:genetics; D004275:DNA, Ribosomal / Q000235:genetics; D005232:Fatty Acids, Volatile / Q000378:metabolism; D005260:Female; D059014:High-Throughput Nucleotide Sequencing / Q000379:methods*; D007774:Lactation; D017013:Methanobacteriaceae / Q000145:classification* / Q000235:genetics / Q000302:isolation & purification*; D058725:Peripartum Period; D049590:Postpartum Period; D012336:RNA, Ribosomal, 16S / Q000235:genetics; D012417:Rumen / Q000378:metabolism / Q000382:microbiology*; D017422:Sequence Analysis, DNA / Q000379:methods*
chemical_list: D004269:DNA, Bacterial; D004275:DNA, Ribosomal; D005232:Fatty Acids, Volatile; D012336:RNA, Ribosomal, 16S
keywords: 16S rRNA gene; Archaea; Diversity; Holstein; Holstein-Jersey; Jersey; Volatile fatty acids; mcrA