title: The genome sequence of the rumen methanogen Methanobrevibacter ruminantium reveals new possibilities for controlling ruminant methane emissions.
abstract: BACKGROUND
  Methane (CH(4)) is a potent greenhouse gas (GHG), having a global warming potential 21 times that of carbon dioxide (CO(2)). Methane emissions from agriculture represent around 40% of the emissions produced by human-related activities, the single largest source being enteric fermentation, mainly in ruminant livestock. Technologies to reduce these emissions are lacking. Ruminant methane is formed by the action of methanogenic archaea typified by Methanobrevibacter ruminantium, which is present in ruminants fed a wide variety of diets worldwide. To gain more insight into the lifestyle of a rumen methanogen, and to identify genes and proteins that can be targeted to reduce methane production, we have sequenced the 2.93 Mb genome of M. ruminantium M1, the first rumen methanogen genome to be completed.
  
  
  RESULTS
  The M1 genome was sequenced, annotated and subjected to comparative genomic and metabolic pathway analyses. Conserved and methanogen-specific gene sets suitable as targets for vaccine development or chemogenomic-based inhibition of rumen methanogens were identified. The feasibility of using a synthetic peptide-directed vaccinology approach to target epitopes of methanogen surface proteins was demonstrated. A prophage genome was described and its lytic enzyme, endoisopeptidase PeiR, was shown to lyse M1 cells in pure culture. A predicted stimulation of M1 growth by alcohols was demonstrated and microarray analyses indicated up-regulation of methanogenesis genes during co-culture with a hydrogen (H(2)) producing rumen bacterium. We also report the discovery of non-ribosomal peptide synthetases in M. ruminantium M1, the first reported in archaeal species.
  
  
  CONCLUSIONS
  The M1 genome sequence provides new insights into the lifestyle and cellular processes of this important rumen methanogen. It also defines vaccine and chemogenomic targets for broad inhibition of rumen methanogens and represents a significant contribution to worldwide efforts to mitigate ruminant methane emissions and reduce production of anthropogenic greenhouse gases.
authors.affiliation: Rumen Microbial Genomics, Food Metabolism and Microbiology Section, Food and Textiles Group, AgResearch Limited, Grasslands Research Centre, Palmerston North, New Zealand.
authors.forename: Sinead C
authors.initials: SC
authors.lastname: Leahy
authors.forename: William J
authors.initials: WJ
authors.lastname: Kelly
authors.forename: Eric
authors.initials: E
authors.lastname: Altermann
authors.forename: Ron S
authors.initials: RS
authors.lastname: Ronimus
authors.forename: Carl J
authors.initials: CJ
authors.lastname: Yeoman
authors.forename: Diana M
authors.initials: DM
authors.lastname: Pacheco
authors.forename: Dong
authors.initials: D
authors.lastname: Li
authors.forename: Zhanhao
authors.initials: Z
authors.lastname: Kong
authors.forename: Sharla
authors.initials: S
authors.lastname: McTavish
authors.forename: Carrie
authors.initials: C
authors.lastname: Sang
authors.forename: Suzanne C
authors.initials: SC
authors.lastname: Lambie
authors.forename: Peter H
authors.initials: PH
authors.lastname: Janssen
authors.forename: Debjit
authors.initials: D
authors.lastname: Dey
authors.forename: Graeme T
authors.initials: GT
authors.lastname: Attwood
mesh_terms: D000818:Animals; D001483:Base Sequence; D017931:DNA Primers; D016521:Electrophoresis, Gel, Pulsed-Field; D016680:Genome, Bacterial; D008697:Methane / Q000378:metabolism*; D041581:Methanobrevibacter / Q000235:genetics* / Q000378:metabolism; D020411:Oligonucleotide Array Sequence Analysis; D016366:Open Reading Frames; D012417:Rumen / Q000382:microbiology*; D012418:Ruminants
chemical_list: D017931:DNA Primers; D008697:Methane