The role of rumen microbiota in enteric methane mitigation for sustainable ruminant production

  • Received : 2023.08.15
  • Accepted : 2023.10.11
  • Published : 2024.02.01


Ruminal methane production functions as the main sink for metabolic hydrogen generated through rumen fermentation and is recognized as a considerable source of greenhouse gas emissions. Methane production is a complex trait affected by dry matter intake, feed composition, rumen microbiota and their fermentation, lactation stage, host genetics, and environmental factors. Various mitigation approaches have been proposed. Because individual ruminants exhibit different methane conversion efficiencies, the microbial characteristics of low-methane-emitting animals can be essential for successful rumen manipulation and environment-friendly methane mitigation. Several bacterial species, including Sharpea, uncharacterized Succinivibrionaceae, and certain Prevotella phylotypes have been listed as key players in low-methane-emitting sheep and cows. The functional characteristics of the unclassified bacteria remain unclear, as they are yet to be cultured. Here, we review ruminal methane production and mitigation strategies, focusing on rumen fermentation and the functional role of rumen microbiota, and describe the phylogenetic and physiological characteristics of a novel Prevotella species recently isolated from low methane-emitting and high propionate-producing cows. This review may help to provide a better understanding of the ruminal digestion process and rumen function to identify holistic and environmentally friendly methane mitigation approaches for sustainable ruminant production.



The study for the characteristics of the Prevotella lacticifex strain was supported by Cabinet Office, Government of Japan, Moonshot R&D Program for Agriculture, Forestry and Fisheries (funding agency: Bio-oriented Technology Research Advancement Institution) (No. JPJ009237).


  1. Rosenzweig C, Mbow C, Barioni LG, et al. Climate change responses benefit from a global food system approach. Nat Food 2020;1:94-7.
  2. FAO, WHO. Sustainable healthy diets: guiding principles. Rome, Italy: FAO, WHO; 2019.
  3. Arndt C, Hristov AN, Price WJ, et al. Full adoption of the most effective strategies to mitigate methane emissions by ruminants can help meet the 1.5 ℃ target by 2030 but not 2050. Proc Natl Acad Sci USA 2022;119:e2111294119.
  4. OECD-FAO Agricultural Outlook 2022-2031. Rome, Italy; Paris, France: FAO; OECD; 2022. Available from:
  5. Ungerfeld EM. Metabolic hydrogen flows in rumen fermentation: Principles and possibilities of interventions. Front Microbiol 2020;11:589.
  6. Johnson KA, Johnson DE. Methane emissions from cattle. J Anim Sci 1995;73:2483-92.
  7. Wright AD, Williams AJ, Winder B, et al. Molecular diversity of rumen methanogens from sheep in Western Australia. Appl Environ Microbiol 2004;70:1263-70.
  8. Shibata M, Terada F. Factors affecting methane production and mitigation in ruminants. Anim Sci J 2010;81:2-10.
  9. Greening C, Geier R, Wang C, et al. Diverse hydrogen production and consumption pathways influence methane production in ruminants. ISME J 2019;13:2617-32.
  10. Tapio I, Snelling TJ, Strozzi F, Wallace RJ. The ruminal microbiome associated with methane emissions from ruminant livestock. J Anim Sci Biotechnol 2017;8:7.
  11. Lyons T, Bielak A, Doyle E, Kuhla B. Variations in methane yield and microbial community profiles in the rumen of dairy cows as they pass through stages of first lactation. J Dairy Sci 2018;101:5102-14.
  12. Difford GF, Plichta DR, Lovendahl P, et al. Host genetics and the rumen microbiome jointly associate with methane emissions in dairy cows. PLoS Genet 2018;14:e1007580.
  13. Wallace RJ, Sasson G, Garnsworthy PC, et al. A heritable subset of the core rumen microbiome dictates dairy cow productivity and emissions. Sci Adv 2019;5:eaav8391.
  14. Kittelmann S, Pinares-Patino CS, Seedorf H, et al. Two different bacterial community types are linked with the low-methane emission trait in sheep. Plos One 2014;9:e103171.
  15. Danielsson R, Dicksved J, Sun L, et al. Methane production in dairy cows correlates with rumen methanogenic and bacterial community structure. Front Microbiol 2017;8:226.
  16. Belanche A, de la Fuente G, Newbold CJ. Effect of progressive inoculation of fauna-free sheep with holotrich protozoa and total-fauna on rumen fermentation, microbial diversity and methane emissions. FEMS Microbiol Ecol 2015;91:fiu026.
  17. Lima FS, Oikonomou G, Lima SF, et al. Prepartum and postpartum rumen fluid microbiomes: characterization and correlation with production traits in dairy cows. Appl Environ Microbiol 2015;81:1327-37.
  18. Liu C, Meng Q, Chen Y, et al. Role of age-related shifts in rumen bacteria and methanogens in methane production in cattle. Front Microbiol 2017;8:1563.
  19. Brask M, Weisbjerg MR, Hellwing ALF, Bannink A, Lund P. Methane production and diurnal variation measured in dairy cows and predicted from fermentation pattern and nutrient or carbon flow. Animal 2015;9:1795-806.
  20. Hristov AN, Kebreab E, Niu M, et al. Symposium review: Uncertainties in enteric methane inventories, measurement techniques, and prediction models. J Dairy Sci 2018;101:6655-74.
  21. Frey M. Hydrogenases: hydrogen-activating enzymes. Chembiochem 2002;3:153-60.<153::AID-CBIC153>3.0.CO;2-B
  22. Reichardt N, Duncan SH, Young P, et al. Phylogenetic distribution of three pathways for propionate production within the human gut microbiota. ISME J 2014;8:1323-35.
  23. Williams SRO, Hannah MC, Jacobs JL, Wales WJ, Moate PJ. Volatile fatty acids in ruminal fluid can be used to predict methane yield of dairy cows. Animals 2019;9:1006.
  24. Janssen PH. Influence of hydrogen on rumen methane formation and fermentation balances through microbial growth kinetics and fermentation thermodynamics. Anim Feed Sci Technol 2010;160:1-22.
  25. Zheng Y, Kahnt J, Kwon IH, Mackie RI, Thauer RK. Hydrogen formation and its regulation in Ruminococcus albus: involvement of an electron-bifurcating [FeFe]-hydrogenase, of a non-electron-bifurcating [FeFe]-hydrogenase, and of a putative hydrogen-sensing [FeFe]-hydrogenase. J Bacteriol 2014;196:3840-52.
  26. Shi Y, Weimer PJ, Ralph J. Formation of formate and hydrogen, and flux of reducing equivalents and carbon in Ruminococcus flavefaciens FD-1. Antonie Van Leeuwenhoek 1997;72:101-9.
  27. Emerson EL, Weimer PJ. Fermentation of model hemicelluloses by Prevotella strains and Butyrivibrio fibrisolvens in pure culture and in ruminal enrichment cultures. Appl Microbiol Biotechnol 2017;101:4269-78.
  28. Paillard D, McKain N, Chaudhary LC, et al. Relation between phylogenetic position, lipid metabolism and butyrate production by different Butyrivibrio-like bacteria from the rumen. Antonie Van Leeuwenhoek 2007;91:417-22.
  29. Cato EP, Moore WEC, Bryant MP. Designation of neotype strains for Bacteroides amylophilus Hamlin and Hungate 1956 and Bacteroides succinogenes Hungate 1950. Int J Syst Bacteriol 1978;28:491-5.
  30. Joblin KN, Matsui H, Naylor GE, Ushida K. Degradation of fresh ryegrass by methanogenic co-cultures of ruminal fungi grown in the presence or absence of Fibrobacter succinogenes. Curr Microbiol 2002;45:46-53.
  31. Aschenbach JR, Kristensen NB, Donkin SS, Hammon HM, Penner GB. Gluconeogenesis in dairy cows: the secret of making sweet milk from sour dough. IUBMB Life 2010;62:869-77.
  32. Allen MS, Bradford BJ, Oba M. Board-invited review: the hepatic oxidation theory of the control of feed intake and its application to ruminants. J Anim Sci 2009;87:3317-34.
  33. Buddle BM, Denis M, Attwood GT, et al. Strategies to reduce methane emissions from farmed ruminants grazing on pasture. Vet J 2011;188:11-7.
  34. Beauchemin KA. Reducing methane emissions form livestock. Scientific achievements in agriculture. In: Agriculture and Agri-Food Canada. 2019.
  35. Abecia L, Toral PG, Martin-Garcia AI, et al. Effect of bromochloromethane on methane emission, rumen fermentation pattern, milk yield, and fatty acid profile in lactating dairy goats. J Dairy Sci 2012;95:2027-36.
  36. Hristov AN, Oh J, Giallongo F, et al. An inhibitor persistently decreased enteric methane emission from dairy cows with no negative effect on milk production. Proc Natl Acad Sci USA 2015;112:10663-8.
  37. Mitsumori M, Shinkai T, Takenaka A, et al. Responses in digestion, rumen fermentation and microbial populations to inhibition of methane formation by a halogenated methane analogue. Br J Nutr 2012;108:482-91.
  38. McCrabb GJ, Berger KT, Magner T, May C, Hunter RA. Inhibiting methane production in Brahman cattle by dietary supplementation with a novel compound and the effects on growth. Aust J Agric Rec 1997;48:323-9.
  39. Denman SE, Tomkins NW, McSweeney CS. Quantitation and diversity analysis of ruminal methanogenic populations in response to the antimethanogenic compound bromochloromethane. FEMS Microbiol Ecol 2007;62:313-22.
  40. Goel G, Makkar HPS, Becker K. Inhibition of methanogens by bromochloromethane: effects on microbial communities and rumen fermentation using batch and continuous fermentations. Br J Nutr 2009;101:1484-92.
  41. Williams AG, Withers SE, Joblin KN. The effect of cocultivation with hydrogen-consuming bacteria on xylanolysis by Ruminococcus flavefaciens. Curr Microbiol 1994;29:133-8.
  42. Denman SE, Martinez-Fernandez G, Shinkai T, Mitsumori M, McSweeney CS. Metagenomic analysis of the rumen microbial community following inhibition of methane formation by a halogenated methane analog. Front Microbiol 2015;6:1087.
  43. Mackie RI, McSweeney CS, Aminov RI. Rumen. 2013. In: Battista J (ed) eLS. New York, USA: John Wiley & Sons Ltd; 2013.
  44. Yarlett N, Coleman GS, Williams AG, Lloyd D. Hydrogenosomes in known species of rumen entodiniomorphid protozoa. FEMS Microbiol Lett 1984;21:15-9.
  45. Finlay BJ, Esteban G, Clarke KJ, Williams AG, Embley TM, Hirt RP. Some rumen ciliates have endosymbiotic methanogens. FEMS Microbiol Lett 1994;117:157-61.
  46. Vogels GD, Hoppe WF, Stumm CK. Association of methanogenic bacteria with rumen ciliates. Appl Environ Microbiol 1980;40:608-12.
  47. Belanche A, de la Fuente G, Newbold CJ. Study of methanogen communities associated with different rumen protozoal populations. FEMS Microbiol Ecol 2014;90:663-77.
  48. Ng F, Kittelmann S, Patchett ML, et al. An adhesin from hydrogen-utilizing rumen methanogen Methanobrevibacter ruminantium M1 binds a broad range of hydrogen-producing microorganisms. Environ Microbiol 2016;18:3010-21.
  49. Morgavi DP, Jouany JP, Martin C. Changes in methane emission and rumen fermentation parameters induced by refaunation in sheep. Aust J Exp Agric 2008;48:69-72.
  50. Morgavi DP, Martin C, Jouany JP, Ranilla MJ. Rumen protozoa and methanogenesis: not a simple cause-effect relationship. Br J Nutr 2012;107:388-97.
  51. Newbold CJ, Lassalas B, Jouany JP. The importance of methanogens associated with ciliate protozoa in ruminal methane production in vitro. Lett Appl Microbiol 1995;21:230-4.
  52. Guyader J, Eugene M, Noziere P, Morgavi DP, Doreau M, Martin C. Influence of rumen protozoa on methane emission in ruminants: a meta-analysis approach. Animal 2014;8:1816-25.
  53. Farra PA, Satter LD. Manipulation of the ruminal fermentation. III. effect of nitrate on ruminal volatile fatty acid production and milk composition. J Dairy Sci 1971;54:1018-24.
  54. Glasson CRK, Kinley RD, de Nys R, et al. Benefits and risks of including the bromoform containing seaweed Asparagopsis in feed for the reduction of methane production from ruminants. Algal Res 2022;64:102673.
  55. Shinkai T, Enishi O, Mitsumori M, et al. Mitigation of methane production from cattle by feeding cashew nut shell liquid. J Dairy Sci 2012;95:5308-16.
  56. Weimar MR, Cheung J, Dey D, et al. Development of multiwell-plate methods using pure cultures of methanogens to identify new inhibitors for suppressing ruminant methane emissions. Appl Environ Microbiol 2017;83:e00396-17.
  57. Bocquier F, Gonzalez-Garcia E. Sustainability of ruminant agriculture in the new context: feeding strategies and features of animal adaptability into the necessary holistic approach. Animal 2010;4:1258-73.
  58. Wasson DE, Yarish C, Hristov AN. Enteric methane mitigation through Asparagopsis taxiformis supplementation and potential algal alternatives. Front Anim Sci 2022;3:999338.
  59. Creevey CJ, Kelly WJ, Henderson G, Leahy SC. Determining the culturability of the rumen bacterial microbiome. Microb Biotechnol 2014;7:467-79.
  60. Henderson G, Cox F, Ganesh S, et al. Rumen microbial community composition varies with diet and host, but a core microbiome is found across a wide geographical range. Sci Rep 2015;5:14567.
  61. Ishler V, Heinrichs AJ, Varga G. From feed to milk: Understanding rumen function. University Park, PA, USA: Pennsylvania State University; 1996. Extension Circular 422.
  62. Wallace RJ, Rooke JA, McKain N, et al. The rumen microbial metagenome associated with high methane production in cattle. BMC Genomics 2015;16:839.
  63. Pope PB, Smith W, Denman SE, et al. Isolation of Succinivibrionaceae implicated in low methane emissions from Tammar wallabies. Science 2011;333:646-8.
  64. McCabe MS, Cormican P, Keogh K, et al. 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. PLoS One 2015;10:e0133234.
  65. Shabat SKB, Sasson G, Doron-Faigenboim A, et al. Specific microbiome-dependent mechanisms underlie the energy harvest efficiency of ruminants. ISME J 2016;10:2958-72.
  66. Lana RP, Russell JB, Van Amburgh ME. The role of pH in regulating ruminal methane and ammonia production. J Anim Sci 1998;76:2190-6.
  67. Henning PH, Horn CH, Steyn DG, Meissner HH, Hagg FM. The potential of Megasphaera elsdenii isolates to control ruminal acidosis. Anim Feed Sci Technol 2010;157:13-9.
  68. Kamke J, Kittelmann S, Soni P, et al. Rumen metagenome and metatranscriptome analyses of low methane yield sheep reveals a Sharpea-enriched microbiome characterised by lactic acid formation and utilisation. Microbiome 2016;4:56.
  69. Malmuthuge N, Guan LL. Understanding host-microbial interactions in rumen: searching the best opportunity for microbiota manipulation. J Anim Sci Biotechnol 2017;8:8.
  70. Stewart CS, Flint HJ, Bryant MP. The rumen bacteria. In: Hobson PN, Stewart CS, editors. The rumen microbial ecosystem. London, UK: Chapman & Hall; 1997. pp. 10-72.
  71. Gross R, Simon J. The hydE gene is essential for the formation of Wolinella succinogenes NiFe-hydrogenase. FEMS Microbiol Lett 2003;227:197-202.
  72. Henderson C. The influence of extracellular hydrogen on the metabolism of Bacteroides ruminicola, Anaerovibrio lipolytica and Selenomonas ruminantium. J Gen Microbiol 1980;119:485-91.
  73. Beauchemin KA, McGinn SM. Methane emissions from beef cattle: Effects of fumaric acid, essential oil, and canola oil. J Anim Sci 2006;84:1489-96.
  74. Wood TA, Wallace RJ, Rowe A, et al. Encapsulated fumaric acid as a feed ingredient to decrease ruminal methane emissions. Anim Feed Sci Technol 2009;152:62-71.
  75. Foley PA, Kenny DA, Callan JJ, Boland TM, O'Mara FP. Effect of DL-malic acid supplementation on feed intake, methane emission, and rumen fermentation in beef cattle. J Anim Sci 2009;87:1048-57.
  76. Asanuma N, Iwamoto M, Hino T. Effect of the addition of fumarate on methane production by ruminal microorganisms in vitro. J Dairy Sci 1999;82:780-7.
  77. Louis P, Duncan SH, Sheridan PO, Walker AW, Flint HJ. Microbial lactate utilisation and the stability of the gut microbiome. Gut Microbiome 2022;3:e3.
  78. Hino T, Kuroda S. Presence of lactate dehydrogenase and lactate racemase in Megasphaera elsdenii grown on glucose or lactate. Appl Envion Microbiol 1993;59:255-9.
  79. Prabhu R, Altman E, Eiteman MA. Lactate and acrylate metabolism by Megasphaera elsdenii under batch and steady-state conditions. Appl Environ Microbiol 2012;78:8564-70.
  80. Asanuma N, Hino T. Prevention of rumen acidosis and suppression of ruminal methanogenesis by augmentation of lactate utilization. Anim Sci J (Japan) 2004;75:543-50. In Japanese.
  81. Mizrahi I, Jami E. The compositional variation of the rumen microbiome and its effect on host performance and methane emission. Animal 2018;12:s220-32. 
  82. Accetto T, Avgustin G. The diverse and extensive plant polysaccharide degradative apparatuses of the rumen and hindgut Prevotella species: A factor in their ubiquity? Syst Appl Microbiol 2019;42:107-16.
  83. Shinkai T, Ikeyama N, Kumagai M, et al. Prevotella lacticifex sp. nov., isolated from the rumen of cows. Int J Syst Evol Microbiol 2022;72:005278.
  84. Ramsak, A, Peterka M, Tajima K, et al. Unravelling the genetic diversity of ruminal bacteria belonging to the CFB phylum. FEMS Microbiol Ecol 2000;33:69-79.
  85. Purushe J, Fouts DE, Morrison M, et al. Comparative genome analysis of Prevotella ruminicola and Prevotella bryantii: insights into their environmental niche. Microb Ecol 2010; 60:721-9.
  86. Bekele AZ, Koike S, Kobayashi Y. Genetic diversity and diet specificity of ruminal Prevotella revealed by 16S rRNA gene-based analysis. FEMS Microbiol Lett 2010;305:49-57.
  87. Stevenson DM, Weimer PJ. Dominance of Prevotella and low abundance of classical ruminal bacterial species in the bovine rumen revealed by relative quantification real-time PCR. Appl Microbiol Biotechnol 2007;75:165-74.
  88. Carberry CA, Kenny DA, Han S, McCabe MS, Waters SM. Effect of phenotypic residual feed intake and dietary forage content on the rumen microbial community of beef cattle. Appl Environ Microbiol 2012;78:4949-58.
  89. Myer PR, Smith TPL, Wells JE, Kuehn LA, Freetly HC. Rumen microbiome from steers differing in feed efficiency. PLoS One 2015;10:e0129174.
  90. Betancur-Murillo CL, Aguilar-Marin SB, Jovel J. Prevotella: A key player in ruminal metabolism. Microorganisms 2022;11:1.
  91. Hitch TCA, Bisdorf K, Afrizal A, et al. A taxonomic note on the genus Prevotella: Description of four novel genera and emended description of the genera Hallella and Xylanibacter. Syst Appl Microbiol 2022;45:126354.
  92. Kogawa M, Hosokawa M, Nishikawa Y, Mori K, Takeyama H. Obtaining high-quality draft genomes from uncultured microbes by cleaning and co-assembly of single-cell amplified genomes. Sci Rep 2018;8:2059.
  93. Chijiiwa R, Hosokawa M, Kogawa M, et al. Single-cell genomics of uncultured bacteria reveals dietary fiber responders in the mouse gut microbiota. Microbiome 2020;8:5.
  94. Gawad C, Koh W, Quake SR. Single-cell genome sequencing: current state of the science. Nat Rev Genet 2016;17:175-88.
  95. Cuomo ASE, Nathan A, Raychaudhuri S, MacArthur DG, Powell JE. Single-cell genomics meets human genetics. Nat Rev Genet 2023;24:535-49.