- Invited Review - Hydrogen production and hydrogen utilization in the rumen: key to mitigating enteric methane production

  • Roderick I. Mackie (Department of Animal Sciences, University of Illinois) ;
  • Hyewon Kim (Department of Animal Sciences, University of Illinois) ;
  • Na Kyung Kim (Department of Animal Sciences, University of Illinois) ;
  • Isaac Cann (Department of Animal Sciences, University of Illinois)
  • Received : 2023.08.11
  • Accepted : 2023.11.08
  • Published : 2024.02.01


Molecular hydrogen (H2) and formate (HCOO-) are metabolic end products of many primary fermenters in the rumen ecosystem. Both play a vital role in fermentation where they are electron sinks for individual microbes in an anaerobic environment that lacks external electron acceptors. If H2 and/or formate accumulate within the rumen, the ability of primary fermenters to regenerate electron carriers may be inhibited and microbial metabolism and growth disrupted. Consequently, H2- and/or formate-consuming microbes such as methanogens and possibly homoacetogens play a key role in maintaining the metabolic efficiency of primary fermenters. There is increasing interest in identifying approaches to manipulate the rumen ecosystem for the benefit of the host and the environment. As H2 and formate are important mediators of interspecies interactions, an understanding of their production and utilization could be a significant starting point for the development of successful interventions aimed at redirecting electron flow and reducing methane emissions. We conclude by discussing in brief ruminant methane mitigation approaches as a model to help understand the fate of H2 and formate in the rumen ecosystem.



The authors acknowledge the scientific wisdom and contributions to this review of numerous rumen microbiologists ranging from Professor Marvin P. Bryant, a pioneering preeminent rumen microbiologist and ecologist, to recent coauthors and collaborators Sinead Leahy, Graeme Attwood, Peter Janssen, Tim McAllister and William Kelly.


  1. Terry SA, Romero CM, Chaves AV, McAllister TA. Nutritional factors affecting greenhouse gas production from ruminants: implications for enteric and manure emissions. In: Improving rumen function. London, UK: Burleigh Dodds Science Publishing; 2020. pp. 505-46.
  2. McAllister TA, Meale SJ, Valle E, et al. Ruminant nutrition symposium: use of genomics and transcriptomics to identify strategies to lower ruminal methanogenesis. J Anim Sci 2015;93:1431-49.
  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 2022; 119:e2111294119.
  4. Gerber PJ, Steinfeld H, Henderson B, et al. Tackling climate change through livestock: a global assessment of emissions and mitigation opportunities. Rome, Italy: Food and Agriculture Organization of the United Nations (FAO); 2013.
  5. Bryant MP. Microbial methane production-theoretical aspects. J Anim Sci 1979;48:193-201.
  6. Mackie RI, White BA, Bryant MP. Methanogenesis, biochemistry. Encycl Microbiol 1992;3:97-109.
  7. Wolin MJ, Miller TL, Stewart CS. Microbe-microbe interactions. In: The rumen microbial ecosystem. Dordrecht, The Netherlands: Springer; 1997. pp. 467-91.
  8. Ungerfeld EM. Metabolic hydrogen flows in rumen fermentation: principles and possibilities of interventions. Front Microbiol 2020;11:589.
  9. Hungate RE, Smith W, Bauchop T, Yu I, Rabinowitz JC. Formate as an intermediate in the bovine rumen fermentation. J Bacteriol 1970;102:389-97.
  10. Leahy SC, Janssen PH, Attwood GT, Mackie RI, McAllister TA, Kelly WJ. Electron flow: key to mitigating ruminant methanogenesis. Trends Microbiol 2022;30:209-12.
  11. Wolin MJ. Fermentation in the rumen and human large intestine. Science 1981;213:1463-8.
  12. Sollinger A, Urich T. Methylotrophic methanogens everywhere - physiology and ecology of novel players in global methane cycling. Biochem Soc Trans 2019;47:1895-907.
  13. Duin EC, Wagner T, Shima S, et al. Mode of action uncovered for the specific reduction of methane emissions from ruminants by the small molecule 3-nitrooxypropanol. Proc Natl Acad Sci 2016;113:6172-7.
  14. Martinez-Fernandez G, Duval S, Kindermann M, Schirra HJ, Denman SE, McSweeney CS. 3-NOP vs. halogenated compound: methane production, ruminal fermentation and microbial community response in forage fed cattle. Front Microbiol 2018;9:1582.
  15. Vijn S, Compart DP, Dutta N, et al. Key considerations for the use of seaweed to reduce enteric methane emissions from cattle. Front Vet Sci 2020;7:597430.
  16. Poulsen M, Schwab C, Jensen BB, et al. Methylotrophic methanogenic Thermoplasmata implicated in reduced methane emissions from bovine rumen. Nat Commun 2013;4:1428.
  17. Sollinger A, Tveit AT, Poulsen M, et al. Holistic assessment of rumen microbiome dynamics through quantitative meta-transcriptomics reveals multifunctional redundancy during key steps of anaerobic feed degradation. mSystems 2018;3: 10.1128/msystems.00038-18.
  18. Shi W, Moon CD, Leahy SC, et al. Methane yield phenotypes linked to differential gene expression in the sheep rumen microbiome. Genome Res 2014;24:1517-25.
  19. Li F, Guan LL. Metatranscriptomic profiling reveals linkages between the active rumen microbiome and feed efficiency in beef cattle. Appl Environ Microbiol 2017;83:e00061-17.
  20. Hungate R. Hydrogen as an intermediate in the rumen fermentation. Arch Mikrobiol 1967;59:158-64.
  21. Zinder SH. Physiological ecology of methanogens. In: Ferry JG, editor. Methanogenesis: ecology, physiology, biochemistry and genetics. Boston, MA, USA: Springer; 1993. pp. 128-206.
  22. Iannotti EL, Kafkewitz D, Wolin MJ, Bryant MP. Glucose fermentation products of Ruminococcus albus grown in continuous culture with Vibrio succinogenes: changes caused by interspecies transfer of H2. J Bacteriol 1973;114:1231-40.
  23. Greening C, Biswas A, Carere CR, et al. Genomic and meta-genomic surveys of hydrogenase distribution indicate H2 is a widely utilised energy source for microbial growth and survival. ISME J 2016;10:761-77.
  24. Poudel S, Tokmina-Lukaszewska M, Colman DR, et al. Unification of [FeFe]-hydrogenases into three structural and functional groups. Biochim Biophys Acta Gen Subj 2016; 1860:1910-21.
  25. Vignais PM, Billoud B. Occurrence, classification, and biological function of hydrogenases: an overview. Chem Rev 2007;107:4206-72.
  26. Buckel W, Thauer RK. Energy conservation via electron bifurcating ferredoxin reduction and proton/Na+ translocating ferredoxin oxidation. Biochim Biophys Acta Bioenerg 2013; 1827:94-113.
  27. 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.
  28. 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.
  29. Seshadri R, Leahy SC, Attwood GT, et al. Cultivation and sequencing of rumen microbiome members from the Hungate1000 Collection. Nat Biotechnol 2018;36:359-67.
  30. Kelly WJ, Mackie RI, Attwood GT, Janssen PH, McAllister TA, Leahy SC. Hydrogen and formate production and utilisation in the rumen and the human colon. Anim Microbiome 2022;4:22.
  31. Belzer C. Nutritional strategies for mucosal health: the interplay between microbes and mucin glycans. Trends Microbiol 2022;30:13-21.
  32. Bergman EN. Energy contributions of volatile fatty acids from the gastrointestinal tract in various species. Physiol Rev 1990;70:567-90.
  33. Modesto A, Cameron NR, Varghese C, et al. Meta-analysis of the composition of human intestinal gases. Dig Dis Sci 2022;67:3842-59.
  34. Sahakian AB, Jee SR, Pimentel M. Methane and the gastrointestinal tract. Dig Dis Sci 2010;55:2135-43.
  35. Polag D, Keppler F. Global methane emissions from the human body: Past, present and future. Atmos Environ 2019;214:116823.
  36. Kumpitsch C, Fischmeister FPS, Mahnert A, et al. Reduced B12 uptake and increased gastrointestinal formate are associated with archaeome-mediated breath methane emission in humans. Microbiome 2021;9:193.
  37. 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.
  38. Xie F, Jin W, Si H, et al. An integrated gene catalog and over 10,000 metagenome-assembled genomes from the gastro-intestinal microbiome of ruminants. Microbiome 2021;9:137.
  39. Newbold CJ, De La Fuente G, Belanche A, Ramos-Morales E, McEwan NR. The role of ciliate protozoa in the rumen. Front Microbiol 2015;6:1313.
  40. Hess M, Paul SS, Puniya AK, et al. Anaerobic fungi: past, present, and future. Front Microbiol 2020;11:584893.
  41. Henderson G, Naylor GE, Leahy SC, et al. Presence of novel, potentially homoacetogenic bacteria in the rumen as determined by analysis of formyltetrahydrofolate synthetase sequences from ruminants. Appl Environ Microbiol 2010;76:2058-66.
  42. Gagen EJ, Denman SE, Padmanabha J, et al. Functional gene analysis suggests different acetogen populations in the bovine rumen and tammar wallaby forestomach. Appl Environ Microbiol 2010;76:7785-95.
  43. Mackie RI, Bryant MP. Acetogenesis and the rumen: syntrophic relationships. In: Drake HL, editor. Acetogenesis. Boston, MA, USA: Springer; 1994. pp. 331-64.
  44. Van Zijderveld SM, Gerrits WJJ, Apajalahti JA, et al. Nitrate and sulfate: Effective alternative hydrogen sinks for mitigation of ruminal methane production in sheep. J Dairy Sci 2010;93:5856-66.
  45. Leng RA. Interactions between microbial consortia in biofilms: a paradigm shift in rumen microbial ecology and enteric methane mitigation. Anim Prod Sci 2014;54:519-43.
  46. Wolin MJ. A theoretical rumen fermentation balance. J Dairy Sci 1960;43:1452-9.
  47. Nakamura N, Lin HC, McSweeney CS, Mackie RI, Gaskins HR. Mechanisms of microbial hydrogen disposal in the human colon and implications for health and disease. Annu Rev Food Sci Technol 2010;1:363-95.
  48. Hylemon PB, Harris SC, Ridlon JM. Metabolism of hydrogen gases and bile acids in the gut microbiome. FEBS Lett 2018;592:2070-82.
  49. Czerkawski JW. Methane production in ruminants and its significance. World Rev Nutr Diet 1969;11:240-82.
  50. Reisinger A, Clark H, Cowie AL, et al. How necessary and feasible are reductions of methane emissions from livestock to support stringent temperature goals? Philos Trans R Soc A Math Phys Eng Sci 2021;379:20200452.
  51. Xu X, Sharma P, Shu S, et al. Global greenhouse gas emissions from animal-based foods are twice those of plant-based foods. Nat Food 2021;2:724-32.
  52. IPCC CC. The physical science basis. Contribution of working group I to the fourth assessment report of the Intergovernmental Panel on Climate Change. Cambridge, United Kingdom and New York, NY, USA: Cambridge University Press; 2007. pp. 113-9.
  53. Beauchemin KA, Ungerfeld EM, Eckard RJ, Wang M. Fifty years of research on rumen methanogenesis: Lessons learned and future challenges for mitigation. Animal 2020;14(S1):s2-s16.
  54. Almeida AK, Hegarty RS, Cowie A. Meta-analysis quantifying the potential of dietary additives and rumen modifiers for methane mitigation in ruminant production systems. Anim Nutr 2021;7:1219-30.
  55. Mizrahi I, Wallace RJ, Morais S. The rumen microbiome: balancing food security and environmental impacts. Nat Rev Microbiol 2021;19:553-66.
  56. Johnson KA, Johnson DE. Methane emissions from cattle. J Anim Sci 1995;73:2483-92.
  57. Pinares-Patino CS, Hickey SM, Young EA, et al. Heritability estimates of methane emissions from sheep. Animal 2013;7:316-21.
  58. Rowe S, Hickey S, Jonker A, et al. Selection for divergent methane yield in New Zealand sheep-a ten-year perspective. Proc Assoc Advmt Anim Breed Genet 2019;23:306-9.
  59. Pinares-Patino C, Ebrahimi SH, McEwan J, et al. Is rumen retention time implicated in sheep differences in methane emission. In: Proceedings of the New Zealand Society of Animal Production; 2011. New Zealand Society of Animal Production Wellington, New Zealand.
  60. Goopy JP, Donaldson A, Hegarty R, et al. Low-methane yield sheep have smaller rumens and shorter rumen retention time. Br J Nutr 2014;111:578-85.
  61. 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.
  62. 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.
  63. Joblin KN. Ruminal acetogens and their potential to lower ruminant methane emissions. Aust J Agric Res 1999;50:1307-14.
  64. Jeyanathan J, Martin C, Morgavi DP. The use of direct-fed microbials for mitigation of ruminant methane emissions: a review. Animal 2014;8:250-61.
  65. Leng RA. Unravelling methanogenesis in ruminants, horses and kangaroos: the links between gut anatomy, microbial biofilms and host immunity. Anim Prod Sci 2018;58:1175-91.
  66. Baca-Gonzalez V, Asensio-Calavia P, Gonzalez-Acosta S, Perez de la Lastra JM, Morales de la Nuez A. Are vaccines the solution for methane emissions from ruminants? A systematic review. Vaccines 2020;8:460.
  67. Kelly WJ, Leahy SC, Kamke J, et al. Occurrence and expression of genes encoding methyl-compound production in rumen bacteria. Anim Microbiome 2019;1:15.
  68. Muetzel S, Clark H. Methane emissions from sheep fed fresh pasture. NZ J Agric Res 2015;58:472-89.
  69. Alam KY, Clark DP. Anaerobic fermentation balance of Escherichia coli as observed by in vivo nuclear magnetic resonance spectroscopy. J Bacteriol 1989;171:6213-7.
  70. Tiffany CR, Lee JY, Rogers AWL, et al. The metabolic footprint of Clostridia and Erysipelotrichia reveals their role in depleting sugar alcohols in the cecum. Microbiome 2021;9:174.
  71. Sun X, Henderson G, Cox F, et al. Lambs fed fresh winter forage rape (Brassica napus L.) emit less methane than those fed perennial ryegrass (Lolium perenne L.), and possible mechanisms behind the difference. PLoS One 2015;10:e0119697.
  72. Sun XZ. Invited review: Glucosinolates might result in low methane emissions from ruminants fed Brassica forages. Front Vet Sci 2020;7:588051.
  73. Mackie RI, McSweeney CS, Aminov RI. Rumen. In: Encyclopedia of Life Sciences. John Wiley & Sons, Ltd; 2013.
  74. Beauchemin KA, Ungerfeld EM, Abdalla AL, et al. Invited review: Current enteric methane mitigation options. J Dairy Sci 2022;105:9297-326.