Modern understanding of the human gut archeoum (narrative review)
https://doi.org/10.23946/2500-0764-2026-11-2-76-87
Abstract
The review presents current information about representatives of the domain Archaea, as part of the human gut microbiome. In the human gastrointestinal tract, 20 species of archaea have been found, the most common are Methanobrevibacter smithii, found in 95.7−100 % of people, Methanosphaera stadtmanae – in 29.4 % and Methanomassiliicoccus luminyensis – in 4 % of people. The species composition of archaea depends on age, with the highest diversity observed in individuals aged 25−60 years. The primary source of archaea colonization in newborns is the intestinal microbiome and the mother's breast milk.
Intestinal archaea are hydrogenotrophs that are unable to break down glycosides and have positive syntrophic relationships with bacteria of the genera Bacteroides, Prevotella, and Ruminococcus, which compete with members of the Desulfovibrionaceae family, indicating their significant contribution to the regulation of the intestinal microbiota.
There is conflicting evidence about the clinical significance of archaea in the gut microbiome. Methane, a metabolite of archaea, regulates the Keap1-Nrf2 system, which provides endogenous antioxidant protection. Some archaea can use pro-atherogenic trimethylamine molecules as electron acceptors, reducing the risk of atherosclerosis. However, archaea have been linked to the development of intestinal cancer and impaired motility, leading to constipation. There is also evidence of a link between archaea and metabolic disorders, as Methanobrevibacter smithii can activate lipogenesis and alter glucose tolerance through hydrogen consumption. Archaea have been implicated in the development of infectious myocarditis and urinary tract diseases. Additionally, there is evidence of the sensitivity of archaea to antibiotics.
In view of the increased attention to the intestinal archaeome, methods for studying methanogenic archaea in humans are described. The main methods are molecular genetic and cultural, but the latter requires complex nutrient media and special atmospheric conditions for cultivation. Data on deposited archaea strains in various microbial collections are provided.
Thus, research on the archaeome of the human intestinal microbiota has far-reaching prospects, both in further assessing the role of archaea for human health and in developing new methods for diagnosing, treating, and preventing microbiome-associated pathological conditions in humans.
About the Author
Yu. V. Zakharova
Kemerovo State Medical University
Russian Federation
Russian Federation
Prof. Yuliyа V. Zakharova, MD, Dr. Sci. (Medicine), Professor of the Department of Microbiology and Virology
Voroshilova Street, 22A, Kemerovo, 650056
References
1. Prokofeva MI, Karaseva AI, Tulenkov AS, Klyukina AA, Suzina NE, Bale NJ, et al. Polysaccharide-degrading archaea dominate acidic hot springs: genomic and cultivation insights into a novel Thermoproteota lineage. mSystems. 2025;10(10):00710–00733. https://doi.org/10.1128/msystems.00710-25.
2. Cena JA, Silvestre-Barbosa Y, Belmok A, Stefani CM, Kyaw CM, Damé-Teixeira N. Meta-analyses on the periodontal archaeome. Advances Experimental Medicine and Biology. 2022;1373:69–93. https:// doi.org/10.1007/978-3-030-96881-6_4
3. Duller S, Moissl-Eichinger C. Archaea in the human microbiome and potential effects on human infectious disease. Emerg Infect Dis. 2024;30(8):1505–1518. https://doi.org/10.3201/eid3008.240181
4. Candeliere F, Sola L, Raimondi S, Rossi M, Amaretti A. Good and bad dispositions between archaea and bacteria in the human gut: New insights from metagenomic survey and co-occurrence analysis. Synth Syst Biotechnol. 2024;9(1):88–98. https://doi.org/10.1016/j.synbio.2023.12.007
5. Wolferen M, Pulschen AA, Baum B, Gribaldo S, Albers SV. The cell biology of archaea. Nat Microbiol. 2022;7(11):1744–1755. https://doi.org/10.1038/s41564-022-01215-8
6. Lyu X, Yu H, Lu Y. Diversity and function of soluble heterodisulfide reductases in methane-metabolizing archaea. Microbiol Spectr. 2025;13(5):03238–24. https://doi.org/10.1128/spectrum.03238-24
7. Tenorio-Salgado S, Villalpando-Aguilar JL, Hernandez-Guerrero R, Poot-Hernández AC, Perez-Rueda E. Exploring the enzymatic repertoires of Bacteria and Archaea and their associations with metabolic maps. Braz J Microbiol. 2024;55(4):3147–3157. https://doi.org/10.1007/s42770-024-01462-3
8. Aparici-Carratalá D, Esclapez J, Bautista V, Bonete M-J, Camacho M. Archaea: current and potential biotechnological applications. Res Microbiol. 2023;174(7):104080–104091. https://doi.org/10.1016/j.resmic.2023.104080
9. Catlett JL, Carr S, Cashman M, Smith MD, Walter M, Sakkaff Z, et al. Metabolic synergy between human symbionts Bacteroides and Methanobrevibacter. Microbiol Spectr. 2022;10(3):e01067–e01022. https:// doi.org/10.1128/spectrum.01067-22
10. Bornemann TLV, Adam PS, Probst AJ. Reconstruction of Archaeal Genomes from Short-Read Metagenomes. Methods in Mol Biol. 2022;2522:487–527. https://doi.org/10.1007/978-1-0716-2445-6_33
11. Sereme Y, Guindo CO, Filleron A, Corbeau P, Tran TA, Drancourt M, et al. Meconial Methanobrevibacter smithii suggests intrauterine methanogen colonization in preterm neonates. Curr Res Microb Sci. 2021;2:100034–100041. https://doi.org/10.1016/j.crmicr.2021.100034
12. Malat I, Drancourt M, Grine G. Methanobrevibacter smithii cell variants in human physiology and pathology: A review. Heliyon. 2024;10(18):36742–36767. https://doi.org/10.1016/j.heliyon.2024.e36742
13. Neumann CJ, Mohammadzadeh R, Woh PY, Kobal T, Pausan M-R, Shinde T, et al. First-year dynamics of the anaerobic microbiome and archaeome in infants' oral and gastrointestinal systems. mSystems. 2025;10(1):e0107124. https://doi.org/10.1128/msystems.01071-24
14. Salas-López M, Vélez-Ixta JM, Rojas-Guerrero DL, Piña-Escobedo A, Hernández-Hernández JM, Rangel-Calvillo MN, et al. Human milk Archaea associated with neonatal gut colonization and its co-occurrence with bacteria. Microorganisms. 2025;13(1):85–104. https://doi.org/10.3390/microorganisms13010085
15. Feehan B, Ran Q, Dorman V, Rumback K, Pogranichniy S, Ward K, et al. Novel complete methanogenic pathways in longitudinal genomic study of monogastric age-associated archaea. Anim Microbiome. 2023;5(1):35–52. https://doi.org/10.1186/s42523-023-00256-6
16. Bai X, Sun Y, Li Y, Li M, Cao Z, Huang Z, et al. Landscape of the gut archaeome in association with geography, ethnicity, urbanization, and diet in the Chinese population. Microbiome. 2022;10(1):147–165. https://doi.org/10.1186/s40168-022-01335-7
17. Mohammadzadeh R, Mahnert A, Duller S, Moissl-Eichinger C. Archaeal key-residents within the human microbiome: characteristics, interactions and involvement in health and disease. Curr Opin in Microbiol. 2022;67:102146–102157. https://doi.org/10.1016/j.mib.2022.102146
18. Wang T, Leibrock N, Plugge CM, Smidt H, Zoetendal EG. In vitro interactions between Blautia hydrogenotrophica, Desulfovibrio piger and Methanobrevibacter smithii under hydrogenotrophic conditions. Gut Microbes. 2023;15(2):2261784. https://doi.org/10.1080/19490976.2023.2261784
19. Ruden DM. The Human Archaeome: Commensals, Opportunists, or Emerging Pathogens? Pathogens. 2025;14(11):1111. https://doi.org/10.3390/pathogens14111111
20. Ou YF, Dong HP, McIlroy SJ, Crowe SA, Hallam SJ, Han P, et al. Expanding the phylogenetic distribution of cytochrome b-containing methanogenic archaea sheds light on the evolution of methanogenesis. ISME J. 2022;16(10):2373–2387. https://doi.org/10.1038/s41396-022-01281-0
21. Wang Y, Wang C, Zhang D, Wang L, Wang H, Hu B, et al. Methane-rich saline protects against sepsis-associated cognitive deficits in mice. Brain Res. 2022;1791:148000. https://doi.org/10.1016/j.brainres.2022.148000
22. Kleikamp HBC, Palacios PA, Kofoed MVW, Papacharalampos G, Bentien A, Nielsen JL. The selenoproteome as a dynamic response mechanism to oxidative stress in hydrogenotrophic methanogenic communities. Environ Sci Technol. 2024;58(15):6637–6646. https://doi.org/10.1021/acs.est.3c07725
23. Musat F, Kjeldsen KU, Rotaru AE, Chen SC, Musat N. Archaea oxidizing alkanes through alkyl-coenzyme M-reductases. Curr Opin Microbiol. 2024;79:102486. https://doi.org/10.1016/j.mib.2024.102486
24. Hoegenauer C, Hammer HF, Mahnert A, Moissl-Eichinger C. Methanogenic archaea in the human gastrointestinal tract. Nat Rev Gastroenterol Hepatol. 2022;19(12):805–813. https://doi.org/10.1038/s41575-022-00673-z
25. Fan Q, Chang H, Tian L, Zheng B, Liu R, Li Z. Methane saline suppresses ferroptosis via the Nrf2/HO-1 signaling pathway to ameliorate intestinal ischemia-reperfusion injury. Redox Rep. 2024;29(1):2373657–2373669. https://doi.org/10.1080/13510002.2024.2373657
26. Mafra D, Ribeiro M, Fonseca L, Regis B, Cardozo LFMF, Fragoso Dos Santos H, et al. Archaea from the gut microbiota of humans: Could be linked to chronic diseases? Anaerobe. 2022;77:102629 https://doi.org/10.1016/j.anaerobe.2022.102629
27. Kuehnast T, Kumpitsch C, Mohammadzadeh R, Weichhart T, Moissl-Eichinger C, Heine H. Exploring the human archaeome: its relevance for health and disease, and its complex interplay with the human immune system. FEBS J. 2025;292(6):1316–1329. https://doi.org/10.1111/febs.17123
28. Kemp JA, Schultz J, Modolon F, Ribeiro-Alves M, Rosado AS, Mafra D. Is there a correlation between TMAO plasma levels and archaea in the gut of patients undergoing hemodialysis? Int Urol Nephrol. 2025;57(4):1269–1275. https://doi.org/10.1007/s11255-024-04273-5
29. Li T, Coker OO, Sun Y, Li S, Liu C, Lin Y, et al. Multi-Cohort Analysis Reveals Altered Archaea in Colorectal Cancer Fecal Samples Across Populations. Gastroenterology. 2025;168(3):525–538. https://doi.org/10.1053/j.gastro.2024.10.023
30. Zuo A, Ba Y, Liu S, Shan D, Liu Z. Gut Archaea in Colorectal Cancer Diagnosis and Ecology. Gastroenterology. 2025;169(2):370–371. https://doi.org/10.1053/j.gastro.2024.11.036
31. Mehravar S, Takakura W, Wang J, Pimentel M, Nasser J, Rezaie A. Symptom profile of patients with intestinal methanogen overgrowth: a systematic review and meta-analysis. Clin Gastroenterol Hepatol. 2025;23(7):1111–1122. https://doi.org/10.1016/j.cgh.2024.07.020
32. Woh PY, Chen Y, Kumpitsch C, Mohammadzadeh R, Schmidt L, Moissl-Eichinger C. Reevaluation of the gastrointestinal methanogenic archaeome in multiple sclerosis and its association with treatment. Microbiol Spectrum. 2025;13(4):e0218324. https://doi.org/10.1128/spectrum.02183-24
33. Fumagalli A, Castells-Nobau A, Trivedi D, Garre-Olmo J, Puig J, Ramos R, et al. Archaea methanogens are associated with cognitive performance through the shaping of gut microbiota, butyrate and histidine metabolism. Gut Microbes. 2025;17(1):2455506. https://doi.org/10.1080/19490976.2025.2455506
34. Su Q, Wong OWH, Lu W, Wan Y, Zhang L, Xu W, et al. Multikingdom and functional gut microbiota markers for autism spectrum disorder. Nat Microbiol. 2024;9(9):2344–2355. https://doi.org/10.1038/s41564-024-01739-1
35. Chue KM, Wong SH, Zuo T, Ali Y. The role of the gut non-bacterial microbiome (virome, mycobiome, archaeome) and its impact on obesity. Mol Metab. 2026;103:102289. https://doi.org/10.1016/j.molmet.2025.102289
36. Malat I, Bossi V, Drancourt M, Grine G, Ruimy R. Methanobrevibacter smithii strain U29 whole genome sequence delineates M. smithii intermediate cell variants. BMC Res Notes. 2025;18(1):414–433. https:// doi.org/10.1186/s13104-025-07444-4
37. Pilliol V, Guindo CO, Terrer E, Aboudharam G, Drancourt M, Grine G. Culturing clinical Methanobrevibacter smithii using GG medium in a minimal anaerobe atmosphere. Journal of Microbiological Methods. 2023;207:106704. https://doi.org/10.1016/j.mimet.2023.106704
38. Weinberger V, Mohammadzadeh R, Blohs M, Kalt K, Mahnert A, Moser S, et al. Expanding the cultivable human archaeome: Methanobrevibacter intestini sp. nov. and strain Methanobrevibacter smithii GRAZ-2' from human faeces. Int J Syst Evol M
Review
For citations:
Zakharova Yu.V. Modern understanding of the human gut archeoum (narrative review). Fundamental and Clinical Medicine. 2026;11(2):76-87. (In Russ.) https://doi.org/10.23946/2500-0764-2026-11-2-76-87
Views:
53
JATS XML
Email this article 