The host-associated archaeome


Host-associated microbial communities have an important role in shaping the health and fitness of plants and animals. Most studies have focused on the bacterial, fungal or viral communities, but often the archaeal component has been neglected. The archaeal community, the so-called archaeome, is now increasingly recognized as an important component of host-associated microbiomes. It is composed of various lineages, including mainly Methanobacteriales and Methanomassiliicoccales (Euryarchaeota), as well as representatives of the Thaumarchaeota. Host–archaeome interactions have mostly been delineated from methanogenic archaea in the gastrointestinal tract, where they contribute to substantial methane production and are potentially also involved in disease-relevant processes. In this Review, we discuss the diversity and potential roles of the archaea associated with protists, plants and animals. We also present the current understanding of the archaeome in humans, the specific adaptations involved in interaction with the resident microbial community as well as with the host, and the roles of the archaeome in both health and disease.

Access options

Rent or Buy article

Get time limited or full article access on ReadCube.


All prices are NET prices.

Fig. 1: Archaeal diversity.
Fig. 2: Methane emission in cattle in comparison to other animals.
Fig. 3: Archaeal taxa detected in human, other animal and plant samples.
Fig. 4: Detailed information on five archaeal genera found in humans, other animals and plants.
Fig. 5: Interaction of the gastrointestinal archaeome with the host and the bacterial microbial community.


  1. 1.

    Rosenberg, E., Koren, O., Reshef, L., Efrony, R. & Zilber-Rosenberg, I. The role of microorganisms in coral health, disease and evolution. Nat. Rev. Microbiol. 5, 355 (2007).

    CAS  PubMed  Google Scholar 

  2. 2.

    Zilber-Rosenberg, I. & Rosenberg, E. Role of microorganisms in the evolution of animals and plants: the hologenome theory of evolution. FEMS Microbiol. Rev. 32, 723–735 (2008).

    CAS  PubMed  Google Scholar 

  3. 3.

    McFall-Ngai, M. et al. Animals in a bacterial world, a new imperative for the life sciences. Proc. Natl Acad. Sci. USA 110, 3229–3236 (2013).

    CAS  PubMed  Google Scholar 

  4. 4.

    Theis, K. R. et al. Getting the hologenome concept right: an eco-evolutionary framework for hosts and their microbiomes. Msystems 1, e00028-16 (2016).

    PubMed  PubMed Central  Google Scholar 

  5. 5.

    Calloway, D. H., Colasito, D. J. & Mathews, R. D. Gases produced by human intestinal microflora. Nature 212, 1238–1239 (1966).

    CAS  PubMed  Google Scholar 

  6. 6.

    Miller, T. L., Wolin, M. J., de Macario, E. C. & Macario, A. J. Isolation of Methanobrevibacter smithii from human feces. Appl. Environ. Microbiol. 43, 227–232 (1982). First isolation of an archaeon from the human gastrointestinal tract.

    CAS  PubMed  PubMed Central  Google Scholar 

  7. 7.

    DeLong, E. F. Archaea in coastal marine environments. Proc. Natl Acad. Sci. USA 89, 5685–5689 (1992).

    CAS  PubMed  Google Scholar 

  8. 8.

    Schleper, C., Jurgens, G. & Jonuscheit, M. Genomic studies of uncultivated archaea. Nat. Rev. Microbiol. 3, 479 (2005).

    CAS  PubMed  Google Scholar 

  9. 9.

    Auguet, J.-C., Barberan, A. & Casamayor, E. O. Global ecological patterns in uncultured Archaea. ISME J. 4, 182 (2010).

    PubMed  Google Scholar 

  10. 10.

    Pereira, O., Hochart, C., Auguet, J. C., Debroas, D. & Galand, P. E. Genomic ecology of Marine Group II, the most common marine planktonic Archaea across the surface ocean. Microbiologyopen 8, e00852 (2019).

    PubMed  PubMed Central  Google Scholar 

  11. 11.

    Santoro, A. E., Richter, R. A. & Dupont, C. L. Planktonic marine archaea. Ann. Rev. Mar. Sci. 11, 131–158 (2019).

    PubMed  Google Scholar 

  12. 12.

    Adam, P. S., Borrel, G., Brochier-Armanet, C. & Gribaldo, S. The growing tree of Archaea: new perspectives on their diversity, evolution and ecology. ISME J. 11, 2407 (2017).

    PubMed  PubMed Central  Google Scholar 

  13. 13.

    Spang, A., Caceres, E. F. & Ettema, T. J. G. Genomic exploration of the diversity, ecology, and evolution of the archaeal domain of life. Science 357, eaaf3883 (2017).

    PubMed  Google Scholar 

  14. 14.

    Brugère, J. F. et al. Archaebiotics: proposed therapeutic use of archaea to prevent trimethylaminuria and cardiovascular disease. Gut Microbes 5, 5–10 (2013). First proposal of providing archaea as live biotherapeutic products in order to prevent some human diseases.

    PubMed  PubMed Central  Google Scholar 

  15. 15.

    Borrel, G. et al. Genomics and metagenomics of trimethylamine-utilizing Archaea in the human gut microbiome. ISME J. 11, 2059–2074 (2017). Study of the (meta)genomic and metabolic diversity of human gut methanogens in a European elderly cohort, with evidence of lower faecal TMA concentration being associated with some specific methanogens.

    CAS  PubMed  PubMed Central  Google Scholar 

  16. 16.

    Probst, A. J., Auerbach, A. K. & Moissl-Eichinger, C. Archaea on human skin. PLoS One 8, e65388 (2013).

    CAS  PubMed  PubMed Central  Google Scholar 

  17. 17.

    Moissl-Eichinger, C. et al. Human age and skin physiology shape diversity and abundance of Archaea on skin. Sci. Rep. 7, 4039 (2017).

    PubMed  PubMed Central  Google Scholar 

  18. 18.

    Bang, C., Weidenbach, K., Gutsmann, T., Heine, H. & Schmitz, R. A. The intestinal archaea Methanosphaera stadtmanae and Methanobrevibacter smithii activate human dendritic cells. PLoS One 9, e99411 (2014). First demonstration of the immunogenic activity of human-associated methanogens (severe pro-inflammatory response of peripheral blood mononuclear cells).

    PubMed  PubMed Central  Google Scholar 

  19. 19.

    Bang, C., Vierbuchen, T., Gutsmann, T., Heine, H. & Schmitz, R. A. Immunogenic properties of the human gut-associated archaeon Methanomassiliicoccus luminyensis and its susceptibility to antimicrobial peptides. PLoS One 12, e0185919 (2017).

    PubMed  PubMed Central  Google Scholar 

  20. 20.

    Koskinen, K. et al. First insights into the diverse human archaeome: specific detection of archaea in the gastrointestinal tract, lung, and nose and on skin. mBio 8, e00824-17 (2017). NGS-based analysis of the archaeome at different body sites, revealing a specific biogeographic pattern.

    PubMed  PubMed Central  Google Scholar 

  21. 21.

    Pausan, M. R. et al. Exploring the archaeome: detection of archaeal signatures in the human body. Front. Microbiol. 10, 2796 (2019).

    PubMed  PubMed Central  Google Scholar 

  22. 22.

    Taffner, J. et al. What is the role of archaea in plants? New insights from the vegetation of alpine bogs. mSphere 3, e00122-18 (2018). Dedicated analyses of a bog plant archaeome.

    PubMed  PubMed Central  Google Scholar 

  23. 23.

    Ross, A. A., Müller, K. M., Weese, J. S. & Neufeld, J. D. Comprehensive skin microbiome analysis reveals the uniqueness of human skin and evidence for phylosymbiosis within the class Mammalia. Proc. Natl Acad. Sci. USA 115, E5786–E5795 (2018).

    CAS  PubMed  Google Scholar 

  24. 24.

    Raymann, K., Moeller, A. H., Goodman, A. L. & Ochman, H. Unexplored archaeal diversity in the great ape gut microbiome. mSphere 2, e00026-17 (2017).

    PubMed  PubMed Central  Google Scholar 

  25. 25.

    Moissl-Eichinger, C. et al. Archaea are interactive components of complex microbiomes. Trends Microbiol. 26, 70–85 (2018).

    CAS  PubMed  Google Scholar 

  26. 26.

    Bang, C. & Schmitz, R. A. Archaea: forgotten players in the microbiome. Emerg. Top. Life Sci. 2, 459–468 (2018).

    CAS  Google Scholar 

  27. 27.

    de Macario, E. C. & Macario, A. J. L. in (Endo)Symbiotic Methanogenic Archaea 103–119 (Springer, 2018).

  28. 28.

    Chaudhary, P. P., Conway, P. L. & Schlundt, J. Methanogens in humans: potentially beneficial or harmful for health. Appl. Microbiol. Biotechnol. 102, 3095–3104 (2018).

    CAS  PubMed  Google Scholar 

  29. 29.

    Bang, C. & Schmitz, R. A. Archaea associated with human surfaces: not to be underestimated. FEMS Microbiol. Rev. 39, 631–648 (2015).

    CAS  PubMed  Google Scholar 

  30. 30.

    Cavicchioli, R., Curmi, P. M. G., Saunders, N. & Thomas, T. Pathogenic archaea: do they exist? BioEssays 25, 1119–1128 (2003).

    CAS  PubMed  Google Scholar 

  31. 31.

    Eckburg, P. B., Lepp, P. W. & Relman, D. A. Archaea and their potential role in human disease. Infect. Immun. 71, 591–596 (2003).

    CAS  PubMed  PubMed Central  Google Scholar 

  32. 32.

    Horz, H.-P. & Conrads, G. The discussion goes on: What is the role of Euryarchaeota in humans? Archaea 2010, 967271 (2010).

    PubMed  PubMed Central  Google Scholar 

  33. 33.

    Aminov, R. I. Role of archaea in human disease. Front. Cell. Infect. Microbiol. 3, 42 (2013).

    PubMed  PubMed Central  Google Scholar 

  34. 34.

    Dridi, B., Raoult, D. & Drancourt, M. Archaea as emerging organisms in complex human microbiomes. Anaerobe 17, 56–63 (2011).

    PubMed  Google Scholar 

  35. 35.

    Gaci, N., Borrel, G., Tottey, W., O’Toole, P. W. & Brugère, J.-F. Archaea and the human gut: new beginning of an old story. World J. Gastroenterol. 20, 16062 (2014).

    CAS  PubMed  PubMed Central  Google Scholar 

  36. 36.

    Saengkerdsub, S. & Ricke, S. C. Ecology and characteristics of methanogenic archaea in animals and humans. Crit. Rev. Microbiol. 40, 97–116 (2014).

    CAS  PubMed  Google Scholar 

  37. 37.

    Levy, B. & Jami, E. Exploring the prokaryotic community associated with the rumen ciliate protozoa population. Front. Microbiol. 9, 2526 (2018).

    PubMed  PubMed Central  Google Scholar 

  38. 38.

    Hackstein, J. H. P. (Endo)Symbiotic Methanogenic Archaea (Springer, 2018).

  39. 39.

    Muller, M. The hydrogenosome. J. Gen. Microbiol. 139, 2879–2889 (1993).

    CAS  PubMed  Google Scholar 

  40. 40.

    Fenchel, T. O. M. & Finlay, B. J. Endosymbiotic methanogenic bacteria in anaerobic ciliates: significance for the growth efficiency of the host. J. Protozool. 38, 18–22 (1991).

    Google Scholar 

  41. 41.

    Holmes, D. E. et al. Methane production from protozoan endosymbionts following stimulation of microbial metabolism within subsurface sediments. Front. Microbiol. 5, 366 (2014).

    PubMed  PubMed Central  Google Scholar 

  42. 42.

    Fenchel, T. Methanogenesis in marine shallow water sediments: the quantitative role of anaerobic protozoa with endosymbiotic methanogenic bacteria. Ophelia 37, 67–82 (1993).

    Google Scholar 

  43. 43.

    Vogels, G. D., Hoppe, W. F. & Stumm, C. K. Association of methanogenic bacteria with rumen ciliates. Appl. Environ. Microbiol. 40, 608–612 (1980).

    CAS  PubMed  PubMed Central  Google Scholar 

  44. 44.

    Lee, M. J., Schreurs, P. J., Messer, A. C. & Zinder, S. H. Association of methanogenic bacteria with flagellated protozoa from a termite hindgut. Curr. Microbiol. 15, 337–341 (1987).

    Google Scholar 

  45. 45.

    Gijzen, H. J., Broers, C. A., Barughare, M. & Stumm, C. K. Methanogenic bacteria as endosymbionts of the ciliate Nyctotherus ovalis in the cockroach hindgut. Appl. Environ. Microbiol. 57, 1630–1634 (1991).

    CAS  PubMed  PubMed Central  Google Scholar 

  46. 46.

    van Hoek, A. H. et al. Multiple acquisition of methanogenic archaeal symbionts by anaerobic ciliates. Mol. Biol. Evol. 17, 251–258 (2000).

    PubMed  Google Scholar 

  47. 47.

    Newbold, C. J., de la Fuente, G., Belanche, A., Ramos-Morales, E. & McEwan, N. R. The role of ciliate protozoa in the rumen. Front. Microbiol. 6, 1313 (2015).

    PubMed  PubMed Central  Google Scholar 

  48. 48.

    Patra, A., Park, T., Kim, M. & Yu, Z. Rumen methanogens and mitigation of methane emission by anti-methanogenic compounds and substances. J. Anim. Sci. Biotechnol. 8, 13 (2017).

    PubMed  PubMed Central  Google Scholar 

  49. 49.

    Ushida, K. in (Endo)Symbiotic Methanogenic Archaea 25–35 (Springer, 2018).

  50. 50.

    Lloyd, D., Hillman, K., Yarlett, N. & Williams, A. G. Hydrogen production by rumen holotrich protozoa: effects of oxygen and implications for metabolic control by in situ conditions. J. Protozool. 36, 205–213 (1989).

    CAS  PubMed  Google Scholar 

  51. 51.

    Guyader, J. et al. Influence of rumen protozoa on methane emission in ruminants: a meta-analysis approach. Animal 8, 1816–1825 (2014).

    CAS  PubMed  Google Scholar 

  52. 52.

    Hegarty, R. S. Reducing rumen methane emissions through elimination of rumen protozoa. Aust. J. Agric. Res. 50, 1321–1328 (1999).

    Google Scholar 

  53. 53.

    Morgavi, D. P., Forano, E., Martin, C. & Newbold, C. J. Microbial ecosystem and methanogenesis in ruminants. Animal 4, 1024–1036 (2010).

    CAS  PubMed  Google Scholar 

  54. 54.

    Morgavi, D. P., Martin, C., Jouany, J.-P. & Ranilla, M. J. Rumen protozoa and methanogenesis: not a simple cause-effect relationship. Br. J. Nutr. 107, 388–397 (2012).

    CAS  PubMed  Google Scholar 

  55. 55.

    Park, T. & Yu, Z. Do ruminal ciliates select their preys and prokaryotic symbionts? Front. Microbiol. 9, 1710 (2018).

    PubMed  PubMed Central  Google Scholar 

  56. 56.

    Henderson, G. et al. Rumen microbial community composition varies with diet and host, but a core microbiome is found across a wide geographical range. Sci. Rep. 5, 14567 (2015).

    CAS  PubMed  PubMed Central  Google Scholar 

  57. 57.

    Lewis, W. H., Sendra, K. M., Embley, T. M. & Esteban, G. F. Morphology and phylogeny of a new species of anaerobic ciliate, Trimyema finlayi n. sp., with endosymbiotic methanogens. Front. Microbiol. 9, 140 (2018).

    PubMed  PubMed Central  Google Scholar 

  58. 58.

    Lind, A. E. et al. Genomes of two archaeal endosymbionts show convergent adaptations to an intracellular lifestyle. ISME J. 12, 2655–2667 (2018).

    CAS  PubMed  PubMed Central  Google Scholar 

  59. 59.

    Beinart, R. A., Rotterová, J., Čepička, I., Gast, R. J. & Edgcomb, V. P. The genome of an endosymbiotic methanogen is very similar to those of its free‐living relatives. Environ. Microbiol. 20, 2538–2551 (2018).

    CAS  PubMed  Google Scholar 

  60. 60.

    Gutiérrez, G. Draft genome sequence of Methanobacterium formicicum DSM 3637, an archaebacterium isolated from the methane producer amoeba Pelomyxa palustris. J. Bacteriol. 194, 6967–6968 (2012).

    PubMed  PubMed Central  Google Scholar 

  61. 61.

    Berg, G., Grube, M., Schloter, M. & Smalla, K. Unraveling the plant microbiome: looking back and future perspectives. Front. Microbiol. 5, 148 (2014).

    PubMed  PubMed Central  Google Scholar 

  62. 62.

    Taffner, J., Cernava, T., Erlacher, A. & Berg, G. Novel insights into plant-associated archaea and their functioning in arugula (Eruca sativa Mill.). J. Adv. Res. 19, 39–48 (2019).

    CAS  PubMed  PubMed Central  Google Scholar 

  63. 63.

    Lu, Y. & Conrad, R. In situ stable isotope probing of methanogenic archaea in the rice rhizosphere. Science 309, 1088–1090 (2005).

    CAS  PubMed  Google Scholar 

  64. 64.

    Lee, H. J., Jeong, S. E., Kim, P. J., Madsen, E. L. & Jeon, C. O. High resolution depth distribution of bacteria, archaea, methanotrophs, and methanogens in the bulk and rhizosphere soils of a flooded rice paddy. Front. Microbiol. 6, 639 (2015).

    PubMed  PubMed Central  Google Scholar 

  65. 65.

    Pump, J., Pratscher, J. & Conrad, R. Colonization of rice roots with methanogenic archaea controls photosynthesis‐derived methane emission. Environ. Microbiol. 17, 2254–2260 (2015).

    CAS  PubMed  Google Scholar 

  66. 66.

    Joabsson, A., Christensen, T. R. & Wallén, B. Vascular plant controls on methane emissions from northern peatforming wetlands. Trends Ecol. Evol. 14, 385–388 (1999).

    CAS  PubMed  Google Scholar 

  67. 67.

    Conrad, R. The global methane cycle: recent advances in understanding the microbial processes involved. Environ. Microbiol. Rep. 1, 285–292 (2009).

    CAS  PubMed  Google Scholar 

  68. 68.

    Müller, H. et al. Plant genotype-specific archaeal and bacterial endophytes but similar Bacillus antagonists colonize Mediterranean olive trees. Front. Microbiol. 6, 138 (2015).

    PubMed  PubMed Central  Google Scholar 

  69. 69.

    Taffner, J., Bergna, A., Cernava, T. & Berg, G. Tomato-associated archaea show a cultivar-specific rhizosphere effect but an unspecific transmission by seeds. Phytobiomes J. 4, 133–141 (2020).

    Google Scholar 

  70. 70.

    Song, G. C. et al. Plant growth‐promoting archaea trigger induced systemic resistance in Arabidopsis thaliana against Pectobacterium carotovorum and Pseudomonas syringae. Environ. Microbiol. 21, 940–948 (2019).

    CAS  PubMed  Google Scholar 

  71. 71.

    Hallam, S. J. et al. Genomic analysis of the uncultivated marine crenarchaeote Cenarchaeum symbiosum. Proc. Natl Acad. Sci. USA 103, 18296–18301 (2006).

    CAS  PubMed  Google Scholar 

  72. 72.

    Preston, C. M., Wu, K. Y., Molinski, T. F. & DeLong, E. F. A psychrophilic crenarchaeon inhabits a marine sponge: Cenarchaeum symbiosum gen. nov., sp. nov. Proc. Natl Acad. Sci. USA 93, 6241–6246 (1996).

    CAS  PubMed  Google Scholar 

  73. 73.

    Jackson, S. A. et al. Archaea appear to dominate the microbiome of Inflatella pellicula deep sea sponges. PLoS One 8, e84438 (2013).

    PubMed  PubMed Central  Google Scholar 

  74. 74.

    Kinsman, R., Sauer, F. D., Jackson, H. A. & Wolynetz, M. S. Methane and carbon dioxide emissions from dairy cows in full lactation monitored over a six-month period. J. Dairy. Sci. 78, 2760–2766 (1995).

    CAS  PubMed  Google Scholar 

  75. 75.

    Duin, E. C. 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. USA 113, 6172–6177 (2016).

    CAS  PubMed  Google Scholar 

  76. 76.

    Shabat, S. K. Ben et al. Specific microbiome-dependent mechanisms underlie the energy harvest efficiency of ruminants. ISME J. 10, 2958–2972 (2016).

    CAS  PubMed  PubMed Central  Google Scholar 

  77. 77.

    Nauer, P. A., Hutley, L. B. & Arndt, S. K. Termite mounds mitigate half of termite methane emissions. Proc. Natl Acad. Sci. USA 115, 13306–13311 (2018).

    CAS  PubMed  Google Scholar 

  78. 78.

    Oxley, A. et al. Halophilic archaea in the human intestinal mucosa. Environ. Microbiol. 12, 2398–2410 (2010).

    PubMed  Google Scholar 

  79. 79.

    Liu, X. et al. Insights into the ecology, evolution, and metabolism of the widespread Woesearchaeotal lineages. Microbiome 6, 102 (2018).

    PubMed  PubMed Central  Google Scholar 

  80. 80.

    Arumugam, M. et al. Enterotypes of the human gut microbiome. Nature 473, 174–180 (2013).

    Google Scholar 

  81. 81.

    Hajishengallis, G., Darveau, R. P. & Curtis, M. A. The keystone-pathogen hypothesis. Nat. Rev. Microbiol. 10, 717–725 (2012).

    CAS  PubMed  PubMed Central  Google Scholar 

  82. 82.

    Dridi, B., Henry, M., El Khechine, A., Raoult, D. & Drancourt, M. High prevalence of Methanobrevibacter smithii and Methanosphaera stadtmanae detected in the human gut using an improved DNA detection protocol. PLoS One 4, e7063 (2009).

    PubMed  PubMed Central  Google Scholar 

  83. 83.

    Polag, D. & Keppler, F. Global methane emissions from the human body: past, present and future. Atmos. Environ. 214, 116823 (2019). Summary of the current knowledge on the methane emission of children and adults in different countries, with the level of human methane production calculated over time.

    CAS  Google Scholar 

  84. 84.

    Saunois, M. et al. The global methane budget 2000–2012. Earth Syst. Sci. Data 8, 697–751 (2016).

    Google Scholar 

  85. 85.

    Gottlieb, K. et al. Selection of a cut-off for high-and low-methane producers using a spot-methane breath test: results from a large north American dataset of hydrogen, methane and carbon dioxide measurements in breath. Gastroenterol. Rep. 5, 193–199 (2017).

    Google Scholar 

  86. 86.

    Morii, H., Oda, K., Suenaga, Y. & Nakamura, T. Low methane concentration in the breath of Japanese. J. UOEH 25, 397–407 (2003).

    CAS  PubMed  Google Scholar 

  87. 87.

    Segal, I., Walker, A. R., Lord, S. & Cummings, J. H. Breath methane and large bowel cancer risk in contrasting African populations. Gut 29, 608–613 (1988).

    CAS  PubMed  PubMed Central  Google Scholar 

  88. 88.

    Hudson, M. J., Tomkins, A. M., Wiggins, H. S. & Drasar, B. S. Breath methane excretion and intestinal methanogenesis in children and adults in rural Nigeria. Scand. J. Gastroenterol. 28, 993–998 (1993).

    CAS  PubMed  Google Scholar 

  89. 89.

    O’Keefe, S. J. D. et al. Why do African Americans get more colon cancer than Native Africans? J. Nutr. 137, 175S–182S (2007).

    PubMed  Google Scholar 

  90. 90.

    Nava, G. M. et al. Hydrogenotrophic microbiota distinguish native Africans from African and European Americans. Environ. Microbiol. Rep. 4, 307–315 (2012).

    CAS  PubMed  PubMed Central  Google Scholar 

  91. 91.

    Levitt, M. D., Furne, J. K., Kuskowski, M. & Ruddy, J. Stability of human methanogenic flora over 35 years and a review of insights obtained from breath methane measurements. Clin. Gastroenterol. Hepatol. 4, 123–129 (2006).

    CAS  PubMed  Google Scholar 

  92. 92.

    Weaver, G. A., Krause, J. A., Miller, T. L. & Wolin, M. J. Incidence of methanogenic bacteria in a sigmoidoscopy population: an association of methanogenic bacteria and diverticulosis. Gut 27, 698–704 (1986).

    CAS  PubMed  PubMed Central  Google Scholar 

  93. 93.

    Stewart, J. A., Chadwick, V. S. & Murray, A. Carriage, quantification, and predominance of methanogens and sulfate‐reducing bacteria in faecal samples. Lett. Appl. Microbiol. 43, 58–63 (2006).

    CAS  PubMed  Google Scholar 

  94. 94.

    Mihajlovski, A., Doré, J., Levenez, F., Alric, M. & Brugère, J. Molecular evaluation of the human gut methanogenic archaeal microbiota reveals an age‐associated increase of the diversity. Environ. Microbiol. Rep. 2, 272–280 (2010).

    CAS  PubMed  Google Scholar 

  95. 95.

    Goodrich, J. K. et al. Genetic determinants of the gut microbiome in UK twins. Cell Host Microbe 19, 731–743 (2016).

    CAS  PubMed  PubMed Central  Google Scholar 

  96. 96.

    Hansen, E. E. et al. Pan-genome of the dominant human gut-associated archaeon, Methanobrevibacter smithii, studied in twins. Proc. Natl Acad. Sci. USA 108, 4599–4606 (2011).

    CAS  PubMed  Google Scholar 

  97. 97.

    Goodrich, J. K., Davenport, E. R., Clark, A. G. & Ley, R. E. The relationship between the human genome and microbiome comes into view. Annu. Rev. Genet. 51, 413–433 (2017).

    CAS  PubMed  PubMed Central  Google Scholar 

  98. 98.

    Bonder, M. J. et al. The effect of host genetics on the gut microbiome. Nat. Genet. 48, 1407–1412 (2016).

    CAS  PubMed  Google Scholar 

  99. 99.

    Goodrich, J. J. K. et al. Human genetics shape the gut microbiome. Cell 159, 789–799 (2014).

    CAS  PubMed  PubMed Central  Google Scholar 

  100. 100.

    Ruaud, A. et al. Syntrophy via interspecies H2 transfer between Christensenella and Methanobrevibacter underlies their global cooccurrence in the human gut. mBio 11, e03235-19 (2020).

    PubMed  PubMed Central  Google Scholar 

  101. 101.

    Hoffmann, C. et al. Archaea and fungi of the human gut microbiome: correlations with diet and bacterial residents. PLoS One 8, e66019 (2013).

    CAS  PubMed  PubMed Central  Google Scholar 

  102. 102.

    Nam, Y.-D. et al. Bacterial, archaeal, and eukaryal diversity in the intestines of Korean people. J. Microbiol. 46, 491–501 (2008).

    CAS  PubMed  Google Scholar 

  103. 103.

    Khelaifia, S. & Raoult, D. Haloferax massiliensis sp. nov., the first human-associated halophilic archaea. N. Microbes N. Infect. 12, 96–98 (2016).

    CAS  Google Scholar 

  104. 104.

    Nkamga, V. D., Henrissat, B. & Drancourt, M. Archaea: essential inhabitants of the human digestive microbiota. Hum. Microbiome J. 3, 1–8 (2017).

    Google Scholar 

  105. 105.

    Samuel, B. S. et al. Genomic and metabolic adaptations of Methanobrevibacter smithii to the human gut. Proc. Natl Acad. Sci. USA 104, 10643–10648 (2007). Study describing the level of adaptation of a human-associated archaeon to the human gastrointestinal tract.

    CAS  PubMed  Google Scholar 

  106. 106.

    Ng, F. et al. An adhesin from hydrogen‐utilizing rumen methanogen Methanobrevibacter ruminantium M1 binds a broad range of hydrogen‐producing microorganisms. Environ. Microbiol. 18, 3010–3021 (2016).

    CAS  PubMed  Google Scholar 

  107. 107.

    Lurie-Weinberger, M. N., Peeri, M., Tuller, T. & Gophna, U. Extensive inter-domain lateral gene transfer in the evolution of the human commensal Methanosphaera stadtmanae. Front. Genet. 3, 182 (2012).

    PubMed  PubMed Central  Google Scholar 

  108. 108.

    Lurie-Weinberger, M. N., Peeri, M. & Gophna, U. Contribution of lateral gene transfer to the gene repertoire of a gut-adapted methanogen. Genomics 99, 52–58 (2012).

    CAS  PubMed  Google Scholar 

  109. 109.

    Bang, C. et al. Biofilm formation of mucosa-associated methanoarchaeal strains. Front. Microbiol. 5, 353 (2014).

    PubMed  PubMed Central  Google Scholar 

  110. 110.

    Lepp, P. W. et al. Methanogenic archaea and human periodontal disease. Proc. Natl Acad. Sci. USA 101, 6176–6181 (2004). First in-depth analysis of the link between archaea and periodontitis, proposing their involvement in this disease.

    CAS  PubMed  Google Scholar 

  111. 111.

    Nkamga, V. D. et al. Methanobrevibacter oralis detected along with Aggregatibacter actinomycetemcomitans in a series of community-acquired brain abscesses. Clin. Microbiol. Infect. 24, 207 (2018).

    CAS  PubMed  Google Scholar 

  112. 112.

    Borrel, G. et al. Comparative genomics highlights the unique biology of Methanomassiliicoccales, a Thermoplasmatales-related seventh order of methanogenic archaea that encodes pyrrolysine. BMC Genomics 15, 679 (2014).

    PubMed  PubMed Central  Google Scholar 

  113. 113.

    Jones, B. V., Begley, M., Hill, C., Gahan, C. G. M. & Marchesi, J. R. Functional and comparative metagenomic analysis of bile salt hydrolase activity in the human gut microbiome. Proc. Natl Acad. Sci. USA 105, 13580–13585 (2008).

    CAS  PubMed  Google Scholar 

  114. 114.

    Bang, C. et al. Effects of antimicrobial peptides on methanogenic archaea. Antimicrob. Agents Chemother. 56, 4123–4130 (2012).

    CAS  PubMed  PubMed Central  Google Scholar 

  115. 115.

    Blais Lecours, P. et al. Immunogenic properties of archaeal species found in bioaerosols. PLoS One 6, e23326 (2011).

    PubMed  PubMed Central  Google Scholar 

  116. 116.

    Vierbuchen, T., Bang, C., Rosigkeit, H., Schmitz, R. A. & Heine, H. The human-associated archaeon Methanosphaera stadtmanae is recognized through its RNA and induces Tlr8-dependent nlrP3 inflammasome activation. Front. Immunol. 8, 1535 (2017). Report on methanoarchaeal RNA as an immune stimulator and identification of the methanoarchaeal receptor.

    PubMed  PubMed Central  Google Scholar 

  117. 117.

    Haines, A., Dilawari, J., Metz, G., Blendis, L. & Wiggins, H. Breath-methane in patients with cancer of the large bowel. Lancet 310, 481–483 (1977).

    Google Scholar 

  118. 118.

    Mahnert, A., Blohs, M., Pausan, M. R. & Moissl-Eichinger, C. The human archaeome: methodological pitfalls and knowledge gaps. Emerg. Top. Life Sci. 2.4, 469–482 (2018).

    Google Scholar 

  119. 119.

    Belay, N., Mukhopadhyay, B., Conway de Macario, E., Galask, R. & Daniels, L. Methanogenic bacteria in human vaginal samples. J. Clin. Microbiol. 28, 1666–1668 (1990).

    CAS  PubMed  PubMed Central  Google Scholar 

  120. 120.

    Grine, G. et al. Detection of Methanobrevibacter smithii in vaginal samples collected from women diagnosed with bacterial vaginosis. Eur. J. Clin. Microbiol. Infect. Dis. 38, 1643–1649 (2019).

    CAS  PubMed  Google Scholar 

  121. 121.

    Pérez-Cobas, A. E., Ginevra, C., Rusniok, C., Jarraud, S. & Buchrieser, C. Legionella pneumophila infection and antibiotic treatment engenders a highly disturbed pulmonary microbiome with decreased microbial diversity. mBio 11, e00889-20 (2019).

    Google Scholar 

  122. 122.

    Grine, G. et al. Co-culture of Methanobrevibacter smithii with enterobacteria during urinary infection. EBioMedicine 43, 333–337 (2019).

    PubMed  PubMed Central  Google Scholar 

  123. 123.

    Sogodogo, E. et al. Nine cases of methanogenic archaea in refractory sinusitis, an emerging clinical entity. Front. Public Health 7, 38 (2019).

    PubMed  PubMed Central  Google Scholar 

  124. 124.

    Drancourt, M. et al. Evidence of archaeal methanogens in brain abscess. Clin. Infect. Dis. 65, 1–5 (2017).

    CAS  PubMed  Google Scholar 

  125. 125.

    Nguyen-Hieu, T., Khelaifia, S., Aboudharam, G. & Drancourt, M. Methanogenic archaea in subgingival sites: a review. APMIS 121, 467–477 (2013).

    PubMed  Google Scholar 

  126. 126.

    Belkacemi, S. et al. Peri-implantitis-associated methanogens: a preliminary report. Sci. Rep. 8, 9447 (2018).

    PubMed  PubMed Central  Google Scholar 

  127. 127.

    Vianna, M. E., Holtgraewe, S., Seyfarth, I., Conrads, G. & Horz, H. P. Quantitative analysis of three hydrogenotrophic microbial groups, methanogenic archaea, sulfate-reducing bacteria, and acetogenic bacteria, within plaque biofilms associated with human periodontal disease. J. Bacteriol. 190, 3779–3785 (2008).

    CAS  PubMed  PubMed Central  Google Scholar 

  128. 128.

    Siqueira, J. F. J. & Rocas, I. N. Community as the unit of pathogenicity: an emerging concept as to the microbial pathogenesis of apical periodontitis. Oral Surg. Oral Med. Oral Pathol. Oral Radiol. Endod. 107, 870–878 (2009).

    PubMed  Google Scholar 

  129. 129.

    de Macario, E. C. & Macario, A. J. L. Methanogenic archaea in health and disease: a novel paradigm of microbial pathogenesis. Int. J. Med. Microbiol. 299, 99–108 (2009).

    PubMed  Google Scholar 

  130. 130.

    Benoit, S. L., Maier, R. J., Sawers, R. G. & Greening, C. Molecular hydrogen metabolism: a widespread trait of pathogenic bacteria and protists. Microbiol. Mol. Biol. Rev. 84, e00092-19 (2020).

    PubMed  Google Scholar 

  131. 131.

    Lecours, P. B. et al. Increased prevalence of Methanosphaera stadtmanae in inflammatory bowel diseases. PLoS One 9, 1–7 (2014).

    Google Scholar 

  132. 132.

    Barnett, D. J. M., Mommers, M., Penders, J., Arts, I. C. W. & Thijs, C. Intestinal archaea inversely associated with childhood asthma. J. Allergy Clin. Immunol. 143, 2305–2307 (2019).

    PubMed  Google Scholar 

  133. 133.

    Pimentel, M. Methane, a gas produced by enteric bacteria, slows intestinal transit and augments small intestinal contractile activity. AJP Gastrointest. Liver Physiol. 290, G1089–G1095 (2006).

    CAS  Google Scholar 

  134. 134.

    Chatterjee, S., Park, S., Low, K., Kong, Y. & Pimentel, M. The degree of breath methane production in IBS correlates with the severity of constipation. Am. J. Gastroenterol. 102, 837 (2007).

    CAS  PubMed  Google Scholar 

  135. 135.

    Attaluri, A., Jackson, M., Valestin, J. & Rao, S. S. C. Methanogenic flora is associated with altered colonic transit but not stool characteristics in constipation without IBS. Am. J. Gastroenterol. 105, 1407 (2010).

    PubMed  Google Scholar 

  136. 136.

    Tottey, W. et al. Colonic transit time is a driven force of the gut microbiota composition and metabolism: in vitro evidence. J. Neurogastroenterol. Motil. 23, 124 (2017).

    PubMed  PubMed Central  Google Scholar 

  137. 137.

    Lurie-Weinberger, M. N. & Gophna, U. Archaea in and on the human body: health implications and future directions. PLoS Pathog. 11, e1004833 (2015).

    PubMed  PubMed Central  Google Scholar 

  138. 138.

    Gottlieb, K., Wacher, V., Sliman, J. & Pimentel, M. Inhibition of methanogenic archaea by statins as a targeted management strategy for constipation and related disorders. Aliment. Pharmacol. Ther. 43, 197–212 (2016).

    CAS  PubMed  Google Scholar 

  139. 139.

    Jia, Y., Li, Z., Liu, C. & Zhang, J. Methane medicine: a rising star gas with powerful anti-inflammation, antioxidant, and antiapoptosis properties. Oxid. Med. Cell. Longev. 2018, 1912746 (2018).

    PubMed  PubMed Central  Google Scholar 

  140. 140.

    Xin, L., Sun, X. & Lou, S. Effects of methane-rich saline on the capability of one-time exhaustive exercise in male SD rats. PLoS One 11, e0150925 (2016).

    PubMed  PubMed Central  Google Scholar 

  141. 141.

    Laverdure, R., Mezouari, A., Carson, M. A., Basiliko, N. & Gagnon, J. A role for methanogens and methane in the regulation of GLP-1. Endocrinol. Diabetes Metab. 1, e00006 (2018).

    PubMed  Google Scholar 

  142. 142.

    Boros, M. & Keppler, F. Methane production and bioactivity—a link to oxido-reductive stress. Front. Physiol. 10, 1244 (2019).

    PubMed  PubMed Central  Google Scholar 

  143. 143.

    Al-Waiz, M., Mikov, M., Mitchell, S. C. & Smith, R. L. The exogenous origin of trimethylamine in the mouse. Metabolism 41, 135–136 (1992).

    CAS  PubMed  Google Scholar 

  144. 144.

    Wang, Z. et al. Gut flora metabolism of phosphatidylcholine promotes cardiovascular disease. Nature 472, 57 (2011).

    CAS  PubMed  PubMed Central  Google Scholar 

  145. 145.

    Tang, W. H. W. et al. Gut microbiota-dependent trimethylamine N-oxide (TMAO) pathway contributes to both development of renal insufficiency and mortality risk in chronic kidney disease. Circ. Res. 116, 448–455 (2015).

    CAS  PubMed  Google Scholar 

  146. 146.

    Mackay, R. J., McEntyre, C. J., Henderson, C., Lever, M. & George, P. M. Trimethylaminuria: causes and diagnosis of a socially distressing condition. Clin. Biochem. Rev. 32, 33 (2011).

    PubMed  PubMed Central  Google Scholar 

  147. 147.

    Srinivasan, G., James, C. M. & Krzycki, J. A. Pyrrolysine encoded by UAG in archaea: charging of a UAG-decoding specialized tRNA. Science 296, 1459–1462 (2002).

    CAS  PubMed  Google Scholar 

  148. 148.

    Gaston, M. A., Jiang, R. & Krzycki, J. A. Functional context, biosynthesis, and genetic encoding of pyrrolysine. Curr. Opin. Microbiol. 14, 342–349 (2011).

    CAS  PubMed  PubMed Central  Google Scholar 

  149. 149.

    Brugère, J.-F., Atkins, J. F., O’Toole, P. W. & Borrel, G. Pyrrolysine in archaea: a 22nd amino acid encoded through a genetic code expansion. Emerg. Top. Life Sci. 2, 607–618 (2018).

    Google Scholar 

  150. 150.

    Dridi, B., Fardeau, M.-L., Ollivier, B., Raoult, D. & Drancourt, M. Methanomassiliicoccus luminyensis gen. nov., sp. nov., a methanogenic archaeon isolated from human faeces. Int. J. Syst. Evol. Microbiol. 62, 1902–1907 (2012).

    CAS  PubMed  Google Scholar 

  151. 151.

    Ramezani, A. et al. Gut colonization with methanogenic archaea lowers plasma trimethylamine N-oxide concentrations in apolipoprotein e−/− mice. Sci. Rep. 8, 14752 (2018).

    PubMed  PubMed Central  Google Scholar 

  152. 152.

    Fadhlaoui, K. et al. Archaea, specific genetic traits, and development of improved bacterial live biotherapeutic products: another face of next-generation probiotics. Appl. Microbiol. Biotechnol. 104, 4705–4716 (2020).

    CAS  PubMed  Google Scholar 

  153. 153.

    Prangishvili, D. et al. Sulfolobicins, specific proteinaceous toxins produced by strains of the extremely thermophilic archaeal genus Sulfolobus. J. Bacteriol. 182, 2985–2988 (2000).

    CAS  PubMed  PubMed Central  Google Scholar 

  154. 154.

    Martin, W. Pathogenic archaebacteria: do they not exist because archaebacteria use different vitamins? BioEssays 26, 592–593 (2004).

    PubMed  Google Scholar 

  155. 155.

    Cavicchioli, R. & Curmi, P. Response to William Martin’s letter. BioEssays 26, 593 (2004).

    Google Scholar 

  156. 156.

    Gill, E. E. & Brinkman, F. S. L. The proportional lack of archaeal pathogens: do viruses/phages hold the key? BioEssays 33, 248–254 (2011).

    PubMed  PubMed Central  Google Scholar 

  157. 157.

    Prangishvili, D. et al. The enigmatic archaeal virosphere. Nat. Rev. Microbiol. 15, 724–739 (2017).

    CAS  PubMed  Google Scholar 

  158. 158.

    No authors listed. Microbiology by numbers. Nat. Rev. Microbiol. 9, 628 (2011).

    Google Scholar 

  159. 159.

    Sachs, J. L., Skophammer, R. G. & Regus, J. U. Evolutionary transitions in bacterial symbiosis. Proc. Natl Acad. Sci. USA 108, 10800–10807 (2011).

    CAS  PubMed  Google Scholar 

  160. 160.

    Valentine, D. L. Adaptations to energy stress dictate the ecology and evolution of the Archaea. Nat. Rev. Microbiol. 5, 316–323 (2007).

    CAS  PubMed  Google Scholar 

  161. 161.

    Castelle, C. J. & Banfield, J. F. Major new microbial groups expand diversity and alter our understanding of the tree of life. Cell 172, 1181–1197 (2018).

    CAS  PubMed  Google Scholar 

  162. 162.

    Borrel, G. et al. Wide diversity of methane and short-chain alkane metabolisms in uncultured archaea. Nat. Microbiol. 4, 603–613 (2019).

    CAS  PubMed  PubMed Central  Google Scholar 

  163. 163.

    Food and Agriculture Organization. Statistical Yearbook of the Food and Agriculture Organization of the United Nations (FAO, 2016).

  164. 164.

    Monteiro, A. L. G. et al. The role of small ruminants on global climate change. Acta Sci. Anim. Sci. 40, 43124 (2018).

    Google Scholar 

  165. 165.

    Sanderson, M. G. Biomass of termites and their emissions of methane and carbon dioxide: a global database. Glob. Biogeochem. Cycles 10, 543–557 (1996).

    CAS  Google Scholar 

  166. 166.

    Daemmgen, U. et al. Enteric methane emissions from German pigs. Agric. For. Res. 3, 83–96 (2012).

    Google Scholar 

  167. 167.

    Brouček, J. & Čermák, B. Emission of harmful gases from poultry farms and possibilities of their reduction. Ekologia 34, 89–100 (2015).

    Google Scholar 

  168. 168.

    Almeida, A. et al. A new genomic blueprint of the human gut microbiota. Nature 568, 499 (2019).

    CAS  PubMed  PubMed Central  Google Scholar 

  169. 169.

    Quast, C. et al. The SILVA ribosomal RNA gene database project: improved data processing and web-based tools. Nucleic Acids Res. 41, D590–D596 (2013).

    CAS  PubMed  Google Scholar 

  170. 170.

    Albers, S.-V. & Meyer, B. H. The archaeal cell envelope. Nat. Rev. Microbiol. 9, 414 (2011).

    CAS  PubMed  Google Scholar 

  171. 171.

    Becker, K. W. et al. Unusual butane- and pentanetriol-based tetraether lipids in Methanomassiliicoccus luminyensis, a representative of the seventh order of methanogens. Appl. Environ. Microbiol. 82, 4505–4516 (2016).

    CAS  PubMed  PubMed Central  Google Scholar 

  172. 172.

    Klingl, A. S-layer and cytoplasmic membrane—exceptions from the typical archaeal cell wall with a focus on double membranes. Front. Microbiol. 5, 1–6 (2014).

    Google Scholar 

  173. 173.

    Shahapure, R., Driessen, R. P. C., Haurat, M. F., Albers, S. & Dame, R. T. The archaellum: a rotating type IV pilus. Mol. Microbiol. 91, 716–723 (2014).

    CAS  PubMed  Google Scholar 

  174. 174.

    Chaudhury, P., Quax, T. E. F. & Albers, S. Versatile cell surface structures of archaea. Mol. Microbiol. 107, 298–311 (2018).

    CAS  PubMed  Google Scholar 

  175. 175.

    Quemin, E. R. J. et al. First insights into the entry process of hyperthermophilic archaeal viruses. J. Virol. 87, 13379–13385 (2013).

    CAS  PubMed  PubMed Central  Google Scholar 

  176. 176.

    Sato, T. & Atomi, H. Novel metabolic pathways in archaea. Curr. Opin. Microbiol. 14, 307–314 (2011).

    CAS  PubMed  Google Scholar 

  177. 177.

    Brasen, C., Esser, D., Rauch, B. & Siebers, B. Carbohydrate metabolism in archaea: current insights into unusual enzymes and pathways and their regulation. Microbiol. Mol. Biol. Rev. 78, 89–175 (2014).

    PubMed  PubMed Central  Google Scholar 

  178. 178.

    Leininger, S. et al. Archaea predominate among ammonia-oxidizing prokaryotes in soils. Nature 442, 806–809 (2006).

    CAS  PubMed  Google Scholar 

  179. 179.

    Stein, L. Y. Insights into the physiology of ammonia-oxidizing microorganisms. Curr. Opin. Chem. Biol. 49, 9–15 (2019).

    CAS  PubMed  Google Scholar 

  180. 180.

    Mand, T. D. & Metcalf, W. W. Energy conservation and hydrogenase function in methanogenic archaea, in particular the genus methanosarcina. Microbiol. Mol. Biol. Rev. 83, e00020-19 (2019).

    PubMed  Google Scholar 

  181. 181.

    Borrel, G., Adam, P. S. & Gribaldo, S. Methanogenesis and the Wood–Ljungdahl pathway: an ancient, versatile, and fragile association. Genome Biol. Evol. 8, 1706–1711 (2016).

    CAS  PubMed  PubMed Central  Google Scholar 

  182. 182.

    Stams, A. J. M. & Plugge, C. M. Electron transfer in syntrophic communities of anaerobic bacteria and archaea. Nat. Rev. Microbiol. 7, 568–577 (2009).

    CAS  PubMed  Google Scholar 

  183. 183.

    Ettwig, K. F. et al. Archaea catalyze iron-dependent anaerobic oxidation of methane. Proc. Natl Acad. Sci. USA 113, 12792–12796 (2016).

    CAS  PubMed  Google Scholar 

  184. 184.

    Cai, C. et al. A methanotrophic archaeon couples anaerobic oxidation of methane to Fe(III) reduction. ISME J. 12, 1929–1939 (2018).

    CAS  PubMed  PubMed Central  Google Scholar 

  185. 185.

    Scheller, S., Yu, H., Chadwick, G. L., McGlynn, S. E. & Orphan, V. J. Artificial electron acceptors decouple archaeal methane oxidation from sulfate reduction. Science 351, 703–707 (2016).

    CAS  PubMed  Google Scholar 

  186. 186.

    Wegener, G., Krukenberg, V., Riedel, D., Tegetmeyer, H. E. & Boetius, A. Intercellular wiring enables electron transfer between methanotrophic archaea and bacteria. Nature 526, 587–590 (2015).

    CAS  PubMed  Google Scholar 

  187. 187.

    Kiener, A., Konig, H., Winter, J. & Leisinger, T. Purification and use of Methanobacterium wolfei pseudomurein endopeptidase for lysis of Methanobacterium thermoautotrophicum. J. Bacteriol. 169, 1010–1016 (1987).

    CAS  PubMed  PubMed Central  Google Scholar 

  188. 188.

    Lee, Z., Bussema, C. & Schmidt, T. rrnDB: documenting the number of rRNA and tRNA genes in bacteria and archaea. Nucleic Acids Res. 37, D489–D493 (2009).

    CAS  PubMed  Google Scholar 

  189. 189.

    Sun, Y., Liu, Y., Pan, J., Wang, F. & Li, M. Perspectives on cultivation strategies of archaea. Microb. Ecol. 79, 770–784 (2020).

    PubMed  Google Scholar 

Download references


The authors gratefully acknowledge A. Mahnert for support in the preparation of Fig. 3, and M. Blohs for input on methane production in humans. Funding given by the Austrian Science Fund (FWF) to C.M.-E. (Project IDs P 30796 and P 32697) is highly appreciated, as is the funding from the German Science Foundation (DFG) given to R.A.S. (SCHM1052/11-1/2). The French National Agency for Research is gratefully acknowledged for funding to G.B. and S.G. (Grants ArchEvol ANR-16-CE02-0005-01 and Methevol ANR-19-CE02-0005-01), and we acknowledge a grant to J.-F.B. from Hub Innovergne (‘Investissements d’Avenir’ 16-IDEX-0001 CAP 20–25).

Author information




The authors contributed equally to all aspects of the article.

Corresponding author

Correspondence to Christine Moissl-Eichinger.

Ethics declarations

Competing interests

The authors declare no competing interests.

Additional information

Peer review information

Nature Reviews Microbiology thanks U. Gophna, I. Mizrahi, D. Relman and the other, anonymous, reviewer(s) for their contribution to the peer review of this work.

Publisher’s note

Springer Nature remains neutral with regard to jurisdictional claims in published maps and institutional affiliations.

Related links

The Food and Agriculture Organization:

Supplementary information



A multicellular eukaryote together with its associated microbial communities.


Describing microorganisms that live in the cells of another organism.


Microorganisms living on the surface of another organism in a symbiotic relationship.


Conversion of a gene into a nonfunctional gene-like sequence in a symbiotic relationship.


Soil area around a plant root, influenced by root exudates and inhabited by a specific population of microorganisms.


Internal regions of plant tissues, which are inhabited by endophytic microorganisms.


All above-ground parts of plants, serving as habitat for microorganisms.


The proportion of variance in the phenotype that can be attributed to genetic differences between individuals.


Microbial consortium attached to a surface or interface and organized in an extracellular matrix.

Horizontal gene transfer

(HGT). A process in which genetic material is acquired from another organism (as opposed to vertical inheritance, in which genetic information is transmitted from parent to offspring).


Enzymes that catalyse the transfer of glycosyl (sugar) residues to an acceptor molecule.

Microorganism-associated molecular patterns

The conserved molecules characteristic of microbes, which are recognized by the immune system.

Rights and permissions

Reprints and Permissions

About this article

Verify currency and authenticity via CrossMark

Cite this article

Borrel, G., Brugère, J., Gribaldo, S. et al. The host-associated archaeome. Nat Rev Microbiol (2020).

Download citation