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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.

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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.


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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).

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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.

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Borrel, G., Brugère, JF., Gribaldo, S. et al. The host-associated archaeome. Nat Rev Microbiol 18, 622–636 (2020).

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