1) Methanogens and fermenter bacteria are known for their syntrophic metabolic model because fermenters break down complex organic compounds/acetate/methane/carbon dioxide/hydrogen sulfide into H2, an

Review Article

Archaea: forgotten players in the microbiome

Corinna Bang* and Ruth A. Schmitz

Institute for General Microbiology, University of Kiel (CAU), Kiel, Germany

Correspondence:Ruth A. Schmitz ([email protected])

Archaea, the third domain of life containing unique membrane composition and highly

diverse cell wall structures, were only recognized 40 years ago. Initially identiﬁed in

extreme environments, they are currently recognized as organisms ubiquitously present

in most, if not all, microbiomes associated with eukaryotic hosts. However, they have

been mostly overseen in microbiome studies due to the lack of standardized detection

protocols and to the fact that no archaeal pathogen is currently known. Recent years

clearly showed that (i) archaea are part of the microbiomes associated with plants,

animals and humans, (ii) form bioﬁlms and (iii) interact and activate the human immune

system. Future studies will not only deﬁne the host-associated diversity of archaea

(referred to as‘archaeome’) but also contribute to our understanding of the comprehen-

sive metabolic interplay between archaea and bacteria and the long-term gain insights

into their role in human health and their potential role(s) during disease development.

Introduction

Archaea belong to the third domain of life [1,2] and their phylogenetic distance to bacteria is reﬂected

by both genetic and structural differences. In contrast to their bacterial counterparts, archaea have not

only a unique and unusual membrane composition, but also higher diversity of different cell wall

structures, e.g. surface layer proteins and heteropolysaccharides, and also for some methanoarchaea,

pseudomurein [3–5]. In addition, many proteins involved in transcription and protein synthesis are

more similar to those found in Eukarya, e.g. RNA polymerase, ribosomal proteins and elongation

factors [6]. During the past 40 years, these properties were mainly thought to be unique adaptions to

the broad variety of extreme environments, in which archaea have been predominantly found [7].

However, in recent years, several studies discovered numerous archaeal species living under non-

extreme conditions, e.g. also in the marine environment (reviewed in refs [8,9]), and particularly, they

were found as part of the microbiome of multicellular host organisms ( plants and animals) (reviewed

in ref. [10], see also Mahnert et al. in this issue [61]). Although bacteria represent the major part of

complex microbial consortia that are associated with animals and plants, recently adapted molecular

tools revealed the additional presence of archaeal species within these communities. To this end, the

actual numbers of archaea in reported microbiomes might still be underestimated depending on the

methods used.

Overall, due to the rapid technological advancement of high-throughput amplicon-based sequen-

cing techniques and metagenome high-throughput sequencing (e.g. using the Illumina technique), the

number of microbiome research studies has increased enormously during the last decade. While the

use of bacteria-speciﬁc primers targeting various variable regions of the 16S rRNA gene (e.g. variable

regions 1–2or3–4) is well established and used in most projects and all sequencing facilities, the

development of primer sets targeting other host-associated microorganisms, such as archaea, is still

not methodologically sound. Archaea are often ignored in medical-based microbiome studies, most

probably due to the absence of a known pathogen. In addition, methodological problems, such as inef-

ﬁcient DNA extraction, unsuitable primer choice or incompleteness of 16S rRNA gene reference data-

bases as well as much lower numbers of complete archaeal genomes, heavily impede data accuracy on

the‘archaeome’[11,12]. Consequently, research on the complexity of the archaeome is still in its

infancy and knowledge on archaeal diversity, particularly within the human microbiome, is mainly

*Present address: Institute of

Clinical Molecular Biology,

University of Kiel (CAU), Kiel,

Germany.

Version of Record published:

22 November 2018 Received: 28 May 2018

Revised: 1 October 2018

Accepted: 4 October 2018

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based onﬁndings by chance based on 16S rRNA amplicon-sequencing of bacteria and more recently on meta-

genomic approaches. However, several studies described suitable techniques for speciﬁc detection of archaeal

microbiome members during the last few years [12,13]. Of particular importance are the studies of Koskinen

et al. [12] and Pausan et al. [14], in which amplicon-based next-generation sequencing methods for archaea

associated with the human body were established and evaluated with samples from different human body sites

as well as quantiﬁcation of archaea by qPCR. During these studies, an astonishing high number of archaeal

members within the human microbiome were discovered—and even more impressive, body site-speciﬁc

archaeal colonization was demonstrated (Figure 1). However, other studies developing archaea-speciﬁc

amplicon-based next-generation sequencing (NGS) methods also enrolled the need for habitat-dependent

adjustment; e.g. archaea-speciﬁc primers used for biogas reactors in a study by Fischer et al. [15] failed to

amplify archaea associated with humans (unpublished data).

Owing to the recent discoveries within theﬁeld of archaeome research, which are based not only on the

overall presence of archaea as part of (most) microbial communities associated with eukaryotic hosts, but also

on the evaluation of their molecular interaction with their eukaryotic hosts, this review aims to summarize the

current knowledge on archaea as the forgotten players in microbiome research.

Occurrence of archaea as part of the microbiome

Although a relevant fraction of the microbial biomass on Earth (in the ocean and on land) is constituted by

archaea, their presence as part of naturally occurring microbial consortia associated with eukaryotic hosts has

been often ignored and thus underestimated for a long time. This fact might be mainly due to the complex cul-

tivation of most archaeal strains as well as their sophisticated handling under standard laboratory conditions.

However, the rapid advancement of archaea-speciﬁc new-generation sequencing methodologies enabled the

discovery of numerous unknown archaeal species associated with every ecosystem studied so far (reviewed in

ref. [10]). This fact is not surprising considering the enormous metabolic capabilities within the domain of

Archaea that comprise phototrophy, organotrophy and lithotrophy [7], and the fact that naturally most micro-

organisms are present and grow in multispecies consortia that enable syntrophic and often symbiotic relation-

ships between all community members.

With respect to their overall abundance in and on eukaryotes, archaeal species are associated with the micro-

biome of plants and of animals, including humans. Today, the‘metaorganism’concept is widely accepted con-

sidering each multicellular organism as a macroscopic host and its associated microorganisms and where the

microbiota is crucially involved in the development, growth,ﬁtness/productivity, adaptation, diversiﬁcation and

health of their eukaryotic host [16]. Composition of this microbiota depends not only on the genotype and diet

of the host [17] but also on the environment [18]. Particularly in higher eukaryotes, this microbiota is speciﬁc

for the diverse body parts [19]. These microbiome characteristics are true not only for bacteria, viruses and

fungi, but also for archaea (archaeome).

Plants

Diverse plant organs carry a unique and highly diverse archaeome; however, information on speciﬁc interac-

tions between archaea and plants is generally scarce. One of the most prominent examples of plant-associated

archaea are methanogens that form part of the anaerobic rhizosphere of rice growing in low-oxygen wetland

plants [20]. Particularly, Methanocellales (Rice Cluster 1) and Methanosaetaceae thereby contribute to 10% of

the worldwide methane release from rice plant photosynthates [21]. Additional community members of low-

oxygen roots and rhizospheres of plants are ammonium-oxidizing archaea, which are found in high abun-

dances and prevent ammonia loss in such environments [22–24]. Furthermore, there is some evidence that

archaea as part of the plant microbiome might be involved in the protection against stress and secondary

metabolite production [25]. There is more evidence to suggest important ecological roles of archaea associated

with plants; future research is required to explore the nature of these interactions.

Animals

Most of the multicellular organisms studied to date were shown to be inhabited not only by trillions of bacteria

and fungi, but also by archaea. The vast majority of archaea that were initially identiﬁed within animals belong

to the phylum Euryarchaeota, with a particular high percentage of anaerobically growing methanogens found

in their digestive tracts. Interestingly, the overwhelming majority of methanoarchaea in the gastrointestinal tract

of most animals are related to theMethanobrevibactergenus [26]. This genus was shown to enhance the

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efﬁciency of bacterial polysaccharide fermentation through the process of methanogenesis, since it is able to

consume several fermentation products of primary and secondary fermenters such as methanol, hydrogen and

carbon dioxide [27,28].Methanobrevibacterspecies are thus highlyﬂexible in forming syntrophic interactions

with a broad range of ( fermenting) bacteria—generating and releasing methane into the surrounding. Since

methane is considered to be a climate relevant gas ( greenhouse gas) with one of the highest global-warming

potential [29], the substantial methane release originating from livestock is an environmental concern and is

frequently considered and discussed [30]. This is mainly because methane is predominantly produced within

the rumen of ruminants before it is released via eructation and breathing [31]. On the one hand, methane yield

could be highly inﬂuenced by diet composition. On the other hand, substances inhibiting methanogenesis are

under development these days. One example for this is the recently found 3-nitrooxypropanol, which speciﬁc-

ally targets the key enzyme of methanogenesis (methyl-coenzyme M reductase) and thereby reduces enteric

methane emissions from livestock without apparent negative side effects for the animals [32]. Besides

Methanobrevibacterspecies, 16S rRNA amplicon-based sequence analysis demonstrated the occurrence of

Methanosphaera,Methanomicroccous,Methanobacterium,Methanomicrobium,Methanomassiliicoccusand

Methanosarcinaspecies in the rumen of cattle, yaks, sheep, reindeers, goats, water buffalos and deer (reviewed

in ref. [10]). In fact, archaeal diversity was also shown for other mammals including horses, pigs and kangar-

oos, though again almost only methanogens were detected therein. Also for non-mammals, a huge diversity of

archaea was demonstrated by 16S rRNA gene-based analysis—besides birds and reptiles, methanogenic

archaea and some crenarchaeal species were found in termites and shrimps (reviewed in ref. [10]). Since all

these studies have been performed based on 16S rRNA gene sequence analysis using mostly universal prokary-

otic primers, the archaeal diversity in the gastrointestinal tract (GIT) of animals might be much higher. For

example, a recent study focused on archaeon-speciﬁc primers to unravel the archaeal diversity in great apes and

found at least 200 archaeal operational taxonomic units (OTUs) in the GIT of orangutans, gorillas, bonobos

Figure 1. The human archaeome.

Timeline overview of the discovery of archaeal species found as a part of the human microbiome at different sites. Since the

ﬁrst discovery of archaeal species in the early 1980s by cultivation, further detection took almost 30 years. Though already in

the late 2010s, some uncultivated species were detected by metagenome and amplicon-sequencing, only the development of

optimized NGS methods in 2017 was able to unravel a niche differentiation of human-associated archaeal communities

including not only methanogenic archaea, but also Thaumarchaeota as well as archaeal species from the DPANN

superphylum.

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and chimpanzees with the highest diversity observed for orangutans [13]. Phylogenetic diversity analysis of the

species revealed numerous OTUs out of three major groups: Methanobacteriales, Methanomassiliicoccales and

Thaumarchaeota. Most interestingly, the authors showed that overall the archaeal diversity was at least twofold

less in humans when compared with their closest relatives—the great apes. However, this study clearly

demonstrated that several archaeal species are conserved across all great ape species, implying a continual

essential function of archaea in the breakdown of dietary compounds throughout hominoid evolution [13].

Humans

Alreadyintheearly1980s,theﬁrst archaeal member has been shown to be part of the human intestine—

Methanobrevibacter smithii[33]. Although only few years later, an additional archaeal strain could be

isolated from stool samples (Methanosphaera stadtmaniae[34]), it took over 30 years to develop

archaea-speciﬁc detection methods in order to unravel their overall high diversity in and on humans

(Figure 2)[12]. In the meantime, the application of universal primer pairs and the development of metagen-

ome analysis revealed the existence of several further archaeal strains—but with overall low reproducibility

within different studies due to missing standardized methods (reviewed in refs [10,35]). However, over the

past few years, three studies using optimized DNA extraction and 16S rRNA gene sequencing demonstrated

overall massive and unexpected archaeal diversity not only in the intestine, but also on human skin, lungs

and nose [12–14]. But, Raymann et al. used primer pair Arch516F/Arch915R for exploring the archaeal

diversity in stool samples from great apes and humans [13]; Koskinen et al. and Pausan et al. focused on

nested-PCR approaches using various speciﬁc primer pairs for studying the human microbiome [12,14]. All

three studies developed speciﬁc computational analysis pipelines adapted to the poor deposition of archaeal

sequences in reference databases. With respect to the overall diversity in the intestine, these studies clearly

demonstrated thatM. smithiiandM. stadtmaniaeare only two exemplary species out of the diverse group of

theMethanobacteriales. In addition, they found a massive diversity ofMethanomassiliicoccalesstrains, a

group whoseﬁrst memberMethanomassiliicoccus luminyensishas been initially found by cultivation in a

study only a few years ago [36,37]. However, only Koskinen et al. and Pausan et al. were able to describe add-

itional thaumarchaeal and archaeal signatures of the DPANN superphylum (

Diapherotrites, Parvarchaeota,

Aenigmarchaeota, Nanoarchaeota, Nanohaloarchaea) by their method in the intestine. This might be due not

only to the used method, but also to the sample selection. In contrast to the study of Raymann et al., who

used exclusively stool samples, the other two studies focused on biopsy samples of different GIT locations in

addition to stool samples.

As detected earlier by Moissl-Eichinger and her collaborators, several thaumarchaeal species were shown

associated with the human skin [12,38]. Most interestingly, Woesearchaeota, Aenigmarchaeota and unclassiﬁed

species from the DPANN superphylum were also identiﬁed in skin samples. Furthermore, Koskinen et al. and

Pausan et al. explored the archaeal diversity of nose and lung samples [12,14]. Interestingly, the nose was

shown to carry a huge abundance of methanoarchaea comparable to that of the intestine, though

Thaumarchaeota were found in higher fractions. In contrast, the lung samples carried roughly no methanoarch-

aea, small fractions of Thaumarchaeota, but vast abundances of Woesearchaeota belonging to the DPANN

superphylum as well as unclassiﬁed members of this superphylum. In summary, an archaea-speciﬁc landscape

of four different human body sites could be demonstrated by these studies, which was not previously recog-

nized and which will change current research on the human-associated archaea (archaeome) as part of the

human microbiome (Figure 2, see also Mahnert et al. in this issue [61]).

With respect to the overall functional role of these human-associated archaeal strains, more detailed studies

dealing with metabolic-association pathways between detected archaea and bacteria are urgently needed.

Indeed, it is well known that methanoarchaea in the intestine can form syntrophic relationships with primary

and secondary fermenters resulting in lower hydrogen partial pressures potentially inﬂuencing the overall com-

munity structure present in the GIT [28,39]. For thaumarchaeal species, ammonia oxidation has been specu-

lated as a very important metabolic process. However, to date, information on metabolic capabilities of

Woesearchaeota and other species belonging to the DPANN superphylum is rare and thus needs to be uncov-

ered to identify their overall importance as part of the human microbiota.

Bioﬁlms

In nature, microorganisms are predominantly surface-associated together with other microbial strains in mixed

consortia or bioﬁlms. For archaea in general, bioﬁlm formation has been shown for various species (reviewed

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in ref. [40]), particularly in extreme environments such as deep lakes, aquifers and/or hydrothermal vents. Even

for the well-studied mucosa-associated strainsM. smithiiandM. stadtmaniae, it was not only shown that their

genetic information potentially allows adhesion to surfaces [39,41], but that they are indeed able to generate bio-

ﬁlms on abiotic surfaces [42](Figure 2). It is thus hypothesized that methanoarchaea in the GIT might also

occur in microbial bioﬁlms settled on the mucosal surface. The huge diversity of archaeal strains on biopsies of

the human intestine found in the study of Koskinen et al. [12] might also argue for this hypothesis. Indeed,

strong adhesion ofM. stadtmaniaeon human immune cells and on epithelial cell lines was frequently observed

during stimulation experiments in our group. It has also been noted that, possibly caused by disposal of exopoly-

saccharides,M. stadtmaniaecells easily aggregate in bioﬁlms (Figure 2). Further evidence comes from studies

elucidating oral bioﬁlms, in whichMethanobrevibacter oralishas been observed in at least every second patient

suffering from periodontal disease [43]. In addition, species of theMethanomassiliicoccusgenus were found to

be part of these subgingival plaques [44]. Bioﬁlm formation appears also most probably for thaumarchaeal

species on the human skin and for Woesearchaeota in the human lung, though this has to be conﬁrmed in the

near future from ongoing studies. One recent study unraveled metabolic potentials of 19 Woesearchaeotal organ-

isms in distinct biotopes [45]. By applying additional co-occurrence analysis, the authors demonstrated the exist-

ence of potential consortia between Woesearchaeota and anaerobic methanoarchaea in anoxic biotopes and

hypothesized a syntrophic metabolic model for a Woesearchaeota-methanogens consortium [45]. Since

Woesearchaeotal species have been found alongside methanoarchaea in GIT biopsy samples [12] such a consor-

tium is plausible, though this warrants future studies.

As a part of the eukaryotic-associated microbiota, archaeal strains are exposed to various defense systems of

their hosts. Oneﬁrst line of epithelial defense is the secretion of antimicrobial agents such as antimicrobial

Figure 2. Bioﬁlm formation of human mucosa-associated archaeal strains.

Structures of static bioﬁlms (incubation time of 3 days) formed byMethanosphaera stadtmaniae(A1–A3) and

Methanobrevibacter smithii(B1–B3). Analysis followed using either a confocal laser scanning microscope (ZEISS LSM 700)

after staining with the Live/Dead viability Kit showing live cells stained with Syto9 ( green) and dead cells with propidium iodide

(red) (A1andB1, site view 2D;A2andB2, 3D) or a scanning electron microscope (Hitachi S-4800) (A3andB3). Scale bars

represent 5mm(A3andB3).

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peptides (AMPs) [46]. Susceptibilities of various mucosa-associated methanoarchaea to several AMPs were

determined during the last years and differed markedly among the tested strains [47,48]. Most

mucosa-associated methanoarchaeal strains belong to the order Methanobacteriales, whose members have a

pseudomurein-containing cell wall and distinct lipid compositions [49]. Interestingly, these strains were more

resistant against the lytic effects of human-derived AMPs than, for example, members of the Methanosarcinales

or Methanomassiliicoccales. However, differences were also found within this order withM. stadtmaniaebeing

the most resistant member to these lytic effects. During these studies, it became evident that particularly this

strain might have evolved various resistance strategies response to AMPs—with bioﬁlm formation and

enhanced heteropolysaccharide production in detail. As mentioned before,M. stadtmaniaeis considered to

form bioﬁlms on gut epithelial cells. Since the concentration of AMPs close to the epithelia is thought to be

higher compared with the concentration in the lumen,M. stadtmaniaemight be exposed to higher concentra-

tions of human AMPs and has thus possibly evolved additional genomic and morphological adaptations.

Interestingly, mucosa-associated microorganisms are currently thought to be much more important regard-

ing the molecular interaction with the host’s immune system, since they are closer to the epithelium compared

with microorganisms in the lumen [50]. Thus, such an interaction between archaea and their human host is

most likely and will be discussed in the following section.

Interaction with the human immune system

Owing to the lack of recognized pathogens within the domain Archaea, their immunological potential was not

questioned for many years. However, during the last years, a few studies demonstrated activation of humane

immune cells and pro-inﬂammatory cytokine responses by peripheral blood mononuclear cells and by

monocyte-derived dendritic cells (moDCs) particularly resulting after inoculation with the gut-associated

archaeonM. stadtmaniae[51,52]. This process was shown to be initiated after phagocytosis and endosomal

lysis ofM. stadtmaniaeby human immune cells. Following increased phosphorylation of mitogen-activated

protein kinases (MAPKs) and transcription factors, high release of pro-inﬂammatory cytokines (including

interleukins and interferons) was observed [51,53]. Although both studies showed recognition and not only

innate, but also adaptive immune response by human immune cells in response to this archaeon, no speciﬁc

receptor involved was identiﬁed. Since archaea in general lack common bacterial-associated molecular patterns

such as lipopolysaccharides, peptidoglycan or bacterial-likeﬂagellin, the question for an archaea-associated

molecular pattern and the receptor involved in recognition emerged. In 2017, our collaborators and we demon-

strated that the puriﬁed RNA ofM. stadtmaniaeserves as a potent immune stimulator in immune cells.

Moreover, this study identiﬁed Toll-like receptors (TLRs) 7 and 8 as the respective involved pattern-recognition

receptors by the use of human myeloid cells and respective mutants [53]. Thus, for theﬁrst time, speciﬁc rec-

ognition of and response to an archaeon by human cells at the molecular level was proved (summarized in

Figure 3). Additionally, this molecular interaction was shown to result in the triggering of the NLRP3 inﬂam-

masome via a TLR8-dependent pathway, which resembles characteristics of both so far known inﬂammasome

activation pathways and thus might represent an archaea-speciﬁc one.

Still, the question remains unclear if (or if not) archaea might be involved in the development of diseases.

Several studies proposed an involvement of methanoarchaea in gastrointestinal diseases such as colon

cancer, obesity, anorexia and inﬂammatory bowel disease (IBD) (reviewed in ref. [35]). However, most of

these studies lack appropriate methods for the quantiﬁcation of archaea and thus reported controversial

results of overall archaeal abundances in studied patient groups—generally failing to conclude any associ-

ation to disease development. On the other hand, the study of Blais-Lecours et al. [54] appropriately deter-

mined increased the abundance ofM. stadtmaniaein patients suffering from IBD, although a relatively

small patient size group was examined. In relationship to the observed high pro-inﬂammatory potential and

inﬂammasome activation that was observed for this strain, a potential involvement in the development and

manifestation of IBD should not be ruled out. In addition, strong B- and T-cell responses within the drain-

ing lymph nodes that further result in adaptive immune responses such as selective immunoglobulin secre-

tion were obtained and strongly argue for systemic immune responses that might occur ifM. stadtmaniae

enters the bloodstream [51,52,54].

Besides potentially direct involvement in inﬂammatory diseases, methanogenic archaea have shown to

support growth of facultative pathogenic bacteria. In the oral cavity, as one example,M. oraliswas identiﬁed in

many studies dealing with periodontal and endodontic diseases [55–57]. Owing to its increased abundance and

its metabolic capabilities, it was hypothesized that this methanoarchaeon is able to enhance growth of

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potentially pathogenic anaerobic bacteria by signiﬁcantly lowering the redox potential in the microhabitats

[55,57]. Arguing in this direction, archaea might represent metabolic key species within microbial consortia

inhabiting the human body ecosystem [58,59] and thus might indeed have the potential to contribute to

disease development. However, this hypothesis urgently warrants future studies that include newly established

methods and optimized protocols.

Conclusions and outlook

With the fast development of high-throughput sequencing analysis during the last decades, our knowledge on

the bacteriome that is involved in health and disease of all multicellular organisms has increased rapidly.

However, due to the lack of standardized protocols for the detection of further members of the complete

microbiome, such as fungi, archaea and viruses, the overall interactions between microbes among each other

and interactions between their hosts remain largely unclear. Complete understanding of effectiveness and inter-

play of present microorganisms is though urgently needed to unravel mechanisms, which are important for

prevention of disease development. Thus, future studies should additionally use established workﬂows for 16S

rRNA gene-based high-throughput analysis speciﬁc for archaea besides the already well-established ones for

bacteria. Results from these studies will not only gain insights into the potential roles of archaea during disease

development, but might also contribute to our understanding of the comprehensive metabolic interplay

between archaea and bacteria, which is certainly an unanswered question important for overall human health

and development.

Summary

Archaea are present in most, if not all, microbiomes associated with eukaryotic hosts—

plants animals and humans

Archaea have been mostly overseen in previous microbiome studies due to the lack of stan-

dardized detection protocols and due to the fact that no archaeal pathogen is currently

known.

Figure 3. Molecular cross-talk between archaea and human immune cells.

Phagocytosis ofM. stadtmaniaeleads to the activation of innate and adaptive immune responses. (A) moDCs were stimulated

withM. stadtmaniaefor a period of 4 h in order to determine phagocytosis. Formed phagolysosomes in moDCs were stained

with LysoTracker Red DND-99 during the time of incubation, and cells were labeled with Hoechst for DAPI staining. Scale bar

indicates 10μm. (B) Schematic simpliﬁcation of immune cell activation. After phagocytosis ofM. stadtmaniae, phagolysosomes

are formed in order to degrade archaeal cells. Subsequently, delivered RNA derived from archaea is recognized by Toll-like

receptors 7 and 8 in the endosomes leading to intracellular signaling cascades. Theﬁnal activation of MAPKs and transcription

factorsﬁnally result in the release of pro-inﬂammatory cytokines, antimicrobial peptides and the expression of modulatory

surface molecules in order to active adaptive immune responses.

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Archaea interact with their human host and activate the human immune system.

Future studies on the host-associated archaeomes will allow to gain insights into their role in

human health and their potential role(s) during disease development.

In the future, interactions between bacteria, archaea, virus and fungi as well as interactions

between their hosts have to be studied to reach a complete understanding of the comprehen-

sive metabolic interplay between microorganisms and hosts.

Complete understanding of effectiveness and interplay of present microorganisms is urgently

needed to unravel mechanisms, which are important for the prevention of disease

development.

Abbreviations

AMPs, antimicrobial peptides; GIT, gastrointestinal tract; IBD, inﬂammatory bowel disease; MAPKs,

mitogen-activated protein kinases; TLRs, Toll-like receptors; moDCs, monocyte-derived dendritic cells; NGS,

next-generation sequencing; OTUs, operational taxonomic units.

Funding

This work was supported by the DFG (German Research Foundation) [HH2758/4-2, SCHM1051/11-2].

Competing Interests

The Authors declare that there are no competing interests associated with the manuscript.

References

1 Woese, C.R. and Fox, G.E. (1977) Phylogenetic structure of the prokaryotic domain: the primary kingdoms.Proc. Natl Acad. Sci. U.S.A.74, 5088–5090

https://doi.org/10.1073/pnas.74.11.5088

2 Woese, C.R., Kandler, O. and Wheelis, M.L. (1990) Towards a natural system of organisms: proposal for the domains archaea, bacteria, and eucarya.

Proc. Natl Acad. Sci. U.S.A.87, 4576–4579https://doi.org/10.1073/pnas.87.12.4576

3 Koga, Y., Nishihara, M., Morii, H. and Akagawa-Matsushita, M. (1993) Ether polar lipids of methanogenic bacteria: structures, comparative aspects, and

biosyntheses.Microbiol. Rev.57, 164–182 PMID:8464404

4 Koga, Y. and Morii, H. (2005) Recent advances in structural research on ether lipids from archaea including comparative and physiological aspects.

Biosci. Biotechnol. Biochem.69, 2019–2034https://doi.org/10.1271/bbb.69.2019

5 Kandler, O. and König, H. (1998) Cell wall polymers in archaea (Archaebacteria).Cell. Mol. Life Sci.54, 305–308https://doi.org/10.1007/

s000180050156

6 Cavicchioli, R. (2007)Archaea: Cellular and Molecular Biology, ASM Press, Washington, DC. xii, 523 p.

7 Valentine, D.L. (2007) Adaptations to energy stress dictate the ecology and evolution of the archaea.Nat. Rev. Microbiol.5, 316–323https://doi.org/10.

1038/nrmicro1619

8 You, J., Das, A., Dolan, E.M. and Hu, Z. (2009) Ammonia-oxidizing archaea involved in nitrogen removal.Water Res.43, 1801–1809https://doi.org/10.

1016/j.watres.2009.01.016

9 Santoro, A.E. and Casciotti, K.L. (2011) Enrichment and characterization of ammonia-oxidizing archaea from the open ocean: phylogeny, physiology and

stable isotope fractionation.ISME J.5, 1796–1808https://doi.org/10.1038/ismej.2011.58

10 Moissl-Eichinger, C., Pausan, M., Taffner, J., Berg, G., Bang, C. and Schmitz, R.A. (2018) Archaea are interactive components of complex microbiomes.

Trends Microbiol.26,70–85https://doi.org/10.1016/j.tim.2017.07.004

11 Dridi, B. (2012) Laboratory tools for detection of archaea in humans.Clin. Microbiol. Infect.18, 825–833https://doi.org/10.1111/j.1469-0691.2012.

03952.x

12 Koskinen, K., Pausan, M.R., Perras, A.K., Beck, M., Bang, C., Mora, M. et al. (2017) First insights into the diverse human archaeome: speciﬁc

detection of archaea in the gastrointestinal tract, lung, and nose and on skin.MBio8, pii: e00824-17https://doi.org/10.1128/mBio.00824-17

13 Raymann, K., Moeller, A.H., Goodman, A.L. and Ochman, H. (2017) Unexplored archaeal diversity in the great ape gut microbiome.mSphere2

https://doi.org/10.1128/mSphere.00026-17

14 Pausan, M.R, Csorba, C., Singer, G., Till, H., Schoepf, V. and Santigli, E., et al. (2018) Measuring the archaeome: detection and quantiﬁcation of

archaea signatures in the human body.bioRxivhttps://doi.org/10.1101/334748

15 Fischer, M.A., Güllert, S., Neulinger, S.C., Streit, W.R. and Schmitz, R.A. (2016) Evaluation of 16S rRNA gene primer pairs for monitoring microbi

community structures showed high reproducibility within and low comparability between datasets generated with multiple archaeal and bacterial primer

pairs.Front. Microbiol.7, 1297https://doi.org/10.3389/fmicb.2016.01297

16 Bosch, T.C. and McFall-Ngai, M.J. (2011) Metaorganisms as the new frontier.Zoology114, 185–190https://doi.org/10.1016/j.zool.2011.04.001

Emerging Topics in Life Sciences (2018)2459–468

https://doi.org/10.1042/ETLS20180035

Downloaded from http://portlandpress.com/emergtoplifesci/article-pdf/2/4/459/484178/etls-2018-0035c.pdf by University of California Santa Barbara (UCSB) user on 25 October 2021

17 Wang, J., Thingholm, L.B., Skiecevič

ienė

, J., Rausch, P., Kummen, M., Hov, J.R. et al. (2016) Genome-wide association analysis identiﬁes variation in

vitamin D receptor and other host factors inﬂuencing the gut microbiota.Nat. Genet.48, 1396–1406https://doi.org/10.1038/ng.3695

18 Rothschild, D., Weissbrod, O., Barkan, E., Kurilshikov, A., Korem, T., Zeevi, D. et al. (2018) Environment dominates over host genetics in shaping

human gut microbiota.Nature555, 210–215https://doi.org/10.1038/nature25973

19 The Human Microbiome Project Consortium (2012) Structure, function and diversity of the healthy human microbiome.Nature486, 207–214

https://doi.org/10.1038/nature11234

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

https://doi.org/10.1111/j.1758-2229.2009.00038.x

21 Pump, J., Pratscher, J. and Conrad, R. (2015) Colonization of rice roots with methanogenic archaea controls photosynthesis-derived methane emission.

Environ. Microbiol.17, 2254–2260https://doi.org/10.1111/1462-2920.12675

22 Treusch, A.H., Leininger, S., Kletzin, A., Schuster, S.C., Klenk, H.-P. and Schleper, C. (2005) Novel genes for nitrite reductase and Amo-relatedproteins

indicate a role of uncultivated mesophilic crenarchaeota in nitrogen cycling.Environ. Microbiol.7, 1985–1995https://doi.org/10.1111/j.1462-2920.

2005.00906.x

23 Herrmann, M., Saunders, A.M. and Schramm, A. (2008) Archaea dominate the ammonia-oxidizing community in the rhizosphere of the freshwater

macrophyteLittorella uniﬂora.Appl. Environ. Microbiol.74, 3279–3283https://doi.org/10.1128/AEM.02802-07

24 Ke, X., Lu, W. and Conrad, R. (2015) High oxygen concentration increases the abundance and activity of bacterial rather than archaeal nitriﬁers in rice

ﬁeld soil.Microb. Ecol.70, 961–970https://doi.org/10.1007/s00248-015-0633-4

25 Taffner, J., Erlacher, A., Bragina, A., Berg, C., Moissl-Eichinger, C. and Berg, G. (2018) What Is the role ofarchaeain plants? New insights from the

vegetation of alpine bogs.mSphere3, e00122-18https://doi.org/10.1128/mSphere.00122-18

26 Henderson, G., Cox, F., Ganesh, S., Jonker, A., Young, W., Global Rumen Census Collaborators et al. (2015) Rumen microbial community composition

varies with diet and host, but a core microbiome is found across a wide geographical range.Sci. Rep.5, 14567https://doi.org/10.1038/srep14567

27 McNeil, N.I. (1984) The contribution of the large intestine to energy supplies in man.Am. J. Clin. Nutr.39, 338–342https://doi.org/10.1093/ajcn/39.2.

338

28 Samuel, B.S. and Gordon, J.I. (2006) A humanized gnotobiotic mouse model of host-archaeal-bacterial mutualism.Proc. Natl Acad. Sci. U.S.A.103,

10011–10016https://doi.org/10.1073/pnas.0602187103

29 Intergovernmental Panel on Climate Change. (2014) Climate change 2013—the physical science basis: working group I contribution to theﬁfth

assessment report of the intergovernmental panel on climate change, pp. 465–570, Cambridge University Press, Cambridge (Carbon and Other

Biogeochemical Cycles)

30 Pérez-Barbería, F.J. (2017) Scaling methane emissions in ruminants and global estimates in wild populations.Sci. Total Environ.579, 1572–1580

https://doi.org/10.1016/j.scitotenv.2016.11.175

31 Sejian, V., Lal, R., Lakritz, J. and Ezeji, T. (2011) Measurement and prediction of enteric methane emission.Int. J. Biometeorol.55,1–16https://doi.

org/10.1007/s00484-010-0356-7

32 Duin, E.C., Wagner, T., Shima, S., Prakash, D., Cronin, B., Yáñez-Ruiz, D.R. et al. (2016) Mode of action uncovered for the speciﬁc reduction of

methane emissions from ruminants by the small molecule 3-nitrooxypropanol.Proc. Natl Acad. Sci. U.S.A.113, 6172–6177https://doi.org/10.1073/

pnas.1600298113

33 Miller, T.L., Wolin, M.J., Conway de Macario, E. and Macario, A.J. (1982) Isolation ofMethanobrevibacter smithiifrom human feces.Appl. Environ.

Microbiol.43, 227–232 PMID:6798932

34 Miller, T.L., Weaver, G.A. and Wolin, M.J. (1984) Methanogens and anaerobes in a colon segment isolated from the normal fecal stream.Appl. Environ.

Microbiol.48, 449–450 PMID:6486788

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

org/10.1093/femsre/fuv010

36 Borrel, G., Harris, H.M., Tottey, W., Mihajlovski, A., Parisot, N., Peyretaillade, E. et al. (2012) Genome sequence of‘CandidatusMethanomethylophilus

alvus’Mx1201, a methanogenic archaeon from the human gut belonging to a seventh order of methanogens.J. Bacteriol.194, 6944–6945https://doi.

org/10.1128/JB.01867-12

37 Borrel, G., Parisot, N., Harris, H.M., Peyretaillade, E., Gaci, N., Tottey, W. et al. (2014) Comparative genomics highlights the unique biology of

Methanomassiliicoccales, a Thermoplasmatales-related seventh order of methanogenic archaea that encodes pyrrolysine.BMC Genomics15, 679

https://doi.org/10.1186/1471-2164-15-679

38 Probst, A.J., Auerbach, A.K. and Moissl-Eichinger, C. (2013) Archaea on human skin.PLoS ONE8, e65388https://doi.org/10.1371/journal.pone.

0065388

39 Samuel, B.S., Hansen, E.E., Manchester, J.K., Coutinho, P.M., Henrissat, B., Fulton, R. et al. (2007) Genomic and metabolic adaptations of

Methanobrevibacter smithiito the human gut.Proc. Natl Acad. Sci. U.S.A.104, 10643

–10648https://doi.org/10.1073/pnas.0704189104

40 Orell, A., Fröls, S. and Albers, S.-V. (2013) Archaeal bioﬁlms: the great unexplored.Annu. Rev. Microbiol.67, 337–354https://doi.org/10.1146/

annurev-micro-092412-155616

41 Fricke, W.F., Seedorf, H., Henne, A., Krüer, M., Liesegang, H., Hedderich, R. et al. (2006) The genome sequence ofMethanosphaera stadtmanae

reveals why this human intestinal archaeon is restricted to methanol and H

2for methane formation and ATP synthesis.J. Bacteriol.188, 642–658

https://doi.org/10.1128/JB.188.2.642-658.2006

42 Bang, C., Ehlers, C., Orell, A., Prasse, D., Spinner, M., Gorb, S.N. et al. (2014) Bioﬁlm formation of mucosa-associated methanoarchaeal strains.Front.

Microbiol.5, 353https://doi.org/10.3389/fmicb.2014.00353

43 Li, C.L., Liu, D.L., Jiang, Y.T., Zhou, Y.B., Zhang, M.Z., Jiang, W. et al. (2009) Prevalence and molecular diversity ofArchaeain subgingival pockets of

periodontitis patients.Oral Microbiol. Immunol.24, 343–346https://doi.org/10.1111/j.1399-302X.2009.00514.x

44 Horz, H.-P., Seyfarth, I. and Conrads, G. (2012)Mcraand 16S rRNA gene analysis suggests a novel lineage ofArchaeaphylogenetically afﬁliated with

Thermoplasmatalesin human subgingival plaque.Anaerobe18, 373–377https://doi.org/10.1016/j.anaerobe.2012.04.006

45 Liu, X., Li, M., Castelle, C.J., Probst, A.J., Zhou, Z., Pan, J. et al. (2018) Insights into the ecology, evolution, and metabolism of the widespread

Woesearchaeotal lineages.Microbiome6, 102https://doi.org/10.1186/s40168-018-0488-2

Emerging Topics in Life Sciences (2018)2459–468https://doi.org/10.1042/ETLS20180035

Downloaded from http://portlandpress.com/emergtoplifesci/article-pdf/2/4/459/484178/etls-2018-0035c.pdf by University of California Santa Barbara (UCSB) user on 25 October 2021

46 Zasloff, M. (1992) Antibiotic peptides as mediators of innate immunity.Curr. Opin. Immunol.4,3–7https://doi.org/10.1016/0952-7915(92)90115-U

47 Bang, C., Schilhabel, A., Weidenbach, K., Kopp, A., Goldmann, T., Gutsmann, T. et al. (2012) Effects of antimicrobial peptides on methanogenic

archaea.Antimicrob. Agents Chemother.56, 4123–4130https://doi.org/10.1128/AAC.00661-12

48 Bang, C., Vierbuchen, T., Gutsmann, T., Heine, H. and Schmitz, R.A. (2017) Immunogenic properties of the human gut-associated archaeon

Methanomassiliicoccus luminyensisand its susceptibility to antimicrobial peptides.PLoS ONE12, e0185919https://doi.org/10.1371/journal.pone.

0185919

49 Steenbakkers, P.J., Geerts, W.J., Ayman-Oz, N.A. and Keltjens, J.T. (2006) Identiﬁcation of pseudomurein cell wall binding domains.Mol. Microbiol.62,

1618–1630https://doi.org/10.1111/j.1365-2958.2006.05483.x

50 Macfarlane, S., Bahrami, B. and Macfarlane, G.T. (2011) Mucosal bioﬁlm communities in the human intestinal tract.Adv. Appl. Microbiol.75, 111–143

https://doi.org/10.1016/B978-0-12-387046-9.00005-0

51 Bang, C., Weidenbach, K., Gutsmann, T., Heine, H. and Schmitz, R.A. (2014) The intestinal archaeaMethanosphaera stadtmanaeand

Methanobrevibacter smithiiactivate human dendritic cells.PLoS ONE9, e99411https://doi.org/10.1371/journal.pone.0099411

52 Blais-Lecours, P., Duchaine, C., Taillefer, M., Tremblay, C., Veillette, M., Cormier, Y. et al. (2011) Immunogenic properties of archaeal species found in

bioaerosols.PLoS ONE6, e23326https://doi.org/10.1371/journal.pone.0023326

53 Vierbuchen, T., Bang, C., Rosigkeit, H., Schmitz, R.A. and Heine, H. (2017) The human-associated archaeonMethanosphaera stadtmanaeis recognized

through Its RNA and induces TLR8-dependent NLRP3 inﬂammasome activation.Front. Immunol.8, 1535https://doi.org/10.3389/ﬁmmu.2017.01535

54 Blais-Lecours, P., Marsolais, D., Cormier, Y., Berberi, M., Hache, C., Bourdages, R. et al. (2014) Increased prevalence ofMethanosphaera stadtmanae

in inﬂammatory bowel diseases.PLoS ONE9, e87734https://doi.org/10.1371/journal.pone.0087734

55 Kulik, E.M., Sandmeier, H., Hinni, K. and Meyer, J. (2001) Identiﬁcation of archaeal rDNA from subgingival dental plaque by PCR ampliﬁcation and

sequence analysis.FEMS Microbiol. Lett.196, 129–133https://doi.org/10.1111/j.1574-6968.2001.tb10553.x

56 Lepp, P.W., Brinig, M.M., Ouverney, C.C., Palm, K., Armitage, G.C. and Relman, D.A. (2004) Methanogenic archaea and human periodontal disease.

Proc. Natl Acad. Sci. U.S.A.101, 6176–6181https://doi.org/10.1073/pnas.0308766101

57 Vianna, M.E., Conrads, G., Gomes, B.P.F.A. and Horz, H.P. (2006) Identiﬁcation and quanti

ﬁcation of archaea involved in primary endodontic infections.

J. Clin. Microbiol.44, 1274–1282https://doi.org/10.1128/JCM.44.4.1274-1282.2006

58 Rousk, J., Brookes, P.C. and Baath, E. (2009) Contrasting soil pH effects on fungal and bacterial growth suggest functional redundancy in carbon

mineralization.Appl. Environ. Microbiol.75, 1589–1596https://doi.org/10.1128/AEM.02775-08

59 Horz, H.P. and Conrads, G. (2011) Methanogenic archaea and oral infections—ways to unravel the black box.J. Oral Microbiol.3https://doi.org/10.

3402/jom.v3i0.5940

60 Eme, L., Spang, A., Lombard, J., Stairs, C.W. and Ettema, T.J.G. (2017) Archaea and the origin of eukaryotes.Nat. Rev. Microbiol.15, 711–723

https://doi.org/10.1038/nrmicro.2017.133

61 Mahnert, A., Blohs, M., Pausan, M.-R. and Moissl-Eichinger, C. (2018) The human archaeome: methodological pitfalls and knowledge gaps.Emerg.

Top. Life Sci., in press.

Emerging Topics in Life Sciences (2018)2459–468

https://doi.org/10.1042/ETLS20180035

Downloaded from http://portlandpress.com/emergtoplifesci/article-pdf/2/4/459/484178/etls-2018-0035c.pdf by University of California Santa Barbara (UCSB) user on 25 October 2021