Pathogenicity, the ability to cause disease in multicellular hosts, is widespread in various domains of life. In total, >1,500 human pathogenic bacterial species belonging to 10 phyla and 24 classes are known (9). The pure ratio observed in the bacterial domain indicates that >16 archaeal pathogens should exist (10); however, despite individual case reports and possible correlations with certain polymicrobial diseases (e.g., periodontitis), archaea are mostly considered nonpathogenic. No single representative of archaea known to date possesses capabilities consistent with Koch’s postulates, which has led to several discussions about possible reasons for that observation (10–13).

In theory, archaea have the prerequisites to evolve into pathogens because they are genetically and metabolically diverse, ubiquitous in the environment, and able to conflict with close relatives by using compounds directed against archaea (10). It is possible that our limited ability to accurately recognize them in disease conditions (not-yet-been-discovered hypothesis) is the reason no archaeal pathogens have been identified (8,11). Other perspectives have proposed that archaeal pathogens might not exist, potentially because they use different cofactors than those found in eukaryotes (14) or are unable to use the organic resources of the host, which are typically exploited by bacterial pathogens on a large scale (metabolism hypothesis) (15; D.J. Harrison, master’s thesis, 2022, https://researchspace.auckland.ac.nz/handle/2292/63414). Alternatively, some argue that pathogenesis in archaea does not exist because they do not possess the required virulence factor genes (gene-absence hypothesis) (D.J. Harrison, master’s thesis, 2022). Related hypotheses suggest that archaea cannot acquire virulence factors from bacteria or eukaryotes, possibly because their viruses and cell walls do not permit transfer between domains (virus hypothesis) (10). All those hypotheses warrant discussion. However, considering the huge lack of knowledge regarding gene annotation (virulence factors might be present, but we cannot identify them; or the metabolic capacities of methanogenic archaea have not yet been fully assessed, and we do not understand their behavior in the host with respect to metabolites taken up), a more superficial view on the principles of bacterial pathogenic traits might be useful.

Several steps are necessary for bacterial pathogenicity to develop: invasion, colonization, damage, and transmission (16) (Figure 1). Some of those traits overlap with archaeal characteristics, including exposure to the host (archaea are commensals) and the ability to adhere to and colonize the host (archaea form biofilms and might be able to attach to surfaces through their adhesins). Furthermore, the immunogenic reaction is highly species-specific; immunogenic potential is low for Methanobrevibacter spp. but stronger for Methanosphaera spp. (17). Transmission to other hosts seems probable; Pausan et al. demonstrated that methanogens can survive extended periods under oxygenated conditions (18). Archaea can team up with bacterial pathogens in harmful groups that can enter hosts’ tissues and benefit from invasion or cause damage to the host. In this context, we should mention the keystone pathogen hypothesis (19), in which some microorganisms could orchestrate the microbiome toward a disease status even in low numbers. Indeed, their metabolic capacity at the end of the food chain, consuming fermentation waste products, indicates that methanogens can influence the entire microbiome; their extraordinarily strong pull toward methane production can result in a microbial community optimized for fiber degradation and coping with B12 shortage (6).

Overall, the discussion on the potential of archaea for bearing pathogenic action at this stage remains highly speculative, underscoring the need for further research to elucidate their role in disease. We will address the different examples for infectious state in the human body that involve archaea and warrant deeper studies.

The involvement of pathogenic bacteria in various infectious diseases is often the focus of studies, but our understanding of the role of archaea in this context is still limited. Although no pathogenic archaea are known to date, the literature has presented some evidence of links between archaea and various infectious diseases (4,20,21) (Figure 2).

Principles of archaeal syntrophy may play a role in shaping specific microbial networks that influence the overall condition but do not cause disease. Studies suggest that methanogenic archaea engage in a symbiotic relationship with bacteria; they use hydrogen (H₂) and other byproducts of bacterial fermentation for methanogenesis, thereby reducing H₂ pressure (1). In addition, they produce metabolites, including short-chain fatty acids or vitamins (e.g., formate, B12) (6) that could support the growth of both archaea and potentially pathogenic bacteria (1,4,21).

We will explore the potential role of archaea in human infectious diseases in the oral cavity, gastrointestinal tract, and urogenital tract. Archaea have also been detected in other parts of the body, such as the skin (22) and the respiratory tract (3). However, for both those sites, the information available is too sparse to elaborate on potential infectious traits.

The literature demonstrates that archaea constitute active components within the human microbiome and are prevalent across a range of different body sites (2). Associations with various infectious diseases, such as periodontitis and endodontic infections within the oral cavity, SIBO in the gastrointestinal tract, and infections of the urogenital tract, have been reported (1,4). Although many of those reports are preliminary and do not fully resolve the archaeal components taxonomically, the genus Methanobrevibacter emerges as the most commonly observed archaea possibly linked to these infectious diseases (Figure 2; Appendix).

Understanding the complexities of detoxifying microbial metabolic products, particularly in the context of methanogenesis, carries substantial implications for both pathogen growth and disease onset. The interaction between archaea and bacteria in syntrophic relationships offers valuable insights into the dynamics within microbial communities. It is essential to conduct a thorough investigation to reveal the complex mechanisms behind these connections, which could play a role in shifting the microbiome toward a diseased state. Those experiments not only would shed light on potential disease mechanisms but also could open up paths for novel therapeutic approaches to address microbial dysbiosis linked to conditions such as periodontitis and other diseases (50).

The extent to which interactions with archaea are beneficial, neutral, or pathogenic is not well understood. Furthermore, advancing research in human health demands an increased focus on clinical studies that consider the inflammatory potential of archaea. In addition, such studies should explore the influence of archaeal metabolisms and their products, including the effects of methane on the human body (1). Although archaea are generally considered nonpathogenic, they could have the potential prerequisites for pathogenesis. Various hypotheses, such as the not-yet-been-discovered, metabolism, gene-absence, and virus hypotheses, are proposed to explain the apparent absence of archaeal pathogens (8,10,11,16). However, because of limited knowledge, challenges in gene annotation, and the complex nature of archaeal behavior in host environments, those hypotheses have not been proven. Although some pathogenic traits overlap between bacteria and archaea, the discussion of potential pathogenic action of archaea is ongoing and emphasizes the need for further research to understand their role in disease.

To gain a more comprehensive understanding of the role of archaea in health and disease requires additional initiatives aimed at effectively characterizing host-associated and disease-associated archaea. Despite the use of molecular biologic techniques in studying the archaeome, detecting archaea presents challenges primarily because standard protocols in research and diagnostics that are optimized for bacteria prove suboptimal for archaea because of their diverse cell structure, physiology, and metabolic activity. Those distinctive features, coupled with inappropriate protocols for sampling, DNA extraction, and PCR primer selection, create obstacles in visualizing, culturing, or analyzing archaea. Moreover, the absence of extensive reference databases hinders a thorough evaluation of the acquired data. Compounding this challenge is the presence of a robust bacterial or host background, further complicating the detection and analysis of archaea (8).

The limited availability of archaeal cultures hinders in-depth, mechanistic, physiologic and comprehensive analyses, including multiomics and interaction studies that could deepen our comprehension of archaea’s role in health and disease (Figure 3). According to the Global Catalog of Microorganisms (https://gcm.wdcm.org/species?taxonid=2173), only a handful of host-associated archaeal isolates are publicly accessible in culture. Those isolates include 3 strains of M. oralis from the human oral cavity and subgingival plaque, along with 4 strains of M. smithii isolated from human feces and the large intestine. The limited availability of cultures presents a substantial hindrance to conducting thorough research. Publications do exist describing the successful isolation of various archaea from patients with diverse health conditions (5), but there is currently no comprehensive culture collection for archaea. Establishing such a collection would be pivotal for advancing research on the archaeome; we have established a cultivation pipeline for the enrichment and cultivation of methanogenic archaea in a highly efficient way (J. Duller, et al., unpub. data, https://doi.org/10.1101/2024.04.10.588852).

Expanding our collection of human-derived isolates is crucial for gaining deeper insights into the functions and roles of archaea, enabling functional analyses in disease models, and determining the effects of their structural elements and metabolites. Microorganisms within a microbiome network engage in various interactions that affect each other and the health of the host. Understanding of such microbial interactions beyond the bacterial sphere is essential for a more comprehensive grasp of disease mechanisms and the search for new diagnostic, preventive, and therapeutic strategies.