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The Human Archaeome: Commensals, Opportunists, or Emerging Pathogens?
1Department of Obstetrics and Gynecology, Charles Stewart Mott Center for Human Growth and Development, Institute of Environmental Health Sciences, Wayne State University, Detroit, MI 48302, USA.
Pathogens (Basel, Switzerland)
|November 27, 2025
Summary
Archaea are common human microbes whose roles in health and disease are unclear. This review synthesizes evidence on archaeal diversity, habitat, and potential indirect disease contributions, exploring the human "archaeome".
Area of Science:
- Microbiology
- Human Microbiome Research
- Eukaryotic Genomics
Background:
- Archaea are a fundamental domain of life, increasingly recognized within the human microbiome.
- Their specific roles in human health and disease pathogenesis remain largely underappreciated and poorly understood.
- Unlike bacteria, no archaeal species are confirmed primary mammalian pathogens, but their ubiquity suggests indirect physiological and pathological influence.
Purpose of the Study:
- To synthesize current evidence on archaeal diversity and habitat specificity across human body sites.
- To evaluate the emerging concept of the human "archaeome" and its potential involvement in disease.
- To highlight technological advancements enabling translational applications in microbiome diagnostics and therapeutics.
Main Methods:
- Review and synthesis of existing scientific literature on human-associated archaea.
- Analysis of archaeal diversity and niche specialization across gastrointestinal, aerodigestive, urogenital tracts, and skin.
- Evaluation of evidence linking archaeal presence to specific diseases and host-microbiome interactions.
Main Results:
- Methanogens dominate the lower gastrointestinal tract, influencing fermentation and methane production.
- Nitrososphaeria are prevalent on skin and in the upper aerodigestive tract, indicating ecological specialization.
- Associations found between methanogens and conditions like IBS, IBD, obesity, CRC, and periodontal disease; archaea detected in cystic fibrosis lungs.
Conclusions:
- Archaea may contribute indirectly to disease through metabolic cross-feeding, immune modulation, and synergistic interactions in polymicrobial infections.
- Understanding the human "archaeome" is crucial for advancing microbiome diagnostics, therapeutic targeting, and microbiome engineering.
- Emerging technologies like MERFISH and multi-omics profiling are key to unlocking the translational potential of archaeal research.
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