Archaeal Microbiome Dynamics in Human Health

Archaea are integral, though often overlooked, members of the human microbiome, inhabiting the gut, skin and respiratory tract. Unlike bacteria, many archaea specialise in methanogenesis, a process that consumes hydrogen gas and influences the overall balance of microbial fermentation. Their interactions with bacterial partners and host tissues shape metabolic outputs such as short-chain fatty acids, modulate immune responses and may contribute to disease states including inflammatory bowel diseases and metabolic disorders. Advances in cultivation and genomic sequencing have begun to illuminate the diversity of the human archaeome, revealing novel taxa, host-adapted functions and a complex associated virome. Archaeal colonisation commences early in life, evolves in response to diet, delivery mode and antibiotic exposure, and persists stably in adulthood. Understanding the dynamics of these communities is critical for harnessing their roles in health maintenance and for developing targeted microbial therapies.

Research from Nature Portfolio

Targeted isolation of human gut methanogens has expanded the roster of cultivable archaeal strains. By combining in silico metabolic modelling, fluorescence-activated cell sorting and optimised media, a recent study achieved stable cultures of previously uncultivated Methanobrevibacter strains. Comparative genomics of these isolates revealed genetic traits linked to gastrointestinal disease contexts and highlighted adaptive mechanisms underlying host colonisation. In parallel, a comprehensive genome catalogue of over 1,100 nonredundant archaeal genomes from diverse human populations has mapped the global diversity of the gut archaeome. Novel genera and species were described, and patterns of protein-coding genes reflected demographic factors such as age and lifestyle. This resource also unveiled a host-associated archaeal virome and provided insights into archaeal functional adaptations, laying the groundwork for future functional and therapeutic investigations.

Archaeal Microbiome Dynamics in Human Health publication trend

The graph below shows the total number of articles in archaeal microbiome dynamics in human health across all publications each year (not limited to Nature Index journals).

Technical terms

Archaeome: The collective community of archaea residing in or on the human body, encompassing diverse lineages and functional capabilities.

Methanogenesis: A metabolic process unique to certain archaea in which carbon compounds (such as CO₂) are reduced to methane, often using hydrogen gas as an electron donor.

Hydrogenotrophy: The utilisation of molecular hydrogen (H₂) by microorganisms to drive energy-yielding reactions, notably including methanogenesis and acetogenesis.

Syntrophy: A mutualistic interaction in which two or more microbial species cooperate to degrade a substrate that neither can utilise efficiently alone, often mediated by interspecies hydrogen transfer.

References

1. First Insights into the Diverse Human Archaeome: Specific Detection of Archaea in the Gastrointestinal Tract, Lung, and Nose and on Skin. mBio (2017).
2. The Intestinal Archaea Methanosphaera stadtmanae and Methanobrevibacter smithii Activate Human Dendritic Cells. PLOS ONE (2014).
3. Increased Prevalence of Methanosphaera stadtmanae in Inflammatory Bowel Diseases. PLOS ONE (2014).
4. Targeted isolation of Methanobrevibacter strains from fecal samples expands the cultivated human archaeome. Nature Communications (2024).
5. A catalogue of 1,167 genomes from the human gut archaeome. Nature Microbiology (2021).
6. Colonization and Succession within the Human Gut Microbiome by Archaea, Bacteria, and Microeukaryotes during the First Year of Life. Frontiers in Microbiology (2017).
7. H2 generated by fermentation in the human gut microbiome influences metabolism and competitive fitness of gut butyrate producers. Microbiome (2023).
8. Alterations in intestinal Archaea composition in pediatric patients with Crohn’s disease based on next-generation sequencing – a pilot study. Gut Microbes (2023).
9. Syntrophy via Interspecies H2 Transfer between Christensenella and Methanobrevibacter Underlies Their Global Cooccurrence in the Human Gut. mBio (2020).