A catalogue of 1,167 genomes from the human gut archaeome

Recovery of 1,167 nonredundant archaeal genomes from the human gut microbiomes reveals previously undescribed genera, associations with sociodemographic factors and the presence of an archaeal virome. The human gut microbiome plays an important role in health, but its archaeal diversity remains largely unexplored. In the present study, we report the analysis of 1,167 nonredundant archaeal genomes (608 high-quality genomes) recovered from human gastrointestinal tract, sampled across 24 countries and rural and urban populations. We identified previously undescribed taxa including 3 genera, 15 species and 52 strains. Based on distinct genomic features, we justify the split of the Methanobrevibacter smithii clade into two separate species, with one represented by the previously undescribed 'CandidatusMethanobrevibacter intestini'. Patterns derived from 28,581 protein clusters showed significant associations with sociodemographic characteristics such as age groups and lifestyle. We additionally show that archaea are characterized by specific genomic and functional adaptations to the host and carry a complex virome. Our work expands our current understanding of the human archaeome and provides a large genome catalogue for future analyses to decipher its impact on human physiology.

Automated summary

The study analyzed 1,167 nonredundant archaeal genomes from human gut microbiomes, revealing previously undescribed genera, associations with sociodemographic factors, and the presence of an archaeal virome. The research demonstrates that archaea exhibit specific genomic and functional adaptations to the host, carrying a complex virome that plays a role in human physiology. This work expands our understanding of the human archaeome and provides a genome catalogue for future studies.