A Comprehensive Analysis of the Global Human Gut Archaeome from a Thousand Genome Catalogue

The human gut microbiome plays an important role in health and disease, but the archaeal diversity therein remains largely unexplored. Here we report the pioneering analysis of 1167 non-redundant archaeal genomes recovered from diverse human gastrointestinal tract microbiomes. We identified 15 novel species including 52 previously unknown archaeal strains. Based on distinct genomic features, we warrant the split of the Methanobrevibacter smithii clade into two separate species. Patterns derived from 1.8 million proteins coded in these genomes showed substantial correlation with socio-demographic characteristics such as age and lifestyle. We infer that archaea are actively replicating in the human gut and are characterized by specific genomic and functional adaptations to the host. The archaeome carries a complex virome, with some species showing unexpected host flexibility. Our work furthers our current understanding of the human archaeome, and provides a large genome catalogue for future analyses to decipher its impact on human physiology.