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

Cynthia Maria Chibani,Almut Werner,Christine Moissl-Eichinger,Jean-François Brugère,Alexandre Almeida,Ruth A Schmitz,Guillaume Borrel,Robert D Finn,Simonetta Gribaldo,Alexander Mahnert

doi:10.1038/s41564-021-01020-9

Abstract

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.

Highlights

Almut Werner[1], Jean-François Brugère 6, Simonetta Gribaldo 3, Robert D
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
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 ‘Candidatus Methanobrevibacter intestini’

Summary

Introduction

Almut Werner[1], Jean-François Brugère 6, Simonetta Gribaldo 3, Robert D. The human gut microbiome plays an important role in health, but its archaeal diversity remains largely unexplored. Most research has focused on the bacterial component[2] and its bacteriophages[3,4], and to some extent unicellular eukaryotes (including fungi) and their viruses, the archaea have been largely overlooked, mainly due to methodological reasons[5,6,7,8,9]. C2 carbon compounds, such as CO2, CO, formate, acetate or methyl compounds serve as substrates for the formation of methane. It is a highly syntrophic metabolism, as end-products of bacterial fermentation are consumed

Methods

Results

Conclusion