Diversity of the class Coriobacteriia within different ecosystems

Members of the class Coriobacteriia are little studied, important fastidious anaerobes within the human gut microbiota. Collinsella aerofaciens is a core member of the gut microbiota that can present several different fermentation profiles within individuals, while Eggerthella lenta is implicated in xenobiotic metabolism. Recent ‘culturomics’ studies have greatly increased the number of Coriobacteriia recovered from human-associated samples, with the names of nine novel genera comprising 12 species published to date. However, the ecological range and genomic diversity of the class Coriobacteriia are poorly understood. Taxonomic assignments within the class Coriobacteriia are unclear, limiting the ways in which data from 16S rRNA gene-based diversity studies in humans and rodent models are interpreted.

Whole-genome and 16S rRNA gene sequences of members of the class Coriobacteriia were analysed and assigned to the families Atopobiaceae, Coriobacteriaceae and Eggerthellaceae. Inconsistencies between 16S rRNA gene sequence and whole genome sequence data deposited in public databases were identified. Newly annotated data searched against 85,000 16S rRNA gene sequence datasets included in the IMNGS (Integrated Microbial Next Generation Sequencing) database demonstrates humans and rodents harbour distinct Coriobacteriia populations. Members of the family Coriobacteriaceae predominate in the human gut, while Eggerthellaceae are more representative of the rodent gut. Metabolic capabilities of the three families of Coriobacteriia vary greatly, with Eggerthellaceae asaccharolytic compared with Coriobacteriaceae and Atopobiaceae. Correct annotation of Coriobacteriia in 16S rRNA gene (and by extension shotgun metagenomic) datasets is required to determine the contributions of these increasingly important bacteria to different ecosystems.