Diversity and prevalence of Anaerostipes in the human gut microbiota

Abstract

Members of the class Clostridia, a polyphyletic group of Gram-positive, spore-forming anaerobes in the Bacillota (Firmicutes) phylum, are prevalent and commonly associated with beneficial functions, such as providing colonization resistance against pathogens. Despite a demonstrated value in maintaining Clostridial populations in the gut, the functional and strain diversity of most commensal Clostridial species remains understudied. Here, we isolated and characterized Clostridial isolates, focusing on the genomic diversity of Anaerostipes, a prevalent butyrate-producing genus within the gut microbiota. We conducted a genomic comparison across 21 Anaerostipes strains isolated from healthy human fecal samples (n = 5) and publicly available genomes (n = 105). Whole genome comparisons across the Anaerostipes genus demonstrated 12 species bins, clustering into three major functionally distinct clusters correlating with host origin. One cluster (representing mostly A. caccae genomes) was distinguished by possessing a complete vitamin B12 biosynthesis pathway. Variability in carbohydrate and amino acid metabolism was demonstrated within dominant species of the human microbiota (A. hadrus, A. caccae, and A. hominis). Collectively, these data indicate metabolic variance across Anaerostipes species that may influence coexistence within the gut environment and variably influence health. IMPORTANCEAnaerostipes is a genus containing species known to produce butyrate upon fermenting lactate. Despite their association with health across studies using 16S rRNA gene-based analyses, little is known about genomic variability within and across species. Our study represents one of the first analyses to define strain variability across the Anaerostipes genus, identifying three functional clusters and close phylogenetic distance within species found in the human gut. Major variability within species prevalent in the human gut included variable carbohydrate and amino acid metabolism genes, suggesting the ability to coexist in the gut environment.