Characterizing the genomic diversity of prevalent gut microbiome bacterial species using metagenome-assembled genomes

Abstract

Metagenome-wide association studies enable the identification of associations between the human microbiome and host physiological traits, such as inflammatory bowel disease, type 2 diabetes, and mental disorders, as well as many other physiological features, including diet, stress, exercise, and drug intake. In these studies, microbiome composition is typically characterized at the species level. As the gut microbiota is known to exhibit structured diversity below the species level, association studies at the within-species level may yield stronger associations. A major challenge is that the within-species structure of most gut microbial species remains poorly defined. In this study, we investigated the within-species structure of the five most abundant and prevalent microbial species using open data. The results showed clear within-species structures for four of the five species.