Geographic patterns of the standing and active human gut microbiome in health and inflammatory bowel disease

The knowledge of species composition and functional aspects of the human microbiome is steadily increasing, but still limited information regarding its variation on a global scale is available. Due to the microbial involvement in inflammatory bowel diseases and their increase in global frequency, shared patterns across populations may hold important clinical relevance. In this study, we analyze a set of 89 mucosal biopsies sampled from individuals of German, Lithuanian and Indian origins, using bacterial community profiling of a roughly equal number of healthy controls, Crohn Disease and Ulcerative Colitis patients from each location. From each individual sample 16S rDNA and rRNA are analyzed as proxies for standing and active microbial community structure, respectively. We find pronounced regional as well as global disease patterns in the major phyla and patterns of diversity, which differ when investigated in the standing or active community. Geography appears to dominate patterns of beta diversity, with European samples being more similar to each other, which is more pronounced in the active microbial community. However, when geographic influence is accounted for, some universal patterns of disease become apparent. In particular, two genera belonging to the Clostridium leptum subgroup, Faecalibacteria and Papillibacter, display consistent patterns with respect to disease status and may thus serve as reliable “microbiomarkers”. These analyses reveal the importance of the interaction of geography and disease in the interpretation of disease-associated changes in microbial communities and highlight the added value of analyzing communities on both the rDNA and rRNA level.