Metagenomics reveals impact of geography and acute diarrheal disease on the Central Indian human gut microbiome
Tanya Monaghan, Tim J. Sloan, Stephen R. Stockdale, Adam Blanchard, Richard D. Emes, Mark H. Wilcox, Rima Biswas, Rupam Nashine, Sonali Manke, Jinal Gandhi, Pratishtha Jain, Shrejal Bhotmange, Shrikant Ambalkar, Ashish Satav, Lorraine A. Draper, Colin Hill, Rajpal S. Kashyap
Abstract
BACKGROUND: , in rural-agricultural and urban populations in Central India, where there is widespread unregulated antibiotic use. We utilized shotgun metagenomics to comprehensively characterize the bacterial and viral fractions of the gut microbiome and their encoded functions in 105 participants. RESULTS: generation cephalosporins and carbapenems. By linking phages present in the microbiome to their bacterial hosts through CRISPR spacers, phage variation could be directly related to shifts in bacterial populations, with the auxiliary metabolic potential of rural-associated phages enriched for carbon and amino acid energy metabolism. CONCLUSIONS: disease exerting a lesser impact. Future studies will be required to understand the potential role of dietary, cultural, and genetic factors in contributing to microbiome differences between rural and urban populations.