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Metagenomics reveals impact of geography and acute diarrheal disease on the Central Indian human gut microbiome

Monaghan, Tanya M.; Sloan, Tim J.; Stockdale, Stephen R.; Blanchard, Adam M.; Emes, Richard D.; Wilcox, Mark; Biswas, Rima; Nashine, Rupam; Manke, Sonali; Gandhi, Jinal; Jain, Pratishtha; Bhotmange, Shrejal; Ambalkar, Shrikant; Satav, Ashish; Draper, Lorraine A.; Hill, Colin; Kashyap, Rajpal Singh

Metagenomics reveals impact of geography and acute diarrheal disease on the Central Indian human gut microbiome Thumbnail


Clinical Associate Professor in Luminal Gastroenterology

Tim J. Sloan

Stephen R. Stockdale

Richard D. Emes

Mark Wilcox

Rima Biswas

Rupam Nashine

Sonali Manke

Jinal Gandhi

Pratishtha Jain

Shrejal Bhotmange

Shrikant Ambalkar

Ashish Satav

Lorraine A. Draper

Colin Hill

Rajpal Singh Kashyap


© 2020, © 2020 The Author(s). Published with license by Taylor & Francis Group, LLC. Background: The Central Indian gut microbiome remains grossly understudied. Herein, we sought to investigate the burden of antimicrobial resistance and diarrheal diseases, particularly Clostridioides difficile, 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: We observed distinct rural-urban differences in bacterial and viral populations, with geography exhibiting a greater influence than diarrheal status. Clostridioides difficile disease was more commonly observed in urban subjects, and their microbiomes were enriched in metabolic pathways relating to the metabolism of industrial compounds and genes encoding resistance to 3rd 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: We report distinct differences in antimicrobial resistance gene profiles, enrichment of metabolic pathways and phage composition between rural and urban populations, as well as a higher burden of Clostridioides difficile disease in the urban population. Our results reveal that geography is the key driver of variation in urban and rural Indian microbiomes, with acute diarrheal disease, including C. difficile 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.

Journal Article Type Article
Acceptance Date Mar 30, 2020
Online Publication Date May 27, 2020
Publication Date May 27, 2020
Deposit Date Jun 8, 2020
Publicly Available Date Jun 9, 2020
Journal Gut Microbes
Print ISSN 1949-0976
Electronic ISSN 1949-0984
Publisher Taylor & Francis Open
Peer Reviewed Peer Reviewed
Volume 12
Issue 1
Article Number 1752605
Keywords Microbiology (medical); Gastroenterology; Microbiology; Infectious Diseases
Public URL
Publisher URL


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