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Metagenomics Reveals Impact of Geography and Acute Diarrhoeal 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; Singh Kashyap, Rajpal


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


Background: The Central Indian gut microbiome remains grossly understudied. Herein, we sought to investigate the burden of antimicrobial resistance and diarrhoeal diseases, particularly Clostridioides difficile, in rural-agricultural and urban populations in Central India, where there is widespread unregulated antibiotic use. We utilised shotgun metagenomics to comprehensively characterise 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 diarrhoeal 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 diarrhoeal 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.


Monaghan, T. M., Sloan, T. J., Stockdale, S. R., Blanchard, A. M., Emes, R. D., Wilcox, M., …Singh Kashyap, R. (2020). Metagenomics Reveals Impact of Geography and Acute Diarrhoeal Disease on the Central Indian Human Gut Microbiome. Gut Microbes, 12(1), Article 1752605

Journal Article Type Article
Acceptance Date Mar 30, 2020
Online Publication Date May 27, 2020
Publication Date May 27, 2020
Deposit Date Apr 20, 2020
Publicly Available Date May 28, 2021
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 Gut microbiome, antibiotic resistome, virome, diarrhoea, Clostridioides difficile, Central India
Public URL
Additional Information This is an Accepted Manuscript of an article published by Taylor & Francis in Gut Microbes on 27 May 2020, available online:


Metagenomics Reveals Impact Of Geography And Acute Diarrhoeal Disease On The Central Indian Human Gut Microbiome (360 Kb)

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