Gut microbial ecology and exposome of a healthy Pakistani cohort

Gul, F., Herrema, H., Davids, M., Keating, C. , Nasir, A., Ijaz, U. Z. and Javed, S. (2024) Gut microbial ecology and exposome of a healthy Pakistani cohort. Gut Pathogens, 16, 5. (doi: 10.1186/s13099-024-00596-x)

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Background Pakistan is a multi-ethnic society where there is a disparity between dietary habits, genetic composition, and environmental exposures. The microbial ecology of healthy Pakistani gut in the context of anthropometric, sociodemographic, and dietary patterns holds interest by virtue of it being one of the most populous countries, and also being a Lower Middle Income Country (LMIC). Methods 16S rRNA profiling of healthy gut microbiome of normo-weight healthy Pakistani individuals from different regions of residence is performed with additional meta-data collected through filled questionnaires. The current health status is then linked to dietary patterns through test of independence and Generalized Linear Latent Variable Model (GLLVM) where distribution of individual microbes is regressed against all recorded sources of variability. To identify the core microbiome signature, a dynamic approach is used that considers into account species occupancy as well as consistency across assumed grouping of samples including organization by gender and province of residence. Fitting neutral modeling then revealed core microbiome that is selected by the environment. Results A strong determinant of disparity is by province of residence. It is also established that the male microbiome is better adapted to the local niche than the female microbiome, and that there is microbial taxonomic and functional diversity in different ethnicities, dietary patterns and lifestyle habits. Some microbial genera, such as, Megamonas, Porphyromonas, Haemophilus, Klebsiella and Finegoldia showed significant associations with consumption of pickle, fresh fruits, rice, and cheese. Our analyses suggest current health status being associated with the diet, sleeping patterns, employment status, and the medical history. Conclusions This study provides a snapshot of the healthy core Pakistani gut microbiome by focusing on the most populous provinces and ethnic groups residing in predominantly urban areas. The study serves a reference dataset for exploring variations in disease status and designing personalized dietary and lifestyle interventions to promote gut health, particularly in LMICs settings.

Item Type:Articles
Additional Information:The authors acknowledge the following fundings: Higher Education Commission of Pakistan’s International Research Support Initiative Programme, Grant No: 1-8/HEC/HRD/2021/11792 (FG, SJ), UKRI Natural Environment Research Council - Independent Research Fellowship NE/L011956/1, (UZI), UKRI Engineering and Physical Sciences Research Council EP/P029329/1 (UZI), UKRI Engineering and Physical Sciences Research Council EP/V030515/1 (UZI), In-kind support by uBiome, USA (AN).
Glasgow Author(s) Enlighten ID:Keating, Dr Ciara and Ijaz, Dr Umer
Creator Roles:
Ijaz, U.Methodology, Investigation, Visualization, Supervision, Writing – original draft
Keating, C.Investigation, Writing – review and editing
Authors: Gul, F., Herrema, H., Davids, M., Keating, C., Nasir, A., Ijaz, U. Z., and Javed, S.
College/School:College of Medical Veterinary and Life Sciences > School of Biodiversity, One Health & Veterinary Medicine
College of Science and Engineering > School of Engineering > Infrastructure and Environment
Journal Name:Gut Pathogens
Publisher:BioMed Central
ISSN (Online):1757-4749
Copyright Holders:Copyright: © The Author(s) 2024
First Published:First published in Gut Pathogens 16: 5
Publisher Policy:Reproduced under a Creative Commons licence

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Project CodeAward NoProject NamePrincipal InvestigatorFunder's NameFunder RefLead Dept
170256Understanding microbial community through in situ environmental 'omic data synthesisUmer Zeeshan IjazNatural Environment Research Council (NERC)NE/L011956/1ENG - Infrastructure & Environment
300451Optimising decentralised low-cost wastewater infrastructure by managing the microbesWilliam SloanEngineering and Physical Sciences Research Council (EPSRC)EP/P029329/1ENG - Infrastructure & Environment
309846Decentralised water technologiesWilliam SloanEngineering and Physical Sciences Research Council (EPSRC)EP/V030515/1ENG - Infrastructure & Environment