Gul, Farzana and Herrema, Hilde and Davids, Mark and Keating, Ciara and Nasir, Arshan and Ijaz, Umer Zeeshan and Javed, Sundus (2024) Gut microbial ecology and exposome of a healthy Pakistani cohort. Gut Pathogens, 16: 5. ISSN 1757-4749
AI Summary:
This study provides a snapshot of the healthy core Pakistani gut microbiome. The study focuses on the most populous provinces and ethnic groups residing in predominantly urban areas.AI Topics:
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.
Gul, Farzana
Author
Gul, Farzana and Herrema, Hilde and Davids, Mark and Keating, Ciara and Nasir, Arshan and Ijaz, Umer Zeeshan and Javed, Sundus (2024) Gut microbial ecology and exposome of a healthy Pakistani cohort. Gut Pathogens, 16: 5. ISSN 1757-4749
See full publications listHerrema, Hilde
Author
Gul, Farzana and Herrema, Hilde and Davids, Mark and Keating, Ciara and Nasir, Arshan and Ijaz, Umer Zeeshan and Javed, Sundus (2024) Gut microbial ecology and exposome of a healthy Pakistani cohort. Gut Pathogens, 16: 5. ISSN 1757-4749
See full publications listDavids, Mark
Author
Gul, Farzana and Herrema, Hilde and Davids, Mark and Keating, Ciara and Nasir, Arshan and Ijaz, Umer Zeeshan and Javed, Sundus (2024) Gut microbial ecology and exposome of a healthy Pakistani cohort. Gut Pathogens, 16: 5. ISSN 1757-4749
See full publications listKeating, Ciara
Author
Ameer, Aqsa and Saleem, Farrukh and Keating, Ciara and Gundogdu, Ozan and Ijaz, Umer and Javed, Sundus (2024) Dataset of 16S rRNA gene sequences of 111 healthy and Newcastle disease infected caecal samples from multiple chicken breeds of Pakistan. Data In Brief, 57: 110957. ISSN 2352-3409
Ameer, Aqsa and Saleem, Farrukh and Keating, Ciara and Gundogdu, Ozan and Ijaz, Umer Zeeshan and Javed, Sundus (2024) Dataset of 130 metagenome-assembled genomes of healthy and diseased broiler chicken caeca from Pakistan. Data In Brief, 54: 110487. ISSN 2352-3409
Saleem, Farrukh and Ameer, Aqsa and Star-Shirko, Banaz and Keating, Ciara and Gundogdu, Ozan and Ijaz, Umer Zeeshan and Javed, Sundus (2024) Dataset of 569 metagenome-assembled genomes from the caeca of multiple chicken breeds from commercial and backyard farming setups of Pakistan. Data In Brief, 54: 110552. ISSN 2352-3409
See full publications listNasir, Arshan
Author
Gul, Farzana and Herrema, Hilde and Davids, Mark and Keating, Ciara and Nasir, Arshan and Ijaz, Umer Zeeshan and Javed, Sundus (2024) Gut microbial ecology and exposome of a healthy Pakistani cohort. Gut Pathogens, 16: 5. ISSN 1757-4749
See full publications listIjaz, Umer
Author
Cholet, Fabien and Vignola, Marta and Quinn, Dominic and Ijaz, Umer Z. and Sloan, William T. and Smith, Cindy J. (2025) Microbial ecology of drinking water biofiltration based on 16S rRNA sequencing: a meta-analysis. Water Research, 281: 123684. ISSN 0043-1354
Saleem, Farrukh and Ameer, Aqsa and Afzal, Farhan and Usman, Muhammad and Irshad, Hamid and Sattar, Sadia and Ijaz, Umer Zeeshan and Javed, Sundus (2025) A cross-sectional survey of poultry management systems, practices and antimicrobial use in relation to disease outbreak in Pakistan. BMC Research Notes, 18: 144. ISSN 1756-0500
Badar, Ayesha and Aqueel, Rhea and Nawaz, Ali and Ijaz, Umer Zeeshan and Malik, Kauser Abdulla (2025) Microbiota transplantation for Cotton Leaf Curl Disease suppression - core microbiome and transcriptome dynamics. Communications Biology, 8 (1): 380. ISSN 2399-3642
See full publications listJaved, Sundus
Author
Ameer, Aqsa and Saleem, Farrukh and Keating, Ciara and Gundogdu, Ozan and Ijaz, Umer Zeeshan and Javed, Sundus (2024) Dataset of 130 metagenome-assembled genomes of healthy and diseased broiler chicken caeca from Pakistan. Data In Brief, 54: 110487. ISSN 2352-3409
Gul, Farzana and Herrema, Hilde and Davids, Mark and Keating, Ciara and Nasir, Arshan and Ijaz, Umer Zeeshan and Javed, Sundus (2024) Gut microbial ecology and exposome of a healthy Pakistani cohort. Gut Pathogens, 16: 5. ISSN 1757-4749
See full publications listAvailable under License Creative Commons Attribution.
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