Compositional and functional differences of the mucosal microbiota along the intestine of healthy individuals
Journal article, 2020

Gut mucosal microbes evolved closest to the host, developing specialized local communities. There is, however, insufficient knowledge of these communities as most studies have employed sequencing technologies to investigate faecal microbiota only. This work used shotgun metagenomics of mucosal biopsies to explore the microbial communities' compositions of terminal ileum and large intestine in 5 healthy individuals. Functional annotations and genome-scale metabolic modelling of selected species were then employed to identify local functional enrichments. While faecal metagenomics provided a good approximation of the average gut mucosal microbiome composition, mucosal biopsies allowed detecting the subtle variations of local microbial communities. Given their significant enrichment in the mucosal microbiota, we highlight the roles of Bacteroides species and describe the antimicrobial resistance biogeography along the intestine. We also detail which species, at which locations, are involved with the tryptophan/indole pathway, whose malfunctioning has been linked to pathologies including inflammatory bowel disease. Our study thus provides invaluable resources for investigating mechanisms connecting gut microbiota and host pathophysiology.


Stefania Vaga

King's College London

Sunjae Lee

King's College London

Boyang Ji

Chalmers, Biology and Biological Engineering, Systems and Synthetic Biology

Anna Andreasson

Stockholm University

Macquarie University

Karolinska Institutet

Nicholas J. Talley

University of Newcastle

Lars Agreus

Karolinska Institutet

Gholamreza Bidkhori

King's College London

Petia Kovatcheva-Datchary

University of Gothenburg

Junseok Park

Korea Advanced Institute of Science and Technology (KAIST)

Doheon Lee

Korea Advanced Institute of Science and Technology (KAIST)

Gordon Proctor

King's College London

Stanislav Dusko Ehrlich

National Institute of Agronomic Research (INRA)

Jens B Nielsen

Chalmers, Biology and Biological Engineering, Systems and Synthetic Biology

Lars Engstrand

Karolinska Institutet

Saeed Shoaie

King's College London

Royal Institute of Technology (KTH)

Scientific Reports

2045-2322 (ISSN)

Vol. 10 1 14977

Subject Categories



Bioinformatics and Systems Biology





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