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.
Author
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) 20452322 (eISSN)
Vol. 10 1 14977Subject Categories
Ecology
Microbiology
Bioinformatics and Systems Biology
DOI
10.1038/s41598-020-71939-2
PubMed
32917913