Compositional and functional differences of the mucosal microbiota along the intestine of healthy individuals

Stefania Vaga, Sunjae Lee, Boyang Ji, Anna Andreasson, Nicholas J. Talley, Lars Agréus, Gholamreza Bidkhori, Petia Kovatcheva-Datchary, Junseok Park, Doheon Lee, Gordon Proctor, Stanislav Dusko Ehrlich, Jens Nielsen, Lars Engstrand, Saeed Shoaie*

*Corresponding author for this work

    Research output: Contribution to journalArticlepeer-review

    57 Citations (Scopus)
    30 Downloads (Pure)


    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.

    Original languageEnglish
    Article number14977
    Pages (from-to)1-12
    Number of pages12
    JournalScientific Reports
    Issue number1
    Publication statusPublished - 11 Sept 2020

    Bibliographical note

    Copyright the Author(s) 2020. Version archived for private and non-commercial use with the permission of the author/s and according to publisher conditions. For further rights please contact the publisher.


    Dive into the research topics of 'Compositional and functional differences of the mucosal microbiota along the intestine of healthy individuals'. Together they form a unique fingerprint.

    Cite this