TY - JOUR
T1 - Compositional and functional differences of the mucosal microbiota along the intestine of healthy individuals
AU - Vaga, Stefania
AU - Lee, Sunjae
AU - Ji, Boyang
AU - Andreasson, Anna
AU - Talley, Nicholas J.
AU - Agréus, Lars
AU - Bidkhori, Gholamreza
AU - Kovatcheva-Datchary, Petia
AU - Park, Junseok
AU - Lee, Doheon
AU - Proctor, Gordon
AU - Ehrlich, Stanislav Dusko
AU - Nielsen, Jens
AU - Engstrand, Lars
AU - Shoaie, Saeed
N1 - 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.
PY - 2020/9/11
Y1 - 2020/9/11
N2 - 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.
AB - 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.
UR - http://www.scopus.com/inward/record.url?scp=85090756810&partnerID=8YFLogxK
U2 - 10.1038/s41598-020-71939-2
DO - 10.1038/s41598-020-71939-2
M3 - Article
C2 - 32917913
AN - SCOPUS:85090756810
SN - 2045-2322
VL - 10
SP - 1
EP - 12
JO - Scientific Reports
JF - Scientific Reports
IS - 1
M1 - 14977
ER -