The Composition and Metabolic Potential of the Human Small Intestinal Microbiota Within the Context of Inflammatory Bowel Disease.
Inflammatory bowel disease
shotgun sequencing
small intestinal microbiota
Journal
Journal of Crohn's & colitis
ISSN: 1876-4479
Titre abrégé: J Crohns Colitis
Pays: England
ID NLM: 101318676
Informations de publication
Date de publication:
02 Aug 2021
02 Aug 2021
Historique:
pubmed:
31
1
2021
medline:
16
12
2021
entrez:
30
1
2021
Statut:
ppublish
Résumé
The human gastrointestinal tract harbours distinct microbial communities essential for health. Little is known about small intestinal communities, despite the small intestine playing a fundamental role in nutrient absorption and host-microbe immune homeostasis. We aimed to explore the small intestine microbial composition and metabolic potential, in the context of inflammatory bowel disease [IBD]. Metagenomes derived from faecal samples and extensive phenotypes were collected from 57 individuals with an ileostomy or ileoanal pouch, and compared with 1178 general population and 478 IBD faecal metagenomes. Microbiome features were identified using MetaPhAn2 and HUMAnN2, and association analyses were performed using multivariate linear regression. Small intestinal samples had a significantly lower bacterial diversity, compared with the general population and, to a lesser extent, IBD samples. Comparing bacterial composition, small intestinal samples clustered furthest from general population samples and closest to IBD samples with intestinal resections. Veillonella atypica, Streptococcus salivarius, and Actinomyces graevenitzii were among the species significantly enriched in the small intestine. Predicted metabolic pathways in the small intestine are predominantly involved in simple carbohydrate and energy metabolism, but also suggest a higher pro-inflammatory potential. We described the bacterial composition and metabolic potential of the small intestinal microbiota. The colonic microbiome of IBD patients, particularly with intestinal resections, showed resemblance to that of the small intestine. Moreover, several features characterising the small intestinal microbiome have been previously associated with IBD. These results highlight the importance of studying the small intestinal microbiota to gain new insight into disease pathogenesis.
Sections du résumé
BACKGROUND AND AIMS
OBJECTIVE
The human gastrointestinal tract harbours distinct microbial communities essential for health. Little is known about small intestinal communities, despite the small intestine playing a fundamental role in nutrient absorption and host-microbe immune homeostasis. We aimed to explore the small intestine microbial composition and metabolic potential, in the context of inflammatory bowel disease [IBD].
METHODS
METHODS
Metagenomes derived from faecal samples and extensive phenotypes were collected from 57 individuals with an ileostomy or ileoanal pouch, and compared with 1178 general population and 478 IBD faecal metagenomes. Microbiome features were identified using MetaPhAn2 and HUMAnN2, and association analyses were performed using multivariate linear regression.
RESULTS
RESULTS
Small intestinal samples had a significantly lower bacterial diversity, compared with the general population and, to a lesser extent, IBD samples. Comparing bacterial composition, small intestinal samples clustered furthest from general population samples and closest to IBD samples with intestinal resections. Veillonella atypica, Streptococcus salivarius, and Actinomyces graevenitzii were among the species significantly enriched in the small intestine. Predicted metabolic pathways in the small intestine are predominantly involved in simple carbohydrate and energy metabolism, but also suggest a higher pro-inflammatory potential.
CONCLUSIONS
CONCLUSIONS
We described the bacterial composition and metabolic potential of the small intestinal microbiota. The colonic microbiome of IBD patients, particularly with intestinal resections, showed resemblance to that of the small intestine. Moreover, several features characterising the small intestinal microbiome have been previously associated with IBD. These results highlight the importance of studying the small intestinal microbiota to gain new insight into disease pathogenesis.
Identifiants
pubmed: 33515008
pii: 6123997
doi: 10.1093/ecco-jcc/jjab020
pmc: PMC8328293
doi:
Types de publication
Comparative Study
Journal Article
Langues
eng
Sous-ensembles de citation
IM
Pagination
1326-1338Subventions
Organisme : VIDI
ID : 016.136.308
Organisme : Netherlands Organization for Scientific Research
Organisme : Diagnostics Grant from the Dutch Digestive Foundation
ID : D16-14
Organisme : University of Groningen
Organisme : Netherlands' Top Institute Food and Nutrition
ID : GH001
Organisme : ERC
ID : ERC-671274
Organisme : CardioVasculair Onderzoek Nederland
ID : CVON 2012-03
Informations de copyright
© The Author(s) 2021. Published by Oxford University Press on behalf of European Crohn’s and Colitis Organisation.
Références
Cell Host Microbe. 2020 Apr 8;27(4):659-670.e5
pubmed: 32101703
Cell Host Microbe. 2018 Apr 11;23(4):458-469.e5
pubmed: 29649441
Front Genet. 2015 Apr 20;6:148
pubmed: 25941533
Sci Rep. 2012;2:332
pubmed: 22451861
Nat Microbiol. 2019 Feb;4(2):293-305
pubmed: 30531976
Am J Physiol Gastrointest Liver Physiol. 2013 Sep 1;305(5):G341-7
pubmed: 23832518
Nat Commun. 2019 May 1;10(1):2012
pubmed: 31043597
Genome Biol. 2012 Apr 16;13(9):R79
pubmed: 23013615
Cell Host Microbe. 2014 Mar 12;15(3):382-392
pubmed: 24629344
Nat Med. 2019 Apr;25(4):701
pubmed: 30846883
Genome Biol. 2019 Nov 25;20(1):252
pubmed: 31767028
Cell Mol Gastroenterol Hepatol. 2020;9(1):33-45
pubmed: 31344510
Genome Biol. 2015 Apr 08;16:67
pubmed: 25887922
Clin Transl Gastroenterol. 2019 May 22;10(5):1-7
pubmed: 31117112
Curr Opin Biotechnol. 2015 Apr;32:14-20
pubmed: 25308830
Cell. 2012 Mar 16;148(6):1258-70
pubmed: 22424233
Cell. 2018 Sep 6;174(6):1388-1405.e21
pubmed: 30193112
Front Nutr. 2019 Apr 17;6:48
pubmed: 31058161
Am J Pathol. 2002 Jun;160(6):2253-7
pubmed: 12057927
Elife. 2019 Feb 12;8:
pubmed: 30747106
Gut. 2017 Jun;66(6):1168-1169
pubmed: 27489239
Case Rep Gastroenterol. 2017 Jun 14;11(2):377-381
pubmed: 28690491
Nat Rev Microbiol. 2012 Nov;10(11):735-42
pubmed: 23000955
ISME J. 2012 Jul;6(7):1415-26
pubmed: 22258098
Sci Rep. 2018 Mar 16;8(1):4736
pubmed: 29549283
Environ Microbiol. 2010 Dec;12(12):3213-27
pubmed: 20626454
BMC Gastroenterol. 2019 Mar 27;19(1):44
pubmed: 30917794
Science. 2017 Oct 20;358(6361):359-365
pubmed: 29051379
Proc Natl Acad Sci U S A. 2018 Apr 17;115(16):4170-4175
pubmed: 29610310
Gut. 2001 Apr;48(4):571-7
pubmed: 11247905
Nat Methods. 2015 Oct;12(10):902-3
pubmed: 26418763
Cell Host Microbe. 2020 Mar 11;27(3):358-375.e7
pubmed: 32101704
Neurogastroenterol Motil. 2012 Feb;24(2):185-90, e92
pubmed: 22097886
Sci Transl Med. 2018 Dec 19;10(472):
pubmed: 30567928
Nat Rev Gastroenterol Hepatol. 2017 Oct;14(10):573-584
pubmed: 28743984
BMJ Open. 2015 Aug 28;5(8):e006772
pubmed: 26319774
Nat Immunol. 2013 Jul;14(7):676-84
pubmed: 23778795
Nat Med. 2015 Aug;21(8):895-905
pubmed: 26214836