The gut microbiome-Does stool represent right?
16S rRNA
Biogeography
Bowel Prep
Bowel prep
Colonoscopy
Drug design
Gut microbiome
Innovation
Microbiome
NGS
Personalized medicine
Prep
Stratification
WGS
Journal
Heliyon
ISSN: 2405-8440
Titre abrégé: Heliyon
Pays: England
ID NLM: 101672560
Informations de publication
Date de publication:
Mar 2023
Mar 2023
Historique:
received:
09
08
2022
revised:
03
02
2023
accepted:
06
02
2023
medline:
27
4
2023
pubmed:
27
4
2023
entrez:
27
4
2023
Statut:
epublish
Résumé
Many stool-based gut microbiome studies have highlighted the importance of the microbiome. However, we hypothesized that stool is a poor proxy for the inner-colonic microbiome and that studying stool samples may be inadequate to capture the true inner-colonic microbiome. To test this hypothesis, we conducted prospective clinical studies with up to 20 patients undergoing an FDA-cleared gravity-fed colonic lavage without oral purgative pre-consumption. The objective of this study was to present the analysis of inner-colonic microbiota obtained non-invasively during the lavage and how these results differ from stool samples. The inner-colonic samples represented the descending, transverse, and ascending colon. All samples were analyzed for 16S rRNA and shotgun metagenomic sequences. The taxonomic, phylogenetic, and biosynthetic gene cluster analyses showed a distinctive biogeographic gradient and revealed differences between the sample types, especially in the proximal colon. The high percentage of unique information found only in the inner-colonic effluent highlights the importance of these samples and likewise the importance of collecting them using a method that can preserve these distinctive signatures. We proposed that these samples are imperative for developing future biomarkers, targeted therapeutics, and personalized medicine.
Identifiants
pubmed: 37101508
doi: 10.1016/j.heliyon.2023.e13602
pii: S2405-8440(23)00809-5
pmc: PMC10123208
doi:
Types de publication
Journal Article
Langues
eng
Pagination
e13602Informations de copyright
©2023PublishedbyElsevierLtd.
Déclaration de conflit d'intérêts
The authors declare no competing interests.
Références
PLoS One. 2011;6(9):e25042
pubmed: 21966408
Annu Rev Pharmacol Toxicol. 2020 Jan 6;60:417-435
pubmed: 31386593
PLoS One. 2013 Apr 22;8(4):e61217
pubmed: 23630581
Mol Cancer. 2019 May 20;18(1):97
pubmed: 31109338
Sci Transl Med. 2019 Jan 30;11(477):
pubmed: 30700573
Gut. 2015 Oct;64(10):1553-61
pubmed: 25596182
Nature. 2021 Sep;597(7877):533-538
pubmed: 34497420
Nat Biotechnol. 2013 Sep;31(9):814-21
pubmed: 23975157
Drug Discov Today. 2017 Jan;22(1):173-179
pubmed: 27818254
Front Cell Infect Microbiol. 2020 Apr 09;10:151
pubmed: 32328469
Cancer Prev Res (Phila). 2018 Jul;11(7):393-402
pubmed: 29636352
Trends Pharmacol Sci. 2019 Jul;40(7):495-505
pubmed: 31171383
mBio. 2019 Apr 16;10(2):
pubmed: 30992349
Nucleic Acids Res. 2014 Jan;42(Database issue):D643-8
pubmed: 24293649
Nat Rev Microbiol. 2019 Jul;17(7):401
pubmed: 31127248
Nat Methods. 2016 Jul;13(7):581-3
pubmed: 27214047
Front Microbiol. 2015 Aug 04;6:771
pubmed: 26300854
ISME J. 2014 Apr;8(4):881-93
pubmed: 24132077
Annu Rev Genomics Hum Genet. 2012;13:151-70
pubmed: 22703178
ISME J. 2011 May;5(5):801-9
pubmed: 21124491
Microbiome. 2018 Mar 20;6(1):50
pubmed: 29554948
Clin Microbiol Infect. 2016 Feb;22(2):178.e1-178.e9
pubmed: 26482265
Nat Rev Drug Discov. 2010 Mar;9(3):203-14
pubmed: 20168317
Front Microbiol. 2016 Apr 20;7:459
pubmed: 27148170
Nucleic Acids Res. 2013 Jan;41(Database issue):D590-6
pubmed: 23193283
Nat Rev Microbiol. 2021 Feb;19(2):77-94
pubmed: 32968241
Trends Cancer. 2019 Sep;5(9):521-524
pubmed: 31474355
Proc Natl Acad Sci U S A. 2009 Aug 25;106(34):14728-33
pubmed: 19667173
Biostatistics. 2019 Apr 1;20(2):273-286
pubmed: 29394327
J Diabetes. 2017 Mar;9(3):226-236
pubmed: 27787945
Curr Opin Biotechnol. 2018 Jun;51:57-63
pubmed: 29223004
Nature. 2019 Jun;570(7762):462-467
pubmed: 31158845
N Engl J Med. 2016 Dec 15;375(24):2369-2379
pubmed: 27974040