Gut-derived Enterococcus faecium from ulcerative colitis patients promotes colitis in a genetically susceptible mouse host.
Animals
Case-Control Studies
Colitis
/ etiology
Colitis, Ulcerative
/ drug therapy
Colon
/ pathology
Crohn Disease
/ microbiology
Disease Models, Animal
Drug Therapy, Combination
Enterococcus faecalis
/ genetics
Fecal Microbiota Transplantation
Feces
/ microbiology
Female
Gastrointestinal Microbiome
Humans
Interleukin-10
/ genetics
Male
Metagenome
Mice
Mice, Inbred C57BL
Crohn’s disease
Inflammatory bowel disease
Metagenome
Microbiota
Journal
Genome biology
ISSN: 1474-760X
Titre abrégé: Genome Biol
Pays: England
ID NLM: 100960660
Informations de publication
Date de publication:
25 11 2019
25 11 2019
Historique:
received:
21
02
2019
accepted:
04
11
2019
entrez:
27
11
2019
pubmed:
27
11
2019
medline:
21
3
2020
Statut:
epublish
Résumé
Recent metagenomic analyses have revealed dysbiosis of the gut microbiota of ulcerative colitis (UC) patients. However, the impacts of this dysbiosis are not fully understood, particularly at the strain level. We perform whole-genome shotgun sequencing of fecal DNA extracts from 13 healthy donors and 16 UC and 8 Crohn's disease (CD) patients. The microbiota of UC and CD patients is taxonomically and functionally divergent from that of healthy donors, with E. faecium being the most differentially abundant species between the two microbial communities. Transplantation of feces from UC or CD patients into Il10 E. faecium strains derived from UC patients display an inflammatory genotype that causes colitis.
Sections du résumé
BACKGROUND
Recent metagenomic analyses have revealed dysbiosis of the gut microbiota of ulcerative colitis (UC) patients. However, the impacts of this dysbiosis are not fully understood, particularly at the strain level.
RESULTS
We perform whole-genome shotgun sequencing of fecal DNA extracts from 13 healthy donors and 16 UC and 8 Crohn's disease (CD) patients. The microbiota of UC and CD patients is taxonomically and functionally divergent from that of healthy donors, with E. faecium being the most differentially abundant species between the two microbial communities. Transplantation of feces from UC or CD patients into Il10
CONCLUSIONS
E. faecium strains derived from UC patients display an inflammatory genotype that causes colitis.
Identifiants
pubmed: 31767028
doi: 10.1186/s13059-019-1879-9
pii: 10.1186/s13059-019-1879-9
pmc: PMC6876129
doi:
Substances chimiques
IL10 protein, mouse
0
Interleukin-10
130068-27-8
Types de publication
Journal Article
Langues
eng
Sous-ensembles de citation
IM
Pagination
252Références
Nat Immunol. 2009 Jun;10(6):603-9
pubmed: 19448631
PLoS Comput Biol. 2012;8(6):e1002358
pubmed: 22719234
Nat Methods. 2012 Jun 10;9(8):811-4
pubmed: 22688413
N Engl J Med. 2016 Nov 17;375(20):1946-1960
pubmed: 27959607
J Infect Dis. 2009 Oct 1;200(7):1162-5
pubmed: 19702507
J Bacteriol. 2009 Sep;191(18):5743-57
pubmed: 19592587
Microb Biotechnol. 2016 Jul;9(4):486-95
pubmed: 27305897
Nature. 2012 Jul 5;487(7405):104-8
pubmed: 22722865
Am J Pathol. 2002 Jun;160(6):2253-7
pubmed: 12057927
Nat Rev Microbiol. 2012 Mar 16;10(4):266-78
pubmed: 22421879
Proc Natl Acad Sci U S A. 2008 Oct 28;105(43):16731-6
pubmed: 18936492
Nat Rev Immunol. 2014 May;14(5):329-42
pubmed: 24751956
Appl Environ Microbiol. 2006 Jul;72(7):5069-72
pubmed: 16820507
Nature. 2016 Jul 06;535(7610):75-84
pubmed: 27383982
N Engl J Med. 2011 Nov 3;365(18):1713-25
pubmed: 22047562
Nature. 2013 Aug 8;500(7461):232-6
pubmed: 23842501
Lancet. 2012 Nov 3;380(9853):1590-605
pubmed: 22914295
Science. 2017 Oct 20;358(6361):359-365
pubmed: 29051379
Bioinformatics. 2002 Jan;18(1):207-8
pubmed: 11836235
Cell Host Microbe. 2017 Aug 9;22(2):247
pubmed: 28799909
Appl Environ Microbiol. 2013 Dec;79(24):7896-904
pubmed: 24123741
Cancer Res. 2010 Aug 15;70(16):6556-65
pubmed: 20663902
Appl Environ Microbiol. 2013 Jan;79(1):196-204
pubmed: 23087032
Diagn Microbiol Infect Dis. 2013 Mar;75(3):245-51
pubmed: 23276768
Nat Rev Gastroenterol Hepatol. 2018 Feb;15(2):111-128
pubmed: 29018272
J Clin Microbiol. 2013 Mar;51(3):849-56
pubmed: 23269735
Nature. 2008 May 29;453(7195):620-5
pubmed: 18509436
Gastroenterology. 2005 Apr;128(4):891-906
pubmed: 15825073
Nat Methods. 2012 Mar 04;9(4):357-9
pubmed: 22388286
Nature. 2017 Jun 15;546(7658):426-430
pubmed: 28607489
Microbiol Insights. 2015 Jul 23;8:7-14
pubmed: 26279626
J Comput Biol. 2012 May;19(5):455-77
pubmed: 22506599
Gastroenterology. 2004 Apr;126(4):989-96; discussion 947
pubmed: 15057738
Infect Immun. 2008 Sep;76(9):4110-9
pubmed: 18591238
Genome Biol. 2011 Jun 24;12(6):R60
pubmed: 21702898
Gut. 2014 Aug;63(8):1275-83
pubmed: 24021287
Nat Methods. 2015 Jan;12(1):59-60
pubmed: 25402007
Cell Host Microbe. 2019 May 8;25(5):695-705.e5
pubmed: 31031170
Nat Rev Gastroenterol Hepatol. 2017 Oct;14(10):573-584
pubmed: 28743984
Proc Natl Acad Sci U S A. 2007 Aug 21;104(34):13780-5
pubmed: 17699621
Am J Gastroenterol. 2002 Apr;97(4):939-46
pubmed: 12003430
J Nutr. 2003 Apr;133(4):1158-62
pubmed: 12672936
Nat Genet. 2010 Dec;42(12):1118-25
pubmed: 21102463
Gut. 2012 Dec;61(12):1693-700
pubmed: 22595313
Genome Biol. 2012 Apr 16;13(9):R79
pubmed: 23013615
Bioinformatics. 2011 Mar 15;27(6):863-4
pubmed: 21278185
Bioinformatics. 2009 Aug 15;25(16):2078-9
pubmed: 19505943
Gastroenterology. 2011 Sep;141(3):959-71
pubmed: 21699778
Nat Methods. 2010 May;7(5):335-6
pubmed: 20383131
Nature. 2011 Jun 15;474(7351):307-17
pubmed: 21677747
Nat Genet. 2008 Nov;40(11):1319-23
pubmed: 18836448
Cell Host Microbe. 2014 Mar 12;15(3):382-392
pubmed: 24629344
Bioinformatics. 2014 Jul 15;30(14):2068-9
pubmed: 24642063
J Cell Biochem. 2019 Apr;120(4):4766-4782
pubmed: 30362597
Science. 2013 Nov 22;342(6161):967-70
pubmed: 24264989
Nat Med. 2000 May;6(5):583-8
pubmed: 10802717
Am J Physiol Gastrointest Liver Physiol. 2001 Sep;281(3):G764-78
pubmed: 11518689