title: Association of gut microbiota with post-operative clinical course in Crohn's disease.
abstract: BACKGROUND
  The gut microbiome is altered in Crohn's disease. Although individual taxa have been correlated with post-operative clinical course, global trends in microbial diversity have not been described in this context.
  
  
  METHODS
  We collected mucosal biopsies from the terminal ileum and ascending colon during surgery and post-operative colonoscopy in 6 Crohn's patients undergoing ileocolic resection (and 40 additional Crohn's and healthy control patients undergoing either surgery or colonoscopy). Using next-generation sequencing technology, we profiled the gut microbiota in order to identify changes associated with remission or recurrence of inflammation.
  
  
  RESULTS
  We performed 16S ribosomal profiling using 101 base-pair single-end sequencing on the Illumina GAIIx platform with deep coverage, at an average depth of 1.3 million high quality reads per sample. At the time of surgery, Crohn's patients who would remain in remission were more similar to controls and more species-rich than Crohn's patients with subsequent recurrence. Patients remaining in remission also exhibited greater stability of the microbiota through time.
  
  
  CONCLUSIONS
  These observations permitted an association of gut microbial profiles with probability of recurrence in this limited single-center study. These results suggest that profiling the gut microbiota may be useful in guiding treatment of Crohn's patients undergoing surgery.
authors: Department of Medicine, Division of Gastroenterology, University of California, San Francisco, 513 Parnassus Avenue, Room S-357, San Francisco, CA 94143-0538, USA. dey@post.harvard.edu.
authors: Neelendu
authors: N
authors: Dey
authors: David A W
authors: DA
authors: Soergel
authors: Susanna
authors: S
authors: Repo
authors: Steven E
authors: SE
authors: Brenner
mesh_terms: D000328:Adult; D016022:Case-Control Studies; D003106:Colon / Q000382:microbiology*; D003424:Crohn Disease / Q000188:drug therapy / Q000382:microbiology* / Q000601:surgery; D005260:Female; D006801:Humans; D007082:Ileum / Q000382:microbiology* / Q000601:surgery; D008297:Male; D064307:Microbiota; D008875:Middle Aged; D012329:RNA, Bacterial / Q000032:analysis*; D012336:RNA, Ribosomal, 16S / Q000032:analysis*; D012008:Recurrence; D012074:Remission Induction; D016896:Treatment Outcome
chemical_list: D012329:RNA, Bacterial; D012336:RNA, Ribosomal, 16S
references: Cochrane Database Syst Rev. 2009 Oct 07;(4):CD006873
references: 19821389
references: Scand J Gastroenterol Suppl. 2001;(234):29-40
references: 11768558
references: FEMS Microbiol Lett. 2010 Sep 1;310(2):138-44
references: 20695899
references: ISME J. 2008 Jul;2(7):716-27
references: 18401439
references: Aliment Pharmacol Ther. 2009 Jan;29(1):75-82
references: 18945264
references: ISME J. 2012 Jan;6(1):183-94
references: 21677692
references: Gut. 1984 Jun;25(6):665-72
references: 6735250
references: Gut. 2011 Jul;60(7):923-9
references: 21262918
references: Gut. 2006 Feb;55(2):205-11
references: 16188921
references: J Clin Microbiol. 2006 Nov;44(11):4136-41
references: 16988016
references: Philos Trans R Soc Lond B Biol Sci. 1994 Jul 29;345(1311):45-58
references: 7972354
references: Nat Genet. 2010 Dec;42(12):1118-25
references: 21102463
references: Inflamm Bowel Dis. 2010 Dec;16(12):2099-108
references: 20848469
references: Gut. 2004 May;53(5):685-93
references: 15082587
references: BMC Microbiol. 2011 Jan 10;11:7
references: 21219646
references: Environ Microbiol. 2010 Jul;12(7):1889-98
references: 20236171
references: Proc Natl Acad Sci U S A. 2008 Oct 28;105(43):16731-6
references: 18936492
references: Genome Res. 2011 Mar;21(3):494-504
references: 21212162
references: PLoS Biol. 2008 Nov 18;6(11):e280
references: 19018661
references: Cochrane Database Syst Rev. 2008 Jul 16;(3):CD006634
references: 18646162
references: Science. 2011 May 20;332(6032):970-4
references: 21596990
references: Nature. 2006 Dec 21;444(7122):1022-3
references: 17183309
references: Nature. 2012 May 09;486(7402):222-7
references: 22699611
references: Appl Environ Microbiol. 2007 Aug;73(16):5261-7
references: 17586664
references: Inflamm Bowel Dis. 2011 Jan;17(1):185-92
references: 20722058
references: J Med Microbiol. 2006 Aug;55(Pt 8):1141-1149
references: 16849736
references: Nat Genet. 2008 Aug;40(8):955-62
references: 18587394
references: Cochrane Database Syst Rev. 2006 Oct 18;(4):CD004826
references: 17054217
references: Gut. 1978 Dec;19(12):1099-104
references: 369959
references: N Engl J Med. 2009 Nov 19;361(21):2066-78
references: 19923578
references: Inflamm Bowel Dis. 2011 Jan;17(1):179-84
references: 20839241
references: Nature. 2009 Jan 22;457(7228):480-4
references: 19043404
references: Science. 2005 Mar 25;307(5717):1915-20
references: 15790844
references: J Gastroenterol Hepatol. 2011 Oct;26(10):1493-9
references: 21777275
references: Inflamm Bowel Dis. 2010 Dec;16(12):2034-42
references: 20848492
references: Gastroenterology. 2009 Feb;136(2):441-50.e1; quiz 716
references: 19109962
references: Gut. 2011 Aug;60(8):1043-9
references: 21317176
references: Clin Gastroenterol Hepatol. 2008 Jun;6(6):616-20
references: 17967564
references: Inflamm Bowel Dis. 2006 Dec;12(12):1136-45
references: 17119388
references: Gastroenterology. 2010 Dec;139(6):1844-1854.e1
references: 20816835
references: Bioinformatics. 2010 Jan 15;26(2):266-7
references: 19914921
references: Gut. 2011 May;60(5):631-7
references: 21209126
references: Appl Environ Microbiol. 2005 Dec;71(12):8228-35
references: 16332807
references: Proc Natl Acad Sci U S A. 2007 Aug 21;104(34):13780-5
references: 17699621
references: Am J Gastroenterol. 2002 Apr;97(4):939-46
references: 12003430
references: Nat Methods. 2010 May;7(5):335-6
references: 20383131
references: J Clin Microbiol. 2005 Jul;43(7):3380-9
references: 16000463
references: J Clin Microbiol. 2006 Nov;44(11):3980-8
references: 16988018
references: Science. 2005 Jun 10;308(5728):1635-8
references: 15831718
references: Mol Biol Evol. 2009 Jul;26(7):1641-50
references: 19377059