16S rRNA gene pyrosequencing reveals bacterial dysbiosis in the Duodenum of dogs with idiopathic inflammatory bowel disease

PLoS ONE

Volumn 7, Issue 6, 2012, Pages

  Suchodolski, Jan S ^a   Dowd, Scot E ^b   Wilke, Vicky ^c   Steiner, Jörg M ^a   Jergens, Albert E ^d  

^a TEXAS A AND M UNIVERSITY   (United States)

^b Molecular Research   (United States)

^c UNIVERSITY OF MINNESOTA   (United States)

^d IOWA STATE UNIVERSITY   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

COMPLEMENTARY DNA; RNA 16S;

ACINETOBACTER; ANIMAL DISEASE; ANIMAL TISSUE; ARTICLE; BACTERIAL DYSBIOSIS; BACTERIUM IDENTIFICATION; BACTEROIDACEAE; BETAPROTEOBACTERIA; BURKHOLDERIA; CLOSTRIDIALES; CONTROLLED STUDY; DIAPHOROBACTER; DISEASE ASSOCIATION; DISEASE SEVERITY; DOG; DUODENUM; ENTERITIS; ERYSIPELOTRICHACEAE; FEMALE; FIRMICUTES; FUSOBACTERIA; GAMMAPROTEOBACTERIA; IDIOPATHIC DISEASE; INTESTINE FLORA; MALE; MICROBIAL COMMUNITY; MIDDLE AGED; NONHUMAN; ORGANISMAL INTERACTION; PREVOTELLACEAE; PYROSEQUENCING; RNA GENE;

ANIMALS; BACTERIA; CASE-CONTROL STUDIES; DOGS; DUODENUM; INFLAMMATORY BOWEL DISEASES; RNA, RIBOSOMAL, 16S;

EID: 84862499724     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0039333     Document Type: Article

References (36)

1. Simpson KW, Jergens AE, (2011) Pitfalls and progress in the diagnosis and management of canine inflammatory bowel disease. Vet Clin North Am Small Anim Pract 41: 381-398.
2. Jergens AE, Moore FM, Haynes JS, Miles KG, (1992) Idiopathic inflammatory bowel disease in dogs and cats: 84 cases (1987-1990). J Am Vet Med Assoc 201: 1603-1608.
3. Jergens AE, Schreiner CA, Frank DE, Niyo Y, Ahrens FE, et al. (2003) A scoring index for disease activity in canine inflammatory bowel disease. J Vet Intern Med 17: 291-297.
4. Craven M, Simpson JW, Ridyard AE, Chandler ML, (2004) Canine inflammatory bowel disease: retrospective analysis of diagnosis and outcome in 80 cases (1995-2002). J Small Anim Pract 45: 336-342.
5. Allenspach K, Wieland B, Groene A, Gaschen F, (2007) Chronic enteropathies in dogs: Evaluation of risk factors for negative outcome. J Vet Intern Med 21 700-708.
6. Suchodolski JS, Xenoulis PG, Paddock CG, Steiner JM, Jergens AE, (2010) Molecular analysis of the bacterial microbiota in duodenal biopsies from dogs with idiopathic inflammatory bowel disease. Vet Microbiol 142: 394-400.
7. Xavier RJ, Podolsky DK, (2007) Unravelling the pathogenesis of inflammatory bowel disease. Nature 448: 427-434.
8. Kathrani A, House A, Catchpole B, Murphy A, Werling D, et al. (2011) Breed-independent toll-like receptor 5 polymorphisms show association with canine inflammatory bowel disease. Tissue Antigens 78: 94-101.
9. Packey CD, Sartor RB, (2009) Commensal bacteria, traditional and opportunistic pathogens, dysbiosis and bacterial killing in inflammatory bowel diseases. Curr Opin Infect Dis 22: 292-301.
10. Barrett JC, Hansoul S, Nicolae DL, Cho JH, Duerr RH, et al. (2008) Genome-wide association defines more than 30 distinct susceptibility loci for Crohn's disease. Nat Genetics 40: 955-962.
11. Frank DN, Amand ALS, Feldman RA, Boedeker EC, Harpaz N, et al. (2007) Molecular-phylogenetic characterization of microbial community imbalances in human inflammatory bowel diseases. Proc Natl Acad Sci USA 104: 13780-13785.
12. Sokol H, Pigneur B, Watterlot L, Lakhdari O, Bermudez-Humaran LG, et al. (2008) Faecalibacterium prausnitzii is an anti-inflammatory commensal bacterium identified by gut microbiota analysis of Crohn disease patients. Proc Natl Acad Sci USA 105: 16731-16736.
13. Allenspach K, House A, Smith K, McNeill FM, Hendricks A, et al. (2010) Evaluation of mucosal bacteria and histopathology, clinical disease activity and expression of Toll-like receptors in German shepherd dogs with chronic enteropathies. Vet Microbiol 146: 326-335.
14. Burgener IA, Konig A, Allenspach K, Sauter SN, Boisclair J, et al. (2008) Upregulation of toll-like receptors in chronic enteropathies in dogs. J Vet Intern Med 22: 553-560.
15. Xenoulis PG, Palculict B, Allenspach K, Steiner JM, Van House AM, et al. (2008) Molecular-phylogenetic characterization of microbial communities imbalances in the small intestine of dogs with inflammatory bowel disease. FEMS Microbiol Ecol 66: 579-589.
16. Suchodolski JS, Dowd SE, Westermarck E, Steiner JM, Wolcott RD, et al. (2009) The effect of the macrolide antibiotic tylosin on microbial diversity in the canine small intestine as demonstrated by massive parallel 16 S rRNA gene sequencing. BMC Microbiol 9: 210.
17. Swanson KS, Dowd SE, Suchodolski JS, Middelbos IS, Vester BM, et al. (2011) Phylogenetic and gene-centric metagenomics of the canine intestinal microbiome reveals similarities with humans and mice. ISME J 5: 639-649.
18. Handl S, Dowd SE, Garcia-Mazcorro JF, Steiner JM, Suchodolski JS, (2011) Massive parallel 16 S rRNA gene pyrosequencing reveals highly diverse fecal bacterial and fungal communities in healthy dogs and cats. FEMS Microbiol Ecol 76: 301-310.
19. Washabau RJ, Day MJ, Willard MD, Hall EJ, Jergens AE, et al. (2010) Endoscopic, Biopsy, and Histopathologic Guidelines for the Evaluation of Gastrointestinal Inflammation in Companion Animals. J Vet Intern Med 24: 10-26.
20. Caporaso JG, Kuczynski J, Stombaugh J, Bittinger K, Bushman FD, et al. (2010) QIIME allows analysis of high-throughput community sequencing data. Nat Methods 7: 335-336.
21. Gontcharova V, Youn E, Wolcott RD, Hollister EB, Gentry TJ, et al. (2010) Black Box Chimera Check (B2C2): a Windows-Based Software for Batch Depletion of Chimeras from Bacterial 16 S rRNA Gene Datasets. Open Microbiol J 4: 47-52.
22. Lauber CL, Hamady M, Knight R, Fierer N, (2009) Pyrosequencing-based assessment of soil pH as a predictor of soil bacterial community structure at the continental scale. Appl Environ Microbiol 75: 5111-5120.
23. Benjamini Y, Hochberg Y, (1995) Controlling the false discovery rate: a practical and powerful approach to multiple testing. J Roy Stat Soc B 57: 289-300.
24. Frank DN, Robertson CE, Hamm CM, Kpadeh Z, Zhang T, et al. (2011) Disease phenotype and genotype are associated with shifts in intestinal-associated microbiota in inflammatory bowel diseases. Inflamm Bowel Dis 17: 179-184.
25. Kathrani A, House A, Catchpole B, Murphy A, German A, et al. (2010) Polymorphisms in the Tlr4 and Tlr5 Gene Are Significantly Associated with Inflammatory Bowel Disease in German Shepherd Dogs. Plos ONE 5: 1-10.
26. Suchodolski JS, Morris EK, Allenspach K, Jergens AE, Harmoinen JA, et al. (2008) Prevalence and identification of fungal DNA in the small intestine of healthy dogs and dogs with chronic enteropathies. Vet Microbiol 132: 379-388.
27. Suchodolski JS, Camacho J, Steiner JM, (2008) Analysis of bacterial diversity in the canine duodenum, jejunum, ileum, and colon by comparative 16 S rRNA gene analysis. FEMS Microbiol Ecol 66: 567-578.
28. Khan ST, Hiraishi A, (2002) Diaphorobacter nitroreducens gen nov, sp nov, a poly(3-hydroxybutyrate)-degrading denitrifying bacterium isolated from activated sludge. J Gen Appl Microbiol 48: 299-308.
29. Stecher B, Hardt WD, (2008) The role of microbiota in infectious disease. Trends Microbiol 16: 107-114.
30. Batt RM, Hall EJ, McLean L, Simpson KW, (1992) Small intestinal bacterial overgrowth and enhanced intestinal permeability in healthy Beagles. Am J Vet Res 53: 1935-1940.
31. Buddington RK, (2003) Postnatal changes in bacterial populations in the gastrointestinal tract of dogs. Am J Vet Res 64: 646-651.
32. Benno Y, Nakao H, Uchida K, Mitsuoka T, (1992) Impact of the advances in age on the gastrointestinal microflora of beagle dogs. J Vet Med Sci 54: 703-706.
33. Simpson JM, Martineau B, Jones WE, Ballam JM, Mackie RI, (2002) Characterization of fecal bacterial populations in canines: effects of age, breed and dietary fiber. Microb Ecol 44: 186-197.
34. Dethlefsen L, Huse S, Sogin ML, Relman DA, (2008) The pervasive effects of an antibiotic on the human gut microbiota, as revealed by deep 16 S rRNA sequencing. PLoS Biol 6: e280.
35. Dethlefsen L, Relman DA, (2011) Incomplete recovery and individualized responses of the human distal gut microbiota to repeated antibiotic perturbation. Proc Natl Acad Sci USA 108: 4554-4561.
36. Sommer MO, Dantas G, Church GM, (2009) Functional characterization of the antibiotic resistance reservoir in the human microflora. Science 325: 1128-1131.