Carrageenan gum and adherent invasive Escherichia coli in a piglet model of inflammatory bowel disease: Impact on intestinal mucosa-associated microbiota

Frontiers in Microbiology

Volumn 7, Issue APR, 2016, Pages

  Munyaka, Peris M ^a   Sepehri, Shadi ^b   Ghia, Jean Eric ^a,b,c   Khafipour, Ehsan ^a,b  

^a UNIVERSITY OF MANITOBA   (Canada)

^b Children's Hospital Foundation of Manitoba   (Canada)

^c Section of Gastroenterology   (Canada)

Author keywords

16S rRNA gene sequencing; Adherent invasive Escherichia coli; Carrageenan gum; Crohn's disease; Microbiome; Pigs; Ulcerative colitis

Indexed keywords

AMMONIA; CARRAGEENAN; INTERLEUKIN 10; INTERLEUKIN 1BETA; INTERLEUKIN 6; INTERLEUKIN 8; RNA 16S; TUMOR NECROSIS FACTOR ALPHA; VOLATILE FATTY ACID;

16S RRNA GENE; ANIMAL EXPERIMENT; ANIMAL MODEL; ANIMAL TISSUE; ARTICLE; BACTERIAL STRAIN; BIOINFORMATICS; CONTROLLED STUDY; CROHN DISEASE; DISCRIMINANT ANALYSIS; DNA EXTRACTION; DYSBIOSIS; ESCHERICHIA COLI; FECES ANALYSIS; GENE; GENE AMPLIFICATION; GRANULOMATOUS INFLAMMATION; HISTOLOGY; INFLAMMATION; INFLAMMATORY BOWEL DISEASE; INOCULATION; INTESTINE MUCOSA; METAGENOME; METAGENOMICS; MICROBIAL DIVERSITY; MICROBIOME; MICROFLORA; NONHUMAN; PATHOGENESIS; PH; PIG; POLYMERASE CHAIN REACTION; ULCERATIVE COLITIS;

EID: 84966389739     PISSN: None     EISSN: 1664302X     Source Type: Journal    
DOI: 10.3389/fmicb.2016.00462     Document Type: Article

References (86)

1. Abraham, C., and Medzhitov, R. (2011). Interactions between the host innate immune system and microbes in inflammatory bowel disease. Gastroenterology 140, 1729-1737. doi: 10.1053/j.gastro.2011.02.012
2. Agus, A., Massier, S., Darfeuille-Michaud, A., Billard, E., and Barnich, N. (2014). Understanding host-adherent-invasive Escherichia coli interaction in Crohn's disease: opening up new therapeutic strategies. Biomed. Res. Int. 2014:567929. doi: 10.1155/2014/567929
3. Anderson, M. (2005). PERMANOVA: A FORTRAN Computer Program For Permutational Multivariate Analysis Of Variance, 24th Edn. Department of Statistics, University of Auckland
4. Andoh, A., Imaeda, H., Aomatsu, T., Inatomi, O., Bamba, S., Sasaki, M., et al. (2011). Comparison of the fecal microbiota profiles between ulcerative colitis and Crohn's disease using terminal restriction fragment length polymorphism analysis. J. Gastroenterol. 46, 479-486. doi: 10.1007/s00535-010-0368-4
5. Bhandari, S. K., Ominski, K. H., Wittenberg, K. M., and Plaizier, J. C. (2007). Effects of chop length of alfalfa and corn silage on milk production and rumen fermentation of dairy cows. J. Dairy Sci. 90, 2355-2366. doi: 10.3168/jds.2006-609
6. CCAC (1993). Guide to the Care and Use of Experimental Animal. Ottawa, ON: Canadian Council of Animal Care
7. Canani, R. B., Costanzo, M. D., Leone, L., Pedata, M., Meli, R., and Calignano, A. (2011). Potential beneficial effects of butyrate in intestinal and extraintestinal diseases. World J. Gastroenterol. 17, 1519-1528. doi: 10.3748/wjg.v17.i12.1519
8. Cao, Y., Shen, J., and Ran, Z. H. (2014). Association between Faecalibacterium prausnitzii reduction and inflammatory bowel disease: a meta-analysis and systematic review of the literature. Gastroenterol. Res. Pract. 2014:872725. doi: 10.1155/2014/872725
9. Caporaso, J. G., Bittinger, K., Bushman, F. D., DeSantis, T. Z., Andersen, G. L., and Knight, R. (2010a). PyNAST: a flexible tool for aligning sequences to a template alignment. Bioinformatics 26, 266-267. doi: 10.1093/bioinformatics/btp636
10. Caporaso, J. G., Kuczynski, J., Stombaugh, J., Bittinger, K., Bushman, F. D., Costello, E. K., et al. (2010b). QIIME allows analysis of high-throughput community sequencing data. Nat. Methods 7, 335-336. doi: 10.1038/nmeth.f.303
11. Caporaso, J. G., Lauber, C. L., Walters, W. A., Berg-Lyons, D., Huntley, J., Fierer, N., et al. (2012). Ultra-high-throughput microbial community analysis on the Illumina HiSeq and MiSeq platforms. ISME J. 6, 1621-1624. doi: 10.1038/ismej.2012.8
12. Chapman, R. W., Selby, W. S., and Jewell, D. P. (1986). Controlled trial of intravenous metronidazole as an adjunct to corticosteroids in severe ulcerative colitis. Gut 27, 1210-1212. doi: 10.1136/gut.27.10.1210
13. Chassaing, B., Koren, O., Carvalho, F. A., Ley, R. E., and Gewirtz, A. T. (2014). AIEC pathobiont instigates chronic colitis in susceptible hosts by altering microbiota composition. Gut 63, 1069-1080. doi: 10.1136/gutjnl-2013-304909
14. Darfeuille-Michaud, A., Boudeau, J., Bulois, P., Neut, C., Glasser, A. L., Barnich, N., et al. (2004). High prevalence of adherent-invasive Escherichia coli associated with ileal mucosa in Crohn's disease. Gastroenterology 127, 412-421. doi: 10.1053/j.gastro.2004.04.061
15. Darfeuille-Michaud, A., Neut, C., Barnich, N., Lederman, E., Di Martino, P., Desreumaux, P., et al. (1998). Presence of adherent Escherichia coli strains in ileal mucosa of patients with Crohn's disease. Gastroenterology 115, 1405-1413. doi: 10.1016/S0016-5085(98)70019-8
16. Derakhshani, H., Tun, H. M., and Khafipour, E. (2016). An extended single-index multiplexed 16S rRNA sequencing for microbial community analysis on MiSeq Illumina platforms. J. Basic Microbiol. 56, 321-326. doi: 10.1002/jobm.201500420
17. DeSantis, T. Z., Hugenholtz, P., Larsen, N., Rojas, M., Brodie, E. L., Keller, K., et al. (2006). Greengenes, a chimera-checked 16S rRNA gene database and workbench compatible with ARB. Appl. Environ. Microbiol. 72, 5069-5072. doi: 10.1128/AEM.03006-05
18. Desilets, M., Deng, X., Rao, C., Ensminger, A. W., Krause, D. O., Sherman, P. M., et al. (2016). Genome-based definition of an inflammatory bowel disease-associated adherent-invasive Escherichia coli pathovar. Inflamm. Bowel Dis. 22, 1-12. doi: 10.1097/MIB.0000000000000574
19. Edgar, R. C. (2010). Search and clustering orders of magnitude faster than BLAST. Bioinformatics 26, 2460-2461. doi: 10.1093/bioinformatics/btq461
20. Edgar, R. C., Haas, B. J., Clemente, J. C., Quince, C., and Knight, R. (2011). UCHIME improves sensitivity and speed of chimera detection. Bioinformatics 27, 2194-2200. doi: 10.1093/bioinformatics/btr381
21. Elson, C. O., Sartor, R. B., Tennyson, G. S., and Riddell, R. H. (1995). Experimental-models of inflammatory bowel-disease. Gastroenterology 109, 1344-1367. doi: 10.1016/0016-5085(95)90599-5
22. Fite, A., Macfarlane, S., Furrie, E., Bahrami, B., Cummings, J. H., Steinke, D. T., et al. (2013). Longitudinal analyses of gut mucosal microbiotas in ulcerative colitis in relation to patient age and disease severity and duration. J. Clin. Microbiol. 51, 849-856. doi: 10.1128/JCM.02574-12
23. Frank, D. N., St. Amand, A. L., Feldman, R. A., Boedeker, E. C., Harpaz, N., and Pace, N. R. (2007). Molecular-phylogenetic characterization of microbial community imbalances in human inflammatory bowel diseases. Proc. Natl. Acad. Sci. U.S.A. 104, 13780-13785. doi: 10.1073/pnas.0706625104
24. Friswell, M., Campbell, B., and Rhodes, J. (2010). The role of bacteria in the pathogenesis of inflammatory bowel disease. Gut Liver 4, 295-306. doi: 10.5009/gnl.2010.4.3.295
25. Guarner, F. (2005). The intestinal flora in inflammatory bowel disease: normal or abnormal? Curr. Opin. Gastroenterol. 21, 414-418
26. Hammer, Ø., Harper, D. A. T., and Ryan, P. D. (2001). PAST: paleontological statistics software package for education and data analysis. Palaeontol. Electron. 4, 1-9
27. Hansen, J. J. (2015). Immune responses to intestinal microbes in inflammatory bowel diseases. Curr. Allergy Asthma Rep. 15, 562. doi: 10.1007/s11882-015-0562-9
28. Heinritz, S. N., Mosenthin, R., and Weiss, E. (2013). Use of pigs as a potential model for research into dietary modulation of the human gut microbiota. Nutr. Res. Rev. 26, 191-209. doi: 10.1017/S0954422413000152
29. Hold, G. L., Smith, M., Grange, C., Watt, E. R., El-Omar, E. M., and Mukhopadhya, I. (2014). Role of the gut microbiota in inflammatory bowel disease pathogenesis: what have we learnt in the past 10 years? World J. Gastroenterol. 20, 1192-1210. doi: 10.3748/wjg.v20.i5.1192
30. Honda, K., and Littman, D. R. (2012). The microbiome in infectious disease and inflammation. Annu. Rev. Immunol. 30, 759-795. doi: 10.1146/annurev-immunol-020711-074937
31. Hooper, L. V., Midtvedt, T., and Gordon, J. I. (2002). How host-microbial interactions shape the nutrient environment of the mammalian intestine. Annu. Rev. Nutr. 22, 283-307. doi: 10.1146/annurev.nutr.22.011602.092259
32. Horwitz, B. H. (2007). The straw that stirs the drink: insight into the pathogenesis of inflammatory bowel disease revealed through the study of microflora-induced inflammation in genetically modified mice. Inflamm. Bowel Dis. 13, 490-500. doi: 10.1002/ibd.20098
33. Jellbauer, S., and Raffatellu, M. (2014). An intestinal arsonist: pathobiont ignites IBD and flees the scene. Gut 63, 1034-1035. doi: 10.1136/gutjnl-2013-305589
34. Khafipour, E., Li, S., Plaizier, J. C., and Krause, D. O. (2009). Rumen microbiome composition determined using two nutritional models of subacute ruminal acidosis. Appl. Environ. Microbiol. 75, 7115-7124. doi: 10.1128/AEM.00739-09
35. Khor, B., Gardet, A., and Xavier, R. J. (2011). Genetics and pathogenesis of inflammatory bowel disease. Nature 474, 307-317. doi: 10.1038/nature10209
36. Kotlowski, R., Bernstein, C. N., Sepehri, S., and Krause, D. O. (2007). High prevalence of Escherichia coli belonging to the B2+D phylogenetic group in inflammatory bowel disease. Gut 56, 669-675. doi: 10.1136/gut.2006.099796
37. Krause, D. O., Little, A. C., Dowd, S. E., and Bernstein, C. N. (2011). Complete genome sequence of adherent invasive Escherichia coli UM146 isolated from Ileal Crohn's disease biopsy tissue. J. Bacteriol. 193, 583-583. doi: 10.1128/JB.01290-10
38. Langille, M. G. I., Zaneveld, J., Caporaso, J. G., McDonald, D., Knights, D., Reyes, J. A., et al. (2013). Predictive functional profiling of microbial communities using 16S rRNA marker gene sequences. Nat. Biotechnol. 31, 814-821. doi: 10.1038/nbt.2676
39. Lara-Villoslada, F., Olivares, M., Sierra, S., Rodríguez, J. M., Boza, J., and Xaus, J. (2007). Beneficial effects of probiotic bacteria isolated from breast milk. Br. J. Nutr. 98(Suppl. 1), S96-S100. doi: 10.1017/S0007114507832910
40. Li, R., Khafipour, E., Krause, D. O., Entz, M. H., de Kievit, T. R., and Fernando, W. G. D. (2012). Pyrosequencing reveals the influence of organic and conventional farming systems on bacterial communities. PLoS ONE 7:e51897. doi: 10.1371/journal.pone.0051897
41. Lupp, C., Robertson, M. L., Wickham, M. E., Sekirov, I., Champion, O. L., Gaynor, E. C., et al. (2007). Host-mediated inflammation disrupts the intestinal microbiota and promotes the overgrowth of Enterobacteriaceae. Cell Host Microbe 2, 119-129. doi: 10.1016/j.chom.2007.06.010
42. Maloy, K. J., and Powrie, F. (2011). Intestinal homeostasis and its breakdown in inflammatory bowel disease. Nature 474, 298-306. doi: 10.1038/nature10208
43. Man, S. M., Kaakoush, N. O., and Mitchell, H. M. (2011). The role of bacteria and pattern-recognition receptors in Crohn's disease. Nat. Rev. Gastroenterol. Hepatol. 8, 152-168. doi: 10.1038/nrgastro.2011.3
44. Manichanh, C., Borruel, N., Casellas, F., and Guarner, F. (2012). The gut microbiota in IBD. Nat. Rev. Gastroenterol. Hepatol. 9, 599-608. doi: 10.1038/nrgastro.2012.152
45. Manichanh, C., Rigottier-Gois, L., Bonnaud, E., Gloux, K., Pelletier, E., Frangeul, L., et al. (2006). Reduced diversity of faecal microbiota in Crohn's disease revealed by a metagenomic approach. Gut 55, 205-211. doi: 10.1136/gut.2005.073817
46. Marcus, S. N., Marcus, A. J., Marcus, R., Ewen, S. W., and Watt, J. (1992). The pre-ulcerative phase of carrageenan-induced colonic ulceration in the guinea-pig. Int. J. Exp. Pathol. 73, 515-526
47. Marquardt, R. R., Jin, L. Z., Kim, J. W., Fang, L., Frohlich, A. A., and Baidoo, S. K. (1999). Passive protective effect of egg-yolk antibodies against enterotoxigenic Escherichia coli K88+ infection in neonatal and early-weaned piglets. FEMS Immunol. Med. Microbiol. 23, 283-288. doi: 10.1111/j.1574-695X.1999.tb01249.x
48. Martin, H. M., Campbell, B. J., Hart, C. A., Mpofu, C., Nayar, M., Singh, R., et al. (2004). Enhanced Escherichia coli adherence and invasion in Crohn's disease and colon cancer. Gastroenterology 127, 80-93. doi: 10.1053/j.gastro.2004.03.054
49. Masella, A. P., Bartram, A. K., Truszkowski, J. M., Brown, D. G., and Neufeld, J. D. (2012). PANDAseq: PAired-eND Assembler for Illumina sequences. BMC Bioinformatics 13:31. doi: 10.1186/1471-2105-13-31
50. Miller, E. R., and Ullrey, D. E. (1987). The pig as a model for human-nutrition. Annu. Rev. Nutr. 7, 361-382. doi: 10.1146/annurev.nu.07.070187.002045
51. Miquel, S., Peyretaillade, E., Claret, L., de Vallée, A., Dossat, C., Vacherie, B., et al. (2010). Complete genome sequence of Crohn's Disease-associated adherent-invasive E. coli strain LF82. PLoS ONE 5:e12714. doi: 10.1371/journal.pone.0012714
52. Morgan, X. C., Tickle, T. L., Sokol, H., Gevers, D., Devaney, K. L., Ward, D. V., et al. (2012). Dysfunction of the intestinal microbiome in inflammatory bowel disease and treatment. Genome Biol. 13:R79. doi: 10.1186/gb-2012-13-9-r79
53. Mukhopadhya, I., Hansen, R., El-Omar, E. M., and Hold, G. L. (2012). IBD-what role do proteobacteria play? Nat. Rev. Gastroenterol. Hepatol. 9, 219-230. doi: 10.1038/nrgastro.2012.14
54. Mylonaki, M., Rayment, N. B., Rampton, D. S., Hudspith, B. N., and Brostoff, J. (2005). Molecular characterization of rectal mucosaassociated bacterial flora in inflammatory bowel disease. Infamm. Bowel Dis. 11, 481-487. doi: 10.1097/01.MIB.0000159663.62651.4f
55. Novozamsky, I. R., Eck, V., Schouwenburg, J. C. H., and Walinga, F. (1974). Total nitrogen determination in plant material by means of the indole-phenol blue method. Neth. J. Agri. Sci. 22, 3-5
56. NRC (2012). Nutrient Requirements of Swine. Washington, DC: National Academies Press
57. Ott, S. J., Musfeldt, M., Wenderoth, D. F., Hampe, J., Brant, O., Fölsch, U. R., et al. (2004). Reduction in diversity of the colonic mucosa associated bacterial microflora in patients with active inflammatory bowel disease. Gut 53, 685-693. doi: 10.1136/gut.2003.025403
58. Parks, D. H., and Beiko, R. G. (2010). Identifying biologically relevant differences between metagenomic communities. Bioinformatics 26, 715-721. doi: 10.1093/bioinformatics/btq041
59. Price, M. N., Dehal, P. S., and Arkin, A. P. (2010). FastTree 2-approximately maximum-likelihood trees for large alignments. PLoS ONE 5:e9490. doi: 10.1371/journal.pone.0009490
60. Qiu, X., Zhang, M., Yang, X., Hong, N., and Yu, C. (2013). Faecalibacterium prausnitzii upregulates regulatory T cells and anti-inflammatory cytokines in treating TNBS-induced colitis. J. Crohns. Colitis 7, e558-e568. doi: 10.1016/j.crohns.2013.04.002
61. Rideout, J. R., He, Y., Navas-Molina, J. A., Walters, W. A., Ursell, L. K., Gibbons, S. M., et al. (2014). Subsampled open-reference clustering creates consistent, comprehensive OTU definitions and scales to billions of sequences. PeerJ 2:e545. doi: 10.7717/peerj.545
62. Sartor, R. B. (2008). Microbial influences in inflammatory bowel diseases. Gastroenterology 134, 577-594. doi: 10.1053/j.gastro.2007.11.059
63. Sartor, R. B., and Mazmanian, S. K. (2012). Intestinal microbes in inflammatory bowel diseases. Am. J. Gastroenterol. Suppl. 1, 15-21. doi: 10.1038/ajgsup.2012.4
64. Schuppler, M., Lötzsch, K., Waidmann, M., and Autenrieth, I. B. (2004). An abundance of Escherichia coli is harbored by the mucosa-associated bacterial flora of interleukin-2-deficient mice. Infect. Immun. 72, 1983-1990. doi: 10.1128/IAI.72.4.1983-1990.2004
65. Sellon, R. K., Tonkonogy, S., Schultz, M., Dieleman, L. A., Grenther, W., Balish, E., et al. (1998). Resident enteric bacteria are necessary for development of spontaneous colitis and immune system activation in interleukin-10-deficient mice. Infect. Immun. 66, 5224-5231
66. Sepehri, S., Khafipour, E., Bernstein, C. N., Coombes, B. K., Pilar, A. V., Karmali, M., et al. (2011). Characterization of Escherichia coli isolated from gut biopsies of newly diagnosed patients with inflammatory bowel disease. Inflamm. Bowel Dis. 17, 1451-1463. doi: 10.1002/ibd.21509
67. Sepehri, S., Kotlowski, R., Bernstein, C. N., and Krause, D. O. (2007). Microbial diversity of inflamed and noninflamed gut biopsy tissues in inflammatory bowel disease. Inflamm. Bowel Dis. 13, 675-683. doi: 10.1002/ibd.20101
68. Sepehri, S., Kotlowski, R., Bernstein, C. N., and Krause, D. O. (2009). Phylogenetic analysis of inflammatory bowel disease associated Escherichia coli and the fimH virulence determinant. Inflamm. Bowel Dis. 15, 1737-1745. doi: 10.1002/ibd.20966
69. Smith, P. M., Howitt, M. R., Panikov, N., Michaud, M., Gallini, C. A., Bohlooly-Y, M., et al. (2013). The microbial metabolites, short-chain fatty acids, regulate colonic Treg cell homeostasis. Science 341, 569-573. doi: 10.1126/science.1241165
70. Sokol, H., Lay, C., Seksik, P., and Tannock, G. W. (2008). Analysis of bacterial bowel communities of IBD patients: what has it revealed? Inflamm. Bowel Dis. 14, 858-867. doi: 10.1002/ibd.20392
71. Sokol, H., Seksik, P., Furet, J. P., Firmesse, O., Nion-Larmurier, I., Beaugerie, L., et al. (2009). Low counts of Faecalibacterium prausnitzii in colitis microbiota. Inflamm. Bowel Dis. 15, 1183-1189. doi: 10.1002/ibd.20903
72. Steiner, T. S. (2007). How flagellin and toll-like receptor 5 contribute to enteric infection. Infect. Immun. 75, 545-552. doi: 10.1128/IAI.01506-06
73. Takaishi, H., Matsuki, T., Nakazawa, A., Takada, T., Kado, S., Asahara, T., et al. (2008). Imbalance in intestinal microflora constitution could be involved in the pathogenesis of inflammatory bowel disease. Int. J. Med. Microbiol. 298, 463-472. doi: 10.1016/j.ijmm.2007.07.016
74. Tobacman, J. (2001). Review of harmful gastrointestinal effects of carrageenan in animal experiments. Environ. Health Perspect. 109, 983-994. doi: 10.1289/ehp.01109983
75. Tong, H. K., Lee, K. H., and Wong, H. A. (1980). The molecular-weight and viscosity of the water-soluble polysaccharide(S) from Eucheuma-Spinosum. Carbohydr. Res. 81, 1-6. doi: 10.1016/S0008-6215(00)85671-2
76. Tsukahara, T., Koyama, H., Okada, M., and Ushida, K. (2002). Stimulation of butyrate production by gluconic acid in batch culture of pig cecal digesta and identification of butyrate-producing bacteria. J. Nutr. 132, 2229-2234
77. van Kruiningen, H. J. (1995). On the use of antibiotics in Crohn's disease J. Clin. Gastroenterol. 20, 310-316. doi: 10.1097/00004836-199506000-00012
78. Vijay-Kumar, M., Aitken, J. D., Carvalho, F. A., Cullender, T. C., Mwangi, S., Srinivasan, S., et al. (2010). Metabolic syndrome and altered gut microbiota in mice lacking Toll-like receptor 5. Science 328, 228-231. doi: 10.1126/science.1179721
79. Vijay-Kumar, M., Sanders, C. J., Taylor, R. T., Kumar, A., Aitken, J. D., Sitaraman, S. V., et al. (2007). Deletion of TLR5 results in spontaneous colitis in mice. J. Clin. Invest. 117, 3909-3921. doi: 10.1172/jci33084
80. Walters, W. A., Xu, Z., and Knight, R. (2014). Meta-analyses of human gut microbes associated with obesity and IBD. FEBS Lett. 588, 4223-4233. doi: 10.1016/j.febslet.2014.09.039
81. Wang, Q., Garrity, G. M., Tiedje, J. M., and Cole, J. R. (2007). Naive Bayesian classifier for rapid assignment of rRNA sequences into the new bacterial taxonomy. Appl. Environ. Microbiol. 73, 5261-5267. doi: 10.1128/AEM.00062-07
82. Wang, Y., Ames, N. P., Tun, H. M., Tosh, S. M., Jones, P. J., and Khafipour, E. (2016). High molecular weight barley β-glucan alters gut microbiota toward reduced cardiovascular disease risk. Front. Microbiol. 7:129. doi: 10.3389/fmicb.2016.00129
83. Watt, J., McLean, C., and Marcus, R. (1979). Degradation of carrageenan for the experimental production of ulcers in the colon. J. Pharm. Pharmacol. 31, 645-646. doi: 10.1111/j.2042-7158.1979.tb13614.x
84. Weiner, M. L. (1991). Toxicological properties of carrageenan. Agents Actions 32, 46-51. doi: 10.1007/BF01983307
85. Wright, E. K., Kamm, M. A., Teo, S. M., Inouye, M., Wagner, J., and Kirkwood, C. D. (2015). Recent advances in characterizing the gastrointestinal microbiome in Crohn's disease: a systematic review. Inflamm. Bowel Dis. 21, 1219-1228. doi: 10.1097/MIB.0000000000000382
86. Xenoulis, P. G., Palculict, B., Allenspach, K., Steiner, J. M., Van House, A. M., and Suchodolski, J. S. (2008). Molecular-phylogenetic characterization of microbial communities imbalances in the small intestine of dogs with inflammatory bowel disease. FEMS Microbiol. Ecol. 66, 579-589. doi: 10.1111/j.1574-6941.2008.00556.x