Comparison of the fecal, cecal, and mucus microbiome in male and female mice after TNBS-induced colitis


Autoři: Ariangela J. Kozik aff001;  Cindy H. Nakatsu aff002;  Hyonho Chun aff004;  Yava L. Jones-Hall aff001
Působiště autorů: Department of Comparative Pathobiology, Purdue University, West Lafayette, Indiana, United States of America aff001;  Interdisciplinary Life Sciences, Purdue University, West Lafayette, Indiana, United States of America aff002;  Department of Agronomy, Purdue University, West Lafayette, Indiana, United States of America aff003;  Department of Mathematics and Statistics, Boston University, Boston, Massachusetts, United States of America aff004
Vyšlo v časopise: PLoS ONE 14(11)
Kategorie: Research Article
doi: 10.1371/journal.pone.0225079

Souhrn

Crohn’s Disease and Ulcerative Colitis are chronic, inflammatory conditions of the digestive tract, collectively known as Inflammatory Bowel Disease (IBD). The combined influence of lifestyle factors, genetics, and the gut microbiome contribute to IBD pathogenesis. Studies of the gut microbiome have shown significant differences in its composition between healthy individuals and those with IBD. Due to the high inter-individual microbiome variation seen in humans, mouse models of IBD are often used to investigate potential IBD mechanisms and their interplay between host, microbial, and environmental factors. While fecal samples are the predominant material used for microbial community analysis, they may not be the ideal sample to use for analysis of the microbiome of mice with experimental colitis, such as that induced by 2, 4, 6 trinitrobenzesulfonic acid (TNBS). As TNBS is administered intrarectally to induce colitis and inflammation is confined to the colon in this model, we hypothesized that the microbiome of the colonic mucus would most closely correlate with TNBS colitis severity. Based on our previous research, we also hypothesized that sex would be associated with both disease severity and microbial differences in mice with chronic TNBS colitis. We examined and compared the fecal, cecal content, and colonic mucus microbiota of 8-week old male and female C57BL/6J wild-type mice prior to and after the induction of TNBS colitis via 16S rRNA gene sequencing. We found that the colonic mucus microbiome was more closely correlated with disease severity than were alterations in the fecal and cecal microbiomes. We also found that the microbiomes of the feces, cecum, and mucus were distinct, but found no significant differences that were associated with sex in either compartment. Our findings highlight the importance of sampling colonic mucus in TNBS-induced colitis. Moreover, consideration of the differential impact of sex on the microbiome across mouse strains may be critical for the appropriate application of TNBS colitis models and robust comparisons across studies in the future.

Klíčová slova:

Cecum – Colitis – Colon – Inflammation – Inflammatory bowel disease – Microbiome – Mouse models – Mucus


Zdroje

1. Ananthakrishnan AN. Environmental Risk Factors for Inflammatory Bowel Disease. Gastroenterol Hepatol. 2013;9: 367–374.

2. Ek WE, D’Amato M, Halfvarson J. The history of genetics in inflammatory bowel disease. Ann Gastroenterol Q Publ Hell Soc Gastroenterol. 2014;27: 294–303.

3. Matsuoka K, Kanai T. The gut microbiota and inflammatory bowel disease. Semin Immunopathol. 2015;37: 47–55. doi: 10.1007/s00281-014-0454-4 25420450

4. Pascal V, Pozuelo M, Borruel N, Casellas F, Campos D, Santiago A, et al. A microbial signature for Crohn’s disease. Gut. 2017; http://gut.bmj.com/content/early/2017/01/31/gutjnl-2016-313235.abstract

5. Levy AN, Allegretti JR. Insights into the role of fecal microbiota transplantation for the treatment of inflammatory bowel disease. Ther Adv Gastroenterol. 2019;12. doi: 10.1177/1756284819836893 30906424

6. Vermeire S, Joossens M, Verbeke K, Wang J, Machiels K, Sabino J, et al. Donor Species Richness Determines Faecal Microbiota Transplantation Success in Inflammatory Bowel Disease. J Crohns Colitis. 2016;10: 387–394. doi: 10.1093/ecco-jcc/jjv203 26519463

7. Zhang S, Cao X, Huang H. Sampling Strategies for Three-Dimensional Spatial Community Structures in IBD Microbiota Research. Front Cell Infect Microbiol. 2017;7. doi: 10.3389/fcimb.2017.00051 28286741

8. Lane ER, Zisman TL, Suskind DL. The microbiota in inflammatory bowel disease: current and therapeutic insights. J Inflamm Res. 2017;10: 63–73. doi: 10.2147/JIR.S116088 28652796

9. Watt E, Gemmell MR, Berry S, Glaire M, Farquharson F, Louis P, et al. Extending colonic mucosal microbiome analysis—assessment of colonic lavage as a proxy for endoscopic colonic biopsies. Microbiome. 2016;4. doi: 10.1186/s40168-016-0207-9 27884202

10. Gevers D, Kugathasan S, Denson LA, Vazquez-Baeza Y, Van Treuren W, Ren B, et al. The treatment-naive microbiome in new-onset Crohn’s disease. Cell Host Microbe. 2014;15: 382–92. doi: 10.1016/j.chom.2014.02.005 24629344

11. Glymenaki M, Singh G, Brass A, Warhurst G, McBain AJ, Else KJ, et al. Compositional Changes in the Gut Mucus Microbiota Precede the Onset of Colitis-Induced Inflammation. Inflamm Bowel Dis. 2017;23: 912–922. doi: 10.1097/MIB.0000000000001118 28498157

12. Tang MS, Poles J, Leung JM, Wolff MJ, Davenport M, Lee SC, et al. Inferred metagenomic comparison of mucosal and fecal microbiota from individuals undergoing routine screening colonoscopy reveals similar differences observed during active inflammation. Gut Microbes. 2015;6: 48–56. doi: 10.1080/19490976.2014.1000080 25559083

13. Costello EK, Lauber CL, Hamady M, Fierer N, Gordon JI, Knight R. Bacterial Community Variation in Human Body Habitats Across Space and Time. Science. 2009;326: 1694–1697. doi: 10.1126/science.1177486 19892944

14. Flores GE, Caporaso JG, Henley JB, Rideout JR, Domogala D, Chase J, et al. Temporal variability is a personalized feature of the human microbiome. Genome Biol. 2014;15. doi: 10.1186/s13059-014-0531-y 25517225

15. Parfrey LW, Knight R. Spatial and temporal variability of the human microbiota. Clin Microbiol Infect. 2012;18: 5–7. doi: 10.1111/j.1469-0691.2012.03861.x

16. Lloyd-Price J, Arze C, Ananthakrishnan AN, Schirmer M, Avila-Pacheco J, Poon TW, et al. Multi-omics of the gut microbial ecosystem in inflammatory bowel diseases. Nature. 2019;569: 655–662. doi: 10.1038/s41586-019-1237-9 31142855

17. Bernbom N, Norrung B, Saadbye P, Molbak L, Vogensen FK, Licht TR. Comparison of methods and animal models commonly used for investigation of fecal microbiota: effects of time, host and gender. J Microbiol Methods. 2006;66: 87–95. doi: 10.1016/j.mimet.2005.10.014 16289391

18. Li H, Limenitakis JP, Fuhrer T, Geuking MB, Lawson MA, Wyss M, et al. The outer mucus layer hosts a distinct intestinal microbial niche. Nat Commun. 2015;6: 8292. doi: 10.1038/ncomms9292 26392213

19. Sartor RB. Gut microbiota: Optimal sampling of the intestinal microbiota for research. Nat Rev Gastroenterol Hepatol. 2015;12: 253–254. doi: 10.1038/nrgastro.2015.46 25802025

20. Li P, Lei J, Hu G, Chen X, Liu Z, Yang J. Matrine Mediates Inflammatory Response via Gut Microbiota in TNBS-Induced Murine Colitis. Front Physiol. 2019;10. doi: 10.3389/fphys.2019.00028 30800071

21. Asfaha S, Bell CJ, Wallace JL, MacNaughton WK. Prolonged colonic epithelial hyporesponsiveness after colitis: role of inducible nitric oxide synthase. Am J Physiol-Gastrointest Liver Physiol. 1999;276: G703–G710. doi: 10.1152/ajpgi.1999.276.3.G703 10070047

22. Wardill HR, Choo JM, Dmochowska N, Mavrangelos C, Campaniello MA, Bowen JM, et al. Acute Colitis Drives Tolerance by Persistently Altering the Epithelial Barrier and Innate and Adaptive Immunity. Inflamm Bowel Dis. 2019;25: 1196–1207. doi: 10.1093/ibd/izz011 30794280

23. Alrafas HR, Busbee PB, Nagarkatti M, Nagarkatti PS. Resveratrol modulates the gut microbiota to prevent murine colitis development through induction of Tregs and suppression of Th17 cells. J Leukoc Biol. 2019;106: 467–480. doi: 10.1002/JLB.3A1218-476RR 30897248

24. Jones-Hall YL, Kozik A, Nakatsu C. Ablation of tumor necrosis factor is associated with decreased inflammation and alterations of the microbiota in a mouse model of inflammatory bowel disease. PLoS One. 2015;10: e0119441. doi: 10.1371/journal.pone.0119441 25775453

25. Kozik AJ, Nakatsu CH, Chun H, Jones-Hall YL. Age, sex, and TNF associated differences in the gut microbiota of mice and their impact on acute TNBS colitis. Exp Mol Pathol. 2017;103: 311–319. doi: 10.1016/j.yexmp.2017.11.014 29175304

26. Wirtz S, Neufert C, Weigmann B, Neurath MF. Chemically induced mouse models of intestinal inflammation. Nat Protoc. 2007;2: 541–6. doi: 10.1038/nprot.2007.41 17406617

27. Erben U, Loddenkemper C, Doerfel K, Spieckermann S, Haller D, Heimesaat MM, et al. A guide to histomorphological evaluation of intestinal inflammation in mouse models. Int J Clin Exp Pathol. 2014;7: 4557–4576. 25197329

28. Masella AP, Bartram AK, Truszkowski JM, Brown DG, Neufeld JD. PANDAseq: paired-end assembler for illumina sequences. BMC Bioinformatics. 2012;13: 31. doi: 10.1186/1471-2105-13-31 22333067

29. Caporaso JG, Kuczynski J, Stombaugh J, Bittinger K, Bushman FD, Costello EK, et al. QIIME allows analysis of high-throughput community sequencing data. Nat Methods. United States; 2010. pp. 335–6. doi: 10.1038/nmeth.f.303 20383131

30. Lozupone C, Knight R. UniFrac: a new phylogenetic method for comparing microbial communities. Appl Env Microbiol. 2005;71. doi: 10.1128/aem.71.12.8228-8235.2005

31. Anderson Marti J. A new method for non-parametric multivariate analysis of variance. Austral Ecol. 2008;26: 32–46. doi: 10.1111/j.1442-9993.2001.01070.pp.x

32. Anderson MJ. Distance-based tests for homogeneity of multivariate dispersions. Biometrics. 2006;62: 245–53. doi: 10.1111/j.1541-0420.2005.00440.x 16542252

33. Mandal S, Van Treuren W, White RA, Eggesbø M, Knight R, Peddada SD. Analysis of composition of microbiomes: a novel method for studying microbial composition. Microb Ecol Health Dis. 2015;26. 26028277

34. ter Braak CJF. Canonical Correspondence Analysis: A New Eigenvector Technique for Multivariate Direct Gradient Analysis. Ecology. 1986;67: 1167–1179. doi: 10.2307/1938672

35. Gu S, Chen D, Zhang J-N, Lv X, Wang K, Duan L-P, et al. Bacterial Community Mapping of the Mouse Gastrointestinal Tract. PLoS ONE. 2013;8. doi: 10.1371/journal.pone.0074957 24116019

36. Suzuki T, Nachman MW. Spatial Heterogeneity of Gut Microbial Composition along the Gastrointestinal Tract in Natural Populations of House Mice. PLOS ONE. 2016;11: e0163720. doi: 10.1371/journal.pone.0163720 27669007

37. Wang Y, Devkota S, Musch MW, Jabri B, Nagler C, Antonopoulos DA, et al. Regional Mucosa-Associated Microbiota Determine Physiological Expression of TLR2 and TLR4 in Murine Colon. PLOS ONE. 2010;5: e13607. doi: 10.1371/journal.pone.0013607 21042588

38. Donaldson GP, Lee SM, Mazmanian SK. Gut biogeography of the bacterial microbiota. Nat Rev Microbiol. 2016;14: 20–32. doi: 10.1038/nrmicro3552 26499895

39. Guo F-F, Yu T-C, Hong J, Fang J-Y. Emerging Roles of Hydrogen Sulfide in Inflammatory and Neoplastic Colonic Diseases. Front Physiol. 2016;7: 156. doi: 10.3389/fphys.2016.00156 27199771

40. Verma R, Verma AK, Ahuja V, Paul J. Real-time analysis of mucosal flora in patients with inflammatory bowel disease in India. J Clin Microbiol. 2010;48: 4279–4282. doi: 10.1128/JCM.01360-10 20861337

41. Jakobsson HE, Rodríguez-Piñeiro AM, Schütte A, Ermund A, Boysen P, Bemark M, et al. The composition of the gut microbiota shapes the colon mucus barrier. EMBO Rep. 2015;16: 164–177. doi: 10.15252/embr.201439263 25525071

42. Roediger WEW, Moore J, Babidge W. Colonic Sulfide in Pathogenesis and Treatment of Ulcerative Colitis. Dig Dis Sci. 1997;42: 1571–1579. doi: 10.1023/a:1018851723920 9286219

43. Figliuolo VR, dos Santos LM, Abalo A, Nanini H, Santos A, Brittes NM, et al. Sulfate-reducing bacteria stimulate gut immune responses and contribute to inflammation in experimental colitis. Life Sci. 2017;189: 29–38. doi: 10.1016/j.lfs.2017.09.014 28912045

44. Nishida A, Inoue R, Inatomi O, Bamba S, Naito Y, Andoh A. Gut microbiota in the pathogenesis of inflammatory bowel disease. Clin J Gastroenterol. 2018;11: 1–10. doi: 10.1007/s12328-017-0813-5 29285689

45. Moen B, Henjum K, Måge I, Knutsen SH, Rud I, Hetland RB, et al. Effect of Dietary Fibers on Cecal Microbiota and Intestinal Tumorigenesis in Azoxymethane Treated A/J Min/+ Mice. PLOS ONE. 2016;11: e0155402. doi: 10.1371/journal.pone.0155402 27196124

46. Ze X, Duncan SH, Louis P, Flint HJ. Ruminococcus bromii is a keystone species for the degradation of resistant starch in the human colon. ISME J. 2012;6: 1535–1543. doi: 10.1038/ismej.2012.4 22343308

47. Hofma BR, Wardill HR, Mavrangelos C, Campaniello MA, Dimasi D, Bowen JM, et al. Colonic migrating motor complexes are inhibited in acute tri-nitro benzene sulphonic acid colitis. PLOS ONE. 2018;13: e0199394. doi: 10.1371/journal.pone.0199394 29933379

48. DeVoss J, Diehl L. Murine Models of Inflammatory Bowel Disease (IBD): Challenges of Modeling Human Disease. Toxicol Pathol. 2014;42: 99–110. doi: 10.1177/0192623313509729 24231829

49. Hugenholtz F, de Vos WM. Mouse models for human intestinal microbiota research: a critical evaluation. Cell Mol Life Sci. 2018;75: 149–160. doi: 10.1007/s00018-017-2693-8 29124307

50. Nguyen TLA, Vieira-Silva S, Liston A, Raes J. How informative is the mouse for human gut microbiota research? Dis Model Mech. 2015;8: 1–16. doi: 10.1242/dmm.017400 25561744

51. Lo Presti A, Zorzi F, Del Chierico F, Altomare A, Cocca S, Avola A, et al. Fecal and Mucosal Microbiota Profiling in Irritable Bowel Syndrome and Inflammatory Bowel Disease. Front Microbiol. 2019;10. doi: 10.3389/fmicb.2019.01655 31379797

52. Elderman M, Hugenholtz F, Belzer C, Boekschoten M, van Beek A, de Haan B, et al. Sex and strain dependent differences in mucosal immunology and microbiota composition in mice. Biol Sex Differ. 2018;9: 26. doi: 10.1186/s13293-018-0186-6 29914546

53. Dominianni C, Sinha R, Goedert JJ, Pei Z, Yang L, Hayes RB, et al. Sex, Body Mass Index, and Dietary Fiber Intake Influence the Human Gut Microbiome. PLOS ONE. 2015;10: e0124599. doi: 10.1371/journal.pone.0124599 25874569

54. Haro C, Rangel-Zúñiga OA, Alcalá-Díaz JF, Gómez-Delgado F, Pérez-Martínez P, Delgado-Lista J, et al. Intestinal Microbiota Is Influenced by Gender and Body Mass Index. PLOS ONE. 2016;11: e0154090. doi: 10.1371/journal.pone.0154090 27228093

55. Mueller S, Saunier K, Hanisch C, Norin E, Alm L, Midtvedt T, et al. Differences in fecal microbiota in different European study populations in relation to age, gender, and country: a cross-sectional study. Appl Environ Microbiol. 2006;72: 1027–1033. doi: 10.1128/AEM.72.2.1027-1033.2006 16461645

56. Consortium THMP, Huttenhower C, Gevers D, Knight R, Abubucker S, Badger JH, et al. Structure, function and diversity of the healthy human microbiome. Nature. 2012;486: 207–214. doi: 10.1038/nature11234 22699609

57. Lay C, Rigottier-Gois L, Holmstrøm K, Rajilic M, Vaughan EE, de Vos WM, et al. Colonic microbiota signatures across five northern European countries. Appl Environ Microbiol. 2005;71: 4153–4155. doi: 10.1128/AEM.71.7.4153-4155.2005 16000838

58. Fransen F, Beek V, A A, Borghuis T, Meijer B, Hugenholtz F, et al. The Impact of Gut Microbiota on Gender-Specific Differences in Immunity. Front Immunol. 2017;8: 754. doi: 10.3389/fimmu.2017.00754 28713378

59. Brotman RM, Ravel J, Bavoil PM, Gravitt PE, Ghanem KG. Microbiome, Sex Hormones, and Immune Responses in the Reproductive Tract: Challenges for Vaccine Development Against Sexually Transmitted Infections. Vaccine. 2014;32: 1543–1552. doi: 10.1016/j.vaccine.2013.10.010 24135572

60. Fairweather D, Frisancho-Kiss S, Rose NR. Sex differences in autoimmune disease from a pathological perspective. Am J Pathol. 2008;173: 600–9. doi: 10.2353/ajpath.2008.071008 18688037

61. Klein SL, Flanagan KL. Sex differences in immune responses. Nat Rev Immunol. 2016;16: 626–38. doi: 10.1038/nri.2016.90 27546235

62. den Besten G, van Eunen K, Groen AK, Venema K, Reijngoud D-J, Bakker BM. The role of short-chain fatty acids in the interplay between diet, gut microbiota, and host energy metabolism. J Lipid Res. 2013;54: 2325–2340. doi: 10.1194/jlr.R036012 23821742

63. Fan N, Lai L. Genetically Modified Pig Models for Human Diseases. J Genet Genomics. 2013;40: 67–73. doi: 10.1016/j.jgg.2012.07.014 23439405

64. Swindle M, Smith AC. Comparative anatomy and physiology of the pig. Scand J Lab Anim Sci. 1998;25: 11–21.

65. Xiao Y, Yan H, Diao H, Yu B, He J, Yu J, et al. Early Gut Microbiota Intervention Suppresses DSS-Induced Inflammatory Responses by Deactivating TLR/NLR Signalling in Pigs. Sci Rep. 2017;7: 3224. doi: 10.1038/s41598-017-03161-6 28607413

66. Merritt AM, Buergelt CD, Sanchez LC. Porcine Ileitis Model Induced by TNBS–Ethanol Instillation. Dig Dis Sci. 2002;47: 879–885. doi: 10.1023/a:1014720923611 11991624


Článek vyšel v časopise

PLOS One


2019 Číslo 11