Dysbiosis in the Gut Microbiota of Patients with Multiple Sclerosis, with a Striking Depletion of Species Belonging to Clostridia XIVa and IV Clusters
Sachiko Miyake, Sangwan Kim, Wataru Suda, Kenshiro Oshima, Masakazu Nakamura, Takako Matsuoka, Norio Chihara, Atsuko Tomita, Wakiro Sato, Seok-Won Kim, Hidetoshi Morita, Masahira Hattori, Takashi Yamamura, Sachiko Miyake, Sangwan Kim, Wataru Suda, Kenshiro Oshima, Masakazu Nakamura, Takako Matsuoka, Norio Chihara, Atsuko Tomita, Wakiro Sato, Seok-Won Kim, Hidetoshi Morita, Masahira Hattori, Takashi Yamamura
Abstract
The pathogenesis of multiple sclerosis (MS), an autoimmune disease affecting the brain and spinal cord, remains poorly understood. Patients with MS typically present with recurrent episodes of neurological dysfunctions such as blindness, paresis, and sensory disturbances. Studies on experimental autoimmune encephalomyelitis (EAE) animal models have led to a number of testable hypotheses including a hypothetical role of altered gut microbiota in the development of MS. To investigate whether gut microbiota in patients with MS is altered, we compared the gut microbiota of 20 Japanese patients with relapsing-remitting (RR) MS (MS20) with that of 40 healthy Japanese subjects (HC40) and an additional 18 healthy subjects (HC18). All the HC18 subjects repeatedly provided fecal samples over the course of months (158 samples in total). Analysis of the bacterial 16S ribosomal RNA (rRNA) gene by using a high-throughput culture-independent pyrosequencing method provided evidence of a moderate dysbiosis in the structure of gut microbiota in patients with MS. Furthermore, we found 21 species that showed significant differences in relative abundance between the MS20 and HC40 samples. On comparing MS samples to the 158 longitudinal HC18 samples, the differences were found to be reproducibly significant for most of the species. These taxa comprised primarily of clostridial species belonging to Clostridia clusters XIVa and IV and Bacteroidetes. The phylogenetic tree analysis revealed that none of the clostridial species that were significantly reduced in the gut microbiota of patients with MS overlapped with other spore-forming clostridial species capable of inducing colonic regulatory T cells (Treg), which prevent autoimmunity and allergies; this suggests that many of the clostridial species associated with MS might be distinct from those broadly associated with autoimmune conditions. Correcting the dysbiosis and altered gut microbiota might deserve consideration as a potential strategy for the prevention and treatment of MS.
Conflict of interest statement
Competing Interests: The authors have declared that no competing interests exist.
Figures
References
- Bach JF. The effect of infections on susceptibility to autoimmune and allergic diseases. N Engl J Med. 2002;347: 911–920.
- Osoegawa M, Kira J, Fukazawa T, Fujihara K, Kikuchi S, Matsui M, et al. Temporal changes and geographical differences in multiple sclerosis phenotypes in Japanese: nationwide survey results over 30 years. Mult Scler. 2009;15: 159–173. 10.1177/1352458508098372
- International Multiple Sclerosis Genetics Consortium; Wellcome Trust Case Control Consortium 2, Sawcer S, Hellenthal G, Pirinen M, et al. Genetic risk and a primary role for cell-mediated immune mechanisms in multiple sclerosis. Nature. 2011;476: 214–219. 10.1038/nature10251
- Ascherio A, Munger KL. Environmental risk factors for multiple sclerosis. Part II: Noninfectious factors. Ann Neurol. 2007;61: 504–513.
- Houzen H, Niino M, Hirotani M, Fukazawa T, Kikuchi S, Tanaka K, et al. Increased prevalence, incidence, and female predominance of multiple sclerosis in northern Japan. J Neurol Sci. 2012;323: 117–122.
- Yamamura T, Miyake S. Diet, gut flora, and multiple sclerosis: current research and future perspectives In: Yamamura T, Gran B, editors. Multiple sclerosis immunology. New York: Springer; 2012. pp. 115–126.
- Belkaid Y, Hand TW. Role of the microbiota in immunity and inflammation. Cell. 2014;157:121–141 10.1016/j.cell.2014.03.011
- Yokote H, Miyake S, Croxford JL, Oki S, Mizusawa H, Yamamura T. NKT cell-dependent amelioration of a mouse model of multiple sclerosis by altering gut flora. Am J Pathol. 2008;173: 1714–1723. 10.2353/ajpath.2008.080622
- Berer K, Mues M, Koutrolos M, Rasbi ZA, Boziki M, Johner C, et al. Commensal microbiota and myelin autoantigen cooperate to trigger autoimmune demyelination. Nature. 2011;479: 538–541. 10.1038/nature10554
- Lee YK, Menezes JS, Umesaki Y, Mazmanian SK. Proinflammatory T-cell responses to gut microbiota promote experimental autoimmune encephalomyelitis. Proc Natl Acad Sci USA. 2011;108: 4612–4622.
- Atarashi K, Tanoue T, Shima T, Imaoka A, Kuwahara T, Momose Y, et al. Induction of colonic regulatory T cells by indigenous Clostridium species. Science. 2011;331:337–341. 10.1126/science.1198469
- Ochoa-Repáraz J, Mielcarz DW, Ditrio LE, Burroughs AR, Begum-Haque S, Dasgupta S, et al. Central nervous system demyelinating disease protection by the human commensal Bacteroides fragilis depends on polysaccharide A expression. J Immunol. 2010;185: 4101–4108. 10.4049/jimmunol.1001443
- Atarashi K, Tanoue T, Oshima K, Suda W, Nagano Y, Nishikawa H, et al. Treg induction by a rationally selected mixture of Clostridia strains from the human microbiota. Nature. 2013;500: 232–236. 10.1038/nature12331
- McDonald WI, Compston A, Edan G, Goodkin D, Hartung HP, Lublin FD, et al. Recommended diagnostic criteria for multiple sclerosis: guidelines from the International Panel on the diagnosis of multiple sclerosis. Ann Neurol. 2011;50: 121–127.
- Kim SW, Suda W, Kim S, Oshima K, Fukuda S, Ohno H, et al. Robustness of gut microbiota of healthy adults in response to probiotic intervention revealed by high-throughput pyrosequencing. DNA Res. 2013;20: 241–53. 10.1093/dnares/dst006
- Said HS, Suda W, Nakagome S, Chinen H, Oshima K, Kim S, et al. Dysbiosis of salivary microbiota in inflammatory bowel disease and its association with oral immunologic biomarkers. DNA Res. 2014;21: 15–25. 10.1093/dnares/dst037
- Lozupone C, Lladser ME, Knight D, Stombaugh J, Knight R. UniFrac: an effective distance metric for microbial community comparison. ISME J. 2011;5: 169–172. 10.1038/ismej.2010.133
- Tindall BJ. The status of the name Lactobacillus rogosae Holdeman and Moore 1974. Opinion 88. Judicial Commission of the International Committee on Systematics of Prokaryotes. Int J Syst Evol Microbiol. 2014; 64: 3578–3579. 10.1099/ijs.0.069146-0
- Ott SJ, Musfeldt M, Wenderoth DF, Hampe J, Brant O, Folsch UR, et al. Reduction in diversity of the colonic mucosa associated bacterial microflora in patients with active inflammatory bowel disease. Gut. 2004;53: 685–693.
- Manichanh C, Rigottier-Gois L, Boonnaud E, Gloux K, Pelletier E, Frangeul L, et al. Reduced diversity of fecal microbiota in Crohn’s disease revealed by a metagenomic approach. Gut. 2006;55: 205–211.
- Frank DN, St Amand AL, Feldman RA, Boedeker EC, Harpaz N, Pace NR. Molecular-phylogenetic characterization of microbial community imbalances in human inflammatory bowel diseases. Proc Natl Acad Sci USA. 2007;104: 13780–13785.
- Peterson DA, Frank DN, Pace NR, Gordon JI. Metagenomic approaches for defining the pathogenesis of inflammatory bowel diseases. Cell Host Microbe. 2008;3: 417–427. 10.1016/j.chom.2008.05.001
- Qin J, Li R, Raes J, Arumugam M, Burgdorf KS, Manichanh C, et al. A human gut microbial gene catalogue established by metagenomic sequencing. Nature. 2010;464: 59–65. 10.1038/nature08821
- Sokol H, Pigneur B, Watterlot L, Lakhdari O, Bermúdez-Humarán LG, Gratadoux JJ, et al. Faecalibacterim prausnitzii is an anti-inflammatory commensal bacterium identified by gut microbiota analysis of Crohn disease patients. Proc Natl Acad Sci USA. 2008;105: 16731–16736. 10.1073/pnas.0804812105
- Mondot S, Kang S, Furet JP, Aguirre de Carcer D, McSweeney C, Morrison M, et al. Highlighting new phylogenetic specificities of Crohn’s disease microbiota. Inflamm Bowel Dis. 2011;17: 185–192.
- Joossens M, Huys G, Cnockaert M, de Preter V, Verbeke K, Rutgeerts P, et al. Dysbiosis of the faecal microbiota in patients with Crohn’s disease and their unaffected relatives. Gut. 2011;60: 631–637. 10.1136/gut.2010.223263
- Furusawa Y, Obata Y, Fukuda S, Endo T, Nakato G, Takahashi D, et al. Commensal microbe-derived butyrate induces the differentiation of the colonic regulatory T cells. Nature. 2013;504: 456–460.
- Smith PM, Howitt MR, Panikov N, Michaud M, Gallini CA, Bohlooly YM, et al. The microbial metabolites, short-chain fatty acids, regulate colonic Treg cell homeostasis. Science. 2013;341: 569–573. 10.1126/science.1241165
- Arpaia N, Campbell C, Fan X, Dikiy S, van der Veeken J, deRoos P, et al. Metabolites produced by commensal bacteria promote peripheral regulatory T-cell generation. Nature. 2013;504: 451–455. 10.1038/nature12726
- Zitomersky NL, Atkinson BJ, Franklin SW, Mitchell PD, Snapper SB, Comstock LE, et al. Characterization of adherent bacteroidales from intestinal biopsies of children and young adults with inflammatory bowel disease. PLoS One. 2013;8: e63686 10.1371/journal.pone.0063686
- Claesson MJ, Jeffery IB, Conde S, Power SE, O’Connor EM, Cusack S, et al. Gut microbiota composition correlates with diet and health in the elderly. Nature. 2012;488: 178–184. 10.1038/nature11319
- Le Chatelier E, Nielsen T, Qin J, Prifti E, Hildebrand F, Falony G, et al. Richness of human gut microbiome correlates with metabolic markers. Nature. 2013;500: 541–546. 10.1038/nature12506
- Scher JU, Sczesnak A, Longman RS, Segata N, Ubeda C, Bielski C, et al. Expansion of intestinal Prevotella copri correlates with enhance susceptibility to arthritis. Elife. 2013; 5: e01202.
- Mukhopadhya I, Hansen R, Nicholl CE, Alhaidan YA, Thomson JM, Berry SH, et al. A comprehensive evaluation of colonic mucosal isolates of Sutterella wadsworthensis from inflammatory bowel disease. PLoS One. 2011;6: e27076 10.1371/journal.pone.0027076
- Williams BL, Hornig M, Parekh T, Lipkin WI. Application of novel PCR-based methods for detection, quantitation, and phylogenetic characterization of Sutterella species in intestinal biopsy samples from children with autism and gastrointestinal disturbances. MBio. 2012;3: pii: e00261–11. 10.1128/mBio.00261-11
- Karlsson FH, Tremaroli V, Nookaew I, Bergström G, Carl Johan Behre CJ, Fagerberg B, et al. Gut metagenome in European women with normal, impaired and diabetic glucose control. Nature. 2013;498: 99–103. 10.1038/nature12198
- Rehman A, Rausch P, Wang J, Skieceviciene J, Kiudelis G, Bhagalia K, et al. Geographical patterns of the standing and active human gut microbiome in health and IBD. Gut. 2015. pii: gutjnl-2014-308341.
- Farrokhi V, Nemati R, Nichols FC, Yao X, Anstadt E, Fujiwara M, et al. Bacterial lipodipeptide, Lipid 654, is a microbiome-associated biomarker for multiple sclerosis. Clin Transl Immunol. 2013; 2:e8.
- Clark RB, Cervantes JL, Maciejewski MW, Farrokhi V, Nemati R, Yao X, et al. Serine lipids of Porphyromonas gingivalis are human and mouse Toll-like receptor 2 ligands. Infect Immun. 2013;81: 3479–3489. 10.1128/IAI.00803-13
Source: PubMed