Abstract
There is substantial potential for the human intestinal microbiota to be mined for its therapeutic potential. Absent exogenous perturbations, the intestinal microbiota tends to be highly stable throughout adult life, and it appears to be associated with a variety of rheumatic diseases. Furthermore, the microbiota can influence the metabolism of many medicines used to treat inflammatory diseases, thus potentially playing a role in the disease process even in the absence of specific abnormalities in its composition. We have multiple tools at hand to alter the microbiota, and the future may hold targeted approaches to remove specific bacteria associated with a particular condition. Finally, there is evidence that an individual’s baseline microbiota might predict his or her response to dietary therapy, thus ushering in an era of individualized medicine targeting the human intestinal microbiota.
This is a preview of subscription content, log in via an institution.
Buying options
Tax calculation will be finalised at checkout
Purchases are for personal use only
Learn about institutional subscriptionsAbbreviations
- AID:
-
Anti-inflammatory diet
- CGR:
-
Cardiac glycoside reductase
- EEN:
-
Exclusive enteral nutrition
- FMT:
-
Fecal microbial transplantation
- HMP:
-
Human Microbiome Project
- IBD:
-
Inflammatory bowel disease
- JIA:
-
Juvenile idiopathic arthritis
- RA:
-
Rheumatoid arthritis
- ReA:
-
Reactive arthritis
- SCFA:
-
Short-chain fatty acids
- SpA:
-
Spondyloarthritis
References
Clunie GP, Lennard L. Relevance of thiopurine methyltransferase status in rheumatology patients receiving azathioprine. Rheumatology (Oxford). 2004;43(1):13–8.
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(7285):59–65.
Brewerton DA, Hart FD, Nicholls A, Caffrey M, James DC, Sturrock RD. Ankylosing spondylitis and HL-A 27. Lancet. 1973;1(7809):904–7.
Backhed F, Roswall J, Peng Y, Feng Q, Jia H, Kovatcheva-Datchary P, et al. Dynamics and stabilization of the human gut Microbiome during the first year of life. Cell Host Microbe. 2015;17(6):852.
Dominguez-Bello MG, Costello EK, Contreras M, Magris M, Hidalgo G, Fierer N, et al. Delivery mode shapes the acquisition and structure of the initial microbiota across multiple body habitats in newborns. Proc Natl Acad Sci U S A. 2010;107(26):11971–5.
Yatsunenko T, Rey FE, Manary MJ, Trehan I, Dominguez-Bello MG, Contreras M, et al. Human gut microbiome viewed across age and geography. Nature. 2012;486(7402):222–7.
Hollister EB, Riehle K, Luna RA, Weidler EM, Rubio-Gonzales M, Mistretta TA, et al. Structure and function of the healthy pre-adolescent pediatric gut microbiome. Microbiome. 2015;3:36.
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(5960):1694–7.
Faith JJ, Guruge JL, Charbonneau M, Subramanian S, Seedorf H, Goodman AL, et al. The long-term stability of the human gut microbiota. Science. 2013;341(6141):1237439.
Franzosa EA, Huang K, Meadow JF, Gevers D, Lemon KP, Bohannan BJ, et al. Identifying personal microbiomes using metagenomic codes. Proc Natl Acad Sci U S A. 2015;112(22):E2930–8.
Taurog JD, Richardson JA, Croft JT, Simmons WA, Zhou M, Fernandez-Sueiro JL, et al. The germfree state prevents development of gut and joint inflammatory disease in HLA-B27 transgenic rats. J Exp Med. 1994;180(6):2359–64.
Wu HJ, Ivanov II, Darce J, Hattori K, Shima T, Umesaki Y, et al. Gut-residing segmented filamentous bacteria drive autoimmune arthritis via T helper 17 cells. Immunity. 2010;32(6):815–27.
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(7374):538–41.
Vieira AT, Macia L, Galvao I, Martins FS, Canesso MC, Amaral FA, et al. A role for gut Microbiota and the metabolite-sensing receptor GPR43 in a murine model of gout. Arthritis Rheumatol. 2015;67(6):1646–56.
Sokol H, Seksik P, Furet JP, Firmesse O, Nion-Larmurier I, Beaugerie L, et al. Low counts of Faecalibacterium prausnitzii in colitis microbiota. Inflamm Bowel Dis. 2009;15(8):1183–9.
Machiels K, Joossens M, Sabino J, De Preter V, Arijs I, Eeckhaut V, et al. A decrease of the butyrate-producing species Roseburia hominis and Faecalibacterium prausnitzii defines dysbiosis in patients with ulcerative colitis. Gut. 2013;63(8):1275–83.
Stoll ML, Kumar R, Morrow CD, Lefkowitz EJ, Cui X, Genin A, et al. Altered microbiota associated with abnormal humoral immune responses to commensal organisms in enthesitis-related arthritis. Arthritis Res Ther. 2014;16(6):486.
Shaw KA, Bertha M, Hofmekler T, Chopra P, Vatanen T, Srivatsa A, et al. Dysbiosis, inflammation, and response to treatment: a longitudinal study of pediatric subjects with newly diagnosed inflammatory bowel disease. Genome Med. 2016;8(1):75.
Maeda Y, Kurakawa T, Umemoto E, Motooka D, Ito Y, Gotoh K, et al. Dysbiosis contributes to arthritis development via activation of autoreactive T cells in the intestine. Arthritis Rheumatol. 2016;68(11):2646–61.
Scher JU, Sczesnak A, Longman RS, Segata N, Ubeda C, Bielski C, et al. Expansion of intestinal Prevotella copri correlates with enhanced susceptibility to arthritis. Elife. 2013;2:e01202.
Tejesvi MV, Arvonen M, Kangas SM, Keskitalo PL, Pirttila AM, Karttunen TJ, et al. Faecal microbiome in new-onset juvenile idiopathic arthritis. Eur J Clin Microbiol Infect Dis. 2015;35(3):363–70.
Giongo A, Gano KA, Crabb DB, Mukherjee N, Novelo LL, Casella G, et al. Toward defining the autoimmune microbiome for type 1 diabetes. ISME J. 2011;5(1):82–91.
Murri M, Leiva I, Gomez-Zumaquero JM, Tinahones FJ, Cardona F, Soriguer F, et al. Gut microbiota in children with type 1 diabetes differs from that in healthy children: a case-control study. BMC Med. 2013;11:46.
Zhou Y, Zhi F. Lower level of Bacteroides in the gut Microbiota is associated with inflammatory bowel disease: a meta-analysis. Biomed Res Int. 2016;2016:5828959.
Durban A, Abellan JJ, Jimenez-Hernandez N, Salgado P, Ponce M, Ponce J, et al. Structural alterations of faecal and mucosa-associated bacterial communities in irritable bowel syndrome. Environ Microbiol Rep. 2012;4(2):242–7.
Scher JU, Ubeda C, Artacho A, Attur M, Isaac S, Reddy SM, et al. Decreased bacterial diversity characterizes the altered gut microbiota in patients with psoriatic arthritis, resembling dysbiosis in inflammatory bowel disease. Arthritis Rheumatol. 2015;67(1):128–39.
Michail S, Durbin M, Turner D, Griffiths AM, Mack DR, Hyams J, et al. Alterations in the gut microbiome of children with severe ulcerative colitis. Inflamm Bowel Dis. 2012;18(10):1799–808.
Taur Y, Jenq RR, Perales MA, Littmann ER, Morjaria S, Ling L, et al. The effects of intestinal tract bacterial diversity on mortality following allogeneic hematopoietic stem cell transplantation. Blood. 2014;124(7):1174–82.
Stoll ML. Gut microbes, immunity, and spondyloarthritis. Clin Immunol. 2015;159(2):134–42.
Thaiss CA, Zmora N, Levy M, Elinav E. The microbiome and innate immunity. Nature. 2016;535(7610):65–74.
Round JL, Lee SM, Li J, Tran G, Jabri B, Chatila TA, et al. The toll-like receptor 2 pathway establishes colonization by a commensal of the human microbiota. Science. 2011;332(6032):974–7.
Farkas AM, Panea C, Goto Y, Nakato G, Galan-Diez M, Narushima S, et al. Induction of Th17 cells by segmented filamentous bacteria in the murine intestine. J Immunol Methods. 2015;421:104–11.
Hussaarts L, Yazdanbakhsh M, Guigas B. Priming dendritic cells for th2 polarization: lessons learned from helminths and implications for metabolic disorders. Front Immunol. 2014;5:499.
Summers RW, Elliott DE, Urban JF Jr, Thompson R, Weinstock JV. Trichuris suis therapy in Crohn’s disease. Gut. 2005;54(1):87–90.
Summers RW, Elliott DE, Urban JF Jr, Thompson RA, Weinstock JV. Trichuris suis therapy for active ulcerative colitis: a randomized controlled trial. Gastroenterology. 2005;128(4):825–32.
Spanogiannopoulos P, Bess EN, Carmody RN, Turnbaugh PJ. The microbial pharmacists within us: a metagenomic view of xenobiotic metabolism. Nat Rev Microbiol. 2016;14(5):273–87.
Jourova L, Anzenbacher P, Anzenbacherova E. Human gut microbiota plays a role in the metabolism of drugs. Biomed Pap Med Fac Univ Palacky Olomouc Czech Repub. 2016;160(3):317–26.
Morgan SL, Baggott JE, Vaughn WH, Austin JS, Veitch TA, Lee JY, et al. Supplementation with folic acid during methotrexate therapy for rheumatoid arthritis. A double-blind, placebo-controlled trial. Ann Intern Med. 1994;121(11):833–41.
Graham LD, Myones BL, Rivas-Chacon RF, Pachman LM. Morbidity associated with long-term methotrexate therapy in juvenile rheumatoid arthritis. J Pediatr. 1992;120(3):468–73.
Nayak RR, O’Loughlin C, Fischbach M, Turnbaugh PJ. Methotrexate is an antibacterial drug metabolized by human gut Bacteria [abstract]. Arthritis Rheum. 2016;68(suppl 10).
Robertson LW, Chandrasekaran A, Reuning RH, Hui J, Rawal BD. Reduction of digoxin to 20R-dihydrodigoxin by cultures of Eubacterium lentum. Appl Environ Microbiol. 1986;51(6):1300–3.
Greenblatt DJ, Smith TW, Koch-Weser J. Bioavailability of drugs: the digoxin dilemma. Clin Pharmacokinet. 1976;1(1):36–51.
Lindenbaum J, Rund DG, Butler VP Jr, Tse-Eng D, Saha JR. Inactivation of digoxin by the gut flora: reversal by antibiotic therapy. N Engl J Med. 1981;305(14):789–94.
Saha JR, Butler VP Jr, Neu HC, Lindenbaum J. Digoxin-inactivating bacteria: identification in human gut flora. Science. 1983;220(4594):325–7.
Haiser HJ, Gootenberg DB, Chatman K, Sirasani G, Balskus EP, Turnbaugh PJ. Predicting and manipulating cardiac drug inactivation by the human gut bacterium Eggerthella lenta. Science. 2013;341(6143):295–8.
Sokol H. Probiotics and antibiotics in IBD. Dig Dis. 2014;32(Suppl 1):10–7.
Carter JD. Reactive arthritis: defined etiologies, emerging pathophysiology, and unresolved treatment. Infect Dis Clin N Am. 2006;20(4):827–47.
Barber CE, Kim J, Inman RD, Esdaile JM, James MT. Antibiotics for treatment of reactive arthritis: a systematic review and metaanalysis. J Rheumatol. 2013;40(6):916–28.
Smieja M, MacPherson DW, Kean W, Schmuck ML, Goldsmith CH, Buchanan W, et al. Randomised, blinded, placebo controlled trial of doxycycline for chronic seronegative arthritis. Ann Rheum Dis. 2001;60(12):1088–94.
Derikx LA, Dieleman LA, Hoentjen F. Probiotics and prebiotics in ulcerative colitis. Best Pract Res Clin Gastroenterol. 2016;30(1):55–71.
Jenks K, Stebbings S, Burton J, Schultz M, Herbison P, Highton J. Probiotic therapy for the treatment of spondyloarthritis: a randomized controlled trial. J Rheumatol. 2010;37(10):2118–25.
Brophy S, Burrows CL, Brooks C, Gravenor MB, Siebert S, Allen SJ. Internet-based randomised controlled trials for the evaluation of complementary and alternative medicines: probiotics in spondyloarthropathy. BMC Musculoskelet Disord. 2008;9:4.
Shukla A, Gaur P, Aggarwal A. Effect of probiotics on clinical and immune parameters in enthesitis-related arthritis category of juvenile idiopathic arthritis. Clin Exp Immunol. 2016;185(3):301–8.
Kristensen NB, Bryrup T, Allin KH, Nielsen T, Hansen TH, Pedersen O. Alterations in fecal microbiota composition by probiotic supplementation in healthy adults: a systematic review of randomized controlled trials. Genome Med. 2016;8(1):52.
Shen TC, Albenberg L, Bittinger K, Chehoud C, Chen YY, Judge CA, et al. Engineering the gut microbiota to treat hyperammonemia. J Clin Invest. 2015;125(7):2841–50.
Wu GD, Chen J, Hoffmann C, Bittinger K, Chen YY, Keilbaugh SA, et al. Linking long-term dietary patterns with gut microbial enterotypes. Science. 2011;334(6052):105–8.
David LA, Maurice CF, Carmody RN, Gootenberg DB, Button JE, Wolfe BE, et al. Diet rapidly and reproducibly alters the human gut microbiome. Nature. 2014;505(7484):559–63.
Bindels LB, Neyrinck AM, Salazar N, Taminiau B, Druart C, Muccioli GG, et al. Non digestible oligosaccharides modulate the gut Microbiota to control the development of Leukemia and associated Cachexia in mice. PLoS One. 2015;10(6):e0131009.
Lukens JR, Gurung P, Vogel P, Johnson GR, Carter RA, McGoldrick DJ, et al. Dietary modulation of the microbiome affects autoinflammatory disease. Nature. 2014;516(7530):246–9.
McAllan L, Skuse P, Cotter PD, O’Connor P, Cryan JF, Ross RP, et al. Protein quality and the protein to carbohydrate ratio within a high fat diet influences energy balance and the gut microbiota in C57BL/6J mice. PLoS One. 2014;9(2):e88904.
Le Leu RK, Young GP, Hu Y, Winter J, Conlon MA, et al. Dig Dis Sci. 2013;58(12):3475–82.
Sprong RC, Schonewille AJ, van der Meer R. Dietary cheese whey protein protects rats against mild dextran sulfate sodium-induced colitis: role of mucin and microbiota. J Dairy Sci. 2010;93(4):1364–71.
Kakodkar S, Farooqui AJ, Mikolaitis SL, Mutlu EA. The specific carbohydrate diet for inflammatory bowel disease: a case series. J Acad Nutr Diet. 2015;115(8):1226–32.
Ruemmele FM. Role of diet in inflammatory bowel disease. Ann Nutr Metab. 2016;68(Suppl 1):33–41.
Arpaia N, Campbell C, Fan X, Dikiy S, van der Veeken J, de Roos P, et al. Metabolites produced by commensal bacteria promote peripheral regulatory T-cell generation. Nature. 2013;504(7480):451–5.
Cao Y, Shen J, Ran ZH. Association between Faecalibacterium prausnitzii reduction and inflammatory bowel disease: a meta-analysis and systematic review of the literature. Gastroenterol Res Pract. 2014;2014:872725.
Brotherton CS, Taylor AG, Bourguignon C, Anderson JG. A high-fiber diet may improve bowel function and health-related quality of life in patients with Crohn disease. Gastroenterol Nurs. 2014;37(3):206–16.
Olendzki BC, Silverstein TD, Persuitte GM, Ma Y, Baldwin KR, Cave D. An anti-inflammatory diet as treatment for inflammatory bowel disease: a case series report. Nutr J. 2014;13:5.
Sigall-Boneh R, Pfeffer-Gik T, Segal I, Zangen T, Boaz M, Levine A. Partial enteral nutrition with a Crohn’s disease exclusion diet is effective for induction of remission in children and young adults with Crohn’s disease. Inflamm Bowel Dis. 2014;20(8):1353–60.
Whitten KE, Rogers P, Ooi CY, Day AS. International survey of enteral nutrition protocols used in children with Crohn’s disease. J Dig Dis. 2012;13(2):107–12.
Heuschkel RB, Menache CC, Megerian JT, Baird AE. Enteral nutrition and corticosteroids in the treatment of acute Crohn’s disease in children. J Pediatr Gastroenterol Nutr. 2000;31(1):8–15.
Berntson L, Hedlund-Treutiger I, Alving K. Anti-inflammatory effect of exclusive enteral nutrition in patients with juvenile idiopathic arthritis. Clin Exp Rheumatol. 2016;34(5):941–5.
Berntson L, Agback P, Dicksved J. Changes in fecal microbiota and metabolomics in a child with juvenile idiopathic arthritis (JIA) responding to two treatment periods with exclusive enteral nutrition (EEN). Clin Rheumatol. 2016;35(6):1501–6.
Kang C, Zhang Y, Zhu X, Liu K, Wang X, Chen M, et al. Healthy subjects differentially respond to dietary capsaicin correlating with the specific gut enterotypes. J Clin Endocrinol Metab. 2016;101(12):4681–9. jc20162786.
Stapel SO, Asero R, Ballmer-Weber BK, Knol EF, Strobel S, Vieths S, et al. Testing for IgG4 against foods is not recommended as a diagnostic tool: EAACI task force report. Allergy. 2008;63(7):793–6.
Shivappa N, Steck SE, Hurley TG, Hussey JR, Hebert JR. Designing and developing a literature-derived, population-based dietary inflammatory index. Public Health Nutr. 2014;17(8):1689–96.
Russell GH, Kaplan JL, Youngster I, Baril-Dore M, Schindelar L, Hohmann E, et al. Fecal transplant for recurrent Clostridium difficile infection in children with and without inflammatory bowel disease. J Pediatr Gastroenterol Nutr. 2014;58(5):588–92.
Zhang FM, Wang HG, Wang M, Cui BT, Fan ZN, Ji GZ. Fecal microbiota transplantation for severe enterocolonic fistulizing Crohn’s disease. World J Gastroenterol. 2013;19(41):7213–6.
Suskind DL, Brittnacher MJ, Wahbeh G, Shaffer ML, Hayden HS, Qin X, et al. Fecal microbial transplant effect on clinical outcomes and fecal microbiome in active Crohn’s disease. Inflamm Bowel Dis. 2015;21(3):556–63.
Suskind DL, Singh N, Nielson H, Wahbeh G. Fecal microbial transplant via nasogastric tube for active pediatric ulcerative colitis. J Pediatr Gastroenterol Nutr. 2015;60(1):27–9.
Quera R, Espinoza R, Estay C, Rivera D. Bacteremia as an adverse event of fecal microbiota transplantation in a patient with Crohn’s disease and recurrent Clostridium difficile infection. J Crohns Colitis. 2014;8(3):252–3.
Kuntz TM, Gilbert JA. Introducing the Microbiome into precision medicine. Trends Pharmacol Sci. 2016;38(1):81–91.
Guo L, McLean JS, Yang Y, Eckert R, Kaplan CW, Kyme P, et al. Precision-guided antimicrobial peptide as a targeted modulator of human microbial ecology. Proc Natl Acad Sci USA. 2015;112(24):7569–74.
Kutter E, De Vos D, Gvasalia G, Alavidze Z, Gogokhia L, Kuhl S, et al. Phage therapy in clinical practice: treatment of human infections. Curr Pharm Biotechnol. 2010;11(1):69–86.
Stoll ML, Kumar R, Lefkowitz EJ, Cron RQ, Morrow CD, Barnes S. Fecal metabolomics in pediatric spondyloarthritis implicate decreased metabolic diversity and altered tryptophan metabolism as pathogenic factors. Genes Immun. 2016;17(7):400–5.
Author information
Authors and Affiliations
Corresponding author
Editor information
Editors and Affiliations
Rights and permissions
Copyright information
© 2018 Springer International Publishing AG, part of Springer Nature
About this chapter
Cite this chapter
Stoll, M.L. (2018). The Promise of Personalized Medicine. In: Ragab, G., Atkinson, T., Stoll, M. (eds) The Microbiome in Rheumatic Diseases and Infection. Springer, Cham. https://doi.org/10.1007/978-3-319-79026-8_35
Download citation
DOI: https://doi.org/10.1007/978-3-319-79026-8_35
Published:
Publisher Name: Springer, Cham
Print ISBN: 978-3-319-79025-1
Online ISBN: 978-3-319-79026-8
eBook Packages: MedicineMedicine (R0)