Long-term effects on luminal and mucosal microbiota and commonly acquired taxa in faecal microbiota transplantation for recurrent Clostridium difficile infection

Jonna Jalanka, Eero Mattila, Hanne Jouhten, Jorn Hartman, Willem M de Vos, Perttu Arkkila, Reetta Satokari, Jonna Jalanka, Eero Mattila, Hanne Jouhten, Jorn Hartman, Willem M de Vos, Perttu Arkkila, Reetta Satokari

Abstract

Background: Faecal microbiota transplantation (FMT) is an effective treatment for recurrent Clostridium difficile infection (rCDI). It restores the disrupted intestinal microbiota and subsequently suppresses C. difficile. The long-term stability of the intestinal microbiota and the recovery of mucosal microbiota, both of which have not been previously studied, are assessed herein. Further, the specific bacteria behind the treatment efficacy are also investigated.

Methods: We performed a high-throughput microbiota profiling using a phylogenetic microarray analysis of 131 faecal and mucosal samples from 14 rCDI patients pre- and post-FMT during a 1-year follow-up and 23 samples from the three universal donors over the same period.

Results: The FMT treatment was successful in all patients. FMT reverted the patients' bacterial community to become dominated by Clostridium clusters IV and XIVa, the major anaerobic bacterial groups of the healthy gut. In the mucosa, the amount of facultative anaerobes decreased, whereas Bacteroidetes increased. Post-FMT, the patients' microbiota profiles were more similar to their own donors than what is generally observed for unrelated subjects and this striking similarity was retained throughout the 1-year follow-up. Furthermore, the universal donor approach allowed us to identify bacteria commonly established in all CDI patients and revealed a commonly acquired core microbiota consisting of 24 bacterial taxa.

Conclusions: FMT induces profound microbiota changes, therefore explaining the high clinical efficacy for rCDI. The identification of commonly acquired bacteria could lead to effective bacteriotherapeutic formulations. FMT can affect microbiota in the long-term and offers a means to modify it relatively permanently for the treatment of microbiota-associated diseases.

Keywords: Bacteriotherapy; Microbiome; Mucosal bacteria; Universal donor.

Figures

Fig. 1
Fig. 1
Study design. Four to eight faecal samples were collected from 14 patients and three donors over the 1-year study period, in addition to two biopsy samples (from 10 patients only). F faecal sample, B biopsy sample
Fig. 2
Fig. 2
Donors’ microbiota and alterations in the patients’ faecal and mucosal microbiota before and after faecal microbiota transplantation (FMT) treatment. a The average microbial composition in faecal samples (see panel d for bacterial groups). Donors’ microbiota shown as average from all time points. b Principle component analysis (PCA) from genus level bacterial groups in faecal samples; donors’ samples in dark blue, patients’ pre-FMT samples coloured red and post-FMT samples coloured turquoise. c Microbial diversity in faecal samples measured from patients and donors (average from all time points), statistical significance from other time points indicated with an asterisk. d The average microbial composition in patients’ mucosal samples. e PCA from genus level bacterial groups in patients’ mucosal samples, pre-FMT samples coloured red (patients with one sample n = 13 and patient P3 with 2 samples, see Additional file 1: Table S1) and post-FMT samples (patient n = 11) coloured turquoise. f The fold change of genus level bacterial groups was significantly different in the pre- and post-FMT mucosal samples. d Phylum level taxonomy
Fig. 3
Fig. 3
Microbiota stability and donor specific microbiota signatures. a Similarity of the patients microbiota to their own donors’ microbiota is significantly higher than the similarity to the other donor. Statistical significance between the groups are indicated with an asterisk (patient similarity to own donor vs. donor intra-individual similarity) and cross variation (patient similarity to own donor vs. patient similarity to other donors) is shown with standard error of mean (SEM). b Patient faecal samples present donor-specific microbial signatures in BaggedRDA analysis
Fig. 4
Fig. 4
The commonly acquired bacteria after faecal microbiota transplantation (FMT). a Flowchart showing how the commonly acquired bacteria were identified. b Heatmap showing the bacterial taxa, abundance and the stability of the therapeutic core. The bacterial groups shown with bold text were increased in all patients and the others were increased in patients from two out of three donors. *The bacteria belonging to C. difficile group include eight commensal species and uncultured representatives (see Additional file 1), which produced the detected signal. C. difficile per se was absent from all donors and patients post-FMT

References

    1. Kelly CP, LaMont JT. Clostridium difficile – More difficult than ever. New Engl J Med. 2008;359(18):1932–40. doi: 10.1056/NEJMra0707500.
    1. Louie TJ, Miller MA, Mullane KM, Weiss K, Lentnek A, Golan Y, Gorbach S, Sears P, Shue YK, OPT-80-003 Clinical Study Group Fidaxomicin versus vancomycin for Clostridium difficile infection. New Engl J Med. 2011;364(5):422–31. doi: 10.1056/NEJMoa0910812.
    1. Honda H, Dubberke ER. The changing epidemiology of Clostridium difficile infection. Curr Opin Gastroenterol. 2014;30(1):54–62. doi: 10.1097/MOG.0000000000000018.
    1. Rupnik M, Wilcox MH, Gerding DN. Clostridium difficile infection: new developments in epidemiology and pathogenesis. Nat Rev Microbiol. 2009;7(7):526–36. doi: 10.1038/nrmicro2164.
    1. Surawicz CM, Brandt LJ, Binion DG, Ananthakrishnan AN, Curry SR, Gilligan PH, McFarland LV, Mellow M, Zuckerbraun BS. Guidelines for diagnosis, treatment, and prevention of Clostridium difficile infections. Am J Gastroenterol. 2013;108(4):478–98. doi: 10.1038/ajg.2013.4.
    1. Mattila E, Arkkila P, Mattila PS, Tarkka E, Tissari P, Anttila VJ. Rifaximin in the treatment of recurrent Clostridium difficile infection. Aliment Pharmacol Ther. 2013;37(1):122–8. doi: 10.1111/apt.12111.
    1. Garey KW, Ghantoji SS, Shah DN, Habib M, Arora V, Jiang ZD, DuPont HL. A randomized, double-blind, placebo-controlled pilot study to assess the ability of rifaximin to prevent recurrent diarrhoea in patients with Clostridium difficile infection. J Antimicrob Chemother. 2011;66(12):2850–5. doi: 10.1093/jac/dkr377.
    1. Borody TJ, Khoruts A. Fecal microbiota transplantation and emerging applications. Nat Rev Gastro Hepat. 2012;9(2):88–96. doi: 10.1038/nrgastro.2011.244.
    1. Tenover FC, Tickler IA, Persing DH. Antimicrobial-resistant strains of Clostridium difficile from North America. Antimicrob Agents Chemother. 2012;56(6):2929–32. doi: 10.1128/AAC.00220-12.
    1. Brandt LJ, Aroniadis OC, Mellow M, Kanatzar A, Kelly C, Park T, Stollman N, Rohlke F, Surawicz C. Long-term follow-up of colonoscopic fecal microbiota transplant for recurrent Clostridium difficile infection. Am J Gastroenterol. 2012;107(7):1079–87. doi: 10.1038/ajg.2012.60.
    1. Mattila E, Uusitalo-Seppala R, Wuorela M, Lehtola L, Nurmi H, Ristikankare M, Moilanen V, Salminen K, Seppala M, Mattila PS, et al. Fecal transplantation, through colonoscopy, is effective therapy for recurrent Clostridium difficile infection. Gastroenterology. 2012;142(3):490–6. doi: 10.1053/j.gastro.2011.11.037.
    1. van Nood E, Vrieze A, Nieuwdorp M, Fuentes S, Zoetendal EG, de Vos WM, Visser CE, Kuijper EJ, Bartelsman JF, Tijssen JG, et al. Duodenal infusion of donor feces for recurrent Clostridium difficile. N Engl J Med. 2013;368(5):407–15. doi: 10.1056/NEJMoa1205037.
    1. Kassam Z, Lee CH, Yuan Y, Hunt RH. Fecal microbiota transplantation for Clostridium difficile infection: systematic review and meta-analysis. Am J Gastroenterol. 2013;108(4):500–8. doi: 10.1038/ajg.2013.59.
    1. Fuentes S, van Nood E, Tims S, Heikamp-de Jong I, ter Braak CJ, Keller JJ, Zoetendal EG, de Vos WM. Reset of a critically disturbed microbial ecosystem: faecal transplant in recurrent Clostridium difficile infection. ISME J. 2014;8(8):1621–33. doi: 10.1038/ismej.2014.13.
    1. Brace C, Gloor GB, Ropeleski M, Allen-Vercoe E, Petrof EO. Microbial composition analysis of Clostridium difficile infections in an ulcerative colitis patient treated with multiple fecal microbiota transplantations. J Crohns Colitis. 2014;8(9):1133–7. doi: 10.1016/j.crohns.2014.01.020.
    1. Shankar V, Hamilton MJ, Khoruts A, Kilburn A, Unno T, Paliy O, Sadowsky MJ. Species and genus level resolution analysis of gut microbiota in Clostridium difficile patients following fecal microbiota transplantation. Microbiome. 2014;2:13. doi: 10.1186/2049-2618-2-13.
    1. Weingarden A, Gonzalez A, Vazquez-Baeza Y, Weiss S, Humphry G, Berg-Lyons D, Knights D, Unno T, Bobr A, Kang J, et al. Dynamic changes in short- and long-term bacterial composition following fecal microbiota transplantation for recurrent Clostridium difficile infection. Microbiome. 2015;3:10. doi: 10.1186/s40168-015-0070-0.
    1. Lee CH, Belanger JE, Kassam Z, Smieja M, Higgins D, Broukhanski G, Kim PT. The outcome and long-term follow-up of 94 patients with recurrent and refractory Clostridium difficile infection using single to multiple fecal microbiota transplantation via retention enema. Eur J Clin Microbiol. 2014;33(8):1425–8. doi: 10.1007/s10096-014-2088-9.
    1. Weingarden AR, Dosa PI, DeWinter E, Steer CJ, Shaughnessy MK, Johnson JR, Khoruts A, Sadowsky MJ. Changes in colonic bile acid composition following fecal microbiota transplantation are sufficient to control Clostridium difficile germination and growth. PLoS One. 2016;11(1) doi: 10.1371/journal.pone.0147210.
    1. Buffie CG, Bucci V, Stein RR, McKenney PT, Ling L, Gobourne A, No D, Liu H, Kinnebrew M, Viale A, et al. Precision microbiome reconstitution restores bile acid mediated resistance to Clostridium difficile. Nature. 2015;517(7533):205–8. doi: 10.1038/nature13828.
    1. Satokari R, Mattila E, Kainulainen V, Arkkila PE. Simple faecal preparation and efficacy of frozen inoculum in faecal microbiota transplantation for recurrent Clostridium difficile infection--an observational cohort study. Aliment Pharmacol Ther. 2015;41(1):46–53. doi: 10.1111/apt.13009.
    1. Lawley TD, Clare S, Walker AW, Stares MD, Connor TR, Raisen C, Goulding D, Rad R, Schreiber F, Brandt C, et al. Targeted restoration of the intestinal microbiota with a simple, defined bacteriotherapy resolves relapsing Clostridium difficile disease in mice. PLoS Pathog. 2012;8(10) doi: 10.1371/journal.ppat.1002995.
    1. Petrof EO, Gloor GB, Vanner SJ, Weese SJ, Carter D, Daigneault MC, Brown EM, Schroeter K, Allen-Vercoe E. Stool substitute transplant therapy for the eradication of Clostridium difficile infection: 'RePOOPulating' the gut. Microbiome. 2013;1(1):3. doi: 10.1186/2049-2618-1-3.
    1. Kalliomaki M, Satokari R, Lahteenoja H, Vahamiko S, Gronlund J, Routi T, Salminen S. Expression of microbiota, Toll-like receptors, and their regulators in the small intestinal mucosa in celiac disease. J Pediatr Gastroenterol Nutr. 2012;54(6):727–32. doi: 10.1097/MPG.0b013e318241cfa8.
    1. Salonen A, Nikkilä J, Jalanka-Tuovinen J, Immonen O, Rajilic-Stojanovic M, Kekkonen RA, Palva A, de Vos WM. Comparative analysis of fecal DNA extraction methods with phylogenetic microarray: effective recovery of bacterial and archaeal DNA using mechanical cell lysis. J Microbiol Methods. 2010;81(2):127–34. doi: 10.1016/j.mimet.2010.02.007.
    1. Dore J, Ehrlich SD, Levenez F, Pelletier E, Alberti A, Bertrand L, Bork P, Costea PI, Sunagawa S, Guarner F, Manichanh C, Santiago A, Zhao L, Shen J, Zhang C, Versalovic J, Luna RA, Petrosino J, Yang H, Li S, Wang J, Allen-Vercoe E, Gloor G, Singh B; IHMS Consortium. IHMS_SOP 06V1: Standard operating procedure for fecal samples DNA extraction, Protocol Q. Int Hum Microbiome Standards. 2015. . Accessed 24 May 2016.
    1. O'Keefe SJ, Li JV, Lahti L, Ou J, Carbonero F, Mohammed K, Posma JM, Kinross J, Wahl E, Ruder E, et al. Fat, fibre and cancer risk in African Americans and rural Africans. Nat Commun. 2015;6:6342. doi: 10.1038/ncomms7342.
    1. Rajilic-Stojanovic M, Heilig HG, Molenaar D, Kajander K, Surakka A, Smidt H, de Vos WM. Development and application of the human intestinal tract chip, a phylogenetic microarray: analysis of universally conserved phylotypes in the abundant microbiota of young and elderly adults. Environ Microbiol. 2009;11(7):1736–51. doi: 10.1111/j.1462-2920.2009.01900.x.
    1. Lahti L, Salojarvi J, Salonen A, Scheffer M, de Vos WM. Tipping elements in the human intestinal ecosystem. Nat Commun. 2014;5:4344. doi: 10.1038/ncomms5344.
    1. Claesson MJ, O’Sullivan O, Wang Q, Nikkilä J, Marchesi JR, Smidt H, de Vos WM, Ross RP, O’Toole PW. Comparative analysis of pyrosequencing and a phylogenetic microarray for exploring microbial community structures in the human distal intestine. PLoS One. 2009;4(8) doi: 10.1371/journal.pone.0006669.
    1. Kainulainen V, Reunanen J, Hiippala K, Guglielmetti S, Vesterlund S, Palva A, Satokari R. BopA does not have a major role in the adhesion of Bifidobacterium bifidum to intestinal epithelial cells, extracellular matrix proteins, and mucus. Appl Environ Microbiol. 2013;79(22):6989–97. doi: 10.1128/AEM.01993-13.
    1. Jalanka-Tuovinen J, Salojarvi J, Salonen A, Immonen O, Garsed K, Kelly FM, Zaitoun A, Palva A, Spiller RC, de Vos WM. Faecal microbiota composition and host-microbe cross-talk following gastroenteritis and in postinfectious irritable bowel syndrome. Gut. 2014;63(11):1737–45. doi: 10.1136/gutjnl-2013-305994.
    1. Qin J, Li R, Raes J, Arumugam M, Burgdorf KS, Manichanh C, Nielsen T, Pons N, Levenez F, Yamada T, et al. A human gut microbial gene catalogue established by metagenomic sequencing. Nature. 2010;464(7285):59–65. doi: 10.1038/nature08821.
    1. Jalanka-Tuovinen J, Salonen A, Nikkilä J, Immonen O, Kekkonen R, Lahti L, Palva A, de Vos WM. Intestinal microbiota in healthy adults: temporal analysis reveals individual and common core and relation to intestinal symptoms. PLoS One. 2011;6(7) doi: 10.1371/journal.pone.0023035.
    1. Rajilic-Stojanovic M, Heilig HG, Tims S, Zoetendal EG, de Vos WM. Long-term monitoring of the human intestinal microbiota composition. Environ Microbiol. 2013;15(4):1146–59. doi: 10.1111/1462-2920.12023.
    1. Tims S, Derom C, Jonkers DM, Vlietinck R, Saris WH, Kleerebezem M, de Vos WM, Zoetendal EG. Microbiota conservation and BMI signatures in adult monozygotic twins. ISME J. 2013;7(4):707–17. doi: 10.1038/ismej.2012.146.
    1. Round JL, Mazmanian SK. The gut microbiota shapes intestinal immune responses during health and disease. Nat Rev Immunol. 2009;9(5):313–23. doi: 10.1038/nri2515.
    1. Hamilton MJ, Weingarden AR, Unno T, Khoruts A, Sadowsky MJ. High-throughput DNA sequence analysis reveals stable engraftment of gut microbiota following transplantation of previously frozen fecal bacteria. Gut Microbes. 2013;4(2):125–35. doi: 10.4161/gmic.23571.
    1. Dethlefsen L, Huse S, Sogin ML, Relman DA. The pervasive effects of an antibiotic on the human gut microbiota, as revealed by deep 16S rRNA sequencing. PLoS Biol. 2008;6(11) doi: 10.1371/journal.pbio.0060280.
    1. Rashid MU, Zaura E, Buijs MJ, Keijser BJF, Crielaard W, Nord CE, Weintraub A. Determining the long-term effect of antibiotic administration on the human normal intestinal microbiota using culture and pyrosequencing methods. Clin Infect Dis. 2015;60:S77–84. doi: 10.1093/cid/civ137.
    1. Zoetendal EG, von Wright A, Vilpponen-Salmela T, Ben-Amor K, Akkermans AD, de Vos WM. Mucosa-associated bacteria in the human gastrointestinal tract are uniformly distributed along the colon and differ from the community recovered from feces. Appl Environ Microbiol. 2002;68(7):3401–7. doi: 10.1128/AEM.68.7.3401-3407.2002.
    1. Satokari R, Fuentes S, Mattila E, Jalanka J, de Vos WM, Arkkila P. Fecal transplantation treatment of antibiotic-induced, noninfectious colitis and long-term microbiota follow-up. Case Rep Med. 2014;2014:913867.
    1. Reunanen J, Kainulainen V, Huuskonen L, Ottman N, Belzer C, Huhtinen H, de Vos WM, Satokari R. Akkermansia muciniphila adheres to enterocytes and strengthens the integrity of the epithelial cell layer. Appl Environ Microbiol. 2015;81(11):3655–62. doi: 10.1128/AEM.04050-14.
    1. Johnson JL, Jones MB, Cobb BA. Polysaccharide A from the capsule of Bacteroides fragilis induces clonal CD4+ T cell expansion. J Biol Chem. 2015;290(8):5007–14. doi: 10.1074/jbc.M114.621771.
    1. Wang Y, Telesford KM, Ochoa-Reparaz J, Haque-Begum S, Christy M, Kasper EJ, Wang L, Wu Y, Robson SC, Kasper DL, et al. An intestinal commensal symbiosis factor controls neuroinflammation via TLR2-mediated CD39 signalling. Nat Commun. 2014;5:4432.
    1. Li SS, Zhu A, Benes V, Costea PI, Hercog R, Hildebrand F, Huerta-Cepas J, Nieuwdorp M, Salojarvi J, Voigt AY, et al. Durable coexistence of donor and recipient strains after fecal microbiota transplantation. Science. 2016;352(6285):586–9. doi: 10.1126/science.aad8852.
    1. Cheng J, Ringel-Kulka T, Heikamp-de Jong I, Ringel Y, Carroll I, de Vos WM, Salojarvi J, Satokari R. Discordant temporal development of bacterial phyla and the emergence of core in the fecal microbiota of young children. ISME J. 2016;10(4):1002–14. doi: 10.1038/ismej.2015.177.
    1. Chu H, Khosravi A, Kusumawardhani IP, Kwon AH, Vasconcelos AC, Cunha LD, Mayer AE, Shen Y, Wu WL, Kambal A, et al. Gene-microbiota interactions contribute to the pathogenesis of inflammatory bowel disease. Science. 2016;352(6289):1116–20. doi: 10.1126/science.aad9948.
    1. Wrzosek L, Miquel S, Noordine ML, Bouet S, Chevalier-Curt MJ, Robert V, Philippe C, Bridonneau C, Cherbuy C, Robbe-Masselot C, et al. Bacteroides thetaiotaomicron and Faecalibacterium prausnitzii influence the production of mucus glycans and the development of goblet cells in the colonic epithelium of a gnotobiotic model rodent. BMC Biol. 2013;11:61. doi: 10.1186/1741-7007-11-61.
    1. Louis P, Hold GL, Flint HJ. The gut microbiota, bacterial metabolites and colorectal cancer. Nat Rev Microbiol. 2014;12(10):661–72. doi: 10.1038/nrmicro3344.
    1. Duncan SH, Louis P, Flint HJ. Lactate-utilizing bacteria, isolated from human feces, that produce butyrate as a major fermentation product. Appl Environ Microbiol. 2004;70(10):5810–7. doi: 10.1128/AEM.70.10.5810-5817.2004.
    1. Watanabe Y, Nagai F, Morotomi M. Characterization of Phascolarctobacterium succinatutens sp nov., an asaccharolytic, succinate-utilizing bacterium isolated from human feces. Appl Environ Microbiol. 2012;78(2):511–8. doi: 10.1128/AEM.06035-11.
    1. Lopez CA, Kingsbury DD, Velazquez EM, Baumler AJ. Collateral damage: microbiota-derived metabolites and immune function in the antibiotic era. Cell Host Microbe. 2014;16(2):156–63. doi: 10.1016/j.chom.2014.07.009.
    1. Atarashi K, Tanoue T, Oshima K, Suda W, Nagano Y, Nishikawa H, Fukuda S, Saito T, Narushima S, Hase K, et al. Treg induction by a rationally selected mixture of Clostridia strains from the human microbiota. Nature. 2013;500(7461):232–6. doi: 10.1038/nature12331.

Source: PubMed

Sponsors and Collaborators

Medical Conditions

Drug Interventions

3
Subscribe