Skip to main content
    • Aa
    • Aa

Challenges and opportunities for faecal microbiota transplantation therapy

  • G. B. ROGERS (a1) and K. D. BRUCE (a1)

The incidence, morbidity, and mortality associated with Clostridium difficile gastrointestinal infections has increased greatly over recent years, reaching epidemic proportions; a trend due, in part, to the emergence of hypervirulent and antibiotic-resistant strains. The need to identify alternative, non-antibiotic, treatment strategies is therefore urgent. The ability of bacteria in faecal matter transplanted from healthy individuals to displace pathogen populations is well recognized. Further, there is growing evidence that such faecal microbiota transplantation can be of benefit in a wide range of conditions associated with gut dysbiosis. Recent technical advances have greatly increased our ability to understand the processes that underpin the beneficial changes in bacterial community composition, as well as to characterize their extent and duration. However, while much of the research into faecal microbiota transplantation focuses currently on achieving clinical efficacy, the potential for such therapies to contribute to the transmission of infective agents also requires careful consideration.

Corresponding author
*Author for correspondence: Dr G. B. Rogers, King's College London, Pharmaceutical Science Division, Franklin–Wilkins Building, 150 Stamford Street, London SE1 9NH, UK. (Email:
Hide All
1. DC Savage . Microbial ecology of the gastrointestinal tract. Annual Review of Microbiology 1977; 31: 107133.

4. JH Gordon , R Dubos . The anaerobic bacterial flora of the mouse cecum. Journal of Experimental Medicine 1970; 132: 251260.

5. BS Drasar , The influence of a diet rich in wheat fibre on the human faecal flora. Journal of Medical Microbiology 1976; 9: 423431.

9. JE Clarridge 3rd. Impact of 16S rRNA gene sequence analysis for identification of bacteria on clinical microbiology and infectious diseases. Clinical Microbiology Reviews 2004; 17: 840862.

10. C Jernberg , Monitorig of antibiotic-induced alterations in the human intestinal microflora and detection of probiotic strains by use of terminal restriction fragment length polymorphism. Applied and Environmental Microbiology 2005; 71: 501506.

11. CJ Donskey , Use of denaturing gradient gel electrophoresis for analysis of the stool microbiota of hospitalized patients. Journal of Microbiological Methods 2003; 54: 249256.

12. F Armougom , D Raoult . Use of pyrosequencing and DNA barcodes to monitor variations in Firmicutes and Bacteroidetes communities in the gut microbiota of obese humans. BMC Genomics 2008; 9: 576.

13. L Dethlefsen , The pervasive effects of an antibiotic on the human gut microbiota, as revealed by deep 16S rRNA sequencing. PLoS Biology 2008; 6: 280.

14. CA Lozupone , Diversity, stability and resilience of the human gut microbiota. Nature 2012; 489: 220230.

16. T Olszak , Microbial exposure during early life has persistent effects on natural killer T cell function. Science 2012; 336: 489493.

17. TS Stappenbeck , LV Hooper , JI Gordon . Developmental regulation of intestinal angiogenesis by indigenous microbes via paneth cells. Proceedings of the National Academy of Sciences USA 2002; 99: 1545115455.

18. S Fukuda , Bifidobacteria can protect from enteropathogenic infection through production of acetate. Nature 2011; 469: 543547.

19. M Candela , Interaction of probiotic Lactobacillus and Bifidobacterium strains with human intestinal epithelial cells: adhesion properties, competition against enteropathogens and modulation of IL-8 production. International Journal of Food Microbiology 2008; 125: 286292.

20. RE Ley , Microbial ecology: human gut microbes associated with obesity. Nature 2006; 444: 10221023.

21. AL Kau , Human nutrition, the gut microbiome and the immune system. Nature 2011; 474: 327336.

22. DN Frank , Molecular-phylogenetic characterization of microbial community imbalances in human inflammatory bowel diseases. Proceedings of the National Academy of Sciences USA 2007; 104: 1378013785.

25. G Duytschaever , Cross-sectional and longitudinal comparisons of the predominant fecal microbiota compositions of a group of pediatric patients with cystic fibrosis and their healthy siblings. Applied and Environmental Microbiology 2011; 77: 80158024.

26. GB Rogers , Comparing the microbiota of the cystic fibrosis lung and human gut. Gut Microbes 2010; 1: 8593.

27. JG Bartlett , DN Gerding . Clinical recognition and diagnosis of Clostridium difficile infection. Clinical Infectious Diseases 2008; 46 (Suppl. 1): S12S18.

28. JS Bakken , Treating Clostridium difficile infection with faecal microbiota transplantation. Clinical Gastroenterology and Hepatology 2011; 9: 10441049.

29. M Rupnik , MH Wilcox , DN Gerding . Clostridium difficile infection: new developments in epidemiology and pathogenesis. Nature Reviews Microbiology 2009; 7: 526536.

30. J Freeman , The changing epidemiology of Clostridium difficile infections. Clinical Microbiology Reviews 2010; 23: 529549.

31. FA Zar , A comparison of vancomycin and metronidazole for the treatment of Clostridium difficile-associated diarrhea, stratified by disease severity. Clinical Infectious Diseases 2007; 45: 302307.

32. LV McFarland , GW Elmer , CM Surawicz . Breaking the cycle: treatment strategies for 163 cases of recurrent Clostridium difficile disease. American Journal of Gastroenterology 2002; 97: 17691775.

33. GB Rogers , MP Carroll , KD Bruce . Enhancing the utility of existing antibiotics by targeting bacterial behaviour? British Journal of Pharmacology 2012; 165: 845–57.

34. SJ Lawrence , JR Korzenik , LM Mundy . Probiotics for recurrent Clostridium difficile disease. Journal of Medical Microbiology 2005; 54: 905906.

39. TJ Borody , A Khoruts . Fecal microbiota transplantation and emerging applications. Nature Reviews Gastroenterology & Hepatology 2011; 9: 8896.

40. TJ Borody , Bacteriotherapy using fecal flora: toying with human motions. Journal of Clinical Gastroenterology 2004; 38: 475483.

41. TJ Borody , Treatment of ulcerative colitis using faecal bacteriotherapy. Journal of Clinical Gastroenterology 2003; 37: 4247.

42. SE Persky , LJ Brandt . Treatment of recurrent Clostridium difficile-associated diarrhea by administration of donated stool directly through a colonoscope. American Journal of Gastroenterology 2000; 95: 32833285.

44. MJ Hamilton , Standardized frozen preparation for transplantation of fecal microbiota for recurrent Clostridium difficile infection. American Journal of Gastroenterology 2012; 107: 761767.

45. JS Bakken . Faecal bacteriotherapy for recurrent Clostridium difficile infection. Anaerobe 2009; 15: 285289.

46. LJ Brandt , TJ Borody , J Campbell . Endoscopic fecal microbiota transplantation: ‘first-line’ treatment for severe Clostridium difficile infection? Journal of Clinical Gastroenterology 2011; 45: 655657.

49. MJ Grehan , Durable alteration of the colonic microbiota by the administration of donor fecal flora. Journal of Clinical Gastroenterology 2010; 44: 551561.

50. EO Petrof , Stool substitute transplant therapy for the eradication of Clostridium difficile infection: ‘RePOOPulating’ the gut. Microbiome 2013; 1: 3.

53. J Jansson , Metabolomics reveals metabolic biomarkers of Crohn's disease. PLoS ONE 2009; 4: e6386.

55. M Roberfroid , Prebiotic effects: metabolic and health benefits. British Journal of Nutrition 2010; 104: S1S63.

58. AM Stephen , JH Cummings . The microbial contribution to human faecal mass. Journal of Medical Microbiology 1980; 13: 4556.

59. J Qin , A human gut microbial gene catalogue established by metagenomic sequencing. Nature 2010; 464: 5965.

60.The Human Microbiome Project Consortium. Structure, function and diversity of the healthy human microbiome. Nature 2012; 486: 207214.

61. CP Kelly . Fecal microbiota transplantation – an old therapy comes of age. New England Journal of Medicine 2013; 368: 474475.

62. S Kunde , Safety, tolerability, and clinical response after fecal transplantation in children and young adults with ulcerative colitis. Journal of Pediatriatric Gastroenterology and Nutrition 2013. doi:10.1097/MPG.0b013e318292fa0d.

Recommend this journal

Email your librarian or administrator to recommend adding this journal to your organisation's collection.

Epidemiology & Infection
  • ISSN: 0950-2688
  • EISSN: 1469-4409
  • URL: /core/journals/epidemiology-and-infection
Please enter your name
Please enter a valid email address
Who would you like to send this to? *



Altmetric attention score

Full text views

Total number of HTML views: 3
Total number of PDF views: 6 *
Loading metrics...

Abstract views

Total abstract views: 144 *
Loading metrics...

* Views captured on Cambridge Core between September 2016 - 19th October 2017. This data will be updated every 24 hours.