Microbiota, Prebiotics, Antibiotics and Fecal Microbiota Transfer

  • Janett Nörenberg
  • Stefanie Vogler
  • Andreas StallmachEmail author


Microbiota is the collectivity of microorganisms settling in the gut of humans and animals. The symbiotic interactions between microbiota and his hosts are of essential physiological and pathophysiological importance. Compositional and metabolic changes in the gastrointestinal microbiota (“dysbiosis”) are associated with the development and maintenance of several inflammatory disorders including chronic inflammatory bowel disease (IBD).

IBD-associated dysbiosis can be treated by the administration of antibiotics and of prebiotics/probiotics and by fecal microbiota transfer (FMT). It was found that treatment with antibiotics can harm beneficial microorganisms leading to a changed composition of microbiota and therefore is no longer the first choice. Prebiotics are food ingredients that induce growth or activity of beneficial microorganisms. Probiotics include nonpathogenic living microorganisms that overpopulate the gut. They have positive impacts on the balance of microbes and improve the absorption of micronutrients. Therefore they may have positive impacts on the course of IBD.

Recently, the effectiveness and safety of a novel therapeutic application such as FMT have been demonstrated. It is about a transplantation of fecal microorganisms from a healthy donor in the form of stool suspensions applicated by endoscopy or gastronasal tubes into the patient’s small or large intestine. Although further research is still needed to understand the relationship between dysbiosis of gut microbiota and extra- and intraintestinal inflammation, FMT is a promising approach to treat IBD.


Crohn’s disease Ulcerative colitis Fecal microbiota transfer Prebiotics Probiotics Microbiome 


  1. Anderson JL, Hedin CR, Benjamin JL et al (2015) Dietary intake of inulin-type fructans in active and inactive Crohn's disease and healthy controls: a case-control study. J Crohns Colitis 9:1024–1031CrossRefGoogle Scholar
  2. Bajer L, Kverka M, Kostovcik M et al (2017) Distinct gut microbiota profiles in patients with primary sclerosing cholangitis and ulcerative colitis. World J Gastroenterol 23:4548–4558CrossRefGoogle Scholar
  3. Benjamin JL, Hedin CR, Koutsoumpas A et al (2011) Randomised, double-blind, placebo-controlled trial of fructo-oligosaccharides in active Crohn’s disease. Gut 60:923–929CrossRefGoogle Scholar
  4. Cammarota G, Ianiro G, Tilg H et al (2017) European consensus conference on faecal microbiota transplantation in clinical practice. Gut 66:569–580CrossRefGoogle Scholar
  5. Chen GL, Zhang Y, Wang WY et al (2017) Partners of patients with ulcerative colitis exhibit a biologically relevant dysbiosis in fecal microbial metacommunities. World J Gastroenterol 23:4624–4631CrossRefGoogle Scholar
  6. Costello S, Waters O, Bryant R et al (2017) Short duration, low intensity pooled faecal microbiota transplantation induces remission in patients with mild-moderately active ulcerative colitis: a randomised controlled trial. J Crohn's Colitis 11:S23CrossRefGoogle Scholar
  7. Feagins LA, Holubar SD, Kane SV et al (2011) Current strategies in the management of intra-abdominal abscesses in Crohn’s disease. Clin Gastroenterol Hepatol 9:842–850CrossRefGoogle Scholar
  8. Gerasimidis K, Bertz M, Hanske L et al (2014) Decline in presumptively protective gut bacterial species and metabolites are paradoxically associated with disease improvement in pediatric Crohn’s disease during enteral nutrition. Inflamm Bowel Dis 20:861–871CrossRefGoogle Scholar
  9. Gevers D, Kugathasan S, Denson LA et al (2014) The treatment-naive microbiome in new-onset Crohn’s disease. Cell Host Microbe 15:382–392CrossRefGoogle Scholar
  10. Gong D, Gong X, Wang L et al (2016) Involvement of reduced microbial diversity in inflammatory bowel disease. Gastroenterol Res Pract 2016:6951091CrossRefGoogle Scholar
  11. Gupta P, Andrew H, Kirschner BS et al (2000) Is lactobacillus GG helpful in children with Crohn’s disease? Results of a preliminary, open-label study. J Pediatr Gastroenterol Nutr 31:453–457CrossRefGoogle Scholar
  12. Harper PH, Truelove SC, Lee EC et al (1983) Split ileostomy and ileocolostomy for Crohn’s disease of the colon and ulcerative colitis: a 20 year survey. Gut 24:106–113CrossRefGoogle Scholar
  13. Hartong WA, Arvanitakis C, Skibba RM et al (1977) Treatment of toxic megacolon. A comparative review of 29 patients. Am J Dig Dis 22:195–200CrossRefGoogle Scholar
  14. Hashash JG, Chintamaneni P, Ramos Rivers CM et al (2015) Patterns of antibiotic exposure and clinical disease activity in inflammatory bowel disease: a 4-year prospective study. Inflamm Bowel Dis 21:2576–2582CrossRefGoogle Scholar
  15. Hold GL (2014) The gut microbiota, dietary extremes and exercise. Gut 63:1838–1839CrossRefGoogle Scholar
  16. Hviid A, Svanstrom H, Frisch M (2011) Antibiotic use and inflammatory bowel diseases in childhood. Gut 60:49–54CrossRefGoogle Scholar
  17. Jonkers D, Penders J, Masclee A et al (2012) Probiotics in the management of inflammatory bowel disease: a systematic review of intervention studies in adult patients. Drugs 72:803–823CrossRefGoogle Scholar
  18. Khan KJ, Ullman TA, Ford AC et al (2011) Antibiotic therapy in inflammatory bowel disease: a systematic review and meta-analysis. Am J Gastroenterol 106:661–673CrossRefGoogle Scholar
  19. König J, Siebenhaar A, Hogenauer C et al (2017) Consensus report: faecal microbiota transfer—clinical applications and procedures. Aliment Pharmacol Ther 45:222–239CrossRefGoogle Scholar
  20. Kronman MP, Zaoutis TE, Haynes K et al (2012) Antibiotic exposure and IBD development among children: a population-based cohort study. Pediatrics 130:e794–e803CrossRefGoogle Scholar
  21. Malchow HA (1997) Crohn’s disease and Escherichia coli. A new approach in therapy to maintain remission of colonic Crohn’s disease? J Clin Gastroenterol 25:653–658CrossRefGoogle Scholar
  22. Mizuno S, Nanki K, Matsuoka K et al (2017) Single fecal microbiota transplantation failed to change intestinal microbiota and had limited effectiveness against ulcerative colitis in Japanese patients. Intest Res 15:68–74CrossRefGoogle Scholar
  23. Moayyedi P, Surette MG, Kim PT et al (2015) Fecal microbiota transplantation induces remission in patients with active ulcerative colitis in a randomized controlled trial. Gastroenterology 149:102–109.e106CrossRefGoogle Scholar
  24. Nagalingam NA, Lynch SV (2012) Role of the microbiota in inflammatory bowel diseases. Inflamm Bowel Dis 18:968–984CrossRefGoogle Scholar
  25. Paramsothy S, Borody TJ, Lin E et al (2015) Donor recruitment for fecal microbiota transplantation. Inflamm Bowel Dis 21:1600–1606CrossRefGoogle Scholar
  26. Paramsothy S, Kamm MA, Kaakoush NO et al (2017a) Multidonor intensive faecal microbiota transplantation for active ulcerative colitis: a randomised placebo-controlled trial. Lancet 389(10075):1218–1228. CrossRefPubMedGoogle Scholar
  27. Paramsothy S, Paramsothy R, Rubin DT et al (2017b) Faecal microbiota transplantation for inflammatory bowel disease: a systematic review and meta-analysis. J Crohns Colitis 11(10):1180–1199. CrossRefPubMedGoogle Scholar
  28. Qin J, Li R, Raes J et al (2010) A human gut microbial gene catalogue established by metagenomic sequencing. Nature 464:59–65CrossRefGoogle Scholar
  29. Reshef L, Kovacs A, Ofer A et al (2015) Pouch inflammation is associated with a decrease in specific bacterial taxa. Gastroenterology 149:718–727CrossRefGoogle Scholar
  30. Rossen NG, Fuentes S, van der Spek MJ et al (2015) Findings from a randomized controlled trial of fecal transplantation for patients with ulcerative colitis. Gastroenterology 149:110–118.e114CrossRefGoogle Scholar
  31. Sartor RB (2008) Microbial influences in inflammatory bowel diseases. Gastroenterology 134:577–594CrossRefGoogle Scholar
  32. Schultz M, Timmer A, Herfarth HH et al (2004) Lactobacillus GG in inducing and maintaining remission of Crohn’s disease. BMC Gastroenterol 4:5CrossRefGoogle Scholar
  33. Selby W, Pavli P, Crotty B et al (2007) Two-year combination antibiotic therapy with clarithromycin, rifabutin, and clofazimine for Crohn’s disease. Gastroenterology 132:2313–2319CrossRefGoogle Scholar
  34. Sender R, Fuchs S, Milo R (2016) Revised estimates for the number of human and bacteria cells in the body. PLoS Biol 14:e1002533CrossRefGoogle Scholar
  35. Singh S, Stroud AM, Holubar SD et al (2015) Treatment and prevention of pouchitis after ileal pouch-anal anastomosis for chronic ulcerative colitis. Cochrane Database Syst Rev (11):CD001176.
  36. Sood A, Midha V, Makharia GK et al (2009) The probiotic preparation, VSL#3 induces remission in patients with mild-to-moderately active ulcerative colitis. Clin Gastroenterol Hepatol 7:1202–1209CrossRefGoogle Scholar
  37. Stallmach A, Carstens O (2002) Role of infections in the manifestation or reactivation of inflammatory bowel diseases. Inflamm Bowel Dis 8:213–218CrossRefGoogle Scholar
  38. Tursi A, Brandimarte G, Giorgetti GM et al (2004) Low-dose balsalazide plus a high-potency probiotic preparation is more effective than balsalazide alone or mesalazine in the treatment of acute mild-to-moderate ulcerative colitis. Med Sci Monit 10:PI126–PI131PubMedGoogle Scholar
  39. Tursi A, Brandimarte G, Papa A et al (2010) Treatment of relapsing mild-to-moderate ulcerative colitis with the probiotic VSL#3 as adjunctive to a standard pharmaceutical treatment: a double-blind, randomized, placebo-controlled study. Am J Gastroenterol 105:2218–2227CrossRefGoogle Scholar
  40. Ungaro R, Bernstein CN, Gearry R et al (2014) Antibiotics associated with increased risk of new-onset Crohn's disease but not ulcerative colitis: a meta-analysis. Am J Gastroenterol 109:1728–1738CrossRefGoogle Scholar
  41. Virta L, Auvinen A, Helenius H et al (2012) Association of repeated exposure to antibiotics with the development of pediatric Crohn’s disease—a nationwide, register-based finnish case-control study. Am J Epidemiol 175:775–784CrossRefGoogle Scholar
  42. Wang SL, Wang ZR, Yang CQ (2012) Meta-analysis of broad-spectrum antibiotic therapy in patients with active inflammatory bowel disease. Exp Ther Med 4:1051–1056CrossRefGoogle Scholar
  43. West RL, van der Woude CJ, Hansen BE et al (2004) Clinical and endosonographic effect of ciprofloxacin on the treatment of perianal fistulae in Crohn’s disease with infliximab: a double-blind placebo-controlled study. Aliment Pharmacol Ther 20:1329–1336CrossRefGoogle Scholar
  44. Youngster I, Russell GH, Pindar C et al (2014) Oral, capsulized, frozen fecal microbiota transplantation for relapsing Clostridium difficile infection. JAMA 312:1772–1778CrossRefGoogle Scholar
  45. Zoetendal EG, von Wright A, Vilpponen-Salmela T et al (2002) 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 68:3401–3407CrossRefGoogle Scholar

Copyright information

© Springer Nature Switzerland AG 2019

Authors and Affiliations

  • Janett Nörenberg
    • 1
  • Stefanie Vogler
    • 1
  • Andreas Stallmach
    • 1
    Email author
  1. 1.Department of Internal Medicine IV (Gastroenterology, Hepatology, and Infectious Diseases)Jena University Hospital, University of JenaJenaGermany

Personalised recommendations