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ESR 3.2: The effect of hospitalization and drug use on the composition of the oral and fecal microbiome



Hospitalization and treatment to cure patients, will also have an effect on the normal functioning of the body and its relationship with microbes. The development of infectious complications in patients may be associated with a dysbiosis caused by these iatrogenic effects. To study these effects, the composition of the oral and fecal microbiota will be analyzed in relation to disease outcome, such as infections, length of stay and number of comorbidities. Patient samples and data will be collected and analyzed in the microbiota research lab. The goal for this is to design clinical interventions, where infections and antibiotics use can be minimized, using strategies such as selective digestive tract decontamination (SDD) or enforcement of the normal microbiota by clinical nutrition with pre- and probiotics. To learn more about the aspects used in the interventions such as the effect of enteral feeding on microbiota and in the safety of probiotics, stays at international expert labs are planned.


  • Dr. H.J.M. (Hermie) Harmsen, PhD, microbial ecologist.
    Department of Medical Microbiology, University of Groningen, University Medical Center Groningen, Hanzeplein 1, 9713 GZ Groningen, Netherlands. [Mail], [Web]
  • Prof. dr. A.M.G.A. (Anne Marie) de Smet, MD PhD, intensivist. Department of Intensive Care Medicine, University of Groningen, University Medical Center Groningen,  Hanzeplein 1, 9713 GZ Groningen, Netherlands.[Mail], [Web]


Johan Hylcema Vlieg, Christian Hansen in Denmark 
Kevin Whelan, King’s College in London 

Relevant publications

  1. Heida FH, van Zoonen AGJF, Hulscher JBF, Te Kiefte BJC, Wessels R, Kooi EMW, et al. A Necrotizing Enterocolitis-Associated Gut Microbiota Is Present in the Meconium. Clin Infect Dis. 2016 Apr 1;62(7):863–70.
  2. de Smet AMGA, Kluytmans JAJW, Cooper BS, Mascini EM, Benus RFJ, van der Werf TS, et al. Decontamination of the Digestive Tract and Oropharynx in ICU Patients. N Engl J Med. 2009 Jan 1;360(1):20–31.
  3. de Jong E, van Oers JA, Beishuizen A, Vos P, Vermeijden WJ, Haas LE, et al. Efficacy and safety of procalcitonin guidance in reducing the duration of antibiotic treatment in critically ill patients. LANCET Infect Dis. 2016 Mar 2.
  4. Benus RFJ, van der Werf TS, Welling GW, Judd PA, Taylor MA, Harmsen HJM, et al. Association between Faecalibacterium prausnitzii and dietary fibre in colonic fermentation in healthy human subjects. Br J Nutr. 2010 Sep;104(5):693–700.


Intensive care (IC); microbiota; enteral feeding; infection​