Carbohydrate-induced resilience of the gut microbiota after exposure to antibiotics


Although antibiotics have drastically reduced infection-associated morbidity and mortality, their use is also associated with detrimental health effects amongst others through perturbations of our intestinal microbes (microbiota). The impact of antibiotics on the extend and degree of microbial perturbations does not only depend on the type of antibiotics, but also on individual microbiota composition and dietary intake among other factors. The mechanisms underlying inter-individual variations in antibiotic-induced microbial perturbations and whether faster recovery of the microbiota can be induced by stimulation of specific microbial groups via non-digestible carbohydrates are largely unknown. Hence, the aim of our research is to identify the subject-specific impact of antibiotics on the intestinal microbiota and its subsequent resilience level, and to study whether administration of non-digestible carbohydrates can improve resilience and metabolic health in subjects with slow microbiota recovery. To realize this, we will use samples obtained from our previous human vancomycin and amoxicillin intervention study to determine how these antibiotics induced individual-specific effects on microbiota composition and activity level, host metabolism, and their resilience. These observations will be simulated in vitro and subsequently, a number of non-digestible carbohydrates will be screened for their potential to improve resilience of slowly-recovering microbiotas. Based on these experiments an intervention trial with healthy overweight adults will be implemented. This study will provide novel insights into the antibiotics-induced resilience of the microbiota that can be used to predict the action of antibiotics, how fast microbial and metabolic recovery can be induced, and identify carbohydrates that improve this resilience.


Project number


Main applicant

Dr. E.G. Zoetendal

Affiliated with

Wageningen University & Research, Agrotechnologie & Voedingswetenschappen, Microbiologie (MIB)

Team members

M. Fassarella MA MSc


01/06/2018 to 31/12/2021