Minimizing the impact of antibiotics: are prebiotics the answer to recover baby’s gut microbiota?

The microbial colonization of the infant gut plays a key role in human health. Consequently, disruptions during this development period have been reported to increase susceptibility to disease during life.


A disturbance, such as antibiotic treatment, may alter microbiota establishment during early life. The use of antibiotics in the first year of life has been associated with an increased risk of allergy, obesity, asthma, and other diseases in later life. Therefore, it is important to minimize the impact of antibiotics and promote the recovery of the gut microbiota.

In early life, diet also plays a key role in shaping the development of the gut microbiota. In the first months of infancy, the gut microbiota of infants is also exposed to prebiotics, such as the human milk oligosaccharides in breast milk and other non-digestible oligosaccharides in infant formula. Prebiotics are defined as compounds that promote the growth of beneficial bacteria.

Aim and set-up

In this project, we will investigate the potential of prebiotics for mitigating the antibiotic burden. For this purpose, an in vitro gut fermentation model will be used to cultivate the complex infant gut microbial communities and simulate the antibiotic perturbation. Several non-digestible oligosaccharides will be tested in the system to study the influence of these prebiotics on the resilience of infant gut microbiota. Further analysis will be performed on prebiotic utilization, microbial metabolites, microbiota composition (16S rRNA gene), and microbiota function (metatranscriptomics). Depending on the stage of the project, there are several possibilities for a BSc- or MSc thesis or internship.


If this project sparks your interest, contact Martha Florencia Endika (