VIMOGUT: In vitro and in vivo analyses and modulation of the chicken gut microbiome to combat AMR

Start: August 2019
Duration: 4 Years
Domain: Antimicrobial Resistance
Members: WBvR, WUR- the Netherlands, APHA- UK
Contact: Dr Michael Brouwer (WUR)

The Project

Based on recent advances in 16s NGS analysis, the microbiome of humans and animals has been shown to have major health effects. As such, modification of the microbiome through changes in diet can have therapeutic effects whereas treatment with antibiotics results in a drop in bacterial abundance which is generally considered a negative effect. While a study on the development of the human infant microbiome has shown three distinct phases of microbiome progression, we have recently shown that the chicken microbiome also develops along three distinct phases, although at a much shorter time-scale.

The intestinal microbiome functions as a barrier for colonisation by ingested bacteria. As such, it is likely also a barrier for bacteria resistant to antimicrobials. Antimicrobial resistance (AMR) is a major public health concern due to a predicted global rise in treatment failure, mortality and the economic burden of rising healthcare costs. Many factors contribute to this including antibiotic use and misuse, global travel, hospitalization abroad and the use of antimicrobials for treatment or as growth promoters in livestock. Although the attribution of AMR in livestock to human health is up for debate, it is desirable to reduce prevalence of AMR in livestock, foremost to decrease the likelihood of AMR bacteria passing through the food chain, but also to retain effective therapeutic treatment of the livestock itself.

Preliminary results show that the microbiome of chickens colonised early in life by extended-spectrum beta-lactamase (ESBL) producing Escherichia coli is less diverse than those of flock mates that are not colonised. This is supported by in vivo studies that have shown that competitive exclusion through probiotics is currently the most effective prevention strategy for colonisation by ESBLs. However, this strategy has been tested with limited attention for chick age. Furthermore, in practice, probiotics is considered too expensive to use throughout the whole production cycle.

An in vitro chicken gut model was developed at APHA as an alternative to study bacterial interactions in complex communities such as the microbiome. This system could be used to evaluate new treatment interventions at different stages of the microbiome development, without the ethical concerns and high cost of in vivo experiments.

The PhD project will study the chicken microbiome development of chickens on farms to determine if the reported microbial progression is reproducible between different production rounds and farms. By screening these samples for the presence of ESBL E. coli, the significance of the reduced diversity of early colonised chickens will be determined. The in vitro chicken gut model will be set up for use at WBVR to test strategies for the reduction of ESBL E. coli and compare these with published data from in vivo studies. When the model can efficiently reproduce these in vivo studies, it can be used for further study of new ESBL E. coli colonisation prevention strategies.

Ingrid Cardenas Rey

About me: I was born in Colombia. Since early life I discovered my passion for animals and their welfare. Furthermore, I got my degree of Doctor of Veterinary Medicine and moved to the US and Australia to work in practice. During this time I got a keen interest in AMR, this is the reason for moving to the Netherlands in 2017 and I started my MSc in Animal Sciences with a focus on quantitative veterinary epidemiology and AMR at Wageningen University and Research (WUR). Besides my professional life, I enjoy dancing, travelling, hiking, and having a nice cup of tea with friends.

What motivated me to do a PhD: My interest in AMR has grown since working as a veterinarian. However, my keen interest in research was not evident until my MSc. That moment was a critical milestone, I realised how much I enjoy scientific research and networking in the scientific environment. Once I heard about VIMOGUT I felt this research was the perfect match for me; I fully connected with the topic! I find it fascinating how microbes can influence our and animals wellbeing or even contribute to reducing AMR. VIMOGUT brings along many challenges but also many opportunities to develop my competences as a young scientist.


A student for this PhD project has been recruited! We would like to welcome Ingrid Cardenas Rey to the One Health EJP consortium.


A student for this PhD project has been recruited! We would like to welcome Ingrid Cardenas Rey to the One Health EJP consortium.


Cárdenas-Rey, I., Bello Gonzalez, T.d.J., van der Goot, J., Ceccarelli, D., Bouwhuis, G., Schillemans, D., Jurburg, S., Veldman, K., De Visser, A., and Brouwer, M. (2022) Succession in the caecal microbiota of developing broilers colonised by extended-spectrum β-lactamase-producing Escherichia colianim microbiome 4, 51. DOI:



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