phd project

Simulating the effects of potable water microbial composition on the microbiome in the human gut

Drinking water can contain different types of bacteria and a large variety of low concentrations of chemical substances. Regarding the microbiological quality only heterotrophic plate counts and a few indicator or pathogenic species are regulated by law whereas the indigenous benign community is disregarded. Recent studies have shown that the water microbiome, a community composed of bacteria with either a low or a high nucleic acid content (LNA or HNA), can be influenced by a variety of biotic and abiotic factors. Whereas the LNA bacteria are thought of as the natural microbes living in nutrient deprived situations like drinking water, HNA bacteria may represent the pathogenic fraction of microbes, normally more likely to thrive in nutrient richer conditions, e.g., in contaminated waters. A high ratio of LNA over HNA bacteria has been suggested to represent a more stable or ‘healthy’ microbiome.

Research challenges
Any water microbiome consumed as drinking water may influence the composition of the microbiome in the human intestinal tract. The importance of the gut microbiome on human health therefore triggers the question on the importance of the microbiomes that are consumed. This project will help forming a better understanding of the direct influence of the LNA/HNA ratio of the water microbiome on the human gut microbiome. Since direct research on the human gut is not feasible in the current state of research, two identical dynamic gut simulators will be run instead (base line and test line). The resilience of the system against the influence of pathogens will be tested to determine any influence of the different LNA/HNA contents of the water microbiome on the gut microbiome, for example how fast a regaining of a healthy composition can be achieved. Moreover, the possibility to drive out a pathogenic organism (an effect that has been observed in an aquatic microbiome after magnetic treatment) will be investigated. The two most challenging aspects of this project are establishing a defined water microbiome with LNA/HNA species that can be used to be tracked in the human gut model, and finding the factors which will give the best insight in the changes in the system.

Your assignment
In order to gain a deeper understanding of the water microbiome on a genetic level, you will apply next generation sequencing methods (NGS); you will collect samples of the treated and base line reactor at predefined time points to compare the development of the gut microbiome under the influence of the different feed water sources. Flow cytometric, culture and (RT)-qPCR based molecular and microbiological approaches will help you further deepen the understanding of the shifts expected in the gut microbiome. Next to microbiological tests, physical and chemical parameters (pH, temperature, electric conductivity) will be conducted.

Your profile
The candidate must hold a MSc degree in biotechnology, microbiology or a comparable discipline, and have an interest in the workings of the human gut. The candidate should have a good understanding and knowledge of the natural sciences; knowledge in medical sciences would be beneficial. An innovative and multi-disciplinary attitude is required. Fluent in spoken and written English, and able to work in multi-disciplinary and international teams. Experience with laboratory and analytical work is required.

Keywords: microbiome gut, gut simulator, HNA/LNA, microbiological water quality

Supervisory team: Prof. Dr. Hauke Smidt (Wageningen University), Gernot Zarfel, Priv.-Doz. Mag. Dr.rer.nat (Medical University of Graz), Dr. Inez Dinkla (Wetsus), Xiaoxia Liu (Wetsus), Dr. Elmar Fuchs (Wetsus)

Project partners: Applied Water Physics theme

Only applications that are complete, in English, and submitted via the application webpage before the deadline will be considered eligible.

Guidelines for applicants:

The call is closed. Please be informed that we no longer accept applications for the current call. We thank you for your interest.