Project number 18

Culturing the unculturable microbes for the improvement of human and plant health

The mammalian gut and the plant roots are key for nutrient uptake. Although the type of absorbed nutrients is entirely different, they both do so by engaging in a complex network of interactions with a wealth of micro-organisms, the so-called microbiota. This taxonomically and functionally diverse microbiota also help in the control of pathogens and the activation of immunity. Additionally, in the plant, these microbes activate growth.
The microbes with whom the mammalian gut and the plant roots cooperate have great potential in the development of new and sustainable methods to increase crop yield and maintain human health. However, biotechnological use of bacteria implies culturability. Deep sequencing technologies gave great insight into the diversity of the bacterial communities inside the gut as well as in and around the plant roots but also revealed that many bacterial members of these ecosystems have not yet been cultured. Hence, there is a need for the development of new methods to improve bacterial isolation and cultivation from natural samples.
In this project, you will develop new methods to isolate and cultivate the “unculturable bugs” from the human gut as well as the maize root. To do so, you will develop innovative screening methods, both based on growth as on function, through the use of novel techniques, such as microfluidics. Furthermore, you will be involved in the molecular characterization of the effects the bacteria exert on their hosts.
The PhD will be executed 50% in the Raes lab and 50% in the Goormachtig lab. In the Raes lab, you will be surrounded by experts in human gut microbiomes, while in the Goormachtig lab all required expertise in root rhizosphere biology is present. Both labs cooperate already on this topic.

Keywords
microfluidics, bacterial cultivation, plant and human health, plant and human microbiome

Supervisors
Sofie Goormachtig, VIB Dept. of Plant Systems Biology, UGent, Gent
Jeroen Raes, VIB lab for Bioinformatics and (eco-)systems biology, KU Leuven, Leuven