3- PhD project: Manipulating horizontal gene transfer for discovery of antibiotics and antibiotic resistance

ESPCI Paris – PSL : ESPCI Paris - PSL is a major institution of higher education (a French "Grande École d’ingénieurs"), an internationally renowned research center (6 Nobel Prizes), and a fertile ground of innovation for industry (3 start-ups created/year). ESPCI is a highly multidisciplinary environment with teaching and research in physics, chemistry and biology.

Project: Soil is a formidable reservoir of microbial biodiversity and existing antibiotics are principally secondary metabolites produced by soil microorganisms, or semisynthetic derivatives thereof. In nature, these compounds serve as weapons in the competition between cells, and their evolution and dissemination are intimately coupled with the evolution and dissemination of antibiotic resistance. This project aims i) to investigate the functional diversity (genes and metabolic pathways) of soil microbial communities involved in antibiotic production, and corresponding resistomes, ii) to develop a better understanding of ecological and evolutionary processes in the soil communities involved in antibiotic production, and as a consequence, to their associated resistomes, iii) to develop a better understanding of the role and mechanisms of horizontal and vertical gene transfer in the evolution and dissemination of antibiotics and antibiotic resistance, and iv) to discover new natural classes of antibiotics, in particular more pathogen-specific antibiotics that reduce the risk of emergence of adapted resistomes.
The project is part of a multi-team programme that brings together a wide range of scientists with expertise in biochemistry, millifluidics, soil science, computational biology, microbial genetics and evolution. The Rainey group contribution builds on work using selfish genetic elements to link genes to microbial community function (see Quistad et al 2020). Specifically, it will exploit the inherent capacity of SGEs to facilitate horizontal spread of genes encoding antibiotics and resitomes and will interface with millifluidic screening platforms developed in the lab of Andrew Griffiths.

Relevant publications from the group:
Quistad, S. Doulcier, G. & Rainey, P. B. (2020). Experimental manipulation of selfish genetic elements connects genes to microbial community function. Philosophical Transactions of the Royal Society. 375, 20190681. DOI: 10.1098/rstb.2019.0681.

Rainey, P. B. & Quistad S. (2020). Toward a dynamical understanding of microbial communities. Philosophical Transactions of the Royal Society 375, 20190248. DOI: 10.1098/rstb.2019.0248.

Funding: The project is funded by Agence National de la Reserche (ANR) as part of the call Antibiorésistance: comprendre, innover, agir (AMR)

Laboratory: The research will be hosted by the Rainey team in the Laboratory of Biophysics and Evolution (https://www.lbe.espci.fr/home/) at ESPCI Paris – PSL University, France (www.espci.psl.eu/en/espci-paris-psl/) in the heart of Paris.

Expected profiles: The project will require hands-on wet-lab-based research using experimental microbial communities, combined with metagenomics and computational biology. Relevant experience is highly desirable, but we place particular emphasis on creative / innovative thinking, confidence to embrace new ideas and techniques, tenacity, and ability to function as part of an interdisciplinary team.

Application: Send a motivation letter, CV with a publication list, and recommendation letters to paul.rainey (arobase) espci.psl.eu. Please be sure to read about our approach to doing science and follow advice for applicants: https://www.lbe.espci.fr/home/jobs/
Starting date : October 2021
Duration : 3 years
Salary : 1 700€ net


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