COL_RES PhD Training Network - Open PhD Positions – Initial Call (# of pos: 8)

Updated: about 2 months ago
Deadline: 22 Mar 2021

COL_RES PhD Training Network - Open PhD Positions – Initial Call

Colonization resistance: training & research towards microbiome derived solutions to foodborne disease

Offer Description:

The COL_RES Innovative Training Network (ITN) comprises a world-leading network of investigators that will examine the mechanisms by which the gut microbiota protects against serious foodborne pathogens (Salmonella, E. coli, Listeria, Citrobacter rodentium and Campylobacter) and lead to the identification of next generation probiotics that can potentially protect against multiple infectious agents. Through intersectoral industry-academia secondments the network will provide state-of-the-art training for 8 early stage researchers (ESR) preparing them for problem solving and entrepreneurial roles in industry and society and underpinning cutting-edge research in infectious disease in the EU. The work will utilize a systems biology-based approach by exploiting existing research models at world-leading laboratories combined with phageomics, metabolomics and bioinformatics to generate multi-omics data that will uncover both pathogen-specific and shared mechanisms by which the gut microbiota protects against foodborne pathogens.

The ESRs will be recruited within 2021 for a duration of 36 months. Each ESR position in COL_RES allows the researcher to work towards a PhD at one of our six leading academic institutions. Every ESR will work on an independent research project with an allied training programme tailored to the career goals of the candidate. ESRs will each undertake two periods of secondment to other academic or industry institutes.

Marie Sklodowska-Curie ESRs are paid an attractive gross salary of 3,270 €/month for 36 months (as defined in MSCA guidelines). The exact (net) salary will be confirmed upon appointment and is dependent on local tax, social and health insurance regulations and on the country correction factor (to allow for the difference in cost of living in the different EU Member States). Each ESR will also be compensated with a Mobility Allowance of 600 €/month, and, for researchers who have a family, a Family Allowance of 500 €/month. All amounts are subject to deductions and taxes. Family is defined as persons linked to the researcher by (i) marriage, or (ii) a relationship with equivalent status to a marriage recognised by the national legislation of the country of the beneficiary or of the nationality of the researcher, or (iii) dependent children who are actually being maintained by the researcher; family status is determined at recruitment and does not evolve.

Applicants for the PhD positions must not yet been awarded a PhD degree and must be in the first 4 years (full-time equivalent) of their research careers prior to the recruitment.

All applicants must not have resided or carried out their main activity (work, studies, etc.) in the country of the organization they are applying to for more than 12 months in the 3 years immediately prior to the recruitment.

Available Positions

ESR1: Role of the microbiota in the pathogenesis of Citrobacter rodentium

Host: Imperial College London, UK

PhD awarding institution: Imperial

Scientific objectives: In this project the ESR will utilise next generation sequencing approaches to analyse microbial community structure in relevant infection models in order to identify commensal taxa that contribute to pathogenesis of C. rodentium. The studies will utilise models that have been established in Prof. Gad Frankels group. The work is expected to identify next generation probiotics to protect against C. rodentium infection and will contribute data which can be integrated into a mathematical model of colonization resistance.

Additional Requirements: B.Sc. / M.Sc. (or equivalent graduation) in relevant area (e.g. Microbiology, Biochemistry, Cell Biology). Practical hands-on experience with molecular biology techniques (e.g. qPCR, gene sequencing and basic bioinformatics) is desired. Proof of English proficiency may be required as the communication and teaching language throughout COL_RES is English (e.g. TOEFL or similar test, not for native speakers).

Contact: Prof. Gad Frankel, g.frankel@imperial.ac.uk

ESR2: Role of the microbiota in the pathogenesis of Listeria monocytogenes

Host: University College Cork, Ireland

PhD awarding institution: University College Cork

Scientific objectives: In this project the ESR will utilise next generation sequencing approaches to analyse microbial community structure in relevant infection models in order to identify commensal taxa that contribute to colonization resistance against the Gram positive foodborne pathogen Listeria monocytogenes. Studies will examine the effect of perturbations of the microbiota upon infection in the context of antibiotic treatment and alterations to diet. The work will also investigate the application of next generation probiotics to protect against L. monocytogenes infection and will contribute data which can be integrated into a mathematical model of colonization resistance.

Additional Requirements: B.Sc. / M.Sc. (or equivalent graduation) in relevant area (e.g. Microbiology, Biochemistry, Cell Biology). Practical hands-on experience with molecular biology techniques (e.g. qPCR, gene sequencing and basic bioinformatics) is desired. Proof of English proficiency may be required as the communication and teaching language throughout COL_RES is English (e.g. TOEFL or similar test, not for native speakers).

Contact: Prof. Cormac Gahan, c.gahan@ucc.ie

ESR3: Role of the microbiota in the pathogenesis Campylobacter jejuni

Host: Charité Universitätsmedizin Berlin, Germany

PhD awarding institution: Charité

Scientific objectives: In this project the ESR will utilise next generation sequencing approaches to analyse microbial community structure in relevant infection models in order to identify commensal taxa that contribute to the pathogenesis of the Gram negative foodborne pathogen Campylobacter jejuni. Studies will examine the effect of perturbations of the microbiota upon infection in the context of alterations to diet. The work will also investigate the application of next generation probiotics to protect against C. jejuni infection and will contribute data which can be integrated into a mathematical model of colonization resistance.

Additional Requirements: M.Sc. (or equivalent graduation) in relevant area (e.g. Microbiology, Biochemistry, Cell Biology). Practical hands-on experience with murine models and molecular biology techniques (e.g. qPCR, gene sequencing and basic bioinformatics) is desired. Proof of English proficiency may be required as the communication and teaching language throughout COL_RES is English (e.g. TOEFL or similar test, not for native speakers).

Contact: Dr. Markus M. Heimesaat markus.heimesaat@charite.de and Prof. Stefan Bereswill stefan.bereswill@charite.de

ESR4: Role of the microbiota in the pathogenesis of Salmonella Typhimurium

Host: Eidgenössische Technische Hochschule (ETH) Zürich, Switzerland

PhD awarding institution: ETH Zürich

Scientific objectives: In this project the ESR will utilise next generation sequencing approaches to analyse microbial community structure in relevant infection models in order to identify commensal taxa that contribute to resistance against Salmonella Typhimurium. Studies will examine the effect of perturbations of the microbiota upon infection in the context of antibiotic treatment and alterations to diet. The work will also investigate the application of next generation probiotics to protect against S. Typhimurium infection and will contribute data which can be integrated into a mathematical model of colonization resistance.

Additional Requirements: M.Sc. (or equivalent graduation) in relevant area (e.g. Microbiology, Biochemistry, Cell Biology). Practical hands-on experience with molecular biology techniques (e.g. qPCR, gene sequencing and basic bioinformatics) is desired. Proof of English proficiency may be required as the communication and teaching language throughout COL_RES is English (e.g. TOEFL or similar test, not for native speakers).

Contact: Prof. Wolf-Dietrich Hardt wolf-dietrich.hardt@micro.biol.ethz.ch

ESR5: Role of the microbiota in the pathogenesis of E. coli (EHEC)

Host: Université Clermont Auvergne, Clermont-Ferrand, France

PhD awarding institution: Université Clermont Auvergne

Scientific objectives: The ESR will investigate the role of the microbiota in resistance to enterohaemorrhagic E. coli (EHEC). The work will identify specific commensal taxa influenced by antibiotics and diet which affect EHEC pathogenesis in an ArCOL (Artificial COLon) fermentation system which mimics the human colon. The research is expected to identify key commensal species required for colonization resistance against EHEC and to test the application of next-generation probiotics to protect against EHEC infection. The work will contribute data which can be integrated into a mathematical model of colonization resistance.

Additional Requirements: M.Sc. (or equivalent graduation) in relevant area (e.g. Microbiology, Biochemistry, Molecular Biology, Physiology). Practical hands-on experience with molecular biology techniques (e.g. qPCR, gene sequencing and basic bioinformatics) is desired. Microbiology skills (aerobic and anaerobic) and experience with use of complex in vitro fermentation systems is also desirable. Proof of English proficiency may be required as the communication and teaching language throughout COL_RES is English (e.g. TOEFL or similar test, not for native speakers).

Contact: Prof. Stéphanie Blanquet-Diot stephanie.blanquet@uca.fr and Dr. Lucie Etienne lucie.etienne-mesmin@uca.fr

ESR6: Gut phage dynamics associated with foodborne infection

Host: University College Cork, Ireland

PhD awarding institution: University College Cork

Scientific objectives: The ESR will extend the work of the Hill group in the area of microbiota phage community structure using state-of-the-art sequencing and bioinformatics approaches. Specifically, the ESR will examine phage populations in murine models before and after antibiotic treatment and determine the influence of phage populations in the context of protection against Listeria and Salmonella infection. The work is expected to develop gut phage therapies targeted at restoring microbiota or specifically targeting pathogens in the gut. The work will generate sophisticated phage profiling data which will integrate into COL_RES datasets and inform an overall colonization resistance model.

Additional Requirements: B.Sc. / M.Sc. (or equivalent graduation) in relevant area (e.g. Microbiology, Biochemistry, Cell Biology). Practical hands-on experience with molecular biology techniques (e.g. qPCR, gene sequencing and basic bioinformatics) is desired. Proof of English proficiency may be required as the communication and teaching language throughout COL_RES is English (e.g. TOEFL or similar test, not for native speakers).

Contact: Prof. Colin Hill, c.hill@ucc.ie

ESR7: Improving metabolomics approaches for microbiome studies

Host: Fundacio Eurecat

PhD awarding institution: Universitat Rovira i Virgili, Tarragona (URV)

Scientific objectives: The ESR will join the research team of Dr. Nuria Canela who runs a state-of-the-art metabolomics platform at Fundacio Eurecat. The ESR is expected to establish improved protocols for the improvement of extraction and analytical protocols for metabolomic analysis of microbiome samples in order to help overcome bottlenecks in the analysis of difficult-to-detect gut-derived metabolites. The research will also focus upon improvement of bioinformatic models for integrating metabolomic datasets with microbiota datasets. The ESR will interact with other ESRs in COL_RES to help provide technical advice and support for metabolomic analysis of samples. The work will provide data to inform an overall colonization resistance model.

Additional Requirements: M.Sc. (or equivalent graduation) in relevant area (e.g. Chemistry, Microbiology, Biochemistry, Cell Biology). Practical hands-on experience with chemical analytical tools and bioinformatics is desired as well as an aptitude for handling large datasets. Proof of English proficiency may be required as the communication and teaching language throughout COL_RES is English (e.g. TOEFL or similar test, not for native speakers).

Contact: Dr. Nuria Canela, nuria.canela@eurecat.org

ESR8: Microbiome analysis and machine-learning to understand colonization resistance mechanisms

Host: University College Cork, Ireland

PhD awarding institution: University College Cork

Scientific objectives: The ESR will join the bioinformatics team of Dr. Marcus Claesson which specialises in machine-learning approaches for multi-omics analysis of microbiome samples and predictive modelling. The research of the ESR is expected to analyse associated microbiome data and to improve machine-learning approaches for multi-omics analysis of microbiomes and related metabolomes from complex systems. The work will use meta-analytical approaches to integrate key datasets from COL_RES in order to develop a predictive model of colonization resistance mechanisms. Overall the work is expected to predict key taxa involved in colonization resistance for subsequent testing as potential probiotics.

Additional Requirements: B.Sc. / M.Sc. (or equivalent graduation) in a relevant area (e.g. Computer Science, Bioinformatics, Cell Biology or Microbiology (with data handling/bioinformatics)). Proven experience of bioinformatics or computational biology is desired as well as an aptitude for handling large datasets. Proof of English proficiency may be required as the communication and teaching language throughout COL_RES is English (e.g. TOEFL or similar test, not for native speakers).

Contacts: Dr Marcus Claesson, M.Claesson@ucc.ie

Positions include interdisciplinary training, summer schools and yearly international meetings.

*Monthly salary is a gross amount including employer costs of employee according to MSCA ITN rules, salary will be paid in currency of respective country.


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