Project Description: microbiome fortification for healthier pigs through metagenomics-driven culturomics and microbial bioactive metabolite discovery
Virtually no microbes live in isolation. Instead, they are part of complex polymicrobial communities where interactions between individual microbial populations shape the composition and biological activities of the community. The project is linked to an ongoing study generating shotgun metagenomic sequences of microbiota DNA samples from tonsil biofilm, small intestine and faeces of young pigs pre-and post-weaning which are either healthy or displaying symptoms of infectious disease such as Streptococcus suis infection, PRRSV, post-weaning diarrhoea or porcine respiratory disease complex. The PhD candidate will contribute to the overall goal of identifying potential antagonists of Streptococcus suis and other porcine bacterial and viral pathogens. The capacity of the porcine tonsil and ileal microbiota to produce specialised metabolites (including antimicrobial molecules) will be assessed using metagenomics data and biosynthetic gene cluster prediction. The data will be used to generate hypotheses about which genetically specified small molecules might mediate beneficial or deleterious microbe-host and microbe-microbe interactions in a microorganism community and how their prevalence differs among individual animals with different health status.
The candidate will work closely with another researcher using a culturomics approach to isolate representative species from tonsil biofilm, small intestine under a range of culture conditions. Plate screens will be used to identify isolates of species predicted by bioinformatics approaches to produce non-ribosomal peptides and, or other small molecules that inhibit S. suis or other pathogens. Genome sequencing of antimicrobial producing isolates and purification / mass-spectrometry will be used to identify and structurally characterise novel antimicrobial compounds.
The PhD project is linked with The Netherlands Centre for One Health (NCOH) and the cohort of PhD candidates funded by the other partners of the NCOH.
The main objectives:
- To characterise diversity, composition and functional capacities of microbiota and key abundant taxa associated with microbiota communities in healthy and diseased piglets.
- To characterise diversity and composition of the virome of the GI-tract/tonsils and its co-occurrence with members of the microbiome, including pathogens
- Identify candidate microbes that might protect piglets against S. suis and other pathogens including viruses based on co-occurrence networks and gene-repertoire enrichment analysis.
- Perform systematic analysis of biosynthetic gene clusters (BGCs) in the metagenome datasets from tonsil and ileum samples and determine the average number and category of BGCs in different microbial taxa.
- Generate hypotheses about which small molecules predicted to be encoded by BGCs mediate beneficial or detrimental microbe-host and microbe-microbe interactions.
- Isolate representative members of identified key taxa, using existing anaerobic microbial cultivation infrastructure and expertise for the targeted isolation of yet uncharacterized respiratory tract and intestinal microorganisms.
- Relevant Bachelor level experience in microbiology, molecular biology, biochemistry
- A Masters degree, with relevant practical experience (e.g. host-pathogen interactions, molecular microbiology or microbiota studies).
- A professional, reliable and organised method of working.
- Good communication skills and being able to maintain effective working relationships
- Good level of English (spoken and written).
We offer a full-time appointment (1.0 fte, 38 hours/week) for 4 years. Salary ranges from € 2222,- (gross) in the first year to € 2840,- (gross) in the fourth year based on full-time employment. We not only offer a competitive salary, but also a good pension of the ABP Pension Fund.
For more information about this position, please send an email to Prof. Jerry Wells email@example.com
For more information about the contractual aspects, please contact Mieke van Laar, Senior Human Resources Advisor, telephone number +31 317 484 224 (firstname.lastname@example.org
Applications have to be submitted before January 15th 2018 via the Wageningen UR
online application system.
This appointment is in the Host-Microbe Interactomics (HMI) Group but involves multi-centre collaboration with Wageningen Bioveterinary Research, Wageningen Livestock Research and Microbiology. Research of the HMI group ranges from work on the molecular mechanisms of diseases caused by pathogenic bacteria, to the interactions between pathogenic and beneficial bacteria and their human or animal hosts.
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