PhD Fellowship: Dissecting the impacts of food structure on gastrointestinal microbial signalling networks to optimise nutrient uptake in humans

The Organisations

AgResearch is a leading Crown Research Institute charged with delivering science and innovation to benefit New Zealand agriculture and its wider economy.  Our internationally recognised scientists are dedicated to this mission and we collaborate with world leading science organisations and universities to achieve exceptional science delivery. We are proud to be unique organisation that is driving prosperity by transforming agriculture to better equip our future generations to come.

The Riddet Institute is a world-best research centre in food and nutritional sciences, providing fundamental scientific understanding and training for a new generation of science leaders.  The Institute is one of New Zealand’s Centres of Research Excellence (CoRE) and as such, integrates partner organisations (Massey University (host), Auckland and Otago Universities, AgResearch and Plant & Food Research) and disciplines, to lead a “NZ Inc” approach to food research, and to generate new knowledge and capability that will transform New Zealand’s food industry.

The Role

The microbes that live in the human body (the human microbiome) profoundly affect how food is digested in the gastrointestinal (GI) tract and nutrient absorption and uptake. Given the vast amounts of available sequencing data from human microbiomes, there is surprisingly little about the precise mechanisms by which these microbes influence each other and how food and food structures influence the GI microbial signalling and biology.

This knowledge gap arises in part from our poor understanding of microbial enzymes, metabolic processes, and the interactions within the microbial ecosystem and the host GI tract. Collectively, the genes present in microbiomes (metagenomes) encode millions of uncharacterised enzymes and metabolites and approaches are needed to connect these genes to biochemical functions.

The critical role that the GI microbiota appears to play in digestion processes and food interactions has stimulated research to identify the microorganisms involved and their functionality, particularly those associated with metabolism of dietary components and food structure. Previous work has uncovered evidence that human GI microbes are capable of influencing each other’s gene transcription.

Stable isotope probing can be applied to metabolomics and metabolite flux studies of a variety of biological systems, including microbial, animal, plant and human studies. A combined omics approach has the potential to provide a more complete picture, utilising biological network analysis to create an understanding of the levels of interaction, inherent complexity, and provide a more comprehensive understanding of the dynamics of food structure, nutrition and the GI microbiome.

The elucidation of GI microbial functions and their role in how food is digested and nutrients absorbed can be utilised to develop foods with optimised a structure and nutrient content to enhance human nutrient uptake.

We are seeking an outstanding PhD candidate to apply the combined methodology of bacterial cultivation, isotope-labelling, metabolomics, and meta-transcriptomics to enhance our understanding of how food structures in the GIT tract impacts interactions between microbiota in a complex ecosystem.  This will involve developing isotopic-labelling systems for measuring microbiome metabolites and their impacts, and characterising the effects of food structures on biochemical mechanisms of the microbiome at the molecular level.

Duties

  • Presenting a research seminar and written report to gain confirmation of PhD programme registration one year after starting.
  • Meeting regularly with supervisors to discuss plans and results.
  • Presenting plans for research and experimental protocols to supervisors for review prior to carrying out.
  • Completing experiments using techniques such as isotope-labelling, microbiology, metabolomics, meta-transcriptomics and culturing of the microbiome.
  • Carrying out data analysis including large data-sets common to metabolomics and meta-transcriptomics.
  • Writing a PhD thesis, including an extensive literature review, 3-5 research chapters and a general discussion.
  • Submitting manuscripts to journals, including a mini-review article and at least two research articles, before the thesis is submitted.
  • Complying with Health and Safety Policies as set by AgResearch and Massey University, and at all times have consideration for the safety of yourself and others in the workplace.
  • Ensuring legislative compliance, (e.g., Department of Labour, HSNO, EPA Animal Ethics) and appropriate data security.

About you

You will have:

  • A relevant Masters or Honor’s degree (e.g. biochemistry, protein chemistry, nutrition) with a grade sufficient to gain entry into a PhD.  The qualification must also include a substantive research project.
  • Excellent written and oral communication skills (IELTS score of 6.5 or equivalent required, if English is not first language).
  • Strong analytical and problem solving skills.
  • Diligence, resilience and enthusiasm.
  • Previous experience in microbiology and cell culture is preferred.

Benefits

The three-year studentship, funded by the Riddet Institute, includes an annual tax-free stipend of NZD$30,000 plus tuition fees. As the successful candidate you will be enrolled at Massey University and based at the Riddet Institute in Palmerston North, and will

  • have the opportunity to take part in leading edge research;
  • be a part of a successful multidisciplinary research team;
  • develop your career as an independent researcher.

PhD Supervisors: Professors Warren McNabb and Nicole Roy, and Dr Karl Fraser.

How to apply

Closing date for applications is January 7th 2018.

Please send your application in the form of a (1) covering letter addressing why you are the ideal candidate, (2) your CV and (3) your academic transcripts to info@riddet.ac.nz.

Please send any other enquiries that you have about this position to Professor Warren McNabb (W.McNabb@massey.ac.nz).

For further information on postgraduate study at Massey University please see: http://www.massey.ac.nz/massey/postgraduate.

 

Job Description

The aim of this position is to complete a PhD thesis is to use the combined methodology of bacterial cultivation, isotope-labelling, metabolomics, and meta-transcriptomics to enhance our understanding of how food structures in the GIT tract impacts interactions between microbiota in a complex ecosystem.

In order to be eligible for this position the candidate must meet the Massey University criteria for enrolment in a PhD programme. This includes:

  • A relevant Masters or Honor’s degree (e.g. biochemistry, protein chemistry, nutrition) with a grade sufficient to gain entry into a PhD.  The qualification must also include a substantive research project.
  • Excellent written and oral communication skills (IELTS score of 6.5 or equivalent required, if English is not first language).

The PhD student’s duties will include:

  • Completing relevant Massey University course(s) deemed necessary by supervisors (depending on previous experience).
  • Presenting a research seminar and written report to gain confirmation of PhD programme registration one year after starting.
  • Meeting regularly with supervisors to discuss plans and results.
  • Presenting plans for research and experimental protocols to supervisors for review prior to carrying out.
  • Completing experiments using techniques such as isotope-labelling, microbiology, metabolomics, meta-transcriptomics and culturing of the microbiome.
  • Carrying out data analysis including large data-sets common to metabolomics and meta-transcriptomics.
  • Writing a PhD thesis, including an extensive literature review, 3-5 research chapters and a general discussion.
  • Submitting manuscripts to journals, including a mini-review article and at least two research articles, before the thesis is submitted.
  • Complying with Health and Safety Policies as set by AgResearch and Massey University and at all times have consideration for the safety of yourself and others in the workplace.
  • Ensuring legislative compliance, (e.g., Department of Labour, HSNO, EPA Animal Ethics) and appropriate data security.