Skip to main content

FOODBIOSYSTEMS - What are the mechanisms driving niche specialisation within rumen plant associated microbiomes?

School of Biological Sciences | PHD

Applications are now CLOSED
Funding
Funded
Reference Number
SBIO-2020-1080
Application Deadline
6 March 2020
Start Date
1 October 2020

Overview

* APPLY VIA: https://research.reading.ac.uk/foodbiosystems/apply-for-a-phd/ * * DO NOT APPLY DIRECTLY TO QUEEN'S FOR THIS PHD PROJECT * Niche specialization is the process by which, through natural selection, a species becomes better adapted to the specific characteristics of a particular habitat. These organisms can be the principal drivers of important processes in the community and therefore are prime targets for researchers looking to engineer microbial communities to achieve desired outcomes. This project aims to identify what drives niche specialization of micro-organisms in the rumen microbiome as they colonize plant material consumed by the host (cows and sheep). The rumen is a complex ecosystem composed of anaerobic bacteria, protozoa, fungi, methanogenic archaea and phages. These microbes interact closely to break down plant material that cannot be digested by humans, whilst providing metabolic energy to the host and, in the case of archaea, producing methane (Huws et al. 2018). Consequently, ruminants produce meat and milk, which are rich in high-quality protein, vitamins and minerals, and therefore contribute to food security. As the world population is predicted to reach approximately 9.7 billion by 2050, an increase in ruminant production to satisfy global protein demand is necessary, despite limited land availability, and whilst ensuring environmental impact is minimized.

Although challenging, these goals can be met, but depend on our understanding of the rumen microbiome. Attempts to manipulate the rumen microbiome to benefit global agricultural challenges have been ongoing for decades with limited success, mostly due to the lack of a detailed understanding of this microbiome. We
recently demonstrated evidence of rumen bacterial competitive niche specialisation and ecological plasticity, through possession of numerous isoforms of genes encoding degradative enzymes (Rubino et al. 2017) and through successional colonisation of the ingested plant material (Huws et al. 2016). This project aims to further this knowledge and address the gaps in our knowledge by generating novel genetic data of the actively expressed functions of all the microorganisms in the rumen as they colonize and break down a variety of plant material consumed by the host. The project is primarily computational and will allow the student to learn highly
sought-after skills in the analysis and interpretation of genetic data from microbiomes but will also involve some
laboratory work involving biochemical characterization of the plant material. The project will contribute to our understanding of the microbial drivers and interactions that promote effective energy harvesting and resultant feed efficiency in ruminant, allowing models and hypotheses to be generated on how to mitigate the impact of future changes in the climate and resulting extreme weather events.

Student profile: Candidates should have an upper second-class degree in a related science (e.g. Bioinformatics, Microbiology, food), and a background interest in -omics technologies and/or bioinformatics. An MSc in relevant science would be advantageous. The ability to learn skills around research conduct/ethics and communication, -
omics technologies, and bioinformatics is essential. Good attention to detail, time-management, organisation, teamwork and independent learning, are also required.

References:
Huws, S.A., Creevey, C.J., Oyama, L.B., et al. 2018. Addressing global ruminant agricultural challenges through understanding the rumen microbiome: past, present, and future. Frontiers in microbiology 9, p. 2161.
Huws, S.A., Edwards, J.E., Creevey, C.J., et al. 2016. Temporal dynamics of the metabolically active rumen bacteria
colonizing fresh perennial ryegrass. FEMS Microbiology Ecology 92(1).
Rubino, F., Carberry, C., Waters, S.M., Kenny, D., McCabe, M.S. and Creevey, C.J. 2017. Divergent functional isoforms drive niche specialisation for nutrient acquisition and use in rumen microbiome. The ISME Journal 11(6), p. 1510

Funding Information

This project is part of the FoodBioSystems BBSRC Doctoral Training Partnership (DTP), it will be funded subject to a competition to identify the strongest applicants. Due to restrictions on the funding, this studentship is only open to UK students and EU students who have lived in the UK for the past three years. The FoodBioSystems DTP is a collaboration between the University of Reading, Cranfield University, Queen’s University Belfast, Aberystwyth University, Surrey University and Brunel University London. Our vision is to develop the next generation of highly skilled UK Agri-Food bioscientists with expertise spanning the entire food
value chain. We have over 60 Associate and Affiliate partners. To find out more about us and the training programme we offer all our postgraduate researchers please visit
https://research.reading.ac.uk/foodbiosystems/

Project Summary
Supervisor
Professor Chris Creevey
Funding Body
FoodBioSystems BBSRC Doctoral Training Partnership
Apply now Register your interest

Biological Sciences overview

COVID-19 UPDATE: The University is open and ready to take new postgraduate research students, though we are having to take precautions in the laboratory environments, involving social distancing and the mandatory use of Personal Protective Equipment (mainly gloves and masks) and strong hygiene measures to ensure safety. Please refer to Our Campus Commitment for further information: http://www.qub.ac.uk/our-campus-commitment/

The School of Biological Sciences provides PhD and MPhil (research degree) programmes in subjects ranging from basic biochemistry, molecular genetics and cancer research, to agricultural science, marine ecology and the economic evaluation of ecosystem services and food retailing. If you have a topic or research question in mind, please use the Find a Supervisor link (see Apply tab) to identify the most appropriate member of staff to support your idea. If not, don't worry, we regularly advertise funded projects and there is no harm in browsing our academic staff profiles for inspiration and then contacting whoever seems best: we are very open to applications from suitably qualified people interested in scientific research. In every case, a PhD or MPhil course provides the means of being part of a cutting edge scientific research team and contributing to genuine new discoveries or the development of new methods for practical use. If you cannot study full time, we offer pro-rata part time research degree programmes as well.

To help orientation, the School is organised into three research theme clusters:

- Ecosystem Biology and Sustainability
- Microbes and Pathogen Biology
- Food Safety and Nutrition

Ecosystem Biology and Sustainability:

In this cluster, you could research biodiversity and ecosystem services for environments ranging from tropical forests to deep oceans, using field techniques and skills such as wildlife tracking, taxonomy, geostatistics, molecular and genetic ecology, foodweb-analysis, microcosm and mesocosm experiments and mathematical/computational methods. Alternatively, you could study the behaviour and temperament of wild, agricultural or domestic animals and their implications for welfare and ability to respond to environmental change. Potential research projects include phylogenetic analysis of rare and newly discovered species, examination of ecological interactions in tropical systems, agricultural soils, or marine communities, using state-of-the-art genetic analysis, surveys using drones or satellite tagging, or experiments in tanks and field plots, including careful and ethical examinations of animal behaviour. Projects range from theoretical analysis of stability in ecosystems, through discovery of new species and mechanisms of interaction, or responses to climate change, to the assessment of EU agri-environment schemes, development of new methods for commercial fisheries management and economic evaluations of conservation measures. Projects very often have an international dimension and include collaboration with other researchers worldwide.

Microbes and Pathogen Biology:

This cluster covers a diverse array of research interests united by an emphasis on molecular approaches applied to both fundamental and applied questions over the range from molecular to ecological systems. These interests include biochemistry, food safety, microbiology and parasite control with applications in human and animal health, nutrition, plant and soil sciences, and agricultural development. We have a long-standing reputation in parasite biology and in applied microbiology (for example in clearing land of contamination) as well as strong contributions to fundamental methods in understanding cancer, developing veterinary vaccines and molecular detectors for toxins and diseases. The common thread is our strong molecular approach using and developing cutting edge genomic, transcriptomic/proteomic methods. Research students in this cluster enjoy a range of strong international links across Europe, Asia, North and South America.

Food Safety and Nutrition:

Research opportunities offered by this cluster span the entire food chain "from farm to fork" with a strong emphasis on food safety and nutrition, public health and food security. In this cluster you would conduct research under the supervision of leading scientists based in the Institute for Global Food Security and benefit from integration with business experts, helping you gain leadership positions nationally and internationally.

Biological Sciences Highlights
Industry Links
  • The School has a wide range of strong, international links with governments, academia and industry, into which postgraduate research students are integrated.
World Class Facilities
  • Students will have the full use of modern, world-class laboratories, equipped with state-of-the-art, highly advanced analytical instruments and facilitated by world-class field work provision.
  • Students studying in the Food Safety and Nutrition programme will gain excellent practical experience of advanced technology and bioanalytical techniques for food safety analysis and monitoring, including:

    1. GC, HPLC and UPLC separation platforms;
    2. ICP, IR, qToF and QqQ mass spectrometers;
    3. Microbiological research facilities;
    4. Antibody production and biomolecule binder development;
    5. Cell culture suite and bioanalytical assay detection systems;
    6. NMR, NIR and Raman spectrometers;
    7. Proteomic and metabolomic profiling tools RT-PCR;
    8. Transcriptomic profiling;
    9. Next-generation sequencing;
    10. Multiplex biosensor platforms and LFD development.
Key Facts

  • Over 80% of science jobs are in areas of Biological Sciences.
  • Most of the critical problems facing humanity - disease, climate change and food security - require biological understanding to solve them.
Brexit Advice

Information on the implications of Brexit for prospective students.

Course content

Research Information

PhD Supervisors
Information on the research interests and activities of academics in Biological Sciences can be accessed via the School website and the Find a Supervisor facility (see Apply tab).

Career Prospects

Introduction
Queen's postgraduates reap exceptional benefits. Unique initiatives, such as Degree Plus and Researcher Plus bolster our commitment to employability, while innovative leadership and executive programmes alongside sterling integration with business experts helps our students gain key leadership positions both nationally and internationally.

Employment after the Course
Graduates have gone on to be professional research scientists, consultants, or hold technical and junior executive positions in commerce and government.

People teaching you

Dr Keith Farnsworth
Chair of School Postgraduate Research Committee
School of Biological Sciences
For a PhD you will have a principal and second supervisor who advise your independent studies and will be supported by a wider team from the academic staff - who they are, of course, depends on your project. For further details on any aspect of postgraduate research degrees within the School of Biological Sciences, contact: biosciences-pg@qub.ac.uk.

Learning Outcomes

A research degree offers students an opportunity to foster their capacity for independent research and critical thought. It also allows students to explore an area of interest and so understand and solve theoretical and practical problems within the field. Undertaking a research degree can enhance a student’s written and oral communication skills and a PhD is almost always a formal requirement for an academic post.

Course structure

0

Assessment

Assessment processes for the Research Degree differ from taught degrees. Students will be expected to present drafts of their work at regular intervals to their supervisor who will provide written and oral feedback; a formal assessment process takes place annually.

This Annual Progress Review requires students to present their work in writing and orally to a panel of academics from within the School. Successful completion of this process will allow students to register for the next academic year.

The final assessment of the doctoral degree is both oral and written. Students will submit their thesis to an internal and external examining team who will review the written thesis before inviting the student to orally defend their work at a Viva Voce.

Feedback

Supervisors will offer feedback on draft work at regular intervals throughout the period of registration on the degree.

Facilities
Full-time research students will have access to a shared office space and access to a desk with personal computer and internet access.

Entrance requirements

Graduate
The minimum academic requirement for admission to a research degree programme is normally an Upper Second Class Honours degree from a UK or ROI HE provider, or an equivalent qualification acceptable to the University. Further information can be obtained by contacting the School.

International Students

For information on international qualification equivalents, please check the specific information for your country.

English Language Requirements

Evidence of an IELTS* score of 6.5, with not less than 5.5 in any component, or an equivalent qualification acceptable to the University is required (*taken within the last 2 years).

International students wishing to apply to Queen's University Belfast (and for whom English is not their first language), must be able to demonstrate their proficiency in English in order to benefit fully from their course of study or research. Non-EEA nationals must also satisfy UK Visas and Immigration (UKVI) immigration requirements for English language for visa purposes.

For more information on English Language requirements for EEA and non-EEA nationals see: www.qub.ac.uk/EnglishLanguageReqs.

If you need to improve your English language skills before you enter this degree programme, INTO Queen's University Belfast offers a range of English language courses. These intensive and flexible courses are designed to improve your English ability for admission to this degree.

As a result of the COVID-19 pandemic, we will be offering Academic English and Pre-sessional courses online only from June to September 2020.

  • Academic English: an intensive English language and study skills course for successful university study at degree level
  • Pre-sessional English: a short intensive academic English course for students starting a degree programme at Queen's University Belfast and who need to improve their English.

Tuition Fees

Northern Ireland (NI) £4,407
England, Scotland or Wales (GB) £4,407
Other (non-UK) EU £4,407
International £21,300

More information on postgraduate tuition fees.

Biological Sciences costs

Students may incur additional costs for small items of clothing and/or equipment necessary for lab or field work

Additional course costs

All Students

Depending on the programme of study, there may also be other extra costs which are not covered by tuition fees, which students will need to consider when planning their studies . Students can borrow books and access online learning resources from any Queen's library. If students wish to purchase recommended texts, rather than borrow them from the University Library, prices per text can range from £30 to £100. Students should also budget between £30 to £100 per year for photocopying, memory sticks and printing charges. Students may wish to consider purchasing an electronic device; costs will vary depending on the specification of the model chosen. There are also additional charges for graduation ceremonies, and library fines. In undertaking a research project students may incur costs associated with transport and/or materials, and there will also be additional costs for printing and binding the thesis. There may also be individually tailored research project expenses and students should consult directly with the School for further information.

How do I fund my study?
1.PhD Opportunities

Find PhD opportunities and funded studentships by subject area.

2.Doctoral Training Centres at Queen's

Queen's has eight outstanding competitive Doctoral Training Centres, with each one providing funding for a number of PhD positions and most importantly a hub for carrying out world class research in key disciplines.

3.PhD loans

The Government offers doctoral loans of up to £26,445 for PhDs and equivalent postgraduate research programmes for English- or Welsh-resident UK and EU students, £10,000 for students in Scotland and up to £5,500 for Northern Ireland students.

4.International Scholarships

Information on Postgraduate Research scholarships for international students.

Funding and Scholarships

The Funding & Scholarship Finder helps prospective and current students find funding to help cover costs towards a whole range of study related expenses.

How to Apply

Apply using our online Postgraduate Applications Portal go.qub.ac.uk/pgapply and follow the step-by-step instructions on how to apply.

Find a supervisor

If you're interested in a particular project, we suggest you contact the relevant academic before you apply, to introduce yourself and ask questions.

To find a potential supervisor aligned with your area of interest, or if you are unsure of who to contact, look through the staff profiles linked here.

You might be asked to provide a short outline of your proposal to help us identify potential supervisors.