NILAB: Integrating AI and Taxonomy-Free Classification for Enhanced Microbiome Analysis of One Health Environments
Overview
This project is a 4-year PhD project with enhanced training and 3+ month placement, which is funded by UKRI BBSRC through the NI Landscape Partnership in AI for Bioscience (NILAB) Programme, delivered by Queen’s University Belfast and Ulster University. Details of the enhanced training will be available later at qub.ac.uk/nilab/. NILAB aims to bridge the gap between biology and artificial intelligence to accelerate bioscience discovery and foster effective collaboration between academia, industrial partners, and government bodies. NILAB’s mission is to train the next generation of researchers to develop and use AI to uncover the rules of life, addressing challenges in human health, animal welfare, and sustainable food systems.
Revolutionizing Microbiome Research for One Health
Scientific Background
In a world where human, animal, and environmental health are deeply interconnected, understanding microbiomes is crucial. The One Health concept highlights the need for integrated approaches to tackle global health challenges. This project is timely and vital as it aims to bridge the gaps in microbiome analysis, making it more accessible and accurate. By focusing applying AI approaches to 16S rRNA-based analysis, the project seeks to overcome the high costs and limitations of traditional shotgun sequencing, paving the way for better health outcomes across all species.
Research Methodology
The student will be at the forefront of innovative research, working within the Creevey lab at Queen's University Belfast (QUB) and collaborating with the Zheng lab at Ulster University (UU). The project involves linking pangenome profiles of available genomes to unique numerical identifiers from an existing database. The student will explore and implement various machine learning (ML) techniques, such as ensemble learning and graph-based approaches, to predict pangenomic profiles from these identifiers. Additionally, they will compare this new approach to existing methods and apply the models to real-world 16S rRNA data from diverse microbiomes, including agriculture, human, and wastewater environments.
Training
The successful candidate will gain hands-on experience in cutting-edge microbial genomics and AI methodologies. They will have access to extensive datasets, including terabytes of amplicon (16S rRNA) and shotgun sequencing data. The project offers a unique opportunity to develop skills in advanced ML techniques, data analysis, and microbiome research. Supported by the expertise of the Creevey and Zheng labs, the student will be well-equipped to make significant contributions to the field of One Health microbiomes, enhancing their career prospects in both academia and industry.
Join us in this exciting journey to revolutionize microbiome research and improve global health outcomes!
Are you passionate about making a real difference in global one health? Join our cutting-edge computational research project to help further improve human, animal, and environmental well-being!
Scientific Background
The One Health concept emphasizes the interconnectedness of human, animal, and environmental health. By investigating the One Health status of various environments, interventions can be developed to improve health outcomes across all species. This involves critical areas such as Disease Surveillance, Antimicrobial Use and Resistance, Biodiversity and Ecosystem Health, and Food Safety and Security. Understanding the role of microbiomes in these environments is essential to achieving these goals. Traditionally, shotgun sequencing has been used for microbiome analysis, but due to its high cost, researchers are increasingly returning to 16S rRNA-based analysis. This method leverages the large quantities of existing genomic information to link 16S data to genomes in public databases, allowing for the prediction of genomic functions from 16S rRNA data alone.
However, further development of these approaches have been hindered by ever-changing, human-derived taxonomies and the reliance on individual genomes as functional representatives for species.
This project will address the limitations of these methods by applying AI/machine learning to a novel taxonomy-free classification approach and pangenome profiles across multiple species, resulting in robust, representative and rapid functional predictions for one-health environments.
Aims and Objectives
This NILAB studentship aims to provide a more comprehensive understanding one-heath environments by applying AI / Machine learning approaches to better understanding the genetic makeup of various species and their relationships to one another. By integrating these profiles, the project seeks to enhance the accuracy of microbiome analysis and facilitate the identification of one-health risks associated with specific organisms.
Methodology
As part of the ongoing EU H2020 project (Holoruminant), the Creevey lab has developed a novel taxonomy-free classification approach for microbiome data. This approach uses sequence similarity to generate unique numerical identifiers for each species, preserving information on their relationships to other species. This method has been applied to create a robust microbiome database, linking various types of data from public repositories.
This studentship will involve:
Integrating pangenome profiles of available genomes with the unique numerical identifiers in the existing database. Exploring and implementing ML techniques, including ensemble learning and graph-based approaches, to predict pangenomic profiles from the unique identifiers. Evaluating the new approach against existing nearest-neighbour methods for functional prediction. Applying the developed models to real-world 16S rRNA data from diverse microbiomes (agriculture, human, wastewater) and validating the prediction accuracy against existing shotgun metagenomic data.
Benefits for the Student
The successful candidate will benefit from the extensive expertise in microbial genomics and AI approaches available in the Creevey lab at Queen's University Belfast (QUB) and the Zheng lab at Ulster University (UU). The project offers access to terabytes of amplicon (16S rRNA) and shotgun sequencing data from various microbiomes, supported by additional data from a newly funded UK/China grant. This studentship provides a unique opportunity to contribute to cutting-edge research in One Health microbiomes, with the potential to make significant advancements in the field.
Funding Information
Funding covers fees and stipend (stipend is £20,780 for the 2025/26 academic year).
Project Summary
Professor Chris Creevey
Full-time: 4 years
Biological Sciences overview
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.
There are three broad themes to research at the School:
- Agri-Food Systems and Human Nutrition
- Understanding Health and Disease
- Sustaining Ecosystems and Biodiversity
Agri-Food Systems and Human Nutrition:
This theme focuses on how Agri-Food systems can be better positioned to provide safe, authentic and healthy diets with high-quality plant, livestock, and aquaculture products, whilst supporting human and animal health in a way that is sustainable and resilient to climactic changes.
Underpinning these goals, the disciplinary expertise of the theme integrates basic and applied research from animal health and welfare, nutrition, performance, and environmental and social impact (e.g. greenhouse gas emissions from livestock) to chemical contaminant and natural toxin detection, food microbiology, food fraud detection, and food systems traceability and transparency, integrated into a holistic total systems approach.
Supporting by underpinning expertise in cutting-edge molecular, genomic, transcriptomic, proteomic, and metabolomic technologies, artificial intelligence and simulation modelling, the goal of the theme is to support the transformation of global Agri-Food systems. This is with the purpose of maximising the benefits both to animal and human nutrition and health, while simultaneously reducing environmental impact, protecting ecological resources, supporting livelihoods and access to affordable safe foods, and upholding social, cultural, and ethical values. A system based on the principles of measurable integrity and impact.
Understanding Health and Disease:
The Understanding Health and Disease research theme covers humans, plants, and animals with research strengths in prevention, diagnostics, surveillance, epidemiology, and treatments. We study how health can be improved through food and nutrition and how diseases can be tackled by understanding their fundamental molecular mechanisms, including those underpinning the biology of pathogens and parasites. Our researchers work in human cancer and genetic diseases, in infections caused by bacteria, fungi, viruses, and parasites, and in how global health and disease will be affected by global warming and climate change.
We recognize that the only way to tackle the problems we face as a society is to take an interdisciplinary approach to our research. This means we have expertise in broad areas including molecular biology, biochemistry, bioinformatics, genomics, transcriptomics, modelling, bioanalytical chemistry, proteomics, metabolomics, microbiology, parasitology, and plant biology. We work internationally with researchers and partners in universities, charities, non-governmental organisations, industry, and government agencies to tackle local and global challenges.
Sustaining Ecosystems and Biodiversity:
This theme covers research in 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, environmental microbiology, microbial ecology, food web analysis, microcosm and mesocosm experiments, and mathematical/computational methods. Within this theme we also 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 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.
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
- Research students will have access to laboratory space as required (in our state-of-the-art research laboratories) and where relevant, also a range of field study sites and equipment (e.g. remote sensing drone equipment). They also have access to local and campus-wide high performance computing facilities and the full strength of our world-class library. Many students also benefit from the strong collaboration network maintained by our academic staff, which could result in working in the laboratories of partner organisations in industry and government as well as in the University, under specific arrangements.
- 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.
Internationally Renowned Experts
- Research at Institute for Global Food Security and the School of Biological Sciences was rated 1st in the UK in the latest Research Exercise Framework (REF) – an independent assessment of research quality, impact and environment at UK universities.
IGFS/Biological Sciences topped the national league table for Agriculture, Veterinary and Food Science, with 94% of research in those areas deemed “world-leading” or “internationally excellent”.
Additionally, the research environment at IGFS/SBS scored a phenomenal 100%.
Key Facts
- Most of the critical problems facing humanity - disease, climate change and food security - require biological understanding to solve them.
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.
Career prospects in the biological sciences are exceptionally good. To some extent it depends on the specific topic, of course, but laboratory-based and especially quantitative skills and the proven innovation of a PhD or MPhil are highly sought after. Degrees are very much in demand, both in commercial science and public sector research and development (e.g. drug discovery and development, crop and animal improvements and welfare, sustainable agriculture and resource use, human nutrition and health, animal health, ecological management, food safety and technology, scientific communications, regulation, and many more fields).
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 Gareth Arnott
Postgraduate Research Director
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.
Research degrees are overseen by the School of Biological Sciences Director of Postgraduate Research, who currently is Dr Gareth Arnott.
Learning Outcomes
A postgraduate research degree involves the undertaking of independent research under the guidance of a professional academic supervisory team, typically using the laboratory facilities on offer in one or more of the teams' labs. The student will be expected to develop their own ideas and learn the methods needed to test them empirically and theoretically. This usually involves learning and practising both laboratory (and or field) skills as well as developing a strong theoretical background in the relevant subject.As well as practical work, all the activities of independent academic scholarship, such as literature searching and critical appraisal, written and verbal communications and academic networking will be developed during a research degree. Independence and innovation will be strongly encouraged, but the student will be supported by regular supervisory guidance and a wide range of courses will also be on offer, both in subject specific skills and generic skills, especially supported by the Graduate School (https://www.qub.ac.uk/graduate-school/).
Students are encouraged to interact with one another and with members of academic staff and postdoctoral scientists to build confidence and informal learning, through a range of ‘research culture’ activities, including peer groups where students get together to discuss topical research papers, or methods, or just chat about their interests.
Course structure
Research degrees vary in length, but typically for a PhD they are three or four years long (full-time) and double that for part-time studies. They follow an annual cycle of progress with formal panel-based appraisals of the progress, the outcome of which is typically practical and academic advice about how to overcome problems encountered and how to move to the next stage. During each year, students are expected to supplement their studies with some tailored courses, ranging from highly specific (e.g. learning to use a piece of apparatus or technique) to generic (e.g. developing oral presentation or leadership skills). Every stage is supported by the supervisory team, augmented by an independent panel of progress monitors as well as the full support of the Graduate School.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 desk in a shared office space.
Entrance requirements
Graduate
The minimum academic requirement for admission to a research degree programme is normally an Upper Second Class Honours degree in a relevant subject 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.
Tuition Fees
Northern Ireland (NI) 1 | £5,005 |
Republic of Ireland (ROI) 2 | £5,005 |
England, Scotland or Wales (GB) 1 | £5,005 |
EU Other 3 | £25,600 |
International | £25,600 |
1 EU citizens in the EU Settlement Scheme, with settled or pre-settled status, are expected to be charged the NI or GB tuition fee based on where they are ordinarily resident, however this is provisional and subject to the publication of the Northern Ireland Assembly Student Fees Regulations. Students who are ROI nationals resident in GB are expected to be charged the GB fee, however this is provisional and subject to the publication of the Northern Ireland Assembly student fees Regulations.
2 It is expected that EU students who are ROI nationals resident in ROI will be eligible for NI tuition fees. The tuition fee set out above is provisional and subject to the publication of the Northern Ireland Assembly student fees Regulations.
3 EU Other students (excludes Republic of Ireland nationals living in GB, NI or ROI) are charged tuition fees in line with international fees.
All tuition fees quoted are for the academic year 2021-22, and relate to a single year of study unless stated otherwise. Tuition fees will be subject to an annual inflationary increase, unless explicitly stated otherwise.
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.
Bench fees
Some research programmes incur an additional annual charge on top of the tuition fees, often referred to as a bench fee. Bench fees are charged when a programme (or a specific project) incurs extra costs such as those involved with specialist laboratory or field work. If you are required to pay bench fees they will be detailed on your offer letter. If you have any questions about Bench Fees these should be raised with your School at the application stage. Please note that, if you are being funded you will need to ensure your sponsor is aware of and has agreed to fund these additional costs before accepting your place.
How do I fund my study?
1.PhD OpportunitiesFind PhD opportunities and funded studentships by subject area.
2.Funded Doctoral Training ProgrammesWe offer numerous opportunities for funded doctoral study in a world-class research environment. Our centres and partnerships, aim to seek out and nurture outstanding postgraduate research students, and provide targeted training and skills development.
3.PhD loansThe 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.
4.International ScholarshipsInformation 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 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.