Fixed-term

OVERVIEW As SARS-CoV-2 is shed in high levels in faeces, wastewater testing has become a complementary, early-warning strategy for outbreaks of Covid-19, aiding governmental decision-making around future infection prevention/control policies. Wastewater monitoring provides a cheap, non-invasive method to determine the level of infection in a large community within a single sample (composite 24-hour sewage samples represent an aggregate of an entire population within the sewerage network). Importantly, as faecal shedding occurs in the pre-symptomatic phase, evidence also suggests that it can be used as an early warning system to indicate when levels of SARS-CoV-2 are rising (or falling) in the community and before individuals require hospitalisation. Moreover, wastewater surveillance also allows for the tracking of other pathogens (e.g. Influenza, Norovirus, Hepatitis A and E, Enterovirus, Adenovirus, Rotavirus) as well as providing information on antimicrobial resistance genes. A number of projects are available within the Queen’s University Wastewater Epidemiology Group covering: 1) Development of methods for SARS-CoV-2 detection in wastewater. 2) Assessment of viral infectivity and stability in wastewater samples. 3) Use of next generation sequencing to study SARS-CoV-2 variants and other pathogens within the wastewater system. 4) Development of strategies for the detection of other microbial pathogens within wastewater, and the evaluation of their viability. 5) Investigation of clinically relevant antimicrobial resistance genes within wastewater microbiomes. Supervisors: Professor John McGrath (School of Biological Sciences), Dr Derek Fairley (Belfast Health and Social Care Trust and School of Medicine, Dentistry and Biomedical Sciences), Dr Connor Bamford (School of Medicine, Dentistry and Biomedical Sciences), and Dr Deirdre Gilpin (School of Pharmacy). Contact: Professor John McGrath (j.mcgrath@qub.ac.uk) 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. Career Prospects Introduction Queen’s postgraduates reap exceptional benefits. Unique initiatives, such as the DegreePlus/Future Ready Award, 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. 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. 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. Apply Now

OVERVIEW Due to the relatively recent discovery of the Domain Archaea, they are hugely understudied compared to their bacterial counterparts. Additionally, as microbiome studies have historically focused on the bacterial component, the global importance of bacteria is well-studied and unquestionable, while the role of archaea in many environments remains unclear. Only within the past few years has it been shown that archaea are present in virtually all environments, and are active participants or major drivers within complex microbial communities in non-extreme terrestrial environments, the ocean, the human body, and in soil, where they carry out vital but poorly understood roles. These findings highlight both the hidden potential of archaea, and the extent of our knowledge gaps regarding their importance. The above studies identified the ability of archaea to directly impact living systems, giving them a new environmental relevance. However, some of our recent work has shown that archaea may also have an impact in another way: they appear to interact with, and influence the behaviour and function of bacteria. We have shown antibacterial activity of haloarchaea isolated from a local salt mine (Megaw et al., 2019), and potential production by archaea of the same signalling molecules that bacteria use to modulate their community behaviour (Megaw and Gilmore, 2017). Other studies have reported failure in isolation of archaea from mixed samples when the bacteria were inhibited. These findings all raise questions about the relationship between archaea and bacteria inhabiting the same environment, concerning the evolution and role of the interactions between these two separate domains of life, and their impact on complex microbial communities. The overall aim of this project is to characterise some of the positive/negative/neutral interactions that occur between bacteria and archaea inhabiting the same environment, in order to gain a better understanding of the relationship between them. This will involve the use of type strains (and environmental isolates where available). Hypersaline environments (the simplest environment from which to isolate and culture both domains) will be used as a model system, but others can also be included. The project will involve the techniques below, in which the student will receive training: – Development and use of co-culture models to investigate population dynamics of bacterial and archaeal species when grown together short and long-term, and subsequent investigation of the cause of any growth-promoting or -inhibitory activities or other observable changes. This will also involve assessment of the antimicrobial susceptibility of archaea and bacteria and other standard culturing techniques. – Investigation of the effects of archaeal metabolic products on bacterial phenotypes (and vice versa), such as growth and biofilm development, followed by potential identification of active metabolites. – Transcriptomic analysis to investigate changes in gene expression when key bacterial and archaeal species are grown together vs. separately. – Screening of archaeal transposon knockouts to identify genes involved in various processes. This will involve molecular biology techniques including PCR and gene sequencing/annotation. Megaw, J., Kelly, S. A., Thompson, T. P., Skvortsov, T. & Gilmore, B. F. (2019). Profiling the microbial community of a Triassic halite deposit in Northern Ireland: an environment with significant potential for biodiscovery. FEMS Microbiology Letters https:doi.org/10.1093/femsle/fnz242. Megaw, J. & Gilmore, B. (2017) Archaeal Persisters: Persister cell formation as a stress response in Haloferax volcanii. Frontiers in Microbiology https://doi.org/10.3389/fmicb.2017.01589. 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. 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. Apply Now

OVERVIEW Microbiomes are defined as the entire habitat, including the microorganisms (bacteria, archaea, lower and higher eukaryotes, and viruses), their genomes (i.e., genes), and the surrounding environmental conditions (Marchesi et al, 2015). Soil and gastrointestinal tracts contain some of the most complex microbiomes in nature, as they are composed of bacteria, archaea, ciliates, fungi and viruses (Huws et al., 2018). The function of these microbes defines host and soil health coupled with other factors such as their environmental impact e.g. greenhouse gas emissions (GHG). Indeed, the rumen microbiome defines ruminant livestock production and environmental impact (nitrogen and methane emissions). Although they have been intensively studied for many years and their importance is well recognised, relatively few of these microorganisms have been isolated, cultured and genome sequenced (Soldenet al., 2016; Seshadri et al., 2018;). Issues regarding cultivability for whole community biodiversity studies led to the onset of sequencing technologies, which bypass the cultivability issue and allow the whole community to be accessed. Nonetheless, our ability to understand the ecology of these microbes and enable development of innovative technologies to reduce environmental impact requires improvements in biodiversity within our microbial culture collections as ’omic technologies are often correlative and lack causal proof which in vitro studies can provide. Before the explosion in sequencing technologies in recent times, culture was the main tool to assess diversity and investigate microbial ecology. The art of culturing has consequently been somewhat lost, but in recent years an insurgence of innovation encompassing so called ’culturomic’ technologies have emerged. These innovations include the dilution to extinction technique, facilitating exclusion of fastidious competitive bacteria, allowing slow growing bacteria to grow, and later be isolated on solid media. These novel technologies have vastly enhanced the cultured biodiversity of microbes available in culture from human gastrointestinal tract, and aquatic and soil environments, and importantly allowed ecological hypothesis to move from correlations to causality. The development of computational techniques to isolate metagenomically-assembled genomes (MAGs) from metagenomic sequences has also helped identify missing genomes from culture collections (Stewart et al., 2018; Sheridan et al., 2020, in press). These MAGs can also be used to develop bespoke culture media based on the metabolic requirements of those microbes. Consequently, the main aim of the PhD is to use innovative technologies to enhance the cow rumen/faecal and soil microbial biodiversity within culture collections. These ecosystems have been chosen due to their connectivity i.e. cow faecal microbes are often also found in abundance in soils, particularly those grazed by ruminants, and consequently the cross-disciplinary expertise required to culture ‘novel’ microbes from both environments will be similar. Following the use of novel culturomics technologies, resultant isolated microbes will then be taxonomically identified using 16S rDNA sequencing and if deemed novel they will then be genome sequenced to understand their functional capacity. A detailed study of the genomes will then be pursued and isolates will then be investigated in terms of ecological function (cellulolytic, proteolytic, amylolytic, etc.) and their evolution. Consequently, this PhD will provide the candidate with an array of skills from classical microbiology through to bioinformatics, much sought after skills for career development. 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. Career Prospects Introduction Queen’s postgraduates reap exceptional benefits. Unique initiatives, such as the DegreePlus/Future Ready Award, 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. 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. 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

OVERVIEW Until recently, human milk (HM) was considered to be sterile and free of microorganisms in healthy mothers. We are now beginning to understand the importance of the microbiome of HM and its role in developing the naïve immune system of new-born babies. Many of the studies exploring the HM microbiome have focused on the use of rRNA gene sequencing techniques. Although valuable information on the composition of the microbiome can be obtained, no functional information on their biochemical characteristics is gained; limiting our understanding of how the microbiome interacts with the new-born host. This project will develop a collection of HM microorganisms using novel culture methods, techniques, and media, with a focus on the use of anaerobic methods. The recovery of microorganisms will be compared to DNA sequencing data to gauge the success of different techniques. Furthermore, the biochemical properties of these microorganisms in response to various culture conditions will be tested using ambient ionisation mass spectrometry techniques to gain an understanding of how they may respond to the new-born gastrointestinal tract. The effect of various treatment and storage conditions (e.g. pasteurisation and freezing) on microbial viability will be pursued; potentially informing guidelines for donor HM banks and at-home storage. This project will be supervised by Dr Simon Cameron and Professor Sharon Huws of Queen’s University School of Biological Sciences. Specific skills/experience required by applicants: A microbiology undergraduate or postgraduate degree would be required or equivalent experience and expertise in standard microbiology laboratory techniques. A willingness to be involved in participant recruitment and sample collection would be beneficial. Experience with statistical analysis, including the use of R, would be beneficial. All applicants must meet the academic entry requirements: https://www.qub.ac.uk/courses/postgraduate-research/biological-sciences-phd.html#entry 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. Career Prospects Introduction Queen’s postgraduates reap exceptional benefits. Unique initiatives, such as the DegreePlus/Future Ready Award, 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. 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. 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. Apply Now