Increasing culture biodiversity and eco-evolutionary understanding of novel bacterial isolates using culturonmics and computational tools

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 supervisors.