In(ph)inity wars - understanding phages-bacteria evolutionary conflict to design new biocontrol strategies.

Dr Giuseppina Mariano, Dr Linda Oyama, Dr Jai Mehat, Prof Claudio Avignone Rossa

CLOSED!!!

About the Project

We seek applicants who are strongly interested in microbial genetics, molecular biology or comparative genomics; have a passion towards microbiology and a commitment towards delivering scientific excellence and developing new methodologies that will improve human health. A background in molecular biology and/or genetics is desirable. 

Additionally, a commitment towards unraveling the complex relationship and the mysteries of how bacteria interact with their viruses(bacteriophages) will be essential.

Project outline

Colibacillosis is a widespread disease in farmed poultry caused by avian pathogenic Escherichia coli (APEC)(1). This disease is responsible for multi-million economic losses due to the high mortality of broiler chickens, treatment costs, vaccinations, and feed supplements (2). The continuous (mis)use of antibiotics to control colibacillosis has caused many E. coli strains to acquire resistance to multiple antibiotics, increasing the costs and difficulty of treating and controlling colibacillosis in the poultry sector(3). With the human population set to reach 10 billion by 2050, the high mortality caused by colibacillosis in poultry represents a major threat to food security and safety. Antibiotic-resistant E. coli can additionally infect humans that come in contact with sick animals, and antibiotic-resistance traits can also be quickly transferred between E. coli strains, further exacerbating the threat to humans, animals, and associated ecosystems(2).

Whilst many efforts have focused on developing vaccinations against APEC, their scarce efficacy and ability to target diverse types of pathogenic E. coli has created an urgent need for alternative measures of control against APEC(3). 

Bacteriophages (aka phages) are specialised viruses of bacteria. Phages can specifically infect and kill bacteria, quickly wiping away a microbial population (4). For this reason, phages/phage cocktails are being considered as alternative therapies for antibiotic-resistant infections in humans and farm animals.

However, recent reports highlighted that bacteria, like humans and plants, have different types of immunity systems, globally known as anti-phage systems. Many of these systems carry similarities with our own innate immunity systems (5). 

The wide variety of anti-phage systems found in bacteria is currently one of the main obstacles to overcome to be able to use phage cocktails in clinical settings or as a measure of biocontrol in the poultry sector. 

With this project, we will explore several aspects of phage-bacteria interaction, including the role of bacterial immunity systems, when using phage cocktails as a control strategy to reduce the burden of APEC colibacillosis infections. 

Milestone 1: Identification of phage types with optimum success rate in killing each pathogenic E. coli lineage.

Milestone 2: Identification of novel anti-phage systems in avian-associated E. coli. 

Milestone 3: Design of probiotic strains to improve avian microbiota health during phage-based treatments

(i)The PhD student will collect >30 diverse coliphages from the environment to supplement our existing collection. Phages’ ability to kill pathogenic E. coli lineages will be tested to establish phages/phage cocktails combinations that are most efficient. The student will develop an in vitro gut model under Dr Mehat’s supervision to track the dynamics of co-evolution between mixed populations of E. coli lineages and phage cocktails. Lineages that show increased resistance to multiple phage combinations will be prioritised in Milestone 2. 

(ii) Using established bioinformatic methods from the Mariano lab (6), the PhD student will identify known and novel anti-phage systems encoded within each E. coli lineage. This analysis will allow to pin-point which anti-phage system can better inhibit the phages/phage cocktails used in Milestone 1. 

(iii) We will use the data from the previous task to generate combinations of efficient phage cocktails against pathogenic E. coli and generate probiotic E. coli strains that carry anti-phage systems that confer resistance to these cocktails. The resistant probiotic strain will maintain a healthy microbiota within the avian gut during phage cocktail treatment, preventing the establishment of other pathogens. We will test our phage-probiotic combinations in our in vitro gut model to ensure that probiotic strains are unable to transfer their anti-phage systems to pathogenic lineages over long periods of co-existence. This will ensure prevention of a new health crisis due to quick transfer of resistance traits between bacterial populations. 

Our findings will provide an extensive phage collection that can be employed against pathogenic E. coli lineages and provide a powerful strategy that combined phage cocktails and engineered probiotic strains to improve health of poultry.

Training opportunities

 The PhD student will learn advanced molecular biology, microbiology, and genetic skills. Furthermore, the student will be trained in using bioinformatic and comparative genomic-based methods in the Mariano lab. Under the supervision of Dr Jai Mehat, they will have the opportunity to develop a new and innovative gut in vitro model, which will be fundamental for the project but will also i) open possibilities for external collaborations for the student and ii) provide the student with a unique skill that will render them highly desirable on the academic, industrial and biomedical job market.

The student will be trained in the investigation of microbial population evolutions through the supervision of Dr Mariano, Dr Oyama and discussion with Dr Mariano’s collaborators' network(6). The student will frequently liaise with the supervisory team, providing constant opportunities for training, scientific discussion, and intellectual exchange. Additionally, the student will be encouraged and supported to attend training courses offered by the ‘Skillfluence hub’ and EMBL-EBI according to any gaps in knowledge or specific skills they want to learn.

How to Apply

Applications will be by online application form only. Do not send CVs. Please go to the FoodBioSystems website to see guidance for applicants, information on academic and funding eligibility and language proficiency.

Equality Diversity and Inclusion:

The FoodBioSystems DTP is committed to equality, diversity and inclusion. We want to build a doctoral researcher and staff body that reflects the diversity of society, and to encourage applications from under-represented and disadvantaged groups. Our actions to promote diversity and inclusion are detailed on the FoodBioSystemsDTP website.

Application Deadline: 22 January, 2024

Start Date: 1 October 2024

Duration: 4 years

How to apply: See details here

Funding Notes

FoodBioSystems DTP students receive a tax free stipend (salary) for four years. For 2023/24 this is £18,622 (or £20,622 for students based at Brunel University). The pay increases slightly each year at rate set by UKRI. The DTP also pays tuition fees at the standard UK rate and makes a contribution to the research project costs.
Most of our funding (minimum 70%) is available to students with UK/home fees status. We welcome applications from international students. However, we can only offer up to 30% of our studentships to international students. In 2024, this will be maximum of 9 projects.

References

1. S. M. Lutful Kabir, Int J Environ Res Public Health. 7, 89–114 (2010).
2. S. E. Rezatofighi, et al., Frontiers in Veterinary Science. 8 (2021)
3. A. R. Elbestawy et al., Journal of King Saud University - Science. 33, 101353 (2021).
4. A. Abd-El Wahab et al., Front Microbiol. 14, 1136638 (2023).
5. D. Mayo-Muñoz, et al., Cell Reports. 42 (2023)
6. E. Macdonald et al., PLOS Genetics. 19, e1010784 (2023).

Innovative encapsulation approaches for seed protection and longevity

  Dr Suzie Hingley-Wilson, Dr Linda Oyama, Prof J Keddie, Dr Giuseppina Mariano

CLOSED!!!

About the Project

This project would suit a student with laboratory experience and a biology background. Some prior physics background would also be desirable.

Project outline

Biocoatings are a mix of beneficial bacteria and colloidal coatings. They can keep bacteria contained, alive and in contact with key surfaces. Seed storage is often problematic with fungal and bacterial spoilage agents rife. This interdisciplinary project aims to combine key anti-fungal and microbial agents with beneficial bacteria in seed-based biocoatings. Maintaining seed longevity would aid human health and nutrition and reduce anti-microbial resistance. 

This novel proposal involves developing seed biocoatings containing protective bacteria and targeted anti-microbial peptides and phages (i.e. bacterial viruses) to achieve seed longevity. This will be based at the University of Surrey and Queens University Belfast, where biocoatings containing key anti-microbial agents and bacilli will be developed and evaluated. These will be tested in collaboration with a world leading industrial partner in seed health Syngenta.

Training opportunities

 The student will receive training at the UofS and QUB, which have a range of doctoral college programmes and offer training in scientific writing, presentation skills, employability, and laboratory safety.

How to Apply

Applications will be by online application form only. Do not send CVs. Please go to the FoodBioSystems website to see guidance for applicants, information on academic and funding eligibility and language proficiency.

Equality Diversity and Inclusion:

The FoodBioSystems DTP is committed to equality, diversity and inclusion. We want to build a doctoral researcher and staff body that reflects the diversity of society, and to encourage applications from under-represented and disadvantaged groups. Our actions to promote diversity and inclusion are detailed on the FoodBioSystemsDTP website.

Application Deadline: 22 January, 2024

Start Date: 1 October 2024

Duration: 4 years

How to apply: See details here

Funding Notes

FoodBioSystems DTP students receive a tax free stipend (salary) for four years. For 2023/24 this is £18,622 (or £20,622 for students based at Brunel University). The pay increases slightly each year at rate set by UKRI. The DTP also pays tuition fees at the standard UK rate and makes a contribution to the research project costs.
Most of our funding (minimum 70%) is available to students with UK/home fees status. We welcome applications from international students. However, we can only offer up to 30% of our studentships to international students. In 2024, this will be maximum of 9 projects.

References

1) Chen et al., Biomacromolecules. 2020 Nov 9;21(11):4545-4558
2) Chen et al., Adv. Sustainable Syst. 2022, 2200312
3) Krings et al., Microbiology Spectrum in press

How and why do rumen bacteria talk to each other?

Prof S Huws, Dr D Whitworth, Dr Linda Oyama

CLOSED!!!

About the Project

This project is suitable for candidates with a background in animal science, microbiology, biochemistry or computational biology.

Project outline

 Ruminants provide an important source of protein and micronutrients for human consumption and health with demand rising due to increases in World population and an increased demand from the Asian continent. In parallel, ruminants are also a contributor to climate change, with agriculture as a whole contributing to around 18% of agricultural greenhouse gases, mainly in the form of eructated methane coming produced by rumen methanogens. Indeed, ruminants possess a complex specialised four-compartment forestomach. The rumen, the primary fermentative compartment, harbouring a dynamic ecosystem comprising bacteria, protozoa, fungi, archaea (containing the methanogens), and bacteriophage, primarily benefiting the host animal by deriving energy from plant material breakdown. 

The microbes which inhabit the rumen, and many other ecosystems in nature, often exist in close communities and they envelop themselves in an extacellular polymeric matrix, such that they exist in what is often termed as the ‘biofilm’ more of existence. Existence as a biofilm affords many evolutionary advantages to the microbes in terms of their ability to coordinate behaviour and survive in a largely hostile environment. In terms of enabling coordinated behaviour, we know that bacteria within a biofilm are densely packed and can often communicate to each other in order to coordinate behaviour via mechanisms such as quorum sensing. Quorum sensing (QS is a density-dependent signalling mechanism involving the release of autoinducer (AIs) compounds which can affect bacterial function, ecology, biofilm dynamics etc. The AIs used in QS are classified as mainly being N-acyl-homoserine lactones (AHL); commonly used by Gram-negative bacteria) or Autoinducer-2 based systems (AI-2; used by Gram-positive and Gram-negative bacteria); although other less common AI systems exist. Most of our understanding of QS comes from bacterial pathogens, with much being unknown on a commensal bacterial and ecosystem level, especially in the context of the rumen microbiome. A small number of studies have explored QS within the rumen bacteria, revealing a prevalence of AI-2 QS systems. Indeed, the lead supervisor has published 2 papers showing that AI-2 based QS systems are prevalent in the rumen microbiome and that these systems are most abundant in the dominant rumen bacteria Prevotella, Butyrivibrio and Pseudobutyrivibrio (Won et al., 2020). We have also published metatranscriptome data tracking the colonization of perennial ryegrass by rumen microbes over time, with the resultant data suggesting that these chemicals may influence transitions in bacterial diversity during colonization, likely through promoting competitive behaviour (Huws et al., 2020).

Objectives:

This is an exciting project as we now have the baseline data on QS chemical communication in the rumen and our aim is to go beyond describing the existence of AI-2 based QS in the rumen to a more fundamental understanding of how these chemicals are transmitted and the consequences of such mechanisms on microbial function, ecological interactions, ability to form biofilms and ultimately their ability to effectively degrade plant material and provide energy to the host. We will also look at mechanisms of transfer of these chemicals from one organism to the next, especially with respect to forming membrane vesicles, in which the supervisory team have vast expertise. These aims are summarised in these project objectives:

1.      Identify AI-2 target genes using genomics, transcriptomics and bioinformatics i.e those affected directly by AI-2 signal molecule binding to the receptor site. 

2.      Understand the consequences of QS on gene regulation to confirm correlations with suspected target genes outlined in 1, using in vitro incubations with and without the QS inhibitor chemical.

3.      To investigate mechanisms of transfer of QS signals via membrane vesicles. We will isolate membrane vesicles using our own standard operating procedures at peak times of AI-2 QS and use proteomic techniques to identify QS molecules in the membrane vesicles.

This project is fundamental in nature with the aim of using this data to ultimately improving the productivity and reducing the environmental impact of ruminant production .

Training opportunities

 Queen’s University Belfast offers an array of courses available through the graduate school https://www.qub.ac.uk/graduate-school/ and it is expected that the student completes a minimum of 10 days training each year. More specifically the student will spend time with the supervisor in Aberystwyth to gain training in proteomic techniques. The placement will take place in the latter part of the PhD when all samples are available. The student will also be encouraged to attend relevant courses outside both universities, attend and present at least two national conferences and 1 international conference throughout the PhD and as outlined in the budget plan. The student will also be able to attend external training events as deemed appropriate.

How to Apply

Applications will be by online application form only. Do not send CVs. Please go to the FoodBioSystems website to see guidance for applicants, information on academic and funding eligibility and language proficiency.

Equality Diversity and Inclusion:

The FoodBioSystems DTP is committed to equality, diversity and inclusion. We want to build a doctoral researcher and staff body that reflects the diversity of society, and to encourage applications from under-represented and disadvantaged groups. Our actions to promote diversity and inclusion are detailed on the FoodBioSystemsDTP website.

Application Deadline: 22 January, 2024

Start Date: 1 October 2024

Duration: 4 years

How to apply: See details here

Funding Notes

FoodBioSystems DTP students receive a tax free stipend (salary) for four years. For 2023/24 this is £18,622 (or £20,622 for students based at Brunel University). The pay increases slightly each year at rate set by UKRI. The DTP also pays tuition fees at the standard UK rate and makes a contribution to the research project costs.
Most of our funding (minimum 70%) is available to students with UK/home fees status. We welcome applications from international students. However, we can only offer up to 30% of our studentships to international students. In 2024, this will be maximum of 9 projects.



References:

Won et al. 2020. Microbiome. 8(1):23. doi: 10.1186/s40168-020-00796-y

Huws SA et al. (2021). Microbiome. 9(1):143. doi: 10.1186/s40168-021-01087-w