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The microbiome of the beehive as an indicator of honeybee pathogens (Ref FHMS - DTP - 06 BIO)

   Faculty of Health & Medical Sciences

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  Dr Jorge Gutierrez-Merino, Dr Beth Nicholls  No more applications being accepted  Funded PhD Project (UK Students Only)

About the Project

Infectious diseases affecting bees pose a serious threat to both biodiversity and food security. Many honeybee pathogens are shared by other wild bee species and crops are experiencing considerable yield gaps owing to insufficient pollination. Therefore, novel strategies that mitigate and prevent infectious agents to pollinators are urgently needed. Here we propose to monitor the microbiome of beehives to forecast the incidence and prevalence of honeybee pathogens. Our group has recently discovered that honey carries DNA of many different bacteria derived from bees, plants, soil, and water (Santorelli et al. 2021; https://doi.org/10.1101/2021.08.25.457643). Furthermore, we have observed that this bacterial diversity is dependent on the geographical location, suggesting a unique microbial feature for every hive that could be exploited as an indicator and predictor of bee pathogens.  

We aim to monitor changes in the microbiome of the beehive using the DNA of honey samples. The DNA sequencing results will be complemented with additional data such as the impact of beekeeping methods and the main environmental bacteria present in the beehives, which, together, will inform of the levels of the gut bacteria in the bee colony and the presence or absence of microbial pathogens. The combination of environmental factors with significant microbial variations will enable us to generate algorithms illustrating the bee gut bacteria that associate with health or disease.  

Training opportunities and student profile 

The selected PhD student will benefit from training in molecular microbiology high throughput technologies such as 16S rRNA sequencing, and advanced computational analysis. Furthermore, the candidate will gain knowledge on beekeeping and farming practices through field sampling, surveys and meetings with beekeepers, farmers and ecologists. This project is therefore suitable for students with a degree in biological sciences, microbiology or a closely related science. The PhD student is expected to contribute intellectually to the development of the project to maximize the results obtained. This person will develop laboratory and scientific skills to become a well-trained molecular & computational microbiologist with expertise in bee ecology. 


  1. Arredondo D, Castelli L, Porrini MP, Garrido PM, Eguaras MJ, Zunino P, Antunez K: Lactobacillus kunkeei strains decreased the infection by honey bee pathogens Paenibacillus larvae and Nosema ceranae. Benef Microbes 2018, 9(2):279-290. 
  2. Borba RS, Hoover SE, Currie RW, Giovenazzo P, Guarna MM, Foster LJ, Zayed A, Pernal SF: Phenomic analysis of the honey bee pathogen-web and its dynamics on colony productivity, health and social immunity behaviors. PLoS One 2022, 17(1):e0263273. 
  3. Floyd AS, Mott BM, Maes P, Copeland DC, McFrederick QS, Anderson KE: Microbial Ecology of European Foul Brood Disease in the Honey Bee (Apis mellifera): Towards a Microbiome Understanding of Disease Susceptibility. Insects 2020, 11(9). 
  4. Kim DR, Cho G, Jeon CW, Weller DM, Thomashow LS, Paulitz TC, Kwak YS: A mutualistic interaction between Streptomyces bacteria, strawberry plants and pollinating bees. Nat Commun 2019, 10. 
  5. Rubanov A, Russell KA, Rothman JA, Nieh JC, McFrederick QS: Intensity of Nosema ceranae infection is associated with specific honey bee gut bacteria and weakly associated with gut microbiome structure. Sci Rep 2019, 9(1):3820. 
  6. Santorelli L, Wilkinson T, Abdulmalik R, Rai Y, Creevey CJ, Huws S, Gutierrez-Merino J: Beehives possess their own distinct microbiomes. 2021. bioRxiv 2021.08.25.457643
  7. Subotic S, Boddicker AM, Nguyen VM, Rivers J, Briles CE, Mosier AC: Honey bee microbiome associated with different hive and sample types over a honey production season. PLoS One 2019, 14(11):e0223834.

This is a collaborative project between The University of Surrey, The University of Sussex, Wisley Gardens, Royal Horticulture Society (RHS), The British Beekeepers Association (BBKA) and Queen’s University Belfast (QUB). 

The principal supervisors are Dr Jorge Gutierrez-Merino, a veterinarian with an extensive track record in Applied Microbiology, particularly in the area of beneficial microbes, and currently working as a Senior Lecturer at Surrey University ([Email Address Removed]); and Dr Elizabeth Nicholls, a bee ecologist with expertise in leading landscape-scale field experiments investigating the impact of pathogens on whole honeybee hive health, and recently awarded a UKRI-Future Leaders Fellowship to study bee foraging decisions at Sussex University. 

Entry requirements

Open to UK students, with the project starting in October 2023. 

You will need to meet the minimum entry requirements for our PhD programme https://www.surrey.ac.uk/postgraduate/biosciences-and-medicine-phd#entry.

Previous education in microbiology and environmental sciences is desirable; and ideally having some experience in genomics and bioinformatics. The person recruited for the PhD is also expected to have (or be willing to develop) beekeeping skills, therefore they will ensure that the beehives selected for the study are carefully managed, and that sample collection is appropriately conducted.

How to apply

Applicants are strongly encouraged to contact the relevant principal supervisor(s) to discuss the project(s) before submitting their application. Please contact Dr Jorge Gutierrez-Merino at [Email Address Removed]

Applications should be submitted via the https://www.surrey.ac.uk/postgraduate/biosciences-and-medicine-phd programme page (N.B. Please select the October 2023 start date when applying).

You may opt to apply for a single project or for 2 of these Pathogens and Host Defences Doctoral Training Partnership studentship projects

When completing your application, in place of a research proposal, please provide a brief motivational document (1 page maximum) which specifies:

  • the reference numbers(s) for the project or two projects you are applying for, 
  • the project title(s) and principal supervisor name(s) 
  • if apply for two projects, please also indicate your order of preference for the projects
  • an explanation of your motivations for wanting to study for a PhD 
  • an explanation of your reasons for selecting the project(s) you have chosen

Additionally, to complete a full application, you MUST also email a copy of your CV and 1-page motivational document directly to the relevant project principal supervisor of each project you apply for. Due to short turnaround times for applicant shortlisting, failure to do this may mean that your application is not considered.

Please note that online interviews for shortlisted applicants are expected to take place during the week commencing 30th January.

Project ref number FHMS-DTP-06 BIO

Funding Notes

Funding is for 3.5 years and includes UKRI-aligned stipend (£17,668 pa for 2022-23), approved University of Surrey fees and a research budget. This studentship is funded jointly by the Faculty of Health and Medical Sciences at the University of Surrey.
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