Landscape scale gut microbiomics in a wild bird; investigating anthropogenic and ecological effects in Berthelot’s pipit


Landscape scale gut microbiomics in a wild bird; investigating anthropogenic and ecological effects in Berthelot’s pipit


Project Description


Professor David S Richardson, University of East Anglia – Contact me

Dr Richard Davies, University of East Anglia, School of Biology

Dr Sarah Worsely, University of East Anglia, School of Biology


The vertebrate gut microbiome -a complex community of microbes- affects many aspects of host biology with considerable consequences for host health (including pathogen resistance) and survival. However, microbiomes differ substantially even among individuals in the same natural population. How ecological and anthropogenic factors shape this variation is not well understood, particularly at a fine spatial scale. Studying this is urgent given the increasing influence of climate change and human disturbance on wild habitats; both factors could impact host-microbe interactions and have important consequences for animals.

Berthelot’s pipit -a bird endemic to the macaronesian islands- provides an excellent system in which to assess the drivers of gut microbiome variation at fine spatial scales. On Tenerife pipits occupy a variety of habitats that span rural-urban and ecological gradients. Individuals have been shown to vary in their exposure to pathogens and exist at different population densities (all predicted to impact the microbiome). Building on previous work on this system you will undertake fieldwork to develop a dataset of host faecal samples and related environmental variables. You will then screen samples using resequencing of a bacteria barcoding gene and resolve microbiome variation using bioinformatic tools.

After characterising the basic pipit bacterial gut microbiome, the following novel objectives can be developed and prioritised according to your interests:

1)         Investigate how anthropogenic disturbance, including urban-rural gradients and livestock, affect this microbiome.
2)         Determine how the microbiome varies in relation to other key environmental variables, e.g. altitude, aridity.
3)         Investigate whether pathogenic infection and gut microbiome differences covary across the landscape (avian malaria and pox are common in the pipit).

At UEA you will join a thriving, friendly, research group, supported by a vibrant ARIES cohort, work with international collaborators in Tenerife, and within a strong evolution, ecology and microbiology research community. We will help you gain diverse research skills in fieldwork, sequencing, bioinformatics, data analysis, geographic information systems, conceptual understanding, scientific writing and public communication. Training to increase transferable skills and enhance employability will also be provided.

Person specification

Degree in biology/zoology/ecology related subject

Field and/or analytical skills preferred

Contact for further details


  • 1 Worsley, SF, Davies, CS, Mannarelli, M-E, Hutchings, MI, Komdeur, J, Burke, T, Dugdale, HL & Richardson, DS (2021). Gut microbiome composition, not alpha diversity, is associated with survival in a natural vertebrate population', Animal Microbiome, 3,1, 84,
  • 2 Davies, CS, Worsley, S, Maher, K, Komdeur, J, Burke, T, Dugdale, H & Richardson, DS (2022). Immunogenetic variation shapes the gut microbiome in a natural vertebrate population. Microbiome 10(1), 1-22Davies, CS, Worsley, S, Maher, K, Komdeur, J, Burke, T, Dugdale, H & Richardson, DS (2022). Immunogenetic variation shapes the gut microbiome in a natural vertebrate population. Microbiome 10(1), 1-22
  • 3 Sheppard, EC, Martin, CA, Armstrong, C, González‐Quevedo, C, Illera, JC, Suh, A, Spurgin, LG & Richardson, DS (2022). Genomic associations with poxvirus across divergent island populations in Berthelot's pipit, Mol. Ecol, 31,11, 3154-3173.
  • 4 Gonzalez-Quevedo, C., Davies, R. G. & Richardson, D. S. Predictors of malaria infection in a wild bird population: landscape-level analyses reveal climatic and anthropogenic factors. J Anim Ecol 83, 1091–1102 (2014).
  • 5 Heni, A.C., Fackelmann, G., Eibner, G. et al. Wildlife gut microbiomes of sympatric generalist species respond differently to anthropogenic landscape disturbances. anim microbiome 5, 22 (2023).

Key Information

  • This project has been shortlisted for funding by the ARIES NERC DTP and will start on 1st October 2024. The closing date for applications is 23:59 on 10th January 2024.
  • Successful candidates who meet UKRI’s eligibility criteria will be awarded a NERC studentship, which covers fees, stipend (£18,622 p.a. for 2023/24) and research funding. International applicants are eligible for fully-funded ARIES studentships including fees. Please note however that ARIES funding does not cover additional costs associated with relocation to, and living in, the UK. We expect to award between 4 and 6 studentships to international candidates in 2024.
  • ARIES students benefit from bespoke graduate training and ARIES provides £2,500 to every student for access to external training, travel and conferences, on top of all Research Costs associated with the project. Excellent applicants from quantitative disciplines with limited experience in environmental sciences may be considered for an additional 3-month stipend to take advanced-level courses.
  • ARIES is committed to equality, diversity, widening participation and inclusion in all areas of its operation. We encourage enquiries and applications from all sections of the community regardless of gender, ethnicity, disability, age, sexual orientation and transgender status. Academic qualifications are considered alongside non-academic experience, and our recruitment process considers potential with the same weighting as past experience.
  • All ARIES studentships may be undertaken on a part-time or full-time basis, visa requirements notwithstanding.
  • For further information, please contact the supervisor. To apply for this Studentship follow the instructions at the bottom of the page or click the 'apply now' link.
  • ARIES is required by our funders to collect Equality and Diversity Information from all of our applicants. The information you provide will be used solely for monitoring and statistical purposes; it will remain confidential, and will be stored on the UEA sharepoint server. Data will not be shared with those involved in making decisions on the award of Studentships, and will have no influence on the success of your application. It will only be shared outside of this group in an anonymised and aggregated form. You will be ask to complete the form by the University to which you apply.
  • ARIES funding is subject to UKRI terms and conditions. Postgraduate Researchers are expected to live within reasonable distance of their host organisation for the duration of their studentship. See for more information

Applications open

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