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Wild Biome: interactions between gut microbiota and parasites

This research project is in competition for funding with one or more projects available across the NERC GW4 Doctoral Training Partnership (DTP). Usually the projects which receive the best applicants will be awarded the funding. Find out more information about the DTP and how to apply.

Application deadline: 7 January 2019

Start date: October 2019

DTP research theme: Living World


In terms of numbers of cells, we are more bacteria than we are human, and the trillions of bacteria that inhabit our gut (our ‘microbiota’) are vital for biological processes and affect many aspects of health. Importantly, the gut is also home to a diverse parasite community (helminths, protozoa, viruses and pathogenic bacteria) with which animals have coevolved for millions of years.

Whilst the impact of microbiota on host health is a burgeoning and important research focus, how parasites and microbiota interact with one another, and the consequences of such interactions for parasite dynamics, host health and the microbiota composition, have largely been overlooked. Here, using wild rodents and their natural parasite community, we aim to tease apart how host, microbiota and parasites interact, and better understand how gut community composition affects the prevalence of zoonotic pathogens (animal pathogens causing disease in humans) and the subsequent risk to public health

Project aims and methods

The broad aim of this project is to examine host-microbiota-parasite interactions. Specific experiments will be agreed in collaboration with you. These experiments will use established field sites in the Italian Alps to live-trap wild rodents and sample their microbiota and natural parasite communities.

These data will be analysed to determine:

  • whether microbiota and parasites alter one another’s diversity, number or infectivity inside and outside the host
  • the implications of interactions between parasites and microbiota for host health
  • how microbiota-parasite interactions alter the risk of zoonotic infection.

The empirical observations will be used together with an existing mechanistic mathematical model of multiple co-circulating microbial species to develop a better understanding of the way species interactions govern microbial community composition, and challenge current concepts of gut health which largely overlook the potential for parasites to interact with microbiota.


You should have a good degree in the area of biological sciences, with a Mbiol, MRes or MSc as desirable. Full training will be provided in field, laboratory and theoretical work, but experience in animal handling and/or basic molecular biology is desirable.

Case or Collaborative Partner

Perkins and Hauffe have collaborated successfully on several innovative projects in host-microbiota-macrobiota interactions. The CASE student will have full access to this combined expertise of these two research groups, including long-term field sites, state-of-the art laboratories, and expertise in data analysis and dissemination of results, in short, a complete preparation for a future career in scientific research.

Exchanges of students between established researchers in different parts of the globe invariably enrich the PhD experience, scientifically, culturally and socially, providing valuable teambuilding and networking skills.


Field work: At the Fondazione E. Mach (FEM) in Italy, training will be provided in small mammal live-trapping (animal handling), biological sampling (health and safety procedures and archiving), plus how to plan and execute logistics for a remote research project.

Laboratory analysis: Dr. Hauffe and her expert technicians at FEM will provide advanced training in metataxonomics of gut microbiota, molecular parasitology, and virology.

Data Analysis: In Cardiff with Drs Perkins and Lello will provide all the necessary bioinformatics, statistical modelling and social network theory training, using ‘R’.

Mathematical modelling: In Bath Dr Adams will provide training in mechanistic modelling using Matlab, including how to run simulations with an existing model, and make minor modifications to it. More advanced training can be provided for an interested student.

Publications: You will receive advanced training in scientific writing and presentations. You will also join ‘CRIPES’ a vibrant discussion group composed of faculty, post-docs and students whose work focuses on infectious diseases.

References and background reading

  • Pascoe EL, Hauffe HC, Marchesi JR, Perkins SE. Network analysis of gut microbiota literature: an overview of the research landscape in non-human animal studies. ISME J. 2017;11:1–8.
  • J Kreisinger, G Bastien, HC Hauffe, J Marchesi, Perkins, S.E. Interactions between multiple helminths and the gut microbiota in wild rodents. Phil. Trans. R. Soc. B, 2015.


Photo of Sarah Perkins

Dr Sarah Perkins


+44 (0)29 2087 0490

Dr Joanne Lello

Senior Lecturer

+44 (0)29 2087 5885


Dr. Ben Adams, University of Bath, Department of Mathematical Sciences.

Dr. Heidi C. Hauffe, Department of Biodiversity and Molecular Ecology, Fondazione Edmund, Mach.

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