Improving livestock resilience by understanding the role of the microbiome in viral infection progression and antibiotic resistance (FoodBioSystems DTP)

The microbes in the gut play an important role in regulating the host’s physiology, thereby influencing the outcome of infections. Conversely, viral infections may alter the composition of gut microbes. We here want to systematically study the impact of viral infections on the intestinal flora of pigs.

Start date
1 October 2021
4 years
Application deadline
Funding information

Funding is for the full 48 months of the studentship

Stipend: £15,609 per annum with annual increases for inflation

Fees:  Studentship fees are covered for UK /EU citizens only.  Up to 30% of the studentships may be awarded to international students. For international FoodBioSystems DTP studentships based at the University of Surrey, the University will be covering the difference in the UK/Republic of Ireland fees and International Fees for international UKRI funded students.

Full eligibility, funding and application details can be found at the FoodBioSystems DTP page.


The microbiome in humans has been well studied and has been shown to influence important physical functions such as energy metabolism and immune system development (Cani et al., 2018). Compared to humans relatively little is known about the role of the gut microbiota in pigs This is despite a number of studies linking the pig microbiome to average daily weight gain, feed efficiency, feed conversion, feed intake and to its capacity to act as a reservoir for antibiotic resistance genes (McCormack et al., 2020, Wang et al., 2019, Ghanbari et al., 2019). This project aims to investigate the impact the viral infection has on the gut microbiome and the resistome (all the genes associated with conferring antibiotic resistance within the microbiome). It has two specific objectives:

1. Uncover the role of the microbiome in viral infection: This aim will involve profiling the microbiome of a healthy cohort of pigs and comparing it to that of animals infected with commercially relevant porcine viruses.

2. Investigating the link between viral infection and the Resistome: Antibiotic resistance is one of the greatest threats to global healthcare systems (McCarthy et al., 2019). Antimicrobials are widely used for disease prevention and growth promotion in pigs. In fact, 80% of antibiotic use in the US is in agriculture (Boeckel et al., 2015). The One Health perspective has been critical in demonstrating the role antibiotic misuse in agriculture has in perpetuating the current antibiotic resistance crisis in hospitals (Manyi- Loh et al., 2018). In this aim, we will explore how viral infection impacts the prevalence of Antibiotic Resistance Genes (ARGs) within the gut microbiome of pigs.

Further information about the project itself can be found here.

Related links
FoodBioSystems DTP website FoodBioSystems DTP - PhD Project

Eligibility criteria

1st or upper 2nd class degree is required in a subject appropriate to the PhD projects applied for (see the project description for more info). Candidates with a lower class of Bachelors degree, but a good performance at the Masters level (“merit” or above) will also be considered.

UK students only.

How to apply

Please go to FoodBioSystems DTP website for information on how to apply for this studentship. The closing date for applications will be 8 February 2021.

Application deadline

Contact details

Falko Steinbach
01 VSM 02
Telephone: +44 (0)1483 682315

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