IAP-24-091

Defining interactions between diet and season on gastrointestinal tract health and microbiome of domestic animals

Simple Summary

The PhD project (Defining interactions between diet and season on gastrointestinal tract health and microbiome of domestic animals) aims to identify consistent seasonally induced changes to the GIT environment (microbiome and transcriptome) which are associated with both behavioural and systemic immunological decline. Furthermore, the project aims to investigate if in-diet bioactive compounds (polyphenols) found in locally grown legumes can mitigate potentially detrimental seasonally induced change in microbial population, GIT tissue and systemic health. The identification of microbial and or tissue markers of seasonally induced change to the GIT will inform animal keepers when action should be taken to mitigate these and systemically associated effects. This mitigation could come in the form of the addition of polyphenols, which act to modulate the GIT microbiome, to the diet.

Background
Changes in both season and diet independently affect the gastrointestinal tract (GIT) microbiome and thereby affect GIT health (Garcia, Bradford and Nagaraja, 2017). However, there is limited understanding of how seasonal changes in the GIT microbiome vary in relation to nutritional input. This interaction between season and the GIT microbiome may enable the anticipation of periods of poorer animal health and, therefore, inferior nutrient utilisation. These periods, when identified, could be attenuated with dietary intervention.
Diets vary based on ingredient source. Specifically, dietary variations in protein source will influence the concentration and diversity of polyphenolic compounds in feed. In this project these compounds will be provided by including different varieties (those containing high and low polyphenol concentrations) of UK-grown legumes. A dose-dependent effect and direct comparison to feeding commercially typical diets on the GIT microbiome will be investigated. Polyphenols have been found to modulate the GIT immune response by inactivating nuclear factor-KB leading to the suppression of pro-inflammatory pathways (Yahfoufi et al. 2018). Further, microbiome level, changes have been observed in both mice and humans with increases in the relative abundance of Lactobacillus, Bifidobacterium, and Akkermansia spp.; potentially leading to upregulation of immune responsiveness (Rodríguez-Daza et al. 2021)
The broad aim of this studentship is to use a comparative approach to characterise dietary-dependent and -independent seasonal changes in the gut microbiome and transcriptome of domestic animals. This studentship will investigate seasonal changes in the gut microbiome of cattle and sheep and identify the impact of diet on seasonal variation in microbe diversity, circulating immune cells and affective behaviour. Moreover, the projects will examine the role of photoperiod and melatonin on the gut microbiome, immune cells and affective behaviour. Finally, the seasonal transcriptome of gastrointestinal tract tissues (e.g. rumen, abomasum, small and large intestine) in cattle and sheep fed different commercially available diets will be characterized. These projects will address three inter-related aims:

1: Identify seasonal variation in GIT microbiome and associate this variation with both behavioural and systemic immunologic change.
2: Assess if the provision of dietary polyphenolic compounds can overcome any deleterious seasonal changes observed in Aim 1.
3: Characterise the seasonal variation in GIT transcriptome

Livestock are exposed to large-scale seasonal changes in environmental cues (i.e., day length) and nutrient supply. Studies will be conducted using cattle and sheep due to the highly reliable and repeatable nature of their seasonal regulation of physiology. Moreover, sheep are excellent animal models to interrogate the molecular and neural underpinnings of seasonal rhythms in gut microbiome health. The research program benefits from;
1) a fully supported farm animal research facility provided by the Cochno Farm at the University of Glasgow, where the student will perform field work with both cattle and sheep.
2) industrial investment and engagement by Harbro Ltd which includes a 4-month placement in a cutting edge animal-nutrition business where the successful candidates will experience a variety of food production models form crop growth and animal production to ingredient processing and industry led research and development.
3) co-supervision by Prof. Pietro Iannetta an international expert in the sustainability of food production systems, especially in legume production, based at the James Hutton Institute who will facilitate agronomy experience.
4) Finally our stakeholder partner (i.e., Ronald Farms, Stirlingshire) will directly benefit from the knowledge gained from the impact of nutrition on seasonal physiology, on gut microbiome health in sheep and cattle

Year 1

• Project 1: Characterize dietary effects on the seasonal adaptation of the GIT microbiome and associated systemic effects
• October-December– NWB induction, literature review, and PGR course work (e.g., Advance Statistical Analyses)
• May –presentation: SBOHVM PGR series
• August –presentation: British Society for Neuroendocrinology (BSN)

Year 2

• Project 2: Characterize hormonal effects on the adaptation of the GIT microbiome and associated systemic effects (RJ, TS, GR, MB, NE).
• September– presentation: British Association of Veterinary Parasitologists (BSVP)
• October– presentation: British Cattle Veterinary Association Congress (BCVA)
• April- presentation: SBOHVM PGR series
• June- Internship: James Hutton Institute

Year 3

• October– CASE partnership internship: 4-month internship (Harbro Ltd)
• Project 3: Delineation of the seasonal GIT transcriptome
• March– presentation: British Society of Animal Scientists
• May– presentation: SBOHVM PGR series
• August– presentation: BSN

Year 3.5

• July-December– fashion dissertation, compose 3 publications and a review manuscript.
• September– presentation: BAVP
• October– presentation: BCVA
• January-February– Viva

The student will gain training and skills from a wide range of expertise provided by the supervisory team. Students will obtain a Personal Home Office License in order to work with animals. Animal handling will include monitoring of animal activity, body condition, faecal and blood sample collection, and a battery of behavioural tests that assess spatial ability, spatial memory, anxiety, and exploratory behaviour. Physiological assays will include measurements of the immune system (e.g., leukocyte counts), and hormone assays (e.g., ELISA). Molecular analyses will include common procedures (e.g., RNA extraction, DNA extraction). The student will learn cutting-edge transcriptome sequencing using Nanopore Flow cells on a GridION and advanced bioinformatic analyses. Students will enroll in advanced bioinformatics courses offered by Glasgow Polyomics. Students will develop writing skills through manuscript preparation and oral communication by presenting research findings in the School seminar series and national/international conferences. The student will receive skills in health and safety, and equality, diversity, and inclusivity. The student will gain industry skills through a 4-month internship with Harbro Ltd.

The student will therefore gain valuable transferable skills sought by both academic and industry-based perspective employers.