Defining environmental regulation of gut microbiome health and welfare in domestic animals

Understanding how gut microbiome varies across the season is important for anticipating environmental induced changes in animal health. The broad aims of the studentship are to use a comparative approach to characterise the seasonal gut microbiome in domestic animals. This will be achieved through three closely related specific objectives: 1) to investigate seasonal changes in the gut microbiome of cattle and sheep and identify the impact of pasture-diet, supplemental-diet (i.e., Harbro premix) and farm-industry practice on microbe diversity, circulating immune cells and affective behaviour; 2) to examine the role of photoperiod and melatonin on the gut microbiome, immune cells and affective behaviour; and 3) to delineate the seasonal transcriptome of gastrointestinal tract tissues (e.g. stomach, small and large intestine) in cattle and sheep. The transcriptomic data will support our efforts to develop a single, online and freely-available source of information, called SeaWave, that contains molecular seasonal cycles in transcript expression across multiple species and tissues. These objectives will allow us to test the hypotheses that 1) environmental conditions govern gut microbiome health to drive seasonal change in animal immune function and affective behaviour; and 2) that environmental conditions induces sex-specific changes on gut microbe diversity.

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Image Captions

Heifers taken by Nicholas Jonsson,Ewe and lambs by Michelle Bellingham


Livestock are exposed to large-scale seasonal changes in environmental cues (i.e., daylength) and nutrients. 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 using fully supported farm animal research facility provided by the Cochno Farm at the University of Glasgow. The project benefits from industrial investment by Harbro Ltd. Harbro will provide the premix diet used in Project 1 and Project 2 so that the projects can determine the impact of grass fed versus supplemental nutrition. Finally, our stakeholder partner (i.e., Ronald Farms, Stirlingshire) will directly benefit from the knowledge gained from the impact of nutrition on seasonal physiology, welfare and gut microbiome health in sheep and cattle.

Project Timeline

Year 1

Project 1 (Oct 2023- Oct 2024) – the student will conduct a seasonal study to characterize the gut microbiome health in cattle and sheep. The projects use a range of pasture-fed, and supplemented diet to investigate the impact on the gut microbe diversity, circulating immune cells (i.e., leukocytes), and affective behaviours. This project will also include farm raised cattle and sheep from the stakeholder Ronald Farms. Animals will be monitored, and samples collected monthly. We hypothesize that some bacteria, such as Anaeroplasmataceae will increase during the winter seasons and coincide with poor spatial abilities/memory and higher anxiety measures. Furthermore, we anticipate that cattle and sheep fed a nutrient supplemented diet provided by Harbro Ltd, will have greater bacterial diversity, lower anxiety, and improved spatial ability/memory compared to pasture fed.
Oct-Dec (2023) – the student will engage in PGR course work (e.g., Advance Statistical Analyses)
May (2024) – presentation in the SBOHVM PGR series
Aug (2024) – presentation at the British Society for Neuroendocrinology

Year 2

Project 2 – (Oct 2024- Oct 2025) – the student will investigate the impact of daylight (e.g., ALAN) and hormones (i.e. melatonin) on gut microbiome health in livestock. Animals will be housed in different light conditions including summer-like, winter-like or ALAN housing environments to determine the effect on microbiome diversity. As previous work as identified a robust sex-difference in photoperiod induced changes in the gut microbiome, this study will include male and female animals. The student will test the hypothesis that female animals elevate Anaeroplasmataceae in response to short winter-like photoperiod and the development of a summer-phenotype will be associated with a reduction in Anaeroplasmataceae. Furthermore, we hypothesize that melatonin induces sex-specific gut microbiome diversity.
Sept (2024) – Present at the British Association of Veterinary Parasitologist annual meeting
Oct (2024) – Present at the British Cattle Veterinary Association Congress
March (2025) – Present at the International Sheep Veterinary Association conference
April (2025)- Present in the SBOHVM PGR seminar series

Year 3

Oct 2025-Dec 2025 – CASE partnership internship. The student will spend 4 months working at Harbro Ltd
Project 3 – (Jan 2026-June 2026) the student will delineate the seasonal transcriptome of the cattle and sheep gastrointestinal tract. This project will take advantage of recent University equipment investment to develop Nanopore GridION sequencing in the Stevenson laboratory. This project will use cattle and sheep samples collected from the local abattoir. Stomach, large and small intestines will be dissected and frozen on dry ice. RNA will be extracted from tissue samples and transcriptomes sequenced using Nanopore Flow cells on a GridION. The Stevenson laboratory has the bioinformatic pipeline established to conduct statistical analyses for differentially expressed genes.
May (2026) – present at the SBOHVM PGR series
Aug (2026) – present at the British Society for Neuroendocrinology

Year 3.5

July 2026-December 2026 – the student will primarily focus on writing their dissertation. Guidance will be provided to format the 3 projects for publication and a review manuscript.
Sept (2026) – Present at the British Association of Veterinary Parasitologist annual meeting
Oct (2026) – Present at the British Cattle Veterinary Association Congress
Jan-Feb (2027) – Viva

& Skills

The student will gain training and skills from a wide range of expertise provided by the supervisory team. Students will obtain a Personal Licence in order to work with animals. Animal handling will include monitoring of animal activity, body condition, faecal samples, blood sample collection and a battery of behavioural tests that assess spatial ability, spatial memory, anxiety (e.g., light:dark box) and exploratory behaviour. Physiological assays will include measurements of immune system (e.g., leukocyte counts), 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 enrol 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.

References & further reading

1. Valdivieso et al., 2022 https://pubmed.ncbi.nlm.nih.gov/35725367/
2. Francesio et al., 2020 https://pubmed.ncbi.nlm.nih.gov/32314683/
3. Bao et al., 2019 https://pubmed.ncbi.nlm.nih.gov/31189592/
4. Hough et al., 2019 https://pubmed.ncbi.nlm.nih.gov/31229635/

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