Interactions between the microbiome, nutrition, behaviour and welfare of domesticated animals

Abstract

This thesis investigated how nutrition influences behaviour, stress physiology, and welfare in domesticated animals through the gut microbiome. The work was guided by a novel conceptual framework, the microbiota-gut-brain-nutrition axis (MGBNA), and applied integrated methodologies including shotgun metagenomics, behavioural testing, and physiological stress markers across three distinct animal studies.

In Holstein bulls, four summer dietary strategies (grazing-only, grazing with 2 kg/day concentrate, grazing with ad libitum concentrate, and full housing with silage and ad libitum concentrate) were evaluated. Bulls in the grazing-only group exhibited higher hair cortisol and lower carcass weights than those receiving concentrate or housed diets. Significant differences were observed in rumen microbial diversity and functional gene profiles, with over 1,400 differentially abundant KEGG orthologs identified across treatments. These differences diminished following transition to a common winter diet, although carcass disparities remained.

In grazing heifers, four sward types (perennial ryegrass, permanent pasture, and multispecies swards with six or twelve plant species) were assessed across a full grazing season. Significant treatment by time interactions were observed for fermentation parameters, hair cortisol, and behaviour. Microbial alpha diversity increased over time, and microbial composition and KEGG based gene functions varied across both time and treatment. The use of rumen fluid cortisol as a physiological biomarker was introduced as a novel measure of stress and rumination.

In breeding dogs, probiotic supplementation was tested for effects on behaviour, physiological stress markers, and gut microbiome composition and function. While no significant treatment differences were detected for HCC, sIgA or FRGM, HCC and sIgA increased over time. Probiotic treated dogs showed greater exploration and reduced escape behaviour, coinciding with microbial restructuring and altered tryptophan metabolism.

Together, these studies demonstrate that diet and environment modulate the gut microbiome and its associations with stress physiology and behaviour, supporting the proposed MGBNA framework across species.

Date of Award	Dec 2025
Original language	English
Awarding Institution	Queen's University Belfast
Sponsors	Devenish Nutrition Limited
Supervisor	Sharon Huws (Supervisor) & Gareth Arnott (Supervisor)