Effects of stress on the microbial ruminal environment in beef cattle and its relationship to feed efficiency and methane emissions

There is currently a poor understanding of the impact of chronic stress on the behaviour and physiology of beef cattle. In monogastrics, hormones released in response to stress can have deleterious effects on the balance of the microbiota present in the gut, which can last long after stress hormone levels have returned to normal. If comparable changes occur in the rumen microbiota, these could have important consequences for ruminal fermentation and digestibility, leading to suboptimal use of nutrients and increased methane emissions. However, there is little information regarding the effects of stress on the rumen microbiome. The overall aim of this thesis was to understand how commercially relevant stressors affect ruminal microbial populations, as well as concurrent effects on behaviour, feed efficiency and methane emissions in beef cattle. The first objective was to assess the direct contribution of glucocorticoids such as cortisol in mediating the effect of stress on the microflora and feed efficiency. Dexamethasone, a potent synthetic cortisol analogue, was used to evaluate the effect of an exogenous glucocorticoid on feed efficiency and the rumen microbial populations. This treatment was applied to 516 ± 50-day old Limousin cross steers selected based on extremes of feed efficiency, to contrast the effects on ruminal microbial communities of more efficient and less efficient animals. Animals in the treatment group (n=24) were injected with 0.05 mg/kg dexamethasone intramuscularly for 3 consecutive days, while matching extremes of feed efficiency controls (n=16) were treated with the equivalent volume of saline solution (Control group). The effect of dexamethasone was assessed on faecal cortisol metabolites, feeding behaviour, locomotor activity, as well as metagenomic information obtained from 16S rRNA gene sequencing of rumen fluid samples. Treatment with exogenous glucocorticoid dexamethasone induced transient changes in activity and faecal cortisol. Nonetheless, this glucocorticoid did not cause any significant changes in the rumen archaea population or microbial diversity, an indication that ruminal microbial populations might be resilient to the direct effects of exogenous glucocorticoids. The second objective was to quantify the behavioural and physiological responses to a putative composite chronic stressor treatment, by applying a series of commercially relevant stressors and assessing any changes in behaviour and HPA axis responsiveness. The commercially relevant stressors used were reduced space allowance, in addition to being subjected every week to regrouping, transport and a short period of isolation. Limousin (n=32) and Angus (n=32) crossbred beef steers, 400 ±13 days old at the beginning of the trial, were assigned in a balanced way to a composite stressor (S) or control (C) treatment, each treatment with four replicate groups. Blood samples and faecal samples were collected to measure cortisol levels. An ACTH challenge was performed using 0.5ug/kg of Synacthen Depot® with blood samples taken just before, 30 min post and 60 min post ACTH challenge to assess changes in HPA axis responsiveness on a subsample of animals (S=22; C=19). Behaviour was assessed from activity monitors, feed intake, an attention bias test, video observations of agonistic behaviour at the feeders and affiliative behaviour (rubbing and licking) in the home pen. Results showed differences between treatments in some parameters of activity and an attention bias test. However, there were no effects of treatment on agonistic or affiliative behaviour. Cortisol responses, although different between groups, could not be specifically attributed to the composite stressor treatment and the ACTH challenge employed did not detect any significant differences in adrenal sensitivity between treatments. Making use of metagenomic information obtained from 16S rRNA gene sequencing of rumen fluid samples taken during the composite stressor experiment, the last objective of this project assessed changes in the rumen microbiota in response to the applied stressors. Although there was a particular interest in the methanogenic populations, analyses also looked at effects on productivity and methane emissions. To this end a small cohort of 12 animals (six from each C and S treatments) was used to assess any effects of the composite stressor treatment on methane emissions. Although changes were detected in some microbial genera throughout the experiment, there were no major changes in the rumen archaea population or microbial diversity directly associated with the composite stressor treatment. Additionally, by the end of the experiment, there was no effect of stress on growth performance or methane emissions. In conclusion, circulating glucocorticoids do not appear to affect the rumen microbiota balance directly, although it is possible that they may affect microbial communities in other sites of the gastrointestinal tract. Some differences in behaviour but not cortisol were found in response to the composite stressor treatment, suggesting that beef cattle might be resilient to repeated but predictable stressors. The stressor regime applied did not cause substantial changes in rumen microbial diversity or methanogenic archaea populations. This thesis was a first step towards enhancing our understanding of the dynamics of the rumen microbiome in response to stress. Further research needs to examine more closely the links between biological changes in response to severe chronic stress and microbiota resilience in the rumen and other sites of the gastrointestinal tract.