Analysis of Hindgut Microbiome of Sheep and Effect of Different Husbandry Conditions

SIMPLE SUMMARY: The purpose of this study was to describe the composition of the hindgut microbiome in sheep and to test whether different husbandry conditions could have an effect in changing the composition and the diversity of the hindgut microbiome, based on the assumption that there is a known influence between stress-related husbandry conditions and the gut microbiome. The results of our study demonstrated very few differences in the sheep hindgut microbiome, basically related to Verrucomicrobia abundance, when compared with previous studies. Additionally, the investigation of the interactions between microbiome and animal husbandry showed few indicators of difference between groups, which might indicate the presence of a low-level stress across the flock, depending on management procedures. Surely, this work represents a contribution for the analysis of the microbiome in animal production and welfare research. ABSTRACT: The microbiome is now seen as an important resource to understand animal health and welfare in many species. However, there are few studies aiming at identifying the association between fecal microbiome composition and husbandry conditions in sheep. A wide range of stressors associated with management and housing of animals increases the hypothalamic–pituitary axis activity, with growing evidence that the microbiome composition can be modified. Therefore, the purpose of the present study was to describe the core microbiome in sheep, characterized using 16S rRNA gene sequencing, and to explore whether exposure to stressful husbandry conditions changed sheep hindgut microbiome composition. Sheep (n = 10) were divided in two groups: isolated group (individually separated for 3 h/day) and control group (housed in the home pen for the entire trial period). Sheep core microbiome was dominated by Firmicutes (43.6%), Bacteroidetes (30.38%), Proteobacteria (10.14%), and Verrucomicrobia (7.55%). Comparative results revealed few operational taxonomic units (OTUs) with significantly different relative abundance between groups. Chao1, abundance-based coverage estimator (ACE), and Fisher’s alpha indices did not show differences between groups. OTU-based Bray–Curtis distances between groups were not significant (p-value = 0.07). In conclusion, these results describing the core microbiome of sheep do not suggest a strong effect of stressful husbandry conditions on microbial composition.