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

Giulietta Minozzi,Simona Cannas,Renata Piccinini,Nicola Ferri,Matteo Chincarini,Giorgio Vignola,Clara Palestrini,Michela Minero,Emanuela Dalla Costa,Filippo Biscarini,Silvia Mazzola

doi:10.3390/ani11010004

Abstract

Simple SummaryThe 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.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.

Highlights

The intestinal microbiome includes microorganisms fundamental for host physiology, immunity, and the central nervous system in both humans and animals [1,2,3]
To check whether sequencing depth and sample size were adequate to characterize the composition of the sheep hindgut microbiome, sequence-based and sample-based rarefaction curves were generated from the operational taxonomic units (OTUs) table before pruning (9134 OTUs)
Both curves tended to plateau asymptotically towards a maximum, indicating that sequencing depth and the number of samples were adequate to characterize the sheep hindgut microbiome in the present study

Summary

Introduction

The intestinal microbiome includes microorganisms fundamental for host physiology, immunity, and the central nervous system in both humans and animals [1,2,3]. Today, this omics approach has been largely used in livestock [4,5,6]. A study conducted in merino sheep analyzed the composition and the stability of the fecal microbiota. Recent studies aimed to define a core gut microbiome across sheep breeds have analyzed its composition in different breed differences as the case of the study on the Tibetan sheep breed [11]

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