Environment rather than breed or body site shapes the skin bacterial community of healthy sheep as revealed by metabarcoding.

Background: The skin is inhabited by a variety of micro-organisms, with bacteria representing the predominant taxon of the skin microbiome. In sheep, the skin bacterial community of healthy animals has been addressed in few studies, only with culture-based methods or sequencing of cloned amplicons.

Objectives: The objectives of this study were to determine the sheep skin bacterial community composition by using metabarcoding for a detailed characterisation and to determine the effect of body part, breed and environment.

Statistical assessment of variability of terminal restriction fragment length polymorphism analysis applied to complex microbial communities.

The variability of terminal restriction fragment polymorphism analysis applied to complex microbial communities was assessed statistically. Recent technological improvements were implemented in the successive steps of the procedure, resulting in a standardized procedure which provided a high level of reproducibility.