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

Abstract

BackgroundThe 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.ObjectivesThe 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.Materials and MethodsOverall, 267 samples were taken from 89 adult female sheep, belonging to three different breeds and kept on nine different farms in Switzerland. From every individual, one sample each was taken from belly, left ear and left leg and metabarcoding of the 16S rRNA V3–V4 hypervariable region was performed.ResultsThe main phyla identified were Actinobacteriota, Firmicutes, Proteobacteria and Bacteriodota. The alpha diversity as determined by Shannon's diversity index was significantly different between sheep from different farms. Beta diversity analysis by principal coordinate analysis (PCoA) showed clustering of the samples by farm and body site, while breed had only a marginal influence. A sparse partial least squares discriminant analysis (sPLS‐DA) revealed seven main groups of operational taxonomic units (OTUs) of which groups of OTUs were specific for some farms.Conclusions and Clinical RelevanceThese findings indicate that environment has a larger influence on skin microbial variability than breed, although the sampled breeds, the most abundant ones in Switzerland, are phenotypically similar. Future studies on the sheep skin microbiome may lead to novel insights in skin diseases and prevention.

Selection of sheep skin bacteria to reduce blood-feeding by biting midges under laboratory conditions

“…Skin bacterial isolation from sheep skin showed that the majority of the species belonged to the families Bacillaceae (43.8 %) and Staphylococcaceae (18.8 %). A previous study analyzing the skin bacterial profile of sheep from different breeds, farms and body sites (Jost et al, 2023) (Haarstad et al, 2014). Interestingly, we also found bacterial species such as B. thuringiensis and Solibacillus sp.…”

“…MALDI-TOF mass spectra were acquired on a microflex Biotyper (Bruker Daltonics, Germany) as described (Cuénod et al, 2021) and the species identified with MABRITECCENTRAL, a database for the comparison and identification of bacterial MALDI-TOF MS spectra (www.mabriteccentral.com) (Mabritec AG). Processed spectra are compared against Bacterial species were selected for the behavioural assays based on their 1) harmlessness (biosafety group 1/1+) ensuring a safe future usage as potential skin probiotic, 2) abundance and 3) VIP-scores as determined in our earlier study (Jost et al, 2023). The VIP-score describes the most influential bacteria for the separation between sheep breeds, body parts and origin by PL-SDA (Jost et al, 2023).…”

“…Processed spectra are compared against Bacterial species were selected for the behavioural assays based on their 1) harmlessness (biosafety group 1/1+) ensuring a safe future usage as potential skin probiotic, 2) abundance and 3) VIP-scores as determined in our earlier study (Jost et al, 2023). The VIP-score describes the most influential bacteria for the separation between sheep breeds, body parts and origin by PL-SDA (Jost et al, 2023).…”

“…Processed spectra are compared against the SARAMIS™ (Spectral ARchive And Microbial Identification System database, Anagnostec GmbH, 14476 Potsdam, Germany) and PAPMID™ (Putative Assigned Protein Masses for Identification Database, Mabritec AG) databases. Bacterial species were selected for the behavioural assays based on their 1) harmlessness (biosafety group 1/1+) ensuring a safe future usage as potential skin probiotic, 2) abundance and 3) VIP-scores as determined in our earlier study (Jost et al, 2023). The VIP-score describes the most influential bacteria for the separation between sheep breeds, body parts and origin by PL-SDA (Jost et al, 2023).…”

“…Little is known about the odour profiles and the associated skin microbiome of animals, though volatiles from cow and chicken skin bacteria were shown to mediate mosquitoes to their animal host as they significantly increased trap catches (Busula et al, 2017). Recently, the skin bacterial profiles of sheep from three different breeds, farms and body sites were investigated by metabarcoding, revealing that environment rather than breed or body site shapes the skin bacterial community (Jost et al, 2023). We assume that sheep also differ in their attractiveness to biting midges based on the volatiles released by their different skin microbiomes.…”