Abstract
Simple SummaryIn the last decade, the number of studies focused on the study of the microbiota of different tissues, organs, or physiological fluids has considerably increased. The milk of dairy species is an important and continuous source of commensal, mutualistic and potentially probiotic bacteria. Second-generation sequencing technologies have been applied to characterise the milk microbiota of dairy cows, whereas the study of the sheep milk microbiota is scarce. In the present study, we aimed to explore the bacterial diversity and composition of milk samples from the Churra sheep breed, a rustic autochthonous breed from the region of Castilla y León (Spain). Moreover, this study tries to clarify the complex bacterial composition of sheep milk comparing the results presented here with previous research on the milk microbiota of the Assaf sheep breed. This assessment has shown that the milk microbiota of ewes from one flock of the Assaf breed is more diverse than the milk microbiota reported here for two different flocks of Churra sheep. The study also provides a step into a better understanding of the link between the bacterial milk composition in these two sheep breeds and somatic cell count, an indicator trait of subclinical mastitis resistance in dairy sheep.Milk from healthy animals has classically been considered a sterile fluid. With the development of massively parallel sequencing and its application to the study of the microbiome of different body fluids, milk microbiota has been documented in several animal species. In this study, the main objective of this work was to access bacterial profiles of healthy milk samples using the next-generation sequencing of amplicons from the 16S rRNA gene to characterise the milk microbiome of the Churra breed. A total of 212 samples were collected from two Churra dairy farms with a different management system. The core milk microbiota in Churra ewes includes lesser genera (only two taxa: Staphylococcus and Escherichia/Shigella) than studies reported in other dairy species or even in a previous study in Assaf sheep milk. We found that diversity values in the two flocks of Churra breed were lower than the diversity of the milk microbiota in Assaf. The non-metric multidimensional scaling (NMDS) ordination using Bray-Curtis distance separates samples based on their microbiota composition. The information reported here might be used to understand the complex issue of milk microbiota composition.
Highlights
The study of the microbial communities found in milk has gained increasing interest in recent years.The classical concept of the sterility of the mammary gland and milk has been challenged by the results obtained in the last decade using bacterial DNA-based methodologies [1,2]
The overall number of amplicon sequences variants (ASVs) detected by the DADA2 analysis for the 212 Churra samples was 2519; only 142 ASVs showed a relative abundance higher than 0.1% (81.8% of all of the analysed sequences)
By exploiting the massive parallel sequencing of the 16S rRNA gene, this study provides a first characterisation of the core microbiota of milk samples of Spanish Churra sheep, which involves genera such as Staphylococcus and Escherichia/Shigella
Summary
The study of the microbial communities found in milk has gained increasing interest in recent years.The classical concept of the sterility of the mammary gland and milk has been challenged by the results obtained in the last decade using bacterial DNA-based methodologies [1,2]. Most studies on the milk microbiota of dairy ruminant species have focused on these changes and the differences between the microbial composition of milk samples obtained from healthy udders and those suffering mastitis or local inflammation [7,8]. These studies have allowed knowing the milk core microbiota for the different species, which refers to all taxa commonly found across all the samples analysed in each study. The relationships between microbiota and udder health may not be applicable from one to other breeds within the same species
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