The Raw Milk Microbiota from Semi-Subsistence Farms Characteristics by NGS Analysis Method.

Bartosz Hornik,Agnieszka Piotrowska-Cyplik,Justyna Staninska-Pięta,Łukasz Wolko,Paweł Cyplik,Jakub Czarny

doi:10.3390/molecules26165029

Bartosz Hornik, Agnieszka Piotrowska-Cyplik + Show 4 more

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https://doi.org/10.3390/molecules26165029

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Abstract

The aim of this study was to analyze the microbiome of raw milk obtained from three semi-subsistence farms (A, B, and C) located in the Kuyavian-Pomeranian Voivodeship in Poland. The composition of drinking milk was assessed on the basis of 16S rRNA gene sequencing using the Ion Torrent platform. Based on the conducted research, significant changes in the composition of the milk microbiome were found depending on its place of origin. Bacteria belonging to the Bacillus (17.0%), Corynebacterium (12.0%) and Escherichia-Shigella (11.0%) genera were dominant in the milk collected from farm A. In the case of the milk from farm B, the dominant bacteria belonged to the Acinetobacter genus (21.0%), whereas in the sample from farm C, Escherichia-Shigella (24.8%) and Bacillus (10.3%) dominated the microbiome. An analysis was performed using the PICRUSt tool (Phylogenetic Investigation of Communities by Reconstruction of Unobserved States) in order to generate a profile of genes responsible for bacterial metabolism. The conducted analysis confirmed the diversity of the profile of genes responsible for bacterial metabolism in all the tested samples. On the other hand, simultaneous analysis of six KEGG Orthologs (KO), which participated in beta-lactam resistance responsible for antibiotic resistance of bacteria, demonstrated that there is no significant relationship between the predicted occurrence of these orthologs and the place of existence of microorganisms. Therefore, it can be supposed that bacterial resistance to beta-lactam antibiotics occurs regardless of the environmental niche, and that the antibiotic resistance maintained in the population is a factor that shapes the functional structure of the microbial consortia.

Highlights

Milk and its products play an important role in human nutrition in many cultures
Microorganisms that developed mechanisms which allow them to survive in the presence of an antimicrobial agent, using the possibilities offered by horizontal gene transfer, can colonize other organisms or transfer their resistance genes to other bacteria
The development of new bioinformatics tools allows for a more accurate description of the diversity of the milk microbiota and the association of taxonomic, physiological and functional characteristics, which allows the dairy industry to improve the quality of milk and dairy products

Summary

Introduction

Milk and its products play an important role in human nutrition in many cultures. It is a source of protein, vitamins and many minerals, which makes it an excellent environment for the growth and development of bacteria [1,2]. The disease is caused by bacteria and other microorganisms that enter the teats The appearance of this disease in high-yielding dairy cows is the cause of huge economic losses [7]. In the subclinical form, there are economic losses caused by the reduced milk yield of cows; the correct diagnosis and implementation of an effective treatment process are very important [8]

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