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      Comparative Analysis of Milk Microbiomes and Their Association with Bovine Mastitis in Two Farms in Central Russia

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          Abstract

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          Bovine mastitis is one of the most common diseases in cattle farms in Russia. In this work we investigate a microbial composition of milk samples collected from farms of Russian Central Region. Our data revealed significant dominance of several operational taxonomic units corresponding mostly to groups of Staphylococcus aureus, Aerococcus spp. and Streptococcus spp. We identify interesting fact of Staphylococcus and Aerococcus genera seemed to be antagonistic to each other, and the disappearance of the Aerococcus genus in milk microbiota may represent a marker for its transition to a subclinical stage of mastitis.

          Abstract

          Bovine mastitis is a widespread infectious disease. In addition to the economic damages associated with reduced milk yield due to mastitis, the problem of food contamination by microorganism metabolites, in particular toxins, is also a concern. Horizontal transfer of microorganisms from animal populations to humans can also be complicated by antibiotic resistance. Therefore, bovine mastitis is relevant to the study of microbiology and veterinary medicine. In this study, we investigated the microbiome of milk samples from healthy cows and cows with different forms of mastitis from individual quarters of the udder of cows during first and second lactation. Total DNA was extracted from milk samples. The V3–V4 regions of the bacterial 16S rRNA genes from each sample were amplified to generate a library via high-throughput sequencing. We revealed significant dominance of several operational taxonomic units (OTUs) corresponding mostly to groups of Staphylococcus aureus, Aerococcus spp., and Streptococcus spp. In addition, we unexpectedly identified Streptococcus thermophilus in samples with high SCC quantities. We found some infectious agents that characterized summer mastitis. We demonstrated that in Central Russia, mastitis is associated with a wide variety of causal organisms. We observed some differences in the diversity of the two investigated farms. However, we did not find any significant difference among healthy, mastitis and subclinical samples according to their SCC status from either farms by principal component analysis. Linear discriminant analysis effect size (LEfSe) confirmed the presence of several indicator genera in farms from Moscow and the Tula Region. These results confirm the complex bacterial etiology of bovine mastitis.

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          QIIME allows analysis of high-throughput community sequencing data.

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            Metagenomic biomarker discovery and explanation

            This study describes and validates a new method for metagenomic biomarker discovery by way of class comparison, tests of biological consistency and effect size estimation. This addresses the challenge of finding organisms, genes, or pathways that consistently explain the differences between two or more microbial communities, which is a central problem to the study of metagenomics. We extensively validate our method on several microbiomes and a convenient online interface for the method is provided at http://huttenhower.sph.harvard.edu/lefse/.
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              UniFrac: a new phylogenetic method for comparing microbial communities.

              We introduce here a new method for computing differences between microbial communities based on phylogenetic information. This method, UniFrac, measures the phylogenetic distance between sets of taxa in a phylogenetic tree as the fraction of the branch length of the tree that leads to descendants from either one environment or the other, but not both. UniFrac can be used to determine whether communities are significantly different, to compare many communities simultaneously using clustering and ordination techniques, and to measure the relative contributions of different factors, such as chemistry and geography, to similarities between samples. We demonstrate the utility of UniFrac by applying it to published 16S rRNA gene libraries from cultured isolates and environmental clones of bacteria in marine sediment, water, and ice. Our results reveal that (i) cultured isolates from ice, water, and sediment resemble each other and environmental clone sequences from sea ice, but not environmental clone sequences from sediment and water; (ii) the geographical location does not correlate strongly with bacterial community differences in ice and sediment from the Arctic and Antarctic; and (iii) bacterial communities differ between terrestrially impacted seawater (whether polar or temperate) and warm oligotrophic seawater, whereas those in individual seawater samples are not more similar to each other than to those in sediment or ice samples. These results illustrate that UniFrac provides a new way of characterizing microbial communities, using the wealth of environmental rRNA sequences, and allows quantitative insight into the factors that underlie the distribution of lineages among environments.
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                Author and article information

                Contributors
                Role: Academic Editor
                Journal
                Animals (Basel)
                Animals (Basel)
                animals
                Animals : an Open Access Journal from MDPI
                MDPI
                2076-2615
                14 May 2021
                May 2021
                : 11
                : 5
                : 1401
                Affiliations
                [1 ]Laboratory of Microbiology, L.K. Ernst Federal Science Center for Animal Husbandry, Dubrovitsy 142132, Russia; dap2189@ 123456gmail.com (D.N.); vijmikrob@ 123456mail.ru (O.A.); Kolodin77@ 123456mail.ru (E.K.); n_zinovieva@ 123456mail.ru (N.Z.); brovko@ 123456bibch.ru (F.B.)
                [2 ]Laboratory of Immunochemistry, Shemyakin and Ovchinnikov Institute of Bioorganic Chemistry of the Russian Academy of Sciences, Pushchino 142290, Russia; phursova_k@ 123456rambler.ru (K.F.); loskutova-i@ 123456mail.ru (I.S.); mshannikova@ 123456gmail.com (M.S.); shepelyakovskaya@ 123456rambler.ru (A.S.)
                [3 ]Laboratory of Plasmid Biology, Federal Research Center “Pushchino Scientific Center for Biological Researches”, G.K. Skryabin Institute of Biochemistry & Physiology of Microorganisms of the Russian Academy of Sciences, Pushchino 142290, Russia
                [4 ]Laboratory of Cell Genome Functioning Mechanisms, Federal Research Center “Pushchino Scientific Center for Biological Researches”, Institute of Cell Biophysics of the Russian Academy of Sciences, Pushchino 142290, Russia; lptolik@ 123456gmail.com (A.S.); dzhelyadin@ 123456bibch.ru (T.D.)
                Author notes
                [* ]Correspondence: sls@ 123456ibpm.pushchino.ru ; Tel.: +7-496-773-3962
                Author information
                https://orcid.org/0000-0002-2775-1248
                https://orcid.org/0000-0001-5164-244X
                https://orcid.org/0000-0003-4017-6863
                Article
                animals-11-01401
                10.3390/ani11051401
                8156869
                34068998
                ba434423-9f3f-47e4-b6c9-da7d6cbf9050
                © 2021 by the authors.

                Licensee MDPI, Basel, Switzerland. This article is an open access article distributed under the terms and conditions of the Creative Commons Attribution (CC BY) license ( https://creativecommons.org/licenses/by/4.0/).

                History
                : 02 April 2021
                : 10 May 2021
                Categories
                Article

                bovine mastitis,milk microbiome,microbial diversity,staphylococcus,aerococcus,central russia

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