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      Identification of the Potential Role of the Rumen Microbiome in Milk Protein and Fat Synthesis in Dairy Cows Using Metagenomic Sequencing

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          Abstract

          Simple Summary

          The rumen is the main digestive and absorption organ of dairy cows. It contains abundant microorganisms and can effectively use human-indigestible plant mass. Therefore, we used metagenomics to explore the role of rumen microbes in the regulation of milk protein and fat in dairy cows. This study showed that Prevotella species and Neocallimastix californiae in the rumen of cows are related to the synthesis of milk components due to their important functions in carbohydrate, amino acid, pyruvate, insulin, and lipid metabolism and transportation metabolic pathways.

          Abstract

          The rumen contains abundant microorganisms that aid in the digestion of lignocellulosic feed and are associated with host phenotype traits. Cows with extremely high milk protein and fat percentages (HPF; n = 3) and low milk protein and fat percentages (LPF; n = 3) were selected from 4000 lactating Holstein cows under the same nutritional and management conditions. We found that the total concentration of volatile fatty acids, acetate, butyrate, and propionate in the rumen fluid was significantly higher in the HPF group than in the LPF group. Moreover, we identified 38 most abundant species displaying differential richness between the two groups, in which Prevotella accounted for 68.8% of the species, with the highest abundance in the HPF group. Functional annotation based on the Kyoto Encyclopedia of Gene and Genome (KEGG), evolutionary genealogy of genes: Non-supervised Orthologous Groups (eggNOG), and Carbohydrate-Active enzymes (CAZy) databases showed that the significantly more abundant species in the HPF group are enriched in carbohydrate, amino acid, pyruvate, insulin, and lipid metabolism and transportation. Furthermore, Spearman’s rank correlation analysis revealed that specific microbial taxa (mainly the Prevotella species and Neocallimastix californiae) are positively correlated with total volatile fatty acids (VFA). Collectively, we found that the HPF group was enriched with several Prevotella species related to the total VFA, acetate, and amino acid synthesis. Thereby, these fulfilled the host’s needs for energy, fat, and rumen microbial protein, which can be used for increased biosynthesis of milk fat and milk protein. Our findings provide novel information for elucidation of the regulatory mechanism of the rumen in the formation of milk composition.

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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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            Fast and sensitive protein alignment using DIAMOND.

            The alignment of sequencing reads against a protein reference database is a major computational bottleneck in metagenomics and data-intensive evolutionary projects. Although recent tools offer improved performance over the gold standard BLASTX, they exhibit only a modest speedup or low sensitivity. We introduce DIAMOND, an open-source algorithm based on double indexing that is 20,000 times faster than BLASTX on short reads and has a similar degree of sensitivity.
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              CD-HIT: accelerated for clustering the next-generation sequencing data

              Summary: CD-HIT is a widely used program for clustering biological sequences to reduce sequence redundancy and improve the performance of other sequence analyses. In response to the rapid increase in the amount of sequencing data produced by the next-generation sequencing technologies, we have developed a new CD-HIT program accelerated with a novel parallelization strategy and some other techniques to allow efficient clustering of such datasets. Our tests demonstrated very good speedup derived from the parallelization for up to ∼24 cores and a quasi-linear speedup for up to ∼8 cores. The enhanced CD-HIT is capable of handling very large datasets in much shorter time than previous versions. Availability: http://cd-hit.org. Contact: liwz@sdsc.edu Supplementary information: Supplementary data are available at Bioinformatics online.
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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
                26 April 2021
                May 2021
                : 11
                : 5
                : 1247
                Affiliations
                [1 ]National Engineering Laboratory for Animal Breeding, Key Laboratory of Animal Genetics, Breeding and Reproduction of Ministry of Agriculture and Rural Affairs, Department of Animal Genetics, Breeding and Reproduction, College of Animal Science and Technology, China Agricultural University, Beijing 100193, China; wuxin0208@ 123456126.com (X.W.); huangjinfeng1003@ 123456126.com (J.H.); pengpeng940203@ 123456126.com (P.P.); liuyanan961102@ 123456126.com (Y.L.); hanbo_98@ 123456126.com (B.H.)
                [2 ]State Key Laboratory of Animal Nutrition, Beijing Engineering Technology Research Center of Raw Milk Quality and Safety Control, College of Animal Science and Technology, China Agricultural University, Beijing 100193, China; huangshuai510@ 123456126.com
                Author notes
                [* ]Correspondence: sundx@ 123456cau.edu.cn
                Article
                animals-11-01247
                10.3390/ani11051247
                8146572
                33926012
                b7264017-8634-476b-8bed-3c8b9aabea15
                © 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
                : 19 February 2021
                : 06 April 2021
                Categories
                Article

                dairy cattle,milk protein,milk fat,metagenome sequencing,rumen microbiome

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