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      Microbial Characteristics and Safety of Dairy Manure ComPosting for Reuse as Dairy Bedding

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          Abstract

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          The cost of cow manure treatment and bedding increases the operating cost of the ranch. Many ranches fill out the recycled manure solids (RMS) process to dry manure as bedding material. However, the microbial safety of RMS bedding is still uncertain, and the change of microbial diversity of the feces after each processing step is not clear. In this study, an amplified fragment sequence was utilized to analyze the microbial flora, bacterial phenotype, and metabolic function prediction of the products in the process of RMS processing. At the same time, samples of sand soil bedding material, rice husk bedding material and RMS bedding material were compared and analyzed. The results will be useful to further study the safety of RMS padding to reduce the operation cost of dairy farms and the incidence rate of mastitis.

          Abstract

          Changes in bacterial community, phenotype, metabolic function, and pathogenic bacteria content in recycled manure solids (RMS) were analyzed by 16S rRNA sequencing, Bugbase, picrost2, and qPCR, respectively. The data from RMS bedding were compared to those of sand bedding and rice husk bedding. The results show that the proportion of potentially pathogenic bacteria among the manure flora of RMS after dry and wet separation, after composting, and after sun-cure storage was 74.00%, 26.03%, and 49.067%, respectively. Compared to RMS bedding, the proportion of potentially pathogenic microorganisms in sand bedding and rice husk bedding was higher. The picrust2 analyses show that the level of lipopolysaccharide biosynthesis changed significantly during RMS processing. In addition, the qPCR results show that composting could effectively reduce the detection and quantification of pathogens, except Streptococcus uberis, in RMS bedding. In general, composting is an essential step to improve the safety of bedding materials in the process of fecal treatment. However, at the same time, RMS bedding may increase the risk of mastitis caused by Streptococcus uberis.

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          Predictive functional profiling of microbial communities using 16S rRNA marker gene sequences

          Profiling phylogenetic marker genes, such as the 16S rRNA gene, is a key tool for studies of microbial communities but does not provide direct evidence of a community’s functional capabilities. Here we describe PICRUSt (Phylogenetic Investigation of Communities by Reconstruction of Unobserved States), a computational approach to predict the functional composition of a metagenome using marker gene data and a database of reference genomes. PICRUSt uses an extended ancestral-state reconstruction algorithm to predict which gene families are present and then combines gene families to estimate the composite metagenome. Using 16S information, PICRUSt recaptures key findings from the Human Microbiome Project and accurately predicts the abundance of gene families in host-associated and environmental communities, with quantifiable uncertainty. Our results demonstrate that phylogeny and function are sufficiently linked that this ‘predictive metagenomic’ approach should provide useful insights into the thousands of uncultivated microbial communities for which only marker gene surveys are currently available.
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            UpSetR: an R package for the visualization of intersecting sets and their properties

            Abstract Motivation: Venn and Euler diagrams are a popular yet inadequate solution for quantitative visualization of set intersections. A scalable alternative to Venn and Euler diagrams for visualizing intersecting sets and their properties is needed. Results: We developed UpSetR, an open source R package that employs a scalable matrix-based visualization to show intersections of sets, their size, and other properties. Availability and implementation: UpSetR is available at https://github.com/hms-dbmi/UpSetR/ and released under the MIT License. A Shiny app is available at https://gehlenborglab.shinyapps.io/upsetr/. Contact: nils@hms.harvard.edu Supplementary information: Supplementary data are available at Bioinformatics online.
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              Application of acute phase protein measurements in veterinary clinical chemistry.

              The body's early defence in response to trauma, inflammation or infection, the acute phase response, is a complex set of systemic reactions seen shortly after exposure to a triggering event. One of the many components is an acute phase protein response in which increased hepatic synthesis leads to increased serum concentration of positive acute phase proteins. The serum concentration of these acute phase proteins returns to base levels when the triggering factor is no longer present. This paper provides a review of the acute phase proteins haptoglobin, C-reactive protein and serum amyloid A and their possible use as non-specific indicators of health in large animal veterinary medicine such as in the health status surveillance of pigs at the herd level, for the detection of mastitis in dairy cattle and for the prognosis of respiratory diseases in horses.
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                Author and article information

                Journal
                Biology (Basel)
                Biology (Basel)
                biology
                Biology
                MDPI
                2079-7737
                28 December 2020
                January 2021
                : 10
                : 1
                : 13
                Affiliations
                [1 ]State Key Laboratory of Animal Nutrition, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing 100193, China; wuhaoming@ 123456caas.cn (H.W.); donglei@ 123456caas.cn (L.D.); 18894311126@ 123456163.com (H.H.); menglu@ 123456caas.cn (L.M.); liuhuiming521@ 123456163.com (H.L.); zhengnan@ 123456caas.cn (N.Z.)
                [2 ]Laboratory of Quality and Safety Risk Assessment for Dairy Products of Ministry of Agriculture and Rural Affairs, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing 100193, China
                [3 ]Key Laboratory of Quality & Safety Control for Milk and Dairy Products of Ministry of Agriculture and Rural Affairs, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing 100193, China
                [4 ]State Key Laboratory of Membrane Biology, Tsinghua University-Peking University Joint Center for Life Sciences, School of Life Sciences, Tsinghua University, Beijing 100084, China; wangyang881229@ 123456mail.tsinghua.edu.cn
                Author notes
                [* ]Correspondence: wangjiaqi@ 123456caas.cn ; Tel.: +86-10-62816069
                Article
                biology-10-00013
                10.3390/biology10010013
                7824547
                33379325
                d388f704-d4c1-42d1-9feb-dc90cd0a8b84
                © 2020 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 ( http://creativecommons.org/licenses/by/4.0/).

                History
                : 25 November 2020
                : 23 December 2020
                Categories
                Article

                recycled manure solids,drum composter,bedding material,pathogenic bacteria,bacterial phenotype

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