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      Effects of the Inclusion of Fermented Mulberry Leaves and Branches in the Gestational Diet on the Performance and Gut Microbiota of Sows and Their Offspring

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          Abstract

          Fermented feed mulberry (FFM), being rich in dietary fiber, has not been fully evaluated to be used in sow’s diet. In this study, we investigated the effects of 25.5% FFM supplemented in gestation diets on the performance and gut microbiota of sows and their offspring. Results showed that the serum concentration of glucose, progesterone, and estradiol were not affected by the dietary treatment, while the level of serum insulin and fecal short chain fatty acid were both reduced in FFM group on gestation day 60 (G60, p < 0.05). Additionally, FFM increased both voluntary feed intake and weaning litter weight ( p < 0.05), while decreased the losses of both Backfat thickness and bodyweight throughout lactation ( p < 0.05). 16S rRNA sequencing showed FFM supplementation significantly increased the diversity and relative abundance of sows’ fecal microbiota on G60 ( p < 0.05). The differential microbiota for sows from FFM group was that Bacteroidetes was increased on G60 while Firmicutes were decreased on Lactation day 7 (L7, p < 0.05), and which for the FFM piglets was that both unclassified_f_Lachnospiraceae on L0 and norank_f_Ruminococcaceae on L7 were increased ( p < 0.05). In short, FFM can be recognized as a potential feed ingredient used in sow’s diet.

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          Controlling the False Discovery Rate: A Practical and Powerful Approach to Multiple Testing

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            Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2

            In comparative high-throughput sequencing assays, a fundamental task is the analysis of count data, such as read counts per gene in RNA-seq, for evidence of systematic changes across experimental conditions. Small replicate numbers, discreteness, large dynamic range and the presence of outliers require a suitable statistical approach. We present DESeq2, a method for differential analysis of count data, using shrinkage estimation for dispersions and fold changes to improve stability and interpretability of estimates. This enables a more quantitative analysis focused on the strength rather than the mere presence of differential expression. The DESeq2 package is available at http://www.bioconductor.org/packages/release/bioc/html/DESeq2.html. Electronic supplementary material The online version of this article (doi:10.1186/s13059-014-0550-8) contains supplementary material, which is available to authorized users.
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              UPARSE: highly accurate OTU sequences from microbial amplicon reads.

              Amplified marker-gene sequences can be used to understand microbial community structure, but they suffer from a high level of sequencing and amplification artifacts. The UPARSE pipeline reports operational taxonomic unit (OTU) sequences with ≤1% incorrect bases in artificial microbial community tests, compared with >3% incorrect bases commonly reported by other methods. The improved accuracy results in far fewer OTUs, consistently closer to the expected number of species in a community.
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                Author and article information

                Contributors
                Role: Academic Editor
                Journal
                Microorganisms
                Microorganisms
                microorganisms
                Microorganisms
                MDPI
                2076-2607
                15 March 2021
                March 2021
                : 9
                : 3
                : 604
                Affiliations
                [1 ]State Key Laboratory of Animal Nutrition, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing 100193, China; zhangyuping@ 123456caas.cn (Y.Z.); 82101186178@ 123456caas.cn (C.Y.); zhanghongfu@ 123456caas.cn (H.Z.)
                [2 ]Precision Livestock and Nutrition Laboratory, TERRA Teaching and Research Centre, Gembloux Agro-Bio Tech, University of Liège, 5030 Gembloux, Belgium; martine.schroyen@ 123456uliege.be (M.S.); nadia.everaert@ 123456uliege.be (N.E.)
                Author notes
                [* ]Correspondence: mateng@ 123456caas.cn ; Tel.: +86-130-2198-3772
                Author information
                https://orcid.org/0000-0003-3336-7426
                https://orcid.org/0000-0002-0244-986X
                Article
                microorganisms-09-00604
                10.3390/microorganisms9030604
                7998242
                33804202
                f5da8cab-e703-4de0-8772-7dc6915f2951
                © 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 ( http://creativecommons.org/licenses/by/4.0/).

                History
                : 24 February 2021
                : 11 March 2021
                Categories
                Article

                mulberry,sows,gestation,lactation,fecal microbiota
                mulberry, sows, gestation, lactation, fecal microbiota

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