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      Exploring the Fecal Microbial Composition and Metagenomic Functional Capacities Associated With Feed Efficiency in Commercial DLY Pigs

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          Abstract

          Gut microbiota has indispensable roles in nutrient digestion and energy harvesting, especially in processing the indigestible components of dietary polysaccharides. Searching for the microbial taxa and functional capacity of the gut microbiome associated with feed efficiency (FE) can provide important knowledge to increase profitability and sustainability of the swine industry. In the current study, we performed a comparative analysis of the fecal microbiota in 50 commercial Duroc × (Landrace × Yorkshire) (DLY) pigs with polarizing FE using 16S rRNA gene sequencing and shotgun metagenomic sequencing. There was a different microbial community structure in the fecal microbiota of pigs with different FE. Random forest analysis identified 24 operational taxonomic units (OTUs) as potential biomarkers to improve swine FE. Multiple comparison analysis detected 8 OTUs with a significant difference or tendency toward a difference between high- and low-FE pigs ( P < 0.01, q < 0.1). The high-FE pigs had a greater abundance of OTUs that were from the Lachnospiraceae and Prevotellaceae families and the Escherichia- Shigella and Streptococcus genera than low-FE pigs. A sub-species Streptococcus gallolyticus subsp. gallolyticus could be an important candidate for improving FE. The functional capacity analysis found 18 KEGG pathways and CAZy EC activities that were different between high- and low-FE pigs. The fecal microbiota in high FE pigs have greater functional capacity to degrade dietary cellulose, polysaccharides, and protein and may have a greater abundance of microbes that can promote intestinal health. These results provided insights for improving porcine FE through modulating the gut microbiome.

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          Most cited references25

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

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            FLASH: fast length adjustment of short reads to improve genome assemblies.

            Next-generation sequencing technologies generate very large numbers of short reads. Even with very deep genome coverage, short read lengths cause problems in de novo assemblies. The use of paired-end libraries with a fragment size shorter than twice the read length provides an opportunity to generate much longer reads by overlapping and merging read pairs before assembling a genome. We present FLASH, a fast computational tool to extend the length of short reads by overlapping paired-end reads from fragment libraries that are sufficiently short. We tested the correctness of the tool on one million simulated read pairs, and we then applied it as a pre-processor for genome assemblies of Illumina reads from the bacterium Staphylococcus aureus and human chromosome 14. FLASH correctly extended and merged reads >99% of the time on simulated reads with an error rate of <1%. With adequately set parameters, FLASH correctly merged reads over 90% of the time even when the reads contained up to 5% errors. When FLASH was used to extend reads prior to assembly, the resulting assemblies had substantially greater N50 lengths for both contigs and scaffolds. The FLASH system is implemented in C and is freely available as open-source code at http://www.cbcb.umd.edu/software/flash. t.magoc@gmail.com.
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              Genetic control of obesity and gut microbiota composition in response to high-fat, high-sucrose diet in mice.

              Obesity is a highly heritable disease driven by complex interactions between genetic and environmental factors. Human genome-wide association studies (GWAS) have identified a number of loci contributing to obesity; however, a major limitation of these studies is the inability to assess environmental interactions common to obesity. Using a systems genetics approach, we measured obesity traits, global gene expression, and gut microbiota composition in response to a high-fat/high-sucrose (HF/HS) diet of more than 100 inbred strains of mice. Here we show that HF/HS feeding promotes robust, strain-specific changes in obesity that are not accounted for by food intake and provide evidence for a genetically determined set point for obesity. GWAS analysis identified 11 genome-wide significant loci associated with obesity traits, several of which overlap with loci identified in human studies. We also show strong relationships between genotype and gut microbiota plasticity during HF/HS feeding and identify gut microbial phylotypes associated with obesity. Copyright © 2013 Elsevier Inc. All rights reserved.
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                Author and article information

                Contributors
                Journal
                Front Microbiol
                Front Microbiol
                Front. Microbiol.
                Frontiers in Microbiology
                Frontiers Media S.A.
                1664-302X
                29 January 2019
                2019
                : 10
                : 52
                Affiliations
                [1] 1College of Animal Science and National Engineering Research Center for Breeding Swine Industry, South China Agricultural University , Guangzhou, China
                [2] 2National Engineering Research Center for Breeding Swine Industry, Guangdong Wens Foodstuffs Group Co., Ltd. , Guangzhou, China
                [3] 3Department of Animal Science, Michigan State University , East Lansing, MI, United States
                Author notes

                Edited by: Xing Chen, China University of Mining and Technology, China

                Reviewed by: Xianwen Ren, Peking University, China; Robert Heyer, Otto-von-Guericke-Universität Magdeburg, Germany

                *Correspondence: Jie Yang, jieyang2012@ 123456hotmail.com Zhenfang Wu, wzfemail@ 123456163.com

                These authors have contributed equally to this work

                This article was submitted to Systems Microbiology, a section of the journal Frontiers in Microbiology

                Article
                10.3389/fmicb.2019.00052
                6361760
                30761104
                1ed97d30-2872-436b-bfb0-51cb0223ae84
                Copyright © 2019 Quan, Cai, Yang, Zeng, Ding, Wang, Zhuang, Zhou, Li, Yang, Li, Zheng, Huang, Yang and Wu.

                This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) and the copyright owner(s) are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms.

                History
                : 22 October 2018
                : 14 January 2019
                Page count
                Figures: 4, Tables: 0, Equations: 0, References: 55, Pages: 12, Words: 0
                Funding
                Funded by: Natural Science Foundation of Guangdong Province 10.13039/501100003453
                Award ID: 2018B030315007
                Award ID: 2018B030313011
                Award ID: 2016A030310447
                Categories
                Microbiology
                Original Research

                Microbiology & Virology
                dly pigs,feed efficiency,gut microbiota,16s rrna gene,metagenome sequencing

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