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      Comparative Genome Analysis and Evaluation of Probiotic Characteristics of Lactobacillus plantarum Strain JDFM LP11

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          Abstract

          In the current study, the probiotic potential of approximately 250 strains of lactic acid bacteria (LAB) isolated from piglet fecal samples were investigated; among them Lactobacillus plantarum strain JDFM LP11, which possesses significant probiotic potential, with enhanced acid/bile tolerance, attachment to porcine intestinal epithelial cells (IPEC-J2), and antimicrobial activity. The genetic characteristics of strain JDFM LP11 were explored by performing whole genome sequencing (WGS) using a PacBio system. The circular draft genome have a total length of 3,206,883 bp and a total of 3,021 coding sequences were identified. Phylogenetically, three genes, possibly related to survival and metabolic activity in the porcine host, were identified. These genes encode p60, lichenan permease IIC component, and protein TsgA, which are a putative endopeptidase, a component of the phosphotransferase system (PTS), and a major facilitator in the gut environment, respectively. Our findings suggest that understanding the functional and genetic characteristics of L. plantarum strain JDFM LP11, with its candidate genes for gut health, could provide new opportunities and insights into applications in the animal food and feed additive industries.

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          Most cited references22

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          Major facilitator superfamily.

          The major facilitator superfamily (MFS) is one of the two largest families of membrane transporters found on Earth. It is present ubiquitously in bacteria, archaea, and eukarya and includes members that can function by solute uniport, solute/cation symport, solute/cation antiport and/or solute/solute antiport with inwardly and/or outwardly directed polarity. All homologous MFS protein sequences in the public databases as of January 1997 were identified on the basis of sequence similarity and shown to be homologous. Phylogenetic analyses revealed the occurrence of 17 distinct families within the MFS, each of which generally transports a single class of compounds. Compounds transported by MFS permeases include simple sugars, oligosaccharides, inositols, drugs, amino acids, nucleosides, organophosphate esters, Krebs cycle metabolites, and a large variety of organic and inorganic anions and cations. Protein members of some MFS families are found exclusively in bacteria or in eukaryotes, but others are found in bacteria, archaea, and eukaryotes. All permeases of the MFS possess either 12 or 14 putative or established transmembrane alpha-helical spanners, and evidence is presented substantiating the proposal that an internal tandem gene duplication event gave rise to a primordial MFS protein prior to divergence of the family members. All 17 families are shown to exhibit the common feature of a well-conserved motif present between transmembrane spanners 2 and 3. The analyses reported serve to characterize one of the largest and most diverse families of transport proteins found in living organisms.
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            WebMGA: a customizable web server for fast metagenomic sequence analysis

            Background The new field of metagenomics studies microorganism communities by culture-independent sequencing. With the advances in next-generation sequencing techniques, researchers are facing tremendous challenges in metagenomic data analysis due to huge quantity and high complexity of sequence data. Analyzing large datasets is extremely time-consuming; also metagenomic annotation involves a wide range of computational tools, which are difficult to be installed and maintained by common users. The tools provided by the few available web servers are also limited and have various constraints such as login requirement, long waiting time, inability to configure pipelines etc. Results We developed WebMGA, a customizable web server for fast metagenomic analysis. WebMGA includes over 20 commonly used tools such as ORF calling, sequence clustering, quality control of raw reads, removal of sequencing artifacts and contaminations, taxonomic analysis, functional annotation etc. WebMGA provides users with rapid metagenomic data analysis using fast and effective tools, which have been implemented to run in parallel on our local computer cluster. Users can access WebMGA through web browsers or programming scripts to perform individual analysis or to configure and run customized pipelines. WebMGA is freely available at http://weizhongli-lab.org/metagenomic-analysis. Conclusions WebMGA offers to researchers many fast and unique tools and great flexibility for complex metagenomic data analysis.
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              Probiotics and the gut microbiota in intestinal health and disease.

              The use of probiotics is increasing in popularity for both the prevention and treatment of a variety of diseases. While a growing number of well-conducted, prospective, randomized, controlled, clinical trials are emerging and investigations of underlying mechanisms of action are being undertaken, questions remain with respect to the specific immune and physiological effects of probiotics in health and disease. This Review considers recent advances in clinical trials of probiotics for intestinal disorders in both adult and pediatric populations. An overview of recent in vitro and in vivo research related to potential mechanisms of action of various probiotic formulations is also considered.
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                Author and article information

                Journal
                Korean J Food Sci Anim Resour
                Korean J Food Sci Anim Resour
                Korean J Food Sci Anim Resour
                kosfa
                Korean Journal for Food Science of Animal Resources
                Korean Society for Food Science of Animal Resources
                1225-8563
                2234-246X
                October 2018
                31 October 2018
                : 38
                : 5
                : 878-888
                Affiliations
                [1 ]International Agricultural Development and Cooperation Center, Chonbuk National University , Jeonju 54896, Korea
                [2 ]Department of Animal Biotechnology, Chonbuk National University , Jeonju 54896, Korea
                [3 ]Department of Animal Science and Institute of Milk Genomics, Chonbuk National University , Jeonju 54896, Korea
                [4 ]Graduate School of Agricultural Convergence Technology, Chonbuk National University , Jeonju 54896, Korea
                [5 ]Department of Functional Food and Biotechnology, Jeonju University , Jeonju 55069, Korea
                Author notes
                [* ]Corresponding author : Sangnam Oh Department of Functional Food and Biotechnology, Jeonju University, Jeonju 55069, Korea Tel: +82-63-220-3109 Fax: +82-63-220-2054 E-mail: osangnam@ 123456jj.ac.kr

                † These authors contributed equally to this study.

                Article
                kosfa-38-5-878
                10.5851/kosfa.2018.e21
                6238035
                28298a29-91e6-4be5-8d20-504d2d7cb7b2
                © Copyright 2018 Korean Society for Food Science of Animal Resources

                This is an Open-Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License ( http://creativecommons.org/licenses/by-nc/3.0) which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited.

                History
                : 28 May 2018
                : 16 July 2018
                : 24 July 2018
                Categories
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                Custom metadata
                2018-10-31

                probiotics,l. plantarum,genome analysis,gut health
                probiotics, l. plantarum, genome analysis, gut health

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