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      The domestication of the probiotic bacterium Lactobacillus acidophilus

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          Abstract

          Lactobacillus acidophilus is a Gram-positive lactic acid bacterium that has had widespread historical use in the dairy industry and more recently as a probiotic. Although L. acidophilus has been designated as safe for human consumption, increasing commercial regulation and clinical demands for probiotic validation has resulted in a need to understand its genetic diversity. By drawing on large, well-characterised collections of lactic acid bacteria, we examined L. acidophilus isolates spanning 92 years and including multiple strains in current commercial use. Analysis of the whole genome sequence data set (34 isolate genomes) demonstrated L. acidophilus was a low diversity, monophyletic species with commercial isolates essentially identical at the sequence level. Our results indicate that commercial use has domesticated L. acidophilus with genetically stable, invariant strains being consumed globally by the human population.

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          Neighbor-net: an agglomerative method for the construction of phylogenetic networks.

          We present Neighbor-Net, a distance based method for constructing phylogenetic networks that is based on the Neighbor-Joining (NJ) algorithm of Saitou and Nei. Neighbor-Net provides a snapshot of the data that can guide more detailed analysis. Unlike split decomposition, Neighbor-Net scales well and can quickly produce detailed and informative networks for several hundred taxa. We illustrate the method by reanalyzing three published data sets: a collection of 110 highly recombinant Salmonella multi-locus sequence typing sequences, the 135 "African Eve" human mitochondrial sequences published by Vigilant et al., and a collection of 12 Archeal chaperonin sequences demonstrating strong evidence for gene conversion. Neighbor-Net is available as part of the SplitsTree4 software package.
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            MLST revisited: the gene-by-gene approach to bacterial genomics.

            Multilocus sequence typing (MLST) was proposed in 1998 as a portable sequence-based method for identifying clonal relationships among bacteria. Today, in the whole-genome era of microbiology, the need for systematic, standardized descriptions of bacterial genotypic variation remains a priority. Here, to meet this need, we draw on the successes of MLST and 16S rRNA gene sequencing to propose a hierarchical gene-by-gene approach that reflects functional and evolutionary relationships and catalogues bacteria 'from domain to strain'. Our gene-based typing approach using online platforms such as the Bacterial Isolate Genome Sequence Database (BIGSdb) allows the scalable organization and analysis of whole-genome sequence data.
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              List of Bacterial Names with Standing in Nomenclature: a folder available on the Internet.

              J Euzéby (1997)
              The List of Bacterial Names with Standing in Nomenclature includes, alphabetically and chronologically, the official names of bacteria as published or validated in the International Journal of Systematic Bacteriology. It encompasses 5,569 taxa (as of 31 December 1996) and is available on the Internet (URL: ftp:@ftp.cict.fr/pub/ bacterio/).
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                Author and article information

                Journal
                Sci Rep
                Sci Rep
                Scientific Reports
                Nature Publishing Group
                2045-2322
                26 November 2014
                2014
                : 4
                : 7202
                Affiliations
                [1 ]Organisms and Environment Division, Cardiff School of Biosciences, Cardiff University , Main Building, Museum Avenue, Cardiff
                [2 ]Department of Zoology, University of Oxford , Oxford, United Kingdom
                [3 ]Laboratorium voor Microbiologie, Universiteit Gent , K. L. Ledeganckstraat 35, B-9000 Gent, Belgium
                [4 ]Centre for Digestive and Gut Health, Imperial College London , London W2 1NY
                Author notes
                Article
                srep07202
                10.1038/srep07202
                4244635
                25425319
                2180e7cf-4f71-4a91-9013-444e8ad463f5
                Copyright © 2014, Macmillan Publishers Limited. All rights reserved

                This work is licensed under a Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International License. The images or other third party material in this article are included in the article's Creative Commons license, unless indicated otherwise in the credit line; if the material is not included under the Creative Commons license, users will need to obtain permission from the license holder in order to reproduce the material. To view a copy of this license, visit http://creativecommons.org/licenses/by-nc-sa/4.0/

                History
                : 25 September 2014
                : 06 November 2014
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