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      Leucobacter musarum subsp. musarum sp. nov., subsp. nov., Leucobacter musarum subsp. japonicus subsp. nov., and Leucobacter celer subsp. astrifaciens subsp. nov., three nematopathogenic bacteria isolated from Caenorhabditis, with an emended description of Leucobacter celer

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          Abstract

          Three Gram-stain-positive, irregular-rod-shaped, non-motile, non-spore-forming bacteria were isolated from nematodes collected from Santa Antao, Cabo Verde (CBX151 T, CBX152 T) and Kakegawa, Japan (CBX130 T). Based on 16S rRNA gene sequence similarity, strains CBX130 T, CBX151 T and CBX152 T were shown to belong to the genus Leucobacter. This affiliation was supported by chemotaxonomic data (2,4-diaminobutyric acid in the cell wall; major respiratory quinones MK-10 and MK-11; major polar lipids phosphatidylglycerol and diphosphatidylglycerol; major fatty acids anteiso-C 15 : 0, anteiso-C 17 : 0 and iso-C 16 : 0). Strains CBX130 T and CBX152 T were found to share salient characteristics. Based on morphological, physiological, chemotaxonomic and biochemical analysis, strain CBX152 T represents a novel species of the genus Leucobacter, for which the name Leucobacter musarum sp. nov. (type strain CBX152 T = DSM 27160 T = CIP 110721 T) is proposed. Two subspecies of Leucobacter musarum sp. nov. are proposed: Leucobacter musarum sp. nov. subsp. musarum subsp. nov. (type strain CBX152 T = DSM 27160 T = CIP 110721 T) and Leucobacter musarum sp. nov. subsp. japonicus subsp. nov. (type strain CBX130 T = DSM 27158 T = CIP 110719 T). The third novel strain, CBX151 T, showed genetic similarities with Leucobacter celer NAL101 T indicating that these strains belong to the same species. Based on morphological, physiological, chemotaxonomic and biochemical differences it is proposed to split the species Leucobacter celer into two novel subspecies, Leucobacter celer subsp. celer subsp. nov. (type strain NAL101 T = KACC 14220 T = JCM 16465 T) and Leucobacter celer subsp. astrifaciens subsp. nov. (type strain CBX151 T = DSM 27159 T = CIP 110720 T), and to emend the description of Leucobacter celer Shin et al. 2011 .

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          Introducing EzTaxon-e: a prokaryotic 16S rRNA gene sequence database with phylotypes that represent uncultured species.

          Ok-Sun Kim, Yong-Joon Cho, Kihyun Lee … (2012)
          Despite recent advances in commercially optimized identification systems, bacterial identification remains a challenging task in many routine microbiological laboratories, especially in situations where taxonomically novel isolates are involved. The 16S rRNA gene has been used extensively for this task when coupled with a well-curated database, such as EzTaxon, containing sequences of type strains of prokaryotic species with validly published names. Although the EzTaxon database has been widely used for routine identification of prokaryotic isolates, sequences from uncultured prokaryotes have not been considered. Here, the next generation database, named EzTaxon-e, is formally introduced. This new database covers not only species within the formal nomenclatural system but also phylotypes that may represent species in nature. In addition to an identification function based on Basic Local Alignment Search Tool (blast) searches and pairwise global sequence alignments, a new objective method of assessing the degree of completeness in sequencing is proposed. All sequences that are held in the EzTaxon-e database have been subjected to phylogenetic analysis and this has resulted in a complete hierarchical classification system. It is concluded that the EzTaxon-e database provides a useful taxonomic backbone for the identification of cultured and uncultured prokaryotes and offers a valuable means of communication among microbiologists who routinely encounter taxonomically novel isolates. The database and its analytical functions can be found at http://eztaxon-e.ezbiocloud.net/.
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            Toward Defining the Course of Evolution: Minimum Change for a Specific Tree Topology

            Walter M. Fitch (1971)
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              Application of tetranucleotide frequencies for the assignment of genomic fragments.

              Hanno Teeling, Anke Meyerdierks, Margarete Bauer … (2004)
              A basic problem of the metagenomic approach in microbial ecology is the assignment of genomic fragments to a certain species or taxonomic group, when suitable marker genes are absent. Currently, the (G + C)-content together with phylogenetic information and codon adaptation for functional genes is mostly used to assess the relationship of different fragments. These methods, however, can produce ambiguous results. In order to evaluate sequence-based methods for fragment identification, we extensively compared (G + C)-contents and tetranucleotide usage patterns of 9054 fosmid-sized genomic fragments generated in silico from 118 completely sequenced bacterial genomes (40 982 931 fragment pairs were compared in total). The results of this systematic study show that the discriminatory power of correlations of tetranucleotide-derived z-scores is by far superior to that of differences in (G + C)-content and provides reasonable assignment probabilities when applied to metagenome libraries of small diversity. Using six fully sequenced fosmid inserts from a metagenomic analysis of microbial consortia mediating the anaerobic oxidation of methane (AOM), we demonstrate that discrimination based on tetranucleotide-derived z-score correlations was consistent with corresponding data from 16S ribosomal RNA sequence analysis and allowed us to discriminate between fosmid inserts that were indistinguishable with respect to their (G + C)-contents.
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                Author and article information

                Journal
                Journal ID (nlm-ta): Int J Syst Evol Microbiol
                Journal ID (iso-abbrev): Int. J. Syst. Evol. Microbiol
                Journal ID (publisher-id): IJSEM
                Title: International Journal of Systematic and Evolutionary Microbiology
                Publisher: Microbiology Society
                ISSN (Print): 1466-5026
                ISSN (Electronic): 1466-5034
                Publication date (Print): November 2015
                Publication date PMC-release: November 2015
                Volume: 65
                Issue: Pt 11
                Pages: 3977-3984
                Affiliations
                [1]Biochemistry Department, University of Oxford, South Parks Road, Oxford OX1 3QU, UK
                Author notes
                Correspondence Laura C. Clark laura.clark@ 123456bioch.ox.ac.uk

                The GenBank/EMBL/DDBJ accession numbers for the 16S rRNA gene sequences of strains CBX151 T, CBX152 T and CBX130 T are KF906844, KF906845 and KF906846, respectively. The GenBank BioProject number for whole genome sequence data from strains CBX151 T, CBX152 T, CBX130 T and Leucobacter celer NAL101 T is PRJNA240071.

                A supplementary figure and two supplementary tables are available with the online Supplementary Material.

                Article
                Publisher ID: 000523
                DOI: 10.1099/ijsem.0.000523
                PMC ID: 4804768
                PubMed ID: 26275616
                SO-VID: 61bda24b-8237-461d-834d-0eb1283eaf67
                Copyright © © 2015 IUMS
                License:

                This is an Open Access article distributed under the terms of the Creative Commons Attribution License ( http://creativecommons.org/licenses/by/3.0/).

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                Subject: Note
                Subject: New Taxa
                Subject: Actinobacteria
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                ScienceOpen disciplines: Microbiology & Virology
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                ScienceOpen disciplines: Microbiology & Virology

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