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      Vibrio paucivorans sp. nov. and Vibrio qingdaonensis sp. nov., two marine bacteria

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          Abstract

          Two Gram-stain-negative, facultatively anaerobic, motile, rod-shaped and flagellated marine bacteria, designated strains DBSS07 T and ZSDZ65 T, were isolated from the surface sediments of the Bohai sea and Qingdao coastal seawater, respectively. Phylogenetic analysis based on 16S rRNA genes, multilocus sequence analysis (MLSA), phylogenomic analysis of single-copy gene families and whole-genome data placed DBSS07 T and ZSDZ65 T within the genus Vibrio . DBSS07 T was most closely related to Vibrio aestivus M22 T, with 97.51 % sequence similarity, whereas ZSDZ65 T was most closely related to Vibrio variabilis R-40492 T with 97.58 % sequence similarity. DBSS07 T grew with 1–7 % (w/v) NaCl (optimum 3 %), at 16–37 °C (optimum 28 °C) and at pH 6.0–9.0 (optimum pH 7.0); whereas ZSDZ65 T grew with 1–5 % (w/v) NaCl (optimum 2 %), at 16–32 °C (optimum 28 °C) and at pH 6.0–9.0 (optimum pH 8.0). Both strains shared the same major fatty acid components (more than 10 % of total fatty acids) of summed feature 3 (C 16 : 1ω7 c or/and C 16 : 1ω6 c), with different proportions. The DNA G+C contents of DBSS07 T and ZSDZ65 T were 44.7 and 44.3 %, respectively. On the basis of the results of polyphasic analysis, DBSS07 T and ZSDZ65 T are considered to represent novel species within the genus Vibrio , for which the names V. paucivorans sp. nov. (type strain, DBSS07 T = KCTC 82896 T= MCCC 1K06284 T) and V. qingdaonensis sp. nov. (type strain, ZSDZ65 T = KCTC 82893 T = MCCC 1K06289 T) are proposed, respectively.

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          MAFFT Multiple Sequence Alignment Software Version 7: Improvements in Performance and Usability

          We report a major update of the MAFFT multiple sequence alignment program. This version has several new features, including options for adding unaligned sequences into an existing alignment, adjustment of direction in nucleotide alignment, constrained alignment and parallel processing, which were implemented after the previous major update. This report shows actual examples to explain how these features work, alone and in combination. Some examples incorrectly aligned by MAFFT are also shown to clarify its limitations. We discuss how to avoid misalignments, and our ongoing efforts to overcome such limitations.
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            MEGA X: Molecular Evolutionary Genetics Analysis across Computing Platforms.

            The Molecular Evolutionary Genetics Analysis (Mega) software implements many analytical methods and tools for phylogenomics and phylomedicine. Here, we report a transformation of Mega to enable cross-platform use on Microsoft Windows and Linux operating systems. Mega X does not require virtualization or emulation software and provides a uniform user experience across platforms. Mega X has additionally been upgraded to use multiple computing cores for many molecular evolutionary analyses. Mega X is available in two interfaces (graphical and command line) and can be downloaded from www.megasoftware.net free of charge.
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              IQ-TREE: A Fast and Effective Stochastic Algorithm for Estimating Maximum-Likelihood Phylogenies

              Large phylogenomics data sets require fast tree inference methods, especially for maximum-likelihood (ML) phylogenies. Fast programs exist, but due to inherent heuristics to find optimal trees, it is not clear whether the best tree is found. Thus, there is need for additional approaches that employ different search strategies to find ML trees and that are at the same time as fast as currently available ML programs. We show that a combination of hill-climbing approaches and a stochastic perturbation method can be time-efficiently implemented. If we allow the same CPU time as RAxML and PhyML, then our software IQ-TREE found higher likelihoods between 62.2% and 87.1% of the studied alignments, thus efficiently exploring the tree-space. If we use the IQ-TREE stopping rule, RAxML and PhyML are faster in 75.7% and 47.1% of the DNA alignments and 42.2% and 100% of the protein alignments, respectively. However, the range of obtaining higher likelihoods with IQ-TREE improves to 73.3-97.1%.
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                Author and article information

                Contributors
                (View ORCID Profile)
                Journal
                International Journal of Systematic and Evolutionary Microbiology
                Microbiology Society
                1466-5026
                1466-5034
                April 11 2023
                April 11 2023
                : 73
                : 4
                Affiliations
                [1 ] Institute of Evolution & Marine Biodiversity, Ocean University of China, Qingdao 266003, PR China
                [2 ] Frontiers Science Center for Deep Ocean Multispheres and Earth System and College of Marine Life Sciences, Ocean University of China, 5 Yushan Road, Qingdao 266003, PR China
                [3 ] Laboratory for Marine Ecology and Environmental Science, Laoshan Laboratory, Qingdao 266071, PR China
                Article
                10.1099/ijsem.0.005822
                c17cfeef-b4d7-4b30-b416-b757c2605e44
                © 2023
                History

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