Vibrio taketomensis sp. nov. by genome taxonomy

Tanaka, Mami; Bi, Hong-Yu; Jiang, Chunqi; Mino, Sayaka; Meirelles, Pedro Milet; Thompson, Fabiano L.; Gómez‐Gil, Bruno; Sawabe, Tomoo

doi:10.1016/j.syapm.2019.126048

Cited by 17 publications

(18 citation statements)

References 28 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…spongicola compared to the other Amphritea species ( Fig 1 ). This observation triggered further assessments of PT3 T using molecular phylogenetic network and genomic approaches, which are frequently used in Vibrionaceae taxonomy [ 11 , 30 ].…”

Section: Resultsmentioning

confidence: 99%

“…opalescens ANRC-JH14 T and A . pacifica ZJ14W T ) were used for pangenome analysis using the program anvi’o v7 [ 25 ] based on previous studies [ 11 , 26 ], with minor modifications. Briefly, contigs databases of each genome were constructed by fasta files (anvi-gen-contigs-database) and decorated with hits from HMM models (anvi-run-hmms).…”

Section: Methodsmentioning

confidence: 99%

“…All strains were cultured on Marine agar 2216 (BD, Franklin Lakes, New Jersey, USA). The phenotypic characteristics were determined according to previously described methods [8][9][10][11].…”

Section: Bacterial Strains and Phenotypic Characterizationmentioning

confidence: 99%

“…A total of eight genomes, including five obtained in this study (PT3 T , A. atlantica JCM 14776 T , A. balenae JCM 14781 T , A. japonica JCM 14782 T , A. spongicola JCM 16668 T and A. ceti KCTC PLOS ONE 42154 T ) and two retrieved from the NCBI database (A. opalescens ANRC-JH14 T and A. pacifica ZJ14W T ) were used for pangenome analysis using the program anvi'o v7 [25] based on previous studies [11,26], with minor modifications. Briefly, contigs databases of each genome were constructed by fasta files (anvi-gen-contigs-database) and decorated with hits from HMM models (anvi-run-hmms).…”

Section: Pan and Core Genome Analysismentioning

confidence: 99%

“…Even after the description of A. pacifica [6], two distinct lineages based on 16S gene sequences in the genus Amphritea have never been discussed yet, but the finding of PT3 T showed phylogenetically more cohesion of the strain to A. ceti and A. spongicola compared to the other Amphritea species (Fig 1). This observation triggered further assessments of PT3 T using molecular phylogenetic network and genomic approaches, which are frequently used in Vibrionaceae taxonomy [11,30].…”

Section: Molecular Phylogenetic Analysis Based On 16s Rrna Gene Nucle...mentioning

confidence: 99%

See 4 more Smart Citations

Taxonomic revision of the genus Amphritea supported by genomic and in silico chemotaxonomic analyses, and the proposal of Aliamphritea gen. nov.

Yamano

Jiang

et al. 2022

PLoS ONE

Self Cite

View full text Add to dashboard Cite

A Gram-staining-negative, aerobic bacterium, designated strain PT3T was isolated from laboratory-reared larvae of the Japanese sea cucumber Apostichopus japonicus. Phylogenetic analysis based on the 16S rRNA gene nucleotide sequences revealed that PT3T was closely related to Amphritea ceti RA1T (= KCTC 42154T = NBRC 110551T) and Amphritea spongicola MEBiC05461T (= KCCM 42943T = JCM 16668T) both with 98.3% sequence similarity, however, average nucleotide identity (ANI) and in silico DNA-DNA hybridization (in silico DDH) values among these three strains were below 95% and 70%, respectively, confirming the novelty of PT3T. Furthermore, the average amino acid identity (AAI) values of PT3T against other Amphritea species were on the reported genus delineation boundary (64–67%). Multilocus sequence analysis using four protein-coding genes (recA, mreB, rpoA, and topA) further demonstrated that PT3T, Amphritea ceti and Amphritea spongicola formed a monophyletic clade clearly separate from other members of the genus Amphritea. Three strains (PT3T, A. ceti　KCTC 42154T and A. spongicola JCM 16668T) also showed higher similarities in their core genomes compared to those of the other Amphritea spp. Based on the genome-based taxonomic approach, Aliamphritea gen. nov. was proposed together with the reclassification of the genus Amphritea and Aliamphritea ceti comb. nov. (type strain RA1T = KCTC 42154T = NBRC 110551T), Aliamphritea spongicola comb. nov. (type strain MEBiC05461T = KCCM 42943T = JCM 16668T), and Aliamphritea hakodatensis sp. nov. (type strain PT3T = JCM 34607T = KCTC 82591T) were suggested.

show abstract

Section: Resultsmentioning

confidence: 99%

Section: Methodsmentioning

confidence: 99%

Section: Bacterial Strains and Phenotypic Characterizationmentioning

confidence: 99%

Section: Pan and Core Genome Analysismentioning

confidence: 99%

Section: Molecular Phylogenetic Analysis Based On 16s Rrna Gene Nucle...mentioning

confidence: 99%

See 3 more Smart Citations

Taxonomic revision of the genus Amphritea supported by genomic and in silico chemotaxonomic analyses, and the proposal of Aliamphritea gen. nov.

Yamano

Jiang

et al. 2022

PLoS ONE

Self Cite

View full text Add to dashboard Cite

show abstract

A MALDI-TOF MS database for fast identification of Vibrio spp. potentially pathogenic to marine mollusks

Moussa

Cauvin

Piouffle³

et al. 2021

Appl Microbiol Biotechnol

View full text Add to dashboard Cite

In mollusk aquaculture, a large number of Vibrio species are considered major pathogens. Conventional methods based on DNA amplification and sequencing used to accurately identify Vibrio species are unsuitable for monitoring programs because they are time-consuming and expensive. The aim of this study was, therefore, to develop the MALDI-TOF MS method in order to establish a rapid identification technique for a large panel of Vibrio species. We created the EnviBase containing 120 main spectra projections (MSP) of the Vibrio species that are potentially responsible for mollusk diseases, comprising 25 species: V. aestuarianus, V. cortegadensis, V. tapetis and species belonging to the Coralliilyticus, Harveyi, Mediterranei, and Orientalis clades. Each MSP was constructed by the merger of raw spectra obtained from three different media and generated by three collaborating laboratories to increase the diversity of the conditions and thus obtain a good technique robustness. Perfect discrimination was obtained with all of the MSP created for the Vibrio species and even for very closely related species as V. europaeus and V. bivalvicida. The new EnviBase library was validated through a blind test on 100 Vibrio strains performed by our three collaborators who used the direct transfer and protein extraction methods. The majority of the Vibrio strains were successfully identified with the newly created EnviBase by the three laboratories for both protocol methods. This study documents the first development of a freely accessible database exclusively devoted to Vibrio found in marine environments, taking into account the high diversity of this genus. Key points • Development of a MALDI-TOF MS database to quickly affiliate Vibrio species. • Increase of the reactivity when faced with Vibrio associated with mollusk diseases. • Validation of MALDI-TOF MS as routine diagnostic tool.

show abstract

Vibrio Clade 3.0: New Vibrionaceae Evolutionary Units Using Genome-Based Approach

et al. 2021

Self Cite

View full text Add to dashboard Cite

 Consent to participate (Not applicable) Consent for publication (Not applicable)  Availability of data and materialThe whole genome sequence data obtained in this study was deposited at DDBJ/EMBL/GenBank under BioProject Accession: PRJDB11924.  Code availability (Not applicable) Author Contributions Chunqi Jiang conceived, designed and performed the experiments, analyzed the data, visualized the data, drafted and reviewed the manuscript. Mami Tanaka and Sayo Nishikawa performed the experiments, reviewed the manuscript.

show abstract

Vibrio taketomensis sp. nov. by genome taxonomy

Cited by 17 publications

References 28 publications

Taxonomic revision of the genus Amphritea supported by genomic and in silico chemotaxonomic analyses, and the proposal of Aliamphritea gen. nov.

Taxonomic revision of the genus Amphritea supported by genomic and in silico chemotaxonomic analyses, and the proposal of Aliamphritea gen. nov.

A MALDI-TOF MS database for fast identification of Vibrio spp. potentially pathogenic to marine mollusks

Vibrio Clade 3.0: New Vibrionaceae Evolutionary Units Using Genome-Based Approach

Contact Info

Product

Resources

About