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PLoS One
2023 Jan 01;188:e0290060. doi: 10.1371/journal.pone.0290060.
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Genome taxonomy of the genus Neptuniibacter and proposal of Neptuniibacter victor sp. nov. isolated from sea cucumber larvae.
Kudo R, Yamano R, Yu J, Koike S, Haditomo AHC, de Freitas MAM, Tsuchiya J, Mino S, Thompson F, Romalde JL, Kasai H, Sakai Y, Sawabe T.
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A Gram-staining-negative, oxidase-positive, strictly aerobic rod-shaped bacterium, designated strain PT1T, was isolated from the laboratory-reared larvae of the sea cucumber Apostichopus japonicus. A phylogenetic analysis based on the 16S rRNA gene nucleotide sequences revealed that PT1T was closely related to Neptuniibacter marinus ATR 1.1T (= CECT 8938T = DSM 100783T) and Neptuniibacter caesariensis MED92T (= CECT 7075T = CCUG 52065T) showing 98.2% and 98.1% sequence similarity, respectively. However, the average nucleotide identity (ANI) and in silico DNA-DNA hybridization (DDH) values among these three strains were 72.0%-74.8% and 18.3%-19.5% among related Neptuniibacter species, which were below 95% and 70%, respectively, confirming the novel status of PT1T. The average amino acid identity (AAI) values of PT1T showing 74-77% among those strains indicated PT1T is a new species in the genus Neptuniibacter. Based on the genome-based taxonomic approach, Neptuniibacter victor sp. nov. is proposed for PT1T. The type strain is PT1T (JCM 35563T = LMG 32868T).
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Fig 1. ML tree based on 16S rRNA gene nucleotide sequences of strain PT1T and related type strains.
Fig 2. MLSA network of PT1T and related Oceanospirillaceae.A list of strains and their assembly accession is provided in Table 1. Sequence regions used for reconstructing the network were 1–995 on mreB, 1–1,041 on recA, 1–981 on rpoA, and 1–2,648 on topA. The clade which PT1T belonged was robust with supported by 100% bootstrap.
Fig 3. Anvi’o representation of the pangenome of strain PT1T and Neptuniibacter.Layers represent each genome, and the darker areas represent the occurrence of gene clusters. The outer colored bars indicate the “Core” or “Unique” bins.
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