Vibrio aphrogenes sp. nov., in the Rumoiensis clade isolated from a seaweed

Abstract

A novel strain Vibrio aphrogenes sp. nov. strain CA-1004T isolated from the surface of seaweed collected on the coast of Mie Prefecture in 1994 [1] was characterized using polyphasic taxonomy including multilocus sequence analysis (MLSA) and a genome based comparison. Both phylogenetic analyses on the basis of 16S rRNA gene sequences and MLSA based on eight protein-coding genes (gapA, gyrB, ftsZ, mreB, pyrH, recA, rpoA, and topA) showed the strain could be placed in the Rumoiensis clade in the genus Vibrio. Sequence similarities of the 16S rRNA gene and the multilocus genes against the Rumoiensis clade members, V. rumoiensis, V. algivorus, V. casei, and V. litoralis, were low enough to propose V. aphrogenes sp. nov. strain CA-1004T as a separate species. The experimental DNA-DNA hybridization data also revealed that the strain CA-1004T was separate from four known Rumoiensis clade species. The G+C content of the V. aphrogenes strain was determined as 42.1% based on the genome sequence. Major traits of the strain were non-motile, halophilic, fermentative, alginolytic, and gas production. A total of 27 traits (motility, growth temperature range, amylase, alginase and lipase productions, and assimilation of 19 carbon compounds) distinguished the strain from the other species in the Rumoiensis clade. The name V. aphrogenes sp. nov. is proposed for this species in the Rumoiensis clade, with CA-1004T as the type strain (JCM 31643T = DSM 103759T).

Microbiome and Functional Analysis of a Traditional Food Process: Isolation of a Novel Species (Vibrio hibernica) With Industrial Potential

“…The species was named due to its country of origin, Ireland. The reconstruction of the phylogenetic history of the Vibrio species was far better supported in the HK tree compared to the 16S rRNA gene tree and this result is further strengthened by other studies with similar outcomes (Tanaka et al, 2017). Phylogenic analysis of this species was seen to be distinct from its closest relatives, V. rumoiensis and V. litoralis.…”

“…Phylogenic analysis of this species was seen to be distinct from its closest relatives, V. rumoiensis and V. litoralis. Both of these species as well as V. algivorus, V. casei and V. aphrogenes belong to the Rumoiensis clade and we propose V. hibernica be included into this clade (Tanaka et al, 2017). Two of the in silico methods of species definition identified V. hibernica as a novel species.…”

Vibrio algicola sp. nov., isolated from the surface of coralline algae

“…The Rumoiensis clade within the genus Vibrio was initially proposed by Bleicher et al [2] and currently comprises six species, i.e. Vibrio casei [2], Vibrio rumoiensis [3], Vibrio litoralis [4], Vibrio aphrogenes [5], Vibrio algivorus [6] and Vibrio gangliei [7]. These species are positive for oxidase and catalase but negative for gelatin hydrolysis and possess summed features 2, 3, 8 and C 16:0 as major fatty acids.…”

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“…Sequencing library for Nanopore sequencing was prepared using the Rapid Barcoding Kit and mate-pair (MP) reads for V. aphrogenes were previously obtained (Tanaka et al, 2017) using the MiSeq platform. Briefly, PE libraries were prepared using the Nextera XT DNA…”

“…As Vibrionaceae are metabolically and genetically diverse, this group of bacteria have always been at the forefront of bacterial taxonomy being tested for new methodologies (Sawabe et al, 2013). Among 24 clades in Vibrionaceae, the Rumoiensis clade consists of species with diverse ecophysiology, but at the same time the clade is phylogenetically robust (Tanaka et al, 2017). As there are currently only five species in the clade, and we were able to finish the genomes of all type strains, Rumoiensis clade species were chosen as a test case for the availability of Nanopore sequencing in creating a rapid, reliable, and ultimately automatic identification scheme for Vibrionaceae.…”