Date Published: June 29, 2017
Publisher: Public Library of Science
Author(s): Mami Tanaka, Shoko Endo, Fumihito Kotake, Nurhidayu Al-saari, A. K. M. Rohul Amin, Gao Feng, Sayaka Mino, Hidetaka Doi, Yoshitoshi Ogura, Tetsuya Hayashi, Wataru Suda, Masahira Hattori, Isao Yumoto, Toko Sawabe, Tomoo Sawabe, Toshiyoshi Araki, Cristiane Thompson.
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  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).
The genus Vibrio, first proposed in 1854, is a large group of bacteria showing Gram negative and with most species requiring salt for growth . Currently 111 Vibrio species have been described (http://www.bacterio.net/) . The genus Vibrio, along with other members of Vibrionaceae, is at the forefront of bacterial taxonomy, having been tested using new methodologies, e.g. amplified fragment length polymorphism (AFLP), multilocus sequence analysis (MLSA), and genome-based sequence comparison [2–6]. Among them, the MLSA has been used as a powerful tool to find “clades” sharing a possible common ancestry among metabolically versatile Vibrionaceae species/strains [3–5]. The 8-gene MLSA defines 23 Vibrio and Photobacterium clades and an Enterovibiro-Grimontia-Salinivibrio super clade, which help us to elucidate the dynamic nature of biodiversity and evolutionary history interacting with the Earth’s ecosystem . Rapid expansion of genome sequencing methodology in bacterial taxonomy also assists and accelerates the accumulation of our knowledge of vibrio biodiversity and has contributed towards the proposals for new clades within the family Vibrionaceae such as Agarivorans  and Swingsii .
The phylogenic analysis based on 16S rRNA gene sequences showed the strain CA-1004T is a member of the genus Vibrio (S1 Fig): more precisely, the strain was closely related to members of the Rumoiensis clade with a high bootstrap support [4–5] (Fig 1). Sequence similarities of the 16S rRNA gene against those of Rumoiensis clade species, V. algivorus NBRC 111146T, V. rumoiensis FERM P-14531T, V. casei DSM 22364T, and V. litoralis DSM 17657T were 98.4%, 98.0%, 97.9%, and 96.8%, respectively. These levels of similarity are below or in the proposed threshold range for the species boundary, 98.2–99.0% [22,23,24]. To further confirm the genetic coherence, DNA-DNA similarity of CA-1004T against Rumoiensis clade species was experimentally measured. Using CA-1004T as a labelled strain, DDH values against V. algivorus NBRC 111146T, V. casei DSM 22364T, V. litoralis DSM 17657T, and V. rumoiensis FERM P-14531T were 15.4%, 12.0%, 4.9%, and 5.6%, respectively. These DDH values were sufficiently below the species boundary (<70%) to propose CA-1004T as a new species in the Rumoiensis clade. MLSA using eight protein-coding genes also showed the clear separation of the Rumoiensis clade containing the CA-1004T from the other clades of Vibrionaceae species, which suggests a common ancestry of the CA-1004T and the other Rumioensis clade species (Fig 2, S2 Fig). Source: http://doi.org/10.1371/journal.pone.0180053