Vibrio mexicanus sp. nov., isolated from a cultured oyster Crassostrea corteziensis

Abstract

A bacterial strain was taxonomically characterised by means of a genomic approach comprising 16S rRNA gene sequence analysis, multilocus sequence analysis (MLSA), the DNA G+C content, whole genome analyses (ANI and GGDC) and phenotypic characterisation. The strain CAIM 1540(T) was isolated from a cultured oyster Crassostrea corteziensis in La Cruz, Sinaloa state, México. The isolate was found to be catalase and oxidase positive, cells were observed to be motile, O/129-sensitive and facultatively anaerobic. The almost-complete 16S rRNA gene sequence placed this strain within the genus Vibrio; the closest related species were found to be Vibrio aestivus, Vibrio marisflavi, Vibrio maritimus and Vibrio variabilis with similarity values of 99.02, 97.05, 96.70, and 96.59 % respectively. MLSA of four housekeeping genes (ftsZ, gapA, recA, and topA) was performed with the closely related species. A draft genome sequence of strain CAIM 1540(T) was obtained. The DNA G+C content of this strain was determined to be 43.7 mol%.The ANI values with V. aestivus were 89.6 % (ANIb), 90.6 % (ANIm) and a GGDC value of 39.5 ± 2.5 % was obtained; with V. marisflavi the genomic similarities were 71.5 % (ANIb), 85.5 % (ANIm) and 20.2 ± 2.3 % (GGDC); with V. maritimus 72.6 % (ANIb), 85.7 % (ANIm) and 22.0 ± 2.0 % (GGDC); and with V. variabilis 72.6 % (ANIb), 85.8 % (ANIm) and 21.6 ± 1.6 % (GGDC). These ANI and GGDC values are below the threshold for the delimitation of prokaryotic species, i.e. 95-96 and 70 %, respectively. Phenotypic characters also showed differences with the closest related species analysed. The results presented here support the description of a novel species, for which the name Vibrio mexicanus sp. nov. is proposed, with strain CAIM 1540(T) (= CECT 8828(T), = DSM 100338(T)) as the type strain. In addition, we found that the recently described species Vibrio thalassae and Vibrio madracius might be a single species because the values of ANIb 95.8 %, ANIm 96.6 % and GGDC 70.2 ± 2.9 % are above the accepted species thresholds.

Classification of the inoculant strain of cowpea UFLA03-84 and of other strains from soils of the Amazon region as Bradyrhizobium viridifuturi (symbiovar tropici)

“…In the place of the traditional DNA-DNA hybridization, new methods of genome comparison, such as ANI and digital DDH (estimated by GGDC) analyses, have been successfully introduced in bacterial taxonomy studies [15,18,24,40]. The cutoff value recommended in traditional DNA-DNA hybridization is 70% for delimitation of species [19].…”

“…The cutoff value recommended for DDH (70%) [19] correlates with 95-96% of ANI [21,23]. ANI and GGDC values have already been successfully used in replacing traditional DDH in definition of the bacterial taxonomic position [15,18,24].…”

Genome-Wide Identification and Functional Characterization of β-Agarases in Vibrio astriarenae Strain HN897

“…According to the latest GTDB taxonomy (r89), V. agarivorans was reclassified as Vibrio sagamiensis and has been moved to the Harveyi clade (Figure 1B), indicating the genomic divergence between these two species was much greater than expected despite sharing agarolytic activity. Interestingly, phenotypic data from our group and others has shown that all the members of the Marisflavi clade can catabolize D-galactose as a sole carbon source (Wang et al, 2011;Gao et al, 2012;Lucena et al, 2012;González-Castillo et al, 2015. It is likely that a combination of phenotypic and genotypic data can be used to provide new insights in resolving the origin and evolution of the Marisflavi clade.…”

“…This clade was originally defined as a group of three species, Vibrio aestivus , Vibrio marisflavi and Vibrio stylophorae ( Sheu et al, 2011 ) based on the 16S rDNA comparisons. Subsequent studies have added a new species, Vibrio mexicanus , together with V. aestivus to form a monophyletic group with V. marisflavi that is well separated from V. stylophorae ( González-Castillo et al, 2015 ). In contrast, analysis based on multilocus sequence typing suggests that the V. mexicanus – V. aestivus cluster is well separated from V. marisflavi .…”

Vibrio japonicus sp. nov., a novel member of the Nereis clade in the genus Vibrio isolated from the coast of Japan

“…Vibrios are comprised of closely related species and are therefore difficult to identify [ 30 ]. MLSA of housekeeping genes has proven to be an accurate tool for delineation of microorganisms [ 31 ], as well as phylogenetic studies of the genus Vibrio [ 25 ].…”