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. 2005 Sep;71(9):5107-15.
doi: 10.1128/AEM.71.9.5107-5115.2005.

Phylogeny and molecular identification of vibrios on the basis of multilocus sequence analysis

F L Thompson  1 , D Gevers, C C Thompson, P Dawyndt, S Naser, B Hoste, C B Munn, J Swings
Affiliations

Phylogeny and molecular identification of vibrios on the basis of multilocus sequence analysis

F L Thompson et al. Appl Environ Microbiol. 2005 Sep.

Abstract

We analyzed the usefulness of rpoA, recA, and pyrH gene sequences for the identification of vibrios. We sequenced fragments of these loci from a collection of 208 representative strains, including 192 well-documented Vibrionaceae strains and 16 presumptive Vibrio isolates associated with coral bleaching. In order to determine the intraspecies variation among the three loci, we included several representative strains per species. The phylogenetic trees constructed with the different genetic loci were roughly in agreement with former polyphasic taxonomic studies, including the 16S rRNA-based phylogeny of vibrios. The families Vibrionaceae, Photobacteriaceae, Enterovibrionaceae, and Salinivibrionaceae were all differentiated on the basis of each genetic locus. Each species clearly formed separated clusters with at least 98, 94, and 94% rpoA, recA, and pyrH gene sequence similarity, respectively. The genus Vibrio was heterogeneous and polyphyletic, with Vibrio fischeri, V. logei, and V. wodanis grouping closer to the Photobacterium genus. V. halioticoli-, V. harveyi-, V. splendidus-, and V. tubiashii-related species formed groups within the genus Vibrio. Overall, the three genetic loci were more discriminatory among species than were 16S rRNA sequences. In some cases, e.g., within the V. splendidus and V. tubiashii group, rpoA gene sequences were slightly less discriminatory than recA and pyrH sequences. In these cases, the combination of several loci will yield the most robust identification. We can conclude that strains of the same species will have at least 98, 94, and 94% rpoA, recA, and pyrH gene sequence similarity, respectively.

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Figures

FIG.1.
FIG.1.
Phylogenetic trees based on neighbor-joining method using 16S rRNA (1,300 nt), rpoA (928 nt), pyrH (443 nt), and recA (613 nt) gene sequences of vibrios. Distance estimations were obtained by the model of Jukes and Cantor (16). Bootstrap percentages (≥50) after 1,000 simulations are shown. Bars, 1% (16S rRNA) and 10% (rpoA, pyrH, and recA) estimated sequence divergence. The Campylobacter NCTC 11168 sequence was used as an outgroup.
FIG. 2.
FIG. 2.
Splits tree showing networks in V. tubiashii (A)- and V. splendidus (B)-related groups on the basis of rpoA gene sequences (931 bp). Bootstrap percentages (≥50) after 500 simulations are shown. Bar, 10% estimated sequence divergence.
FIG. 3.
FIG. 3.
Phylogenetic tree based on neighbor-joining method using the concatenated sequences (3,284 nt) of 16S rRNA, rpoA, pyrH, and recA of type strains. Distance estimations were obtained by the model of Jukes and Cantor (16). Bootstrap percentages (≥50) after 1,000 simulations are shown. Bar, 2% estimated sequence divergence.
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