Vibrio mexicanus sp. nov., isolated from a cultured oyster Crassostrea
corteziensis, a new member of the Marisflavi clade.
Antonie van Leeuwenhoek
Adrián González-Castilloa, Julissa Enciso-Ibarrraa, M. Carmen Bolán-Mejiaa, Sabela
Balboab, Jesús L. Romaldeb, Hector Cabanillas-Beltránc, Bruno Gomez-Gila*
a
b
CIAD, A.C., Mazatlán Unit for Aquaculture, AP. 711 Mazatlán, Sinaloa 82000, México
Departamento de Microbiología y Parasitología, CIBUS, Universidad de Santiago de
Compostela, Campus Sur s/n, 15782 Santiago de Compostela, Spain
c
Instituto Tecnológico de Tepic, Av. Tecnológico 2595, Tepic, Nayarit 63175, México.
*Corresponding author. bruno@ciad.mx. 52 (669) 989 8700 fax 52 (669) 989 8701
Supplementary material
Figure S1. Mean values and standard deviation (n = 3) of the strain CAIM 1540T grown different
salinity concentrations in TSB broth at 24 hours of incubation (30 °C).
Figure S2. Mean values and standard deviation (n = 3) of the strain CAIM 1540T grown different
pH in TSB broth at 24 hours of incubation (30 °C).
Figure S3. Mean values and standard deviation (n = 3) of the strain CAIM 1540T grown different
temperatures in TSB broth at 24 hours of incubation.
Figure S4. Phylogenetic tree based on partial ftsZ housekeeping gene sequences,
obtained by the Neighbour Joining method. GenBank sequence accession
numbers are given in parentheses. Numbers at nodes denote the level of bootstrap
based on 1000 replicates; only values greater than 50% are shown. Vibrio
cholerae was used as bacterial out-group. Scale bar, base substitutions per site.
Figure S5. Phylogenetic tree based on partial gapA housekeeping gene sequences,
obtained by the Neighbour Joining method. GenBank sequence accession
numbers are given in parentheses. Numbers at nodes denote the level of bootstrap
based on 1000 replicates; only values greater than 50% are shown. Vibrio
cholerae was used as bacterial out-group. Scale bar, base substitutions per site.
Figure S6. Phylogenetic tree based on partial recA housekeeping gene sequences,
obtained by the Neighbour Joining method. GenBank sequence accession
numbers are given in parentheses. Numbers at nodes denote the level of bootstrap
based on 1000 replicates; only values greater than 50% are shown. Vibrio
cholerae was used as bacterial out-group. Scale bar, base substitutions per site.
Figure S7. Phylogenetic tree based on partial topA housekeeping gene sequences,
obtained by the Neighbour Joining method. GenBank sequence accession
numbers are given in parentheses. Numbers at nodes denote the level of bootstrap
based on 1000 replicates; only values greater than 50% are shown. Vibrio
cholerae was used as bacterial out-group. Scale bar, base substitutions per site.
Figure S8. Phylogenetic tree based on concatenated sequences of the four
housekeeping genes ftsZ, gapA, recA, and topA, and the 16S rRNA gene, and
obtained by the maximum-likelihood method. Numbers at nodes denote the level
of bootstrap based on 1000 replicates; only values greater than 50% are shown.
Vibrio cholerae was used as bacterial out-group. Scale bar, base substitutions per
site.
Figure S9. Phylogenetic tree based on concatenated sequences of the four
housekeeping genes ftsZ, gapA, recA, and topA, and the 16S rRNA gene, and
obtained by the maximum parsimony method. Numbers at nodes denote the level
of bootstrap based on 1000 replicates; only values greater than 50% are shown.
Vibrio cholerae was used as bacterial out-group.
Figure S10. Phylogenetic tree based on partial recA (Included V. stylophorae)
housekeeping gene sequences, obtained by the Neighbour Joining method.
GenBank sequence accession numbers are given in parentheses. Numbers at nodes
denote the level of bootstrap based on 1000 replicates; only values greater than
50% are shown. Vibrio cholerae was used as bacterial out-group. Scale bar, base
substitutions per site.
Figure S11. NeighborNet analysis. SplitsTree v4 NeighborNet analysis from 20 taxa were
reconstructed based on the 16S rRNA gene (1200 bp). Distances were corrected with the
Jukes-Cantor correlation. The phi test did find statistically significant evidence for
recombination (p=4.922E-7).
Figure S12. NeighborNet analysis. SplitsTree v4 NeighborNet analysis from 20 taxa were
reconstructed based on the ftsZ gene (431 bp). Distances were corrected with the JukesCantor correlation. The phi test did not find statistically significant evidence for
recombination (p=0.5536).
Figure S13. NeighborNet analysis. SplitsTree v4 NeighborNet analysis from 20 taxa were
reconstructed based on the gapA gene (600 bp). Distances were corrected with the JukesCantor correlation. The phi test did find statistically significant evidence for recombination
(p=4.395E-8).
Figure S14. NeighborNet analysis. SplitsTree v4 NeighborNet analysis from 20 taxa were
reconstructed based on the recA gene (493 bp). Distances were corrected with the JukesCantor correlation. The phi test did not find statistically significant evidence for
recombination (p=0.2461).
Figure S16. NeighborNet analysis. SplitsTree v4 NeighborNet analysis from 20 taxa were
reconstructed based on the topA gene (401 bp). Distances were corrected with the JukesCantor correlation. The phi test did not find statistically significant evidence for
recombination (p=0.6368).
Figure S17. NeighborNet analysis. SplitsTree v4 NeighborNet analysis from 20 taxa were
concatenated and reconstructed based on the four housekeeping genes ftsZ, gapA, recA,
topA and the 16S rRNA gene. Distances were corrected with the Jukes-Cantor correlation.
The phi test did find statistically significant evidence for recombination (p=5.049E-5).
Figure S18. NeighborNet analysis. SplitsTree v4 NeighborNet analysis from 21 taxa
(Included V. stylophorae) were reconstructed based on the recA gene (493 bp). Distances
were corrected with the Jukes-Cantor correlation. The phi test did not find statistically
significant evidence for recombination (p=0.3134).
Supplementary table 1. Accession number for the gene sequences used in this study. NA
= not available.
Species
16S rRNA
ftsZ
gapA
recA
topA
V. mexicanus
sp. nov.
JQ434105
KP698215
KP698212
KP698213
KP698214
V. aestivus
HE613734
KP698216
KF666670
KF666733
KF666757
V. marisflavi
FJ847833
HM036067 HM036070 HM036066 GU366193
V. maritimus
GU929925
GU929927
KF666681
GU929935
GU929939
V. variabilis
GU929924
GU929926
KF666686
GU929934
GU929938
V. brasiliensis
AEVS01000097
HM771354 HM771359 HM771379 HM771333
V. neonatus
AY426979
DQ907363
AY546644
KF697298
DQ907502
V. halioticoli
BAUJ01000001
DQ907349
AY546638
EU871966
DQ907487
V. tubiashii
X74725
DQ907381
DQ907312
AJ842518
DQ907521
V. sagamiensis
AB428909
AB428915
AB428919
KF796612
KJ616413
V. sinaloensis
DQ451211
HM771357 HM771362 JN039138
V. ezurae
BATM01000062 DQ907343
AY546645
AJ842413
HM771336
DQ907481
V. caribbeanicus AEIU01000064
HM771358 HM771363 HM771383 HM771337
V. fortis
AJ514916
DQ907346
DQ907282
AJ842422
DQ907484
V. penaeicida
AJ421444
DQ907370
DQ907303
AJ842496
DQ907512
V. hepatarius
AJ345063
DQ907352
DQ907285
AJ842444
DQ907491
V. breoganii
EF599161
KF666649
KF666675
EU541585
KF666760
V. nereis
X74716
DQ907362
DQ449617
AJ580870
DQ907504
V. mediterranei
AB680921
DQ907356
DQ907290
AJ842459
DQ907495
V. cholerae
EF032498
HE805627
HE805629
FM204835
HE805631
V. stylophorae
GQ281380
NA
NA
GU993996
NA