Strain identifier
BacDive ID: 17326
Type strain:
Species: Beneckea nigripulchritudo
Strain Designation: 164
Strain history: CIP <- 1988, NCIB <- 1972, P. Baumann: strain 164, Beneckea nigripulchrituda
NCBI tax ID(s): 1051649 (strain), 28173 (species)
General
@ref: 15841
BacDive-ID: 17326
DSM-Number: 21607
keywords: genome sequence, 16S sequence, Bacteria, mesophilic, Gram-negative, motile, rod-shaped
description: Beneckea nigripulchritudo 164 is a mesophilic, Gram-negative, motile bacterium that was isolated from Sea water.
NCBI tax id
NCBI tax id | Matching level |
---|---|
28173 | species |
1051649 | strain |
strain history
@ref | history |
---|---|
15841 | <- NCIMB <- P. Baumann, University of Hawaii; 164 |
121300 | CIP <- 1988, NCIB <- 1972, P. Baumann: strain 164, Beneckea nigripulchrituda |
doi: 10.13145/bacdive17326.20230509.8.1
Name and taxonomic classification
LPSN
- @ref: 20215
- description: domain/bacteria
- keyword: phylum/pseudomonadota
- domain: Bacteria
- phylum: Pseudomonadota
- class: Gammaproteobacteria
- order: Vibrionales
- family: Vibrionaceae
- genus: Beneckea
- species: Beneckea nigripulchritudo
- full scientific name: Beneckea nigripulchritudo corrig. Baumann et al. 1971 (Approved Lists 1980)
synonyms
@ref synonym 20215 Beneckea nigrapulchrituda 20215 Beneckea nigrapulchritoda 20215 Vibrio nigripulchritudo
@ref: 15841
domain: Bacteria
phylum: Proteobacteria
class: Gammaproteobacteria
order: Vibrionales, not validated
family: Vibrionaceae
genus: Vibrio
species: Vibrio nigripulchritudo
full scientific name: Vibrio nigripulchritudo (Baumann et al. 1971) Baumann et al. 1981
strain designation: 164
type strain: yes
Morphology
cell morphology
- @ref: 121300
- gram stain: negative
- cell shape: rod-shaped
- motility: yes
Culture and growth conditions
culture medium
@ref | name | growth | link | composition |
---|---|---|---|---|
15841 | BACTO MARINE BROTH (DIFCO 2216) (DSMZ Medium 514) | yes | https://mediadive.dsmz.de/medium/514 | Name: BACTO MARINE BROTH (DIFCO 2216) (DSMZ Medium 514) Composition: NaCl 19.45 g/l MgCl2 5.9 g/l Bacto peptone 5.0 g/l Na2SO4 3.24 g/l CaCl2 1.8 g/l Yeast extract 1.0 g/l KCl 0.55 g/l NaHCO3 0.16 g/l Fe(III) citrate 0.1 g/l KBr 0.08 g/l SrCl2 0.034 g/l H3BO3 0.022 g/l Na2HPO4 0.008 g/l Na-silicate 0.004 g/l NaF 0.0024 g/l (NH4)NO3 0.0016 g/l Distilled water |
35504 | Marine agar (MA) | yes | Distilled water make up to (1000.000 ml);Marine agar (55.100 g) | |
121300 | CIP Medium 13 | yes | https://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=13 |
culture temp
@ref | growth | type | temperature | range |
---|---|---|---|---|
15841 | positive | growth | 28 | mesophilic |
35504 | positive | growth | 25 | mesophilic |
121300 | positive | growth | 15-41 | |
121300 | no | growth | 5 | psychrophilic |
Physiology and metabolism
halophily
@ref | salt | growth | tested relation | concentration |
---|---|---|---|---|
121300 | NaCl | positive | growth | 2-6 % |
121300 | NaCl | no | growth | 0 % |
121300 | NaCl | no | growth | 8 % |
121300 | NaCl | no | growth | 10 % |
metabolite utilization
@ref | Chebi-ID | metabolite | utilization activity | kind of utilization tested |
---|---|---|---|---|
68369 | 25115 | malate | + | assimilation |
68369 | 17128 | adipate | + | assimilation |
68369 | 27689 | decanoate | - | assimilation |
68369 | 24265 | gluconate | - | assimilation |
68369 | 17306 | maltose | + | assimilation |
68369 | 59640 | N-acetylglucosamine | - | assimilation |
68369 | 16899 | D-mannitol | + | assimilation |
68369 | 30849 | L-arabinose | - | assimilation |
68369 | 17634 | D-glucose | - | assimilation |
68369 | 5291 | gelatin | + | hydrolysis |
68369 | 4853 | esculin | + | hydrolysis |
68369 | 16199 | urea | - | hydrolysis |
68369 | 29016 | arginine | - | hydrolysis |
68369 | 17634 | D-glucose | + | fermentation |
68369 | 27897 | tryptophan | - | energy source |
68369 | 17632 | nitrate | + | reduction |
121300 | 16947 | citrate | - | carbon source |
121300 | 4853 | esculin | - | hydrolysis |
121300 | 17632 | nitrate | + | reduction |
121300 | 16301 | nitrite | - | reduction |
metabolite production
@ref | Chebi-ID | metabolite | production |
---|---|---|---|
68369 | 35581 | indole | no |
121300 | 35581 | indole | yes |
metabolite tests
@ref | Chebi-ID | metabolite | indole test | voges-proskauer-test | methylred-test |
---|---|---|---|---|---|
68369 | 35581 | indole | - | ||
121300 | 15688 | acetoin | - | ||
121300 | 17234 | glucose | - |
enzymes
@ref | value | activity | ec |
---|---|---|---|
68369 | cytochrome oxidase | + | 1.9.3.1 |
68369 | gelatinase | + | |
68369 | beta-glucosidase | + | 3.2.1.21 |
68369 | urease | - | 3.5.1.5 |
68369 | arginine dihydrolase | - | 3.5.3.6 |
121300 | oxidase | + | |
121300 | beta-galactosidase | + | 3.2.1.23 |
121300 | alcohol dehydrogenase | - | 1.1.1.1 |
121300 | gelatinase | + | |
121300 | amylase | + | |
121300 | caseinase | + | 3.4.21.50 |
121300 | catalase | + | 1.11.1.6 |
121300 | tween esterase | + | |
121300 | gamma-glutamyltransferase | + | 2.3.2.2 |
121300 | lecithinase | + | |
121300 | lipase | + | |
121300 | lysine decarboxylase | - | 4.1.1.18 |
121300 | ornithine decarboxylase | - | 4.1.1.17 |
121300 | phenylalanine ammonia-lyase | - | 4.3.1.24 |
121300 | protease | + | |
121300 | tryptophan deaminase | - | |
121300 | urease | - | 3.5.1.5 |
68382 | alkaline phosphatase | + | 3.1.3.1 |
68382 | esterase (C 4) | + | |
68382 | esterase lipase (C 8) | + | |
68382 | lipase (C 14) | - | |
68382 | leucine arylamidase | + | 3.4.11.1 |
68382 | valine arylamidase | + | |
68382 | cystine arylamidase | - | 3.4.11.3 |
68382 | trypsin | - | 3.4.21.4 |
68382 | alpha-chymotrypsin | - | 3.4.21.1 |
68382 | acid phosphatase | + | 3.1.3.2 |
68382 | naphthol-AS-BI-phosphohydrolase | + | |
68382 | alpha-galactosidase | - | 3.2.1.22 |
68382 | beta-galactosidase | - | 3.2.1.23 |
68382 | beta-glucuronidase | - | 3.2.1.31 |
68382 | alpha-glucosidase | - | 3.2.1.20 |
68382 | beta-glucosidase | - | 3.2.1.21 |
68382 | N-acetyl-beta-glucosaminidase | + | 3.2.1.52 |
68382 | alpha-mannosidase | - | 3.2.1.24 |
68382 | alpha-fucosidase | - | 3.2.1.51 |
API zym
@ref | Control | Alkaline phosphatase | Esterase | Esterase Lipase | Lipase | Leucine arylamidase | Valine arylamidase | Cystine arylamidase | Trypsin | alpha- Chymotrypsin | Acid phosphatase | Naphthol-AS-BI-phosphohydrolase | alpha- Galactosidase | beta- Galactosidase | beta- Glucuronidase | alpha- Glucosidase | beta- Glucosidase | N-acetyl-beta- glucosaminidase | alpha- Mannosidase | alpha- Fucosidase |
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
121300 | - | + | + | + | - | + | + | - | - | - | + | + | - | - | - | - | - | + | - | - |
API 20NE
@ref | NO3 | TRP | GLU_ Ferm | ADH Arg | URE | ESC | GEL | PNPG | GLU_ Assim | ARA | MNE | MAN | NAG | MAL | GNT | CAP | ADI | MLT | CIT | PAC | OX |
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
15841 | + | - | + | - | - | + | + | + | - | - | +/- | + | - | + | - | - | + | + | + | + | + |
API biotype100
@ref | GLU | FRU | GAL | TRE | MNE | SBE | MEL | SAC | RAF | MTE | MAL | LAC | LTE | MbGa | MaGa | CEL | GEN | MbGu | ESC | RIB | ARA | XYL | PLE | RHA | FUC | MLZ | DARL | LARL | XLT | DUL | TAG | GLY | INO | MAN | MTL | TUR | SOR | ADO | HBG | LYX | ERY | MDG | 3MDG | SAT | MUC | LTAT | DTAT | MTAT | DMLT | LMLT | CATE | TATE | TTE | CIT | GRT | GAT | 2KG | 5KG | TRY | NAG | GNT | PAC | PAT | pOBE | QAT | GTE | mOBE | BAT | PPAT | CMT | TGE | BET | PCE | ABT | HIN | LAT | CAP | CYT | HIS | SUC | FUM | GRE | GYT | AVT | ETN | TTN | GLN | ITA | 3OBU | APT | GTT | PRO | DALA | LALA | SER | MNT | PROP | TYR | 2KT |
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
121300 | + | - | - | + | - | - | + | + | - | - | - | + | - | + | + | - | - | - | + | + | - | - | - | - | + | - | - | - | - | - | + | + | - | + | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | + | - | - | - | - | + | - | - | - | - | - | - | - | + | - | - | + | - | - | - | - | - | - | - | - | - | + | - | - | - | + | + | - | - | - | - | - | + | - | - | + | + | - | - | + | + | - | - | - | - |
Isolation, sampling and environmental information
isolation
@ref | sample type |
---|---|
15841 | Sea water |
121300 | Environment, Seawater enriched with chitin |
isolation source categories
- Cat1: #Environmental
- Cat2: #Aquatic
- Cat3: #Marine
taxonmaps
- @ref: 69479
- File name: preview.99_641.png
- url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_14;96_71;97_312;98_520;99_641&stattab=map
- Last taxonomy: Vibrio
- 16S sequence: X74717
- Sequence Identity:
- Total samples: 231
- soil counts: 22
- aquatic counts: 192
- animal counts: 17
Safety information
risk assessment
@ref | biosafety level | biosafety level comment |
---|---|---|
15841 | 1 | Risk group (German classification) |
121300 | 2 | Risk group (French classification) |
Sequence information
16S sequences
@ref | description | accession | length | database | NCBI tax ID |
---|---|---|---|---|---|
20218 | Vibrio nigripulchritudo DNA, 16S-23S rRNA intergenic spacer and 23S rRNA, partial sequence, strain: ATCC 27043 | AB255726 | 291 | ena | 1051649 |
20218 | Vibrio nigripulchritudo DNA, 16S-23S ribosomal RNA intergenic spacer, type G, including tRNA-Glu, strain: ATCC 27043 | AB515338 | 468 | ena | 1051649 |
20218 | Vibrio nigripulchritudo DNA, 16S-23S ribosomal RNA intergenic spacer, type GLV, including tRNA-Glu, tRNA-Lys, tRNA-Val, strain: ATCC 27043 | AB515339 | 723 | ena | 1051649 |
20218 | Vibrio nigripulchritudo DNA, 16S-23S ribosomal RNA intergenic spacer, type GLAV, including tRNA-Glu, tRNA-Lys, tRNA-Ala, tRNA-Val, strain: ATCC 27043 | AB515340 | 762 | ena | 1051649 |
20218 | Vibrio nigripulchritudo strain ATCC 27043 16S-23S ribosomal RNA intergenic spacer, partial sequence; tRNA-Glu gene, complete sequence | AF413009 | 492 | ena | 1051649 |
20218 | Vibrio nigripulchritudo strain ATCC 27043 16S-23S ribosomal RNA intergenic spacer, partial sequence; tRNA-Glu and tRNA-Val genes, complete sequence | AF413010 | 729 | ena | 1051649 |
20218 | Vibrio nigripulchritudo strain ATCC 27043 16S-23S ribosomal RNA intergenic spacer, partial sequence; tRNA-Glu and tRNA-Val genes, complete sequence | AF413011 | 766 | ena | 1051649 |
20218 | Vibrio nigripulchritudo strain ATCC 27043 16S-23S ribosomal RNA intergenic spacer, partial sequence; tRNA-Glu, tRNA-Ala, and tRNA-Val genes, complete sequence | AF413012 | 800 | ena | 1051649 |
20218 | Vibrio nigripulchritudo strain ATCC 27043 16S-23S ribosomal RNA intergenic spacer, partial sequence; tRNA-Ala gene, complete sequence | AF413013 | 472 | ena | 1051649 |
20218 | Vibrio nigripulchritudo strain ATCC 27043 16S-23S ribosomal RNA intergenic spacer, partial sequence; tRNA-Ala gene, complete sequence | AF413014 | 474 | ena | 1051649 |
20218 | Vibrio nigripulchritudo strain ATCC 27043 16S-23S ribosomal RNA intergenic spacer, partial sequence; tRNA-Ile and tRNA-Ala genes, complete sequence | AF413015 | 571 | ena | 1051649 |
20218 | Vibrio nigripulchritudo 16S rRNA | D11213 | 218 | ena | 1051649 |
20218 | Vibrio nigripulchritudo 16S rRNA | D11262 | 214 | ena | 1051649 |
20218 | Vibrio nigripulchritudo 16S rRNA | D11311 | 191 | ena | 1051649 |
20218 | Vibrio nigripulchritudo 16S ribosomal RNA gene, partial sequence | HM771352 | 1470 | ena | 1051649 |
15841 | V.nigripulchritudo (ATCC 27043T) gene for 16S ribosomal RNA | X74717 | 1434 | ena | 1051649 |
Genome sequences
@ref | description | accession | assembly level | database | NCBI tax ID |
---|---|---|---|---|---|
66792 | Vibrio nigripulchritudo ATCC 27043 | GCA_000222685 | contig | ncbi | 1051649 |
66792 | Vibrio nigripulchritudo ATCC 27043 | 1051649.3 | wgs | patric | 1051649 |
66792 | Vibrio nigripulchritudo ATCC 27043 | 2512047078 | draft | img | 1051649 |
Genome-based predictions
predictions
trait | prediction | confidence | training_data |
---|---|---|---|
motile | yes | 92.233 | no |
flagellated | yes | 92.928 | no |
gram-positive | no | 98.682 | no |
anaerobic | no | 98.363 | no |
aerobic | yes | 81.535 | no |
halophile | no | 53.366 | no |
spore-forming | no | 94.411 | no |
thermophile | no | 99.687 | yes |
glucose-util | yes | 92.395 | no |
glucose-ferment | yes | 85.412 | no |
External links
@ref: 15841
culture collection no.: DSM 21607, ATCC 27043, CAIM 323, CCUG 16376, CCUG 28586, CIP 103195, LMG 3896, NCIMB 1904
straininfo link
- @ref: 86326
- straininfo: 5108
Reference
@id | authors | catalogue | doi/url | title | journal | pubmed |
---|---|---|---|---|---|---|
15841 | Curators of the DSMZ | Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 21607) | https://www.dsmz.de/collection/catalogue/details/culture/DSM-21607 | |||
20215 | Parte, A.C., Sardà Carbasse, J., Meier-Kolthoff, J.P., Reimer, L.C. and Göker, M. | 10.1099/ijsem.0.004332 | List of Prokaryotic names with Standing in Nomenclature (LPSN) moves to the DSMZ | |||
20218 | Verslyppe, B., De Smet, W., De Baets, B., De Vos, P., Dawyndt P. | 10.1016/j.syapm.2013.11.002 | StrainInfo introduces electronic passports for microorganisms. | Syst Appl Microbiol. 37: 42-50 2014 | 24321274 | |
35504 | Curators of the CIP | https://brclims.pasteur.fr/brcWeb/souche/detail/1/14965 | ||||
66792 | Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmann | https://diaspora-project.de/progress.html#genomes | Automatically annotated for the DiASPora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information) | |||
66794 | Antje Chang, Lisa Jeske, Sandra Ulbrich, Julia Hofmann, Julia Koblitz, Ida Schomburg, Meina Neumann-Schaal, Dieter Jahn, Dietmar Schomburg | 10.1093/nar/gkaa1025 | BRENDA, the ELIXIR core data resource in 2021: new developments and updates | Nucleic Acids Res. 49: D498-D508 2020 | 33211880 | |
68369 | Automatically annotated from API 20NE | |||||
68382 | Automatically annotated from API zym | |||||
69479 | João F Matias Rodrigues, Janko Tackmann,Gregor Rot, Thomas SB Schmidt, Lukas Malfertheiner, Mihai Danaila,Marija Dmitrijeva, Daniela Gaio, Nicolas Näpflin and Christian von Mering. University of Zurich. | https://microbeatlas.org/ | MicrobeAtlas 1.0 beta | |||
86326 | Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J. | 10.60712/SI-ID5108.1 | StrainInfo: A central database for resolving microbial strain identifiers | |||
121300 | Curators of the CIP | Collection of Institut Pasteur (CIP 103195) | https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20103195 |