Strain identifier
BacDive ID: 6015
Type strain:
Species: Halomonas cupida
Strain history: CIP <- 2005, DSM, ATCC <- P. Baumann, Hawaii Univ., USA: strain 79, Alcaligenes cupidus
NCBI tax ID(s): 44933 (species)
General
@ref: 1746
BacDive-ID: 6015
DSM-Number: 4740
keywords: genome sequence, 16S sequence, Bacteria, mesophilic, motile
description: Halomonas cupida DSM 4740 is a mesophilic, motile bacterium that was isolated from seawater.
NCBI tax id
- NCBI tax id: 44933
- Matching level: species
strain history
@ref | history |
---|---|
1746 | <- ATCC <- P. Baumann |
67770 | IAM 12552 <-- ATCC 27124 <-- P. Baumann 79. |
118818 | CIP <- 2005, DSM, ATCC <- P. Baumann, Hawaii Univ., USA: strain 79, Alcaligenes cupidus |
doi: 10.13145/bacdive6015.20230509.8.1
Name and taxonomic classification
LPSN
- @ref: 20215
- description: domain/bacteria
- keyword: phylum/pseudomonadota
- domain: Bacteria
- phylum: Pseudomonadota
- class: Gammaproteobacteria
- order: Oceanospirillales
- family: Halomonadaceae
- genus: Halomonas
- species: Halomonas cupida
- full scientific name: Halomonas cupida (Baumann et al. 1972) Dobson and Franzmann 1996
synonyms
@ref synonym 20215 Alcaligenes cupidus 20215 Deleya cupida
@ref: 1746
domain: Bacteria
phylum: Proteobacteria
class: Gammaproteobacteria
order: Oceanospirillales
family: Halomonadaceae
genus: Halomonas
species: Halomonas cupida
full scientific name: Halomonas cupida (Baumann et al. 1972) Dobson and Franzmann 1996
type strain: yes
Morphology
cell morphology
@ref | motility | confidence | gram stain | cell shape |
---|---|---|---|---|
69480 | yes | 96.526 | ||
69480 | 99.881 | negative | ||
118818 | no | negative | rod-shaped |
Culture and growth conditions
culture medium
@ref | name | growth | link | composition |
---|---|---|---|---|
1746 | 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 |
1746 | MARINE AGAR (DSMZ Medium 123) | yes | https://mediadive.dsmz.de/medium/123 | Name: MARINE AGAR (DSMZ Medium 123) Composition: NaCl 24.0 g/l Agar 15.0 g/l MgCl2 x 6 H2O 11.0 g/l Bacto peptone 5.0 g/l Na2SO4 4.0 g/l CaCl2 x 6 H2O 2.0 g/l Yeast extract 1.0 g/l KCl 0.7 g/l KBr 0.1 g/l SrCl2 x 6 H2O 0.04 g/l H3BO3 0.03 g/l NaSiO3 x 9 H2O 0.005 g/l NaF 0.003 g/l NH4NO3 0.002 g/l Fe(III)PO4 x 4 H2O 0.001 g/l Distilled water |
34123 | Marine agar (MA) | yes | Distilled water make up to (1000.000 ml);Marine agar (55.100 g) | |
118818 | CIP Medium 72 | yes | https://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=72 | |
118818 | CIP Medium 13 | yes | https://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=13 |
culture temp
@ref | growth | type | temperature | range |
---|---|---|---|---|
1746 | positive | growth | 25 | mesophilic |
1746 | positive | growth | 26 | mesophilic |
34123 | positive | growth | 30 | mesophilic |
46437 | positive | growth | 26 | mesophilic |
67770 | positive | growth | 25 | mesophilic |
118818 | positive | growth | 5-41 | |
118818 | no | growth | 45 | thermophilic |
Physiology and metabolism
spore formation
@ref | spore formation | confidence |
---|---|---|
69481 | no | 100 |
69480 | no | 99.957 |
halophily
- @ref: 118818
- salt: NaCl
- growth: positive
- tested relation: growth
- concentration: 0-10 %
observation
- @ref: 67770
- observation: quinones: Q-9
metabolite utilization
@ref | Chebi-ID | metabolite | utilization activity | kind of utilization tested |
---|---|---|---|---|
118818 | 16947 | citrate | + | carbon source |
118818 | 4853 | esculin | - | hydrolysis |
118818 | 606565 | hippurate | + | hydrolysis |
118818 | 17632 | nitrate | + | reduction |
118818 | 16301 | nitrite | - | reduction |
118818 | 15792 | malonate | + | assimilation |
118818 | 17632 | nitrate | - | respiration |
metabolite production
- @ref: 118818
- Chebi-ID: 35581
- metabolite: indole
- production: no
enzymes
@ref | value | activity | ec |
---|---|---|---|
68382 | alpha-fucosidase | - | 3.2.1.51 |
68382 | alpha-mannosidase | - | 3.2.1.24 |
68382 | N-acetyl-beta-glucosaminidase | - | 3.2.1.52 |
68382 | beta-glucosidase | + | 3.2.1.21 |
68382 | alpha-glucosidase | + | 3.2.1.20 |
68382 | beta-glucuronidase | - | 3.2.1.31 |
68382 | beta-galactosidase | - | 3.2.1.23 |
68382 | alpha-galactosidase | - | 3.2.1.22 |
68382 | naphthol-AS-BI-phosphohydrolase | + | |
68382 | acid phosphatase | + | 3.1.3.2 |
68382 | alpha-chymotrypsin | - | 3.4.21.1 |
68382 | trypsin | - | 3.4.21.4 |
68382 | cystine arylamidase | - | 3.4.11.3 |
68382 | valine arylamidase | + | |
68382 | leucine arylamidase | + | 3.4.11.1 |
68382 | lipase (C 14) | - | |
68382 | esterase lipase (C 8) | + | |
68382 | esterase (C 4) | + | |
68382 | alkaline phosphatase | + | 3.1.3.1 |
118818 | oxidase | + | |
118818 | beta-galactosidase | + | 3.2.1.23 |
118818 | alcohol dehydrogenase | - | 1.1.1.1 |
118818 | gelatinase | +/- | |
118818 | amylase | - | |
118818 | DNase | + | |
118818 | caseinase | - | 3.4.21.50 |
118818 | catalase | + | 1.11.1.6 |
118818 | tween esterase | + | |
118818 | gamma-glutamyltransferase | + | 2.3.2.2 |
118818 | lecithinase | - | |
118818 | lipase | - | |
118818 | lysine decarboxylase | - | 4.1.1.18 |
118818 | ornithine decarboxylase | - | 4.1.1.17 |
118818 | phenylalanine ammonia-lyase | - | 4.3.1.24 |
118818 | protease | - | |
118818 | tryptophan deaminase | - | |
118818 | urease | - | 3.5.1.5 |
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 |
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
118818 | - | + | + | + | - | + | + | - | - | - | + | + | - | - | - | + | + | - | - | - |
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 |
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
118818 | + | + | + | + | + | - | + | + | + | + | + | + | + | - | - | + | + | + | + | + | + | + | + | - | - | - | + | + | + | - | - | + | + | + | + | + | + | + | - | + | + | + | + | + | + | - | + | + | + | + | + | - | - | + | + | + | + | - | - | + | + | - | + | + | - | - | - | - | - | - | - | + | + | + | - | + | + | - | + | + | + | + | + | + | - | - | + | - | + | + | + | + | + | + | + | + | + | + | + |
Isolation, sampling and environmental information
isolation
@ref | sample type | geographic location | country | origin.country | continent |
---|---|---|---|---|---|
1746 | seawater | ||||
46437 | Seawater enrichment with allantoin | off coast of Oahu Hawaii | USA | USA | North America |
118818 | Environment, Seawater | Hawaii | United States of America | USA | North America |
isolation source categories
- Cat1: #Environmental
- Cat2: #Aquatic
- Cat3: #Marine
taxonmaps
- @ref: 69479
- File name: preview.99_5920.png
- url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_48;96_430;97_491;98_562;99_5920&stattab=map
- Last taxonomy: Halomonas cupida
- 16S sequence: AB681733
- Sequence Identity:
- Total samples: 376
- soil counts: 42
- aquatic counts: 157
- animal counts: 145
- plant counts: 32
Safety information
risk assessment
@ref | biosafety level | biosafety level comment |
---|---|---|
1746 | 1 | Risk group (German classification) |
118818 | 1 | Risk group (French classification) |
Sequence information
16S sequences
@ref | description | accession | length | database | NCBI tax ID |
---|---|---|---|---|---|
20218 | Halomonas cupida partial 16S rRNA gene, strain DSM 4740 | FN257742 | 1464 | ena | 44933 |
20218 | Halomonas cupida genes for 16S ribosomal RNA, internal transcribed spacer 1 and 23S ribosomal RNA, partial and complete sequence, clone: 1207 | AB367211 | 1207 | ena | 44933 |
20218 | Halomonas cupida genes for 16S ribosomal RNA, internal transcribed spacer 1 and 23S ribosomal RNA, partial and complete sequence, clone: 1268 | AB367212 | 1268 | ena | 44933 |
20218 | Halomonas cupida gene for 16S rRNA, partial sequence, strain: NBRC 102219 | AB681733 | 1465 | ena | 44933 |
1746 | Halomonas cupida strain DSM 4740 16S ribosomal RNA gene, partial sequence | L42615 | 1471 | ena | 44933 |
Genome sequences
@ref | description | accession | assembly level | database | NCBI tax ID |
---|---|---|---|---|---|
66792 | Halomonas cupida strain DSM 4740 | 44933.4 | wgs | patric | 44933 |
66792 | Halomonas cupida strain NBRC 102219 | 44933.8 | wgs | patric | 44933 |
66792 | Halomonas cupida DSM 4740 | 2599185207 | draft | img | 44933 |
67770 | Halomonas cupida NBRC 102219 | GCA_007991155 | contig | ncbi | 44933 |
67770 | Halomonas cupida DSM 4740 | GCA_900142755 | scaffold | ncbi | 44933 |
GC content
@ref | GC-content | method |
---|---|---|
67770 | 60 | thermal denaturation, midpoint method (Tm) |
67770 | 60.7 | Buoyant density centrifugation (BD) |
Genome-based predictions
predictions
trait | prediction | confidence | training_data |
---|---|---|---|
spore-forming | no | 100 | no |
gram-positive | no | 98.511 | no |
anaerobic | no | 99.297 | no |
halophile | yes | 84.289 | no |
spore-forming | no | 97.284 | no |
glucose-util | yes | 94.187 | no |
aerobic | yes | 96.021 | no |
flagellated | yes | 66.399 | no |
thermophile | no | 98.821 | no |
motile | yes | 91.29 | no |
glucose-ferment | no | 72.255 | no |
External links
@ref: 1746
culture collection no.: DSM 4740, ATCC 27124, CCUG 16075, LMG 3448, CIP 74.06, JCM 20632, CECT 5001, CIP 103199, IAM 12552, NBRC 102219, NCIMB 1978, CIP 74.6
straininfo link
- @ref: 75501
- straininfo: 2161
literature
topic | Pubmed-ID | title | authors | journal | DOI | year | mesh | topic2 |
---|---|---|---|---|---|---|---|---|
Phylogeny | 24425813 | Halomonas huangheensis sp. nov., a moderately halophilic bacterium isolated from a saline-alkali soil. | Miao C, Jia F, Wan Y, Zhang W, Lin M, Jin W | Int J Syst Evol Microbiol | 10.1099/ijs.0.056556-0 | 2013 | Alkalies, Base Composition, China, DNA, Bacterial/genetics, Fatty Acids/chemistry, Halomonas/*classification/genetics/isolation & purification, Molecular Sequence Data, Nucleic Acid Hybridization, *Phylogeny, RNA, Ribosomal, 16S/genetics, Salinity, *Soil Microbiology, Ubiquinone/chemistry | Genetics |
Phylogeny | 27380915 | Halomonas sediminicola sp. nov., a moderately halophilic bacterium isolated from a solar saltern sediment. | Lee JC, Kim SJ, Whang KS | Int J Syst Evol Microbiol | 10.1099/ijsem.0.001278 | 2016 | Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, Fatty Acids/chemistry, Geologic Sediments/*microbiology, Halomonas/*classification/genetics/isolation & purification, Nucleic Acid Hybridization, Phospholipids/chemistry, *Phylogeny, Ponds/*microbiology, RNA, Ribosomal, 16S/genetics, Republic of Korea, *Salinity, Sequence Analysis, DNA, Ubiquinone/chemistry | Transcriptome |
Reference
@id | authors | catalogue | doi/url | title | journal | pubmed |
---|---|---|---|---|---|---|
1746 | Curators of the DSMZ | Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 4740) | https://www.dsmz.de/collection/catalogue/details/culture/DSM-4740 | |||
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 | |
34123 | Curators of the CIP | https://brclims.pasteur.fr/brcWeb/souche/detail/1/14970 | ||||
46437 | Curators of the CCUG | Culture Collection University of Gothenburg (CCUG) (CCUG 16075) | https://www.ccug.se/strain?id=16075 | |||
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) | |||
67770 | Curators of the JCM | https://jcm.brc.riken.jp/en/ | ||||
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 | |||
69480 | Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmann | https://diaspora-project.de/progress.html#genomes | Predictions based on genome sequence made in the Diaspora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information) | |||
69481 | Xiao-Yin To, René Mreches, Martin Binder, Alice C. McHardy, Philipp C. Münch | 10.21203/rs.3.rs-2527258/v1 | Predictions based on the model GenomeNet Sporulation v. 1 | |||
75501 | Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J. | 10.60712/SI-ID2161.1 | StrainInfo: A central database for resolving microbial strain identifiers | |||
118818 | Curators of the CIP | Collection of Institut Pasteur (CIP 103199) | https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20103199 |