Strain identifier
BacDive ID: 6075
Type strain: 
Species: Halomonas stevensii
Strain Designation: S18214
Strain history: <- K. K. Kim, KCTC; S18214 <- D. A. Stevens, Santa Clara Valley Medical Center (SCVMC), San Jose, California, USA
NCBI tax ID(s): 502821 (species)
version 8.1 (current version)
General
@ref: 15440
BacDive-ID: 6075
DSM-Number: 21198
keywords: genome sequence, 16S sequence, Bacteria, aerobe, mesophilic, Gram-negative, motile, rod-shaped, human pathogen
description: Halomonas stevensii S18214 is an aerobe, mesophilic, Gram-negative human pathogen that was isolated from blood of a renal care patient.
NCBI tax id
- NCBI tax id: 502821
- Matching level: species
strain history
- @ref: 15440
- history: <- K. K. Kim, KCTC; S18214 <- D. A. Stevens, Santa Clara Valley Medical Center (SCVMC), San Jose, California, USA
doi: 10.13145/bacdive6075.20230509.8.1
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 stevensii
- full scientific name: Halomonas stevensii Kim et al. 2010
synonyms
- @ref: 20215
- synonym: Vreelandella stevensii
@ref: 15440
domain: Bacteria
phylum: Proteobacteria
class: Gammaproteobacteria
order: Oceanospirillales
family: Halomonadaceae
genus: Halomonas
species: Halomonas stevensii
full scientific name: Halomonas stevensii Kim et al. 2010
strain designation: S18214
type strain: yes
Morphology
cell morphology
- @ref: 29031
- gram stain: negative
- cell length: 2.5 µm
- cell width: 1 µm
- cell shape: rod-shaped
- motility: yes
pigmentation
- @ref: 29031
- production: yes
Culture and growth conditions
culture medium
- @ref: 15440
- name: BACTO MARINE BROTH (DIFCO 2216) (DSMZ Medium 514)
- growth: yes
- link: https://mediadive.dsmz.de/medium/514
- composition: 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
culture temp
| @ref | growth | type | temperature | range |
|---|---|---|---|---|
| 15440 | positive | growth | 28 | mesophilic |
| 29031 | positive | growth | 10-40 | |
| 29031 | positive | optimum | 32.5 | mesophilic |
culture pH
| @ref | ability | type | pH | PH range |
|---|---|---|---|---|
| 29031 | positive | growth | 07-11 | alkaliphile |
| 29031 | positive | optimum | 8.5 |
Physiology and metabolism
oxygen tolerance
- @ref: 29031
- oxygen tolerance: aerobe
spore formation
- @ref: 29031
- spore formation: no
halophily
| @ref | salt | growth | tested relation | concentration |
|---|---|---|---|---|
| 29031 | NaCl | positive | growth | 0-20 % |
| 29031 | NaCl | positive | optimum | 5.25 % |
metabolite utilization
| @ref | Chebi-ID | metabolite | utilization activity | kind of utilization tested |
|---|---|---|---|---|
| 29031 | 30089 | acetate | + | carbon source |
| 29031 | 16449 | alanine | + | carbon source |
| 29031 | 16947 | citrate | + | carbon source |
| 29031 | 16236 | ethanol | + | carbon source |
| 29031 | 28757 | fructose | + | carbon source |
| 29031 | 24265 | gluconate | + | carbon source |
| 29031 | 17234 | glucose | + | carbon source |
| 29031 | 17754 | glycerol | + | carbon source |
| 29031 | 25115 | malate | + | carbon source |
| 29031 | 17306 | maltose | + | carbon source |
| 29031 | 17268 | myo-inositol | + | carbon source |
| 29031 | 26271 | proline | + | carbon source |
| 29031 | 17272 | propionate | + | carbon source |
| 29031 | 17822 | serine | + | carbon source |
| 29031 | 30031 | succinate | + | carbon source |
| 29031 | 17992 | sucrose | + | carbon source |
| 29031 | 27082 | trehalose | + | carbon source |
metabolite production
- @ref: 29031
- Chebi-ID: 16136
- metabolite: hydrogen sulfide
- production: yes
enzymes
| @ref | value | activity | ec |
|---|---|---|---|
| 29031 | catalase | + | 1.11.1.6 |
| 29031 | cytochrome oxidase | + | 1.9.3.1 |
| 29031 | urease | + | 3.5.1.5 |
Isolation, sampling and environmental information
isolation
- @ref: 15440
- sample type: blood of a renal care patient
- geographic location: California, San Jose, Santa Clara Valley Medical Center
- country: USA
- origin.country: USA
- continent: North America
isolation source categories
| Cat1 | Cat2 | Cat3 |
|---|---|---|
| #Infection | #Patient | |
| #Host Body Product | #Fluids | #Blood |
taxonmaps
- @ref: 69479
- File name: preview.99_136.png
- url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_48;96_104;97_111;98_121;99_136&stattab=map
- Last taxonomy: Halomonas
- 16S sequence: AM941388
- Sequence Identity:
- Total samples: 9461
- soil counts: 614
- aquatic counts: 3901
- animal counts: 4865
- plant counts: 81
Safety information
risk assessment
- @ref: 15440
- pathogenicity human: yes, in single cases
- biosafety level: 1
- biosafety level comment: Risk group (German classification)
Sequence information
16S sequences
- @ref: 15440
- description: Halomonas stevensii S18214 partial 16S rRNA gene, type strain S18214T
- accession: AM941388
- length: 1455
- database: ena
- NCBI tax ID: 1177117
Genome sequences
| @ref | description | accession | assembly level | database | NCBI tax ID |
|---|---|---|---|---|---|
| 66792 | Halomonas stevensii S18214 | GCA_000275725 | contig | ncbi | 1177117 |
| 66792 | Halomonas stevensii S18214 | 1177117.3 | wgs | patric | 1177117 |
| 66792 | Halomonas stevensii S18214 | 2551306145 | draft | img | 1177117 |
GC content
| @ref | GC-content | method |
|---|---|---|
| 15440 | 62.0 | high performance liquid chromatography (HPLC) |
| 29031 | 62 |
Genome-based predictions
predictions
| trait | prediction | confidence | training_data |
|---|---|---|---|
| motile | yes | 92.511 | yes |
| gram-positive | no | 98.782 | yes |
| anaerobic | no | 97.391 | yes |
| halophile | yes | 91.859 | yes |
| spore-forming | no | 95.891 | yes |
| flagellated | yes | 78.734 | no |
| thermophile | no | 99.49 | yes |
| glucose-util | yes | 88.468 | yes |
| aerobic | yes | 91.463 | no |
| glucose-ferment | no | 78.06 | no |
External links
@ref: 15440
culture collection no.: DSM 21198, KCTC 22148
straininfo link
- @ref: 75562
- straininfo: 407909
literature
| topic | Pubmed-ID | title | authors | journal | DOI | year | mesh | topic2 |
|---|---|---|---|---|---|---|---|---|
| Phylogeny | 19651714 | Halomonas stevensii sp. nov., Halomonas hamiltonii sp. nov. and Halomonas johnsoniae sp. nov., isolated from a renal care centre. | Kim KK, Lee KC, Oh HM, Lee JS | Int J Syst Evol Microbiol | 10.1099/ijs.0.004424-0 | 2009 | Bacteremia/etiology/*microbiology, Base Composition, Base Sequence, California, DNA, Bacterial/chemistry, Equipment and Supplies, Hospital/*microbiology, Halomonas/*classification/genetics/isolation & purification, *Hemodialysis Units, Hospital, Humans, Molecular Sequence Data, Phylogeny, RNA, Bacterial/genetics, RNA, Ribosomal, 16S/genetics, Renal Dialysis/*instrumentation, Sequence Homology, Nucleic Acid | Pathogenicity |
| Pathogenicity | 21167477 | O-chain structure from the lipopolysaccharide of the human pathogen Halomonas stevensii strain S18214. | Pieretti G, Carillo S, Kim KK, Lee KC, Lee JS, Lanzetta R, Parrilli M, Corsaro MM | Carbohydr Res | 10.1016/j.carres.2010.11.023 | 2010 | Carbohydrate Sequence, Halomonas/*immunology, Humans, Molecular Sequence Data, O Antigens/*chemistry/immunology | Genetics |
| Genetics | 22933767 | Draft genome sequence of the human pathogen Halomonas stevensii S18214T. | Kim KK, Lee KC, Jeong H, Stevens DA, Lee JS | J Bacteriol | 10.1128/JB.01071-12 | 2012 | DNA, Bacterial/*chemistry/*genetics, Dialysis/adverse effects, Environmental Microbiology, *Genome, Bacterial, Halomonas/*genetics/isolation & purification, Humans, Molecular Sequence Data, *Sequence Analysis, DNA | Pathogenicity |
| Phylogeny | 24510978 | Halomonas songnenensis sp. nov., a moderately halophilic bacterium isolated from saline and alkaline soils. | Jiang J, Pan Y, Hu S, Zhang X, Hu B, Huang H, Hong S, Meng J, Li C, Wang K | Int J Syst Evol Microbiol | 10.1099/ijs.0.056499-0 | 2014 | Bacterial Typing Techniques, Base Composition, China, DNA, Bacterial/genetics, Fatty Acids/chemistry, Genes, Bacterial, Halomonas/*classification/genetics/isolation & purification, Hydrogen-Ion Concentration, Molecular Sequence Data, Nucleic Acid Hybridization, Phospholipids/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, Salinity, Sequence Analysis, DNA, Soil/chemistry, *Soil Microbiology, Ubiquinone/chemistry | Genetics |
| Phylogeny | 32195651 | Halomonas montanilacus sp. nov., isolated from hypersaline Lake Pengyanco on the Tibetan Plateau. | Lu H, Xing P, Zhai L, Li H, Wu Q | Int J Syst Evol Microbiol | 10.1099/ijsem.0.004109 | 2020 | Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, Fatty Acids/chemistry, Halomonas/*classification/isolation & purification, Lakes/*microbiology, Nucleic Acid Hybridization, Phospholipids/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, *Saline Waters, Sequence Analysis, DNA, Tibet, Vitamin K 2/analogs & derivatives/chemistry | Transcriptome |
Reference
| @id | authors | catalogue | doi/url | title | ID_cross_reference | pubmed |
|---|---|---|---|---|---|---|
| 15440 | Curators of the DSMZ | Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 21198) | https://www.dsmz.de/collection/catalogue/details/culture/DSM-21198 | |||
| 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 | |||
| 29031 | Barberan A, Caceres Velazquez H, Jones S, Fierer N. | 10.1128/mSphere.00237-17 | Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information | 25461 | 28776041 | |
| 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) | |||
| 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 | |||
| 75562 | Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J. | 10.60712/SI-ID407909.1 | StrainInfo: A central database for resolving microbial strain identifiers |