Strain identifier
BacDive ID: 6074
Type strain:
Species: Halomonas johnsoniae
Strain Designation: T68687
Strain history: <- D A Stevens, Santa Clara Valley Medical Center, USA
NCBI tax ID(s): 502832 (species)
General
@ref: 15439
BacDive-ID: 6074
DSM-Number: 21197
keywords: genome sequence, 16S sequence, Bacteria, aerobe, mesophilic, Gram-negative, motile, rod-shaped
description: Halomonas johnsoniae T68687 is an aerobe, mesophilic, Gram-negative bacterium that was isolated from waste handling option port of a dialysis machine.
NCBI tax id
- NCBI tax id: 502832
- Matching level: species
strain history
@ref | history |
---|---|
15439 | <- K. K. Kim, KCTC; T68687 <- D. A. Stevens, Santa Clara Valley Medical Center (SCVMC), San Jose, California, USA |
67771 | <- D A Stevens, Santa Clara Valley Medical Center, USA |
doi: 10.13145/bacdive6074.20230509.8.1
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 johnsoniae
- full scientific name: Halomonas johnsoniae Kim et al. 2010
@ref: 15439
domain: Bacteria
phylum: Proteobacteria
class: Gammaproteobacteria
order: Oceanospirillales
family: Halomonadaceae
genus: Halomonas
species: Halomonas johnsoniae
full scientific name: Halomonas johnsoniae Kim et al. 2010
strain designation: T68687
type strain: yes
Morphology
cell morphology
@ref | gram stain | cell length | cell width | cell shape | motility | confidence |
---|---|---|---|---|---|---|
29031 | negative | 2.75 µm | 0.8 µm | rod-shaped | yes | |
67771 | negative | |||||
69480 | yes | 96.918 | ||||
69480 | negative | 99.995 |
pigmentation
- @ref: 29031
- production: yes
Culture and growth conditions
culture medium
- @ref: 15439
- name: TRYPTONE SOYA BROTH (TSB) (DSMZ Medium 545)
- growth: yes
- link: https://mediadive.dsmz.de/medium/545
- composition: Name: TRYPTONE SOYA BROTH (TSB) (DSMZ Medium 545) Composition: Casein peptone 17.0 g/l NaCl 5.0 g/l Soy peptone 3.0 g/l D(+)-Glucose 2.5 g/l K2HPO4 2.5 g/l Distilled water
culture temp
@ref | growth | type | temperature | range |
---|---|---|---|---|
15439 | positive | growth | 28 | mesophilic |
29031 | positive | growth | 10-40 | |
29031 | positive | optimum | 32.5 | mesophilic |
67771 | positive | growth | 28 | mesophilic |
culture pH
@ref | ability | type | pH | PH range |
---|---|---|---|---|
29031 | positive | growth | 07-10 | alkaliphile |
29031 | positive | optimum | 8.5 |
Physiology and metabolism
oxygen tolerance
@ref | oxygen tolerance |
---|---|
29031 | aerobe |
67771 | aerobe |
spore formation
@ref | spore formation | confidence |
---|---|---|
29031 | no | |
69481 | no | 100 |
69480 | no | 99.751 |
halophily
@ref | salt | growth | tested relation | concentration |
---|---|---|---|---|
29031 | NaCl | positive | growth | 0-20 % |
29031 | NaCl | positive | optimum | 2.5 % |
metabolite utilization
@ref | Chebi-ID | metabolite | utilization activity | kind of utilization tested |
---|---|---|---|---|
29031 | 17879 | 4-hydroxybenzoate | + | carbon source |
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 | 29864 | mannitol | + | carbon source |
29031 | 26271 | proline | + | carbon source |
29031 | 17272 | propionate | + | carbon source |
29031 | 17822 | serine | + | carbon source |
29031 | 30911 | sorbitol | + | carbon source |
29031 | 30031 | succinate | + | carbon source |
29031 | 17992 | sucrose | + | carbon source |
29031 | 27082 | trehalose | + | carbon source |
29031 | 17632 | nitrate | + | reduction |
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 |
Isolation, sampling and environmental information
isolation
@ref | sample type | geographic location | country | origin.country | continent |
---|---|---|---|---|---|
15439 | waste handling option port of a dialysis machine | California, San Jose, Santa Clara Valley Medical Center | USA | USA | North America |
67771 | From dialysis center environment and machines | USA | USA | North America |
isolation source categories
Cat1 | Cat2 |
---|---|
#Engineered | #Waste |
#Infection | #Medical device |
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: AM941399
- Sequence Identity:
- Total samples: 9461
- soil counts: 614
- aquatic counts: 3901
- animal counts: 4865
- plant counts: 81
Safety information
risk assessment
- @ref: 15439
- biosafety level: 1
- biosafety level comment: Risk group (German classification)
Sequence information
16S sequences
- @ref: 15439
- description: Halomonas johnsoniae partial 16S rRNA gene, type strain T68687T
- accession: AM941399
- length: 1455
- database: ena
- NCBI tax ID: 502832
Genome sequences
@ref | description | accession | assembly level | database | NCBI tax ID |
---|---|---|---|---|---|
66792 | Halomonas johnsoniae KCTC 22157 | GCA_014651795 | contig | ncbi | 502832 |
66792 | Halomonas johnsoniae strain KCTC 22157 | 502832.6 | wgs | patric | 502832 |
GC content
@ref | GC-content | method |
---|---|---|
15439 | 64.4 | high performance liquid chromatography (HPLC) |
29031 | 64.4-65.2 |
Genome-based predictions
predictions
trait | prediction | confidence | training_data |
---|---|---|---|
spore-forming | no | 100 | no |
gram-positive | no | 98.741 | no |
anaerobic | no | 98.73 | yes |
halophile | yes | 93.047 | no |
spore-forming | no | 96.057 | no |
glucose-util | yes | 88.512 | yes |
aerobic | yes | 93.088 | yes |
thermophile | no | 99.484 | yes |
motile | yes | 91.023 | no |
flagellated | yes | 72.222 | no |
glucose-ferment | no | 74.803 | no |
External links
@ref: 15439
culture collection no.: DSM 21197, KCTC 22157
straininfo link
- @ref: 75561
- straininfo: 405345
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 |
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 |
---|---|---|---|---|---|---|
15439 | Curators of the DSMZ | Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 21197) | https://www.dsmz.de/collection/catalogue/details/culture/DSM-21197 | |||
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) | |||
67771 | Curators of the KCTC | https://kctc.kribb.re.kr/En/Kctc | ||||
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 | |||
75561 | Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J. | 10.60712/SI-ID405345.1 | StrainInfo: A central database for resolving microbial strain identifiers |