Strain identifier
BacDive ID: 14259
Type strain:
Species: Sphingomonas japonica
Strain Designation: KC7
Strain history: CIP <- 2012, JCM <- 2008, N. Tanaka: strain KC7
NCBI tax ID(s): 511662 (species)
General
@ref: 16495
BacDive-ID: 14259
DSM-Number: 22753
keywords: genome sequence, 16S sequence, Bacteria, aerobe, mesophilic, Gram-negative, motile, rod-shaped
description: Sphingomonas japonica KC7 is an aerobe, mesophilic, Gram-negative bacterium that was isolated from marine crustacean specimen Paralithodes camtschatica.
NCBI tax id
- NCBI tax id: 511662
- Matching level: species
strain history
@ref | history |
---|---|
16495 | <- L. A. Romanenko, Pacific Inst. Bioorg. Chem., RAS, Vladivostok, Russia; KMM 3038 <- N. Tanaka; KC7 |
67770 | N. Tanaka KC7. |
120316 | CIP <- 2012, JCM <- 2008, N. Tanaka: strain KC7 |
doi: 10.13145/bacdive14259.20230509.8.1
Name and taxonomic classification
LPSN
- @ref: 20215
- description: domain/bacteria
- keyword: phylum/pseudomonadota
- domain: Bacteria
- phylum: Pseudomonadota
- class: Alphaproteobacteria
- order: Sphingomonadales
- family: Sphingomonadaceae
- genus: Sphingomonas
- species: Sphingomonas japonica
- full scientific name: Sphingomonas japonica Romanenko et al. 2009
@ref: 16495
domain: Bacteria
phylum: Proteobacteria
class: Alphaproteobacteria
order: Sphingomonadales
family: Sphingomonadaceae
genus: Sphingomonas
species: Sphingomonas japonica
full scientific name: Sphingomonas japonica Romanenko et al. 2009 emend. Feng et al. 2017
strain designation: KC7
type strain: yes
Morphology
cell morphology
@ref | gram stain | cell length | cell width | cell shape | motility | confidence |
---|---|---|---|---|---|---|
28989 | negative | 1.65 µm | 0.7 µm | rod-shaped | yes | |
69480 | negative | 99.986 | ||||
120316 | negative | rod-shaped | yes |
pigmentation
- @ref: 28989
- production: yes
Culture and growth conditions
culture medium
@ref | name | growth | link | composition |
---|---|---|---|---|
16495 | 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 |
36629 | Marine agar (MA) | yes | Distilled water make up to (1000.000 ml);Marine agar (55.100 g) | |
120316 | CIP Medium 13 | yes | https://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=13 |
culture temp
@ref | growth | type | temperature | range |
---|---|---|---|---|
16495 | positive | growth | 28 | mesophilic |
28989 | positive | growth | 04-37 | |
28989 | positive | optimum | 26.5 | mesophilic |
36629 | positive | growth | 25 | mesophilic |
67770 | positive | growth | 25 | mesophilic |
Physiology and metabolism
oxygen tolerance
- @ref: 28989
- oxygen tolerance: aerobe
spore formation
@ref | spore formation | confidence |
---|---|---|
69481 | no | 99 |
69480 | no | 99.99 |
observation
- @ref: 28989
- observation: aggregates in clumps
metabolite utilization
@ref | Chebi-ID | metabolite | utilization activity | kind of utilization tested |
---|---|---|---|---|
28989 | 25115 | malate | + | carbon source |
28989 | 53426 | tween 80 | + | carbon source |
28989 | 4853 | esculin | + | hydrolysis |
68369 | 25115 | malate | - | assimilation |
68369 | 17128 | adipate | - | assimilation |
68369 | 27689 | decanoate | - | assimilation |
68369 | 24265 | gluconate | - | assimilation |
68369 | 59640 | N-acetylglucosamine | - | assimilation |
68369 | 16899 | D-mannitol | - | assimilation |
68369 | 16024 | D-mannose | - | assimilation |
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 |
metabolite production
@ref | Chebi-ID | metabolite | production |
---|---|---|---|
28989 | 16136 | hydrogen sulfide | yes |
68369 | 35581 | indole | no |
metabolite tests
- @ref: 68369
- Chebi-ID: 35581
- metabolite: indole
- indole test: -
enzymes
@ref | value | activity | ec |
---|---|---|---|
28989 | acid phosphatase | + | 3.1.3.2 |
28989 | alkaline phosphatase | + | 3.1.3.1 |
28989 | catalase | + | 1.11.1.6 |
28989 | gelatinase | + | |
28989 | cytochrome oxidase | + | 1.9.3.1 |
68369 | cytochrome oxidase | - | 1.9.3.1 |
68369 | beta-glucosidase | + | 3.2.1.21 |
68369 | urease | - | 3.5.1.5 |
68369 | arginine dihydrolase | - | 3.5.3.6 |
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 |
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
16495 | - | - | - | - | - | + | - | + | + | + | - | - | - | + | - | - | - | - | - | - | - |
16495 | - | - | - | - | - | + | + | + | - | - | - | - | - | - | - | - | - | - | - | - | - |
Isolation, sampling and environmental information
isolation
@ref | sample type | host species | geographic location | country | origin.country | continent |
---|---|---|---|---|---|---|
16495 | marine crustacean specimen Paralithodes camtschatica | Paralithodes camtschatica | Sea of Japan, Peter the Great Bay | Russia | RUS | Asia |
67770 | Paralithodes camtschatica collected from Peter the Great Bay | Paralithodes camtschatica | Sea of Japan | Russia | RUS | |
120316 | Paralithodes camtschatica collected from Peter the Great Bay | Sea of Japan | Russian Federation | RUS | Europe |
isolation source categories
Cat1 | Cat2 | Cat3 |
---|---|---|
#Environmental | #Aquatic | #Marine |
#Host | #Arthropoda | #Crustacea |
Safety information
risk assessment
@ref | biosafety level | biosafety level comment |
---|---|---|
16495 | 1 | Risk group (German classification) |
120316 | 1 | Risk group (French classification) |
Sequence information
16S sequences
- @ref: 16495
- description: Sphingomonas japonica gene for 16S rRNA, partial sequence, strain: KC7
- accession: AB428568
- length: 1480
- database: ena
- NCBI tax ID: 511662
Genome sequences
@ref | description | accession | assembly level | database | NCBI tax ID |
---|---|---|---|---|---|
66792 | Sphingomonas japonica strain DSM 22753 | 511662.4 | wgs | patric | 511662 |
66792 | Sphingomonas japonica DSM 22753 | 2828348002 | draft | img | 511662 |
67770 | Sphingomonas japonica DSM 22753 | GCA_011762085 | contig | ncbi | 511662 |
GC content
- @ref: 16495
- GC-content: 66.7
- method: high performance liquid chromatography (HPLC)
Genome-based predictions
predictions
trait | prediction | confidence | training_data |
---|---|---|---|
spore-forming | no | 99 | no |
gram-positive | no | 97.126 | yes |
anaerobic | no | 99.434 | yes |
halophile | no | 89.519 | no |
spore-forming | no | 95.999 | no |
glucose-util | yes | 82.842 | no |
aerobic | yes | 96.524 | yes |
thermophile | no | 96.814 | yes |
flagellated | no | 87.287 | no |
motile | yes | 77.713 | yes |
glucose-ferment | no | 92.468 | yes |
External links
@ref: 16495
culture collection no.: DSM 22753, JCM 15438, KMM 3038, NRIC 0738, CIP 110395
straininfo link
- @ref: 83418
- straininfo: 362852
literature
topic | Pubmed-ID | title | authors | journal | DOI | year | mesh | topic2 |
---|---|---|---|---|---|---|---|---|
Phylogeny | 19406815 | Sphingomonas japonica sp. nov., isolated from the marine crustacean Paralithodes camtschatica. | Romanenko LA, Tanaka N, Frolova GM, Mikhailov VV | Int J Syst Evol Microbiol | 10.1099/ijs.0.003285-0 | 2009 | Animals, Anomura/*microbiology, Bacterial Typing Techniques, DNA, Bacterial/analysis, DNA, Ribosomal/analysis, Fatty Acids/analysis, Genes, rRNA, Genotype, Molecular Sequence Data, Phenotype, Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Species Specificity, Sphingomonas/*classification/genetics/isolation & purification/physiology | Genetics |
Phylogeny | 28691655 | Sphingomonas spermidinifaciens sp. nov., a novel bacterium containing spermidine as the major polyamine, isolated from an abandoned lead-zinc mine and emended descriptions of the genus Sphingomonas and the species Sphingomonas yantingensis and Sphingomonas japonica. | Feng GD, Yang SZ, Xiong X, Li HP, Zhu HH | Int J Syst Evol Microbiol | 10.1099/ijsem.0.001905 | 2017 | Bacterial Typing Techniques, Base Composition, China, DNA, Bacterial/genetics, Fatty Acids/chemistry, *Mining, Nucleic Acid Hybridization, Phospholipids/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, *Soil Microbiology, Spermidine/chemistry, Sphingomonas/*classification/genetics/isolation & purification, Ubiquinone/chemistry, Zinc | Transcriptome |
Phylogeny | 36173732 | Sphingomonas baiyangensis sp. nov., isolated from water in Baiyang Lake. | Wei DW, Yang Y, Zeng Y, Wang C, Feng J | Int J Syst Evol Microbiol | 10.1099/ijsem.0.005326 | 2022 | Bacterial Typing Techniques, Base Composition, Cardiolipins, DNA, Bacterial/genetics, Fatty Acids/chemistry, Glycolipids/chemistry, Glycosphingolipids, Lakes/microbiology, Nucleotides, Phosphatidylcholines, Phosphatidylethanolamines, Phospholipids/chemistry, Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Soil Microbiology, *Sphingomonas, Water | Transcriptome |
Reference
@id | authors | catalogue | doi/url | title | ID_cross_reference | pubmed |
---|---|---|---|---|---|---|
16495 | Curators of the DSMZ | Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 22753) | https://www.dsmz.de/collection/catalogue/details/culture/DSM-22753 | |||
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 | |||
28989 | 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 | 25422 | 28776041 | |
36629 | Curators of the CIP | https://brclims.pasteur.fr/brcWeb/souche/detail/1/8250 | ||||
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/ | ||||
68369 | Automatically annotated from API 20NE | |||||
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 | |||
83418 | Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J. | 10.60712/SI-ID362852.1 | StrainInfo: A central database for resolving microbial strain identifiers | |||
120316 | Curators of the CIP | Collection of Institut Pasteur (CIP 110395) | https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20110395 |