Strain identifier
BacDive ID: 13045
Type strain:
Species: Chryseomonas luteola
Strain Designation: 4239, KS 0921
Strain history: CIP <- 1987, IAM <- G.L. Gilardi: strain 4239
NCBI tax ID(s): 1215106 (strain), 47886 (species)
General
@ref: 2931
BacDive-ID: 13045
DSM-Number: 6975
keywords: genome sequence, 16S sequence, Bacteria, obligate aerobe, mesophilic, motile
description: Chryseomonas luteola 4239 is an obligate aerobe, mesophilic, motile bacterium that was isolated from human wound.
NCBI tax id
NCBI tax id | Matching level |
---|---|
47886 | species |
1215106 | strain |
strain history
@ref | history |
---|---|
2931 | <- ATCC; ATCC 43273 (Chryseomonas luteola) <- JCM; JCM 3352 <- K. Kodama, University of Tokyo, Tokyo, Japan; KS 0921 <- G. Gilardi; 4239 |
67770 | K. Kodama KS 0921 <-- G. L. Gilardi #4239. |
120689 | CIP <- 1987, IAM <- G.L. Gilardi: strain 4239 |
doi: 10.13145/bacdive13045.20230509.8.1
Name and taxonomic classification
LPSN
- @ref: 20215
- description: domain/bacteria
- keyword: phylum/pseudomonadota
- domain: Bacteria
- phylum: Pseudomonadota
- class: Gammaproteobacteria
- order: Pseudomonadales
- family: Pseudomonadaceae
- genus: Chryseomonas
- species: Chryseomonas luteola
- full scientific name: Chryseomonas luteola (Kodama et al. 1985) Holmes et al. 1987
synonyms
@ref synonym 20215 Pseudomonas luteola 20215 Chryseomonas polytricha 20215 Pseudomonas zeshuii
@ref: 2931
domain: Bacteria
phylum: Proteobacteria
class: Gammaproteobacteria
order: Pseudomonadales
family: Pseudomonadaceae
genus: Pseudomonas
species: Pseudomonas luteola
full scientific name: Pseudomonas luteola Kodama et al. 1985
strain designation: 4239, KS 0921
type strain: yes
Morphology
cell morphology
@ref | motility | confidence | gram stain | cell shape |
---|---|---|---|---|
69480 | yes | 98.902 | ||
69480 | 99.993 | negative | ||
120689 | no | negative | rod-shaped |
pigmentation
- @ref: 120689
- production: no
- name: Pyocyanin
Culture and growth conditions
culture medium
@ref | name | growth | composition | link |
---|---|---|---|---|
33753 | MEDIUM 3 - Columbia agar | yes | Columbia agar (39.000 g);distilled water (1000.000 ml) | |
2931 | TRYPTICASE SOY YEAST EXTRACT MEDIUM (DSMZ Medium 92) | yes | Name: TRYPTICASE SOY YEAST EXTRACT MEDIUM (DSMZ Medium 92) Composition: Trypticase soy broth 30.0 g/l Agar 15.0 g/l Yeast extract 3.0 g/l Distilled water | https://mediadive.dsmz.de/medium/92 |
2931 | COLUMBIA BLOOD MEDIUM (DSMZ Medium 693) | yes | Name: COLUMBIA BLOOD MEDIUM (DSMZ Medium 693) Composition: Defibrinated sheep blood 50.0 g/l Columbia agar base | https://mediadive.dsmz.de/medium/693 |
120689 | CIP Medium 3 | yes | https://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=3 |
culture temp
@ref | growth | type | temperature | range |
---|---|---|---|---|
2931 | positive | growth | 30 | mesophilic |
33753 | positive | growth | 30 | mesophilic |
67770 | positive | growth | 30 | mesophilic |
120689 | positive | growth | 10-41 | |
120689 | no | growth | 5 | psychrophilic |
Physiology and metabolism
oxygen tolerance
- @ref: 120689
- oxygen tolerance: obligate aerobe
spore formation
- @ref: 69480
- spore formation: no
- confidence: 99.992
halophily
@ref | salt | growth | tested relation | concentration |
---|---|---|---|---|
120689 | NaCl | positive | growth | 0-8 % |
120689 | NaCl | no | growth | 10 % |
observation
- @ref: 67770
- observation: quinones: Q-9
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 | 16024 | D-mannose | + | 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 |
120689 | 16947 | citrate | + | carbon source |
120689 | 4853 | esculin | + | hydrolysis |
120689 | 17632 | nitrate | + | reduction |
120689 | 16301 | nitrite | - | reduction |
120689 | 17632 | nitrate | - | respiration |
antibiotic resistance
- @ref: 120689
- metabolite: 0129 (2,4-Diamino-6,7-di-iso-propylpteridine phosphate)
- is antibiotic: yes
- is sensitive: no
- is resistant: yes
metabolite production
@ref | Chebi-ID | metabolite | production |
---|---|---|---|
68369 | 35581 | indole | no |
120689 | 35581 | indole | no |
metabolite tests
- @ref: 68369
- Chebi-ID: 35581
- metabolite: indole
- indole test: -
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 |
120689 | oxidase | + | |
120689 | beta-galactosidase | + | 3.2.1.23 |
120689 | alcohol dehydrogenase | - | 1.1.1.1 |
120689 | gelatinase | - | |
120689 | amylase | - | |
120689 | DNase | - | |
120689 | caseinase | - | 3.4.21.50 |
120689 | catalase | + | 1.11.1.6 |
120689 | tween esterase | - | |
120689 | lecithinase | - | |
120689 | lipase | - | |
120689 | lysine decarboxylase | - | 4.1.1.18 |
120689 | ornithine decarboxylase | - | 4.1.1.17 |
120689 | phenylalanine ammonia-lyase | - | 4.3.1.24 |
120689 | tryptophan deaminase | - | |
120689 | 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 |
fatty acid profile
fatty acids
@ref fatty acid percentage ECL 53991 C12:0 6.9 12 53991 C14:0 1 14 53991 C16:0 18 16 53991 C18:0 0.2 18 53991 C10:0 3OH 3.8 11.423 53991 C12:0 2OH 3.2 13.178 53991 C12:0 3OH 3.5 13.455 53991 C16:1 ω7c 23.3 15.819 53991 C18:1 ω7c /12t/9t 39.7 17.824 53991 C19:0 CYCLO ω8c 0.3 18.9 - type of FA analysis: whole cell analysis
- method/protocol: CCUG
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 |
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
120689 | - | + | + | + | - | + | + | - | + | - | + | + | - | - | + | - | + | - | - | - |
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 |
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
2931 | + | - | - | + | - | + | - | + | + | + | + | + | - | + | + | + | - | + | + | - | + |
2931 | + | - | - | + | - | + | - | + | + | + | + | + | - | + | + | + | - | + | + | - | + |
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 |
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
120689 | + | + | + | + | + | - | - | - | - | + | + | - | - | - | - | - | - | - | + | + | + | + | - | + | + | - | + | - | - | - | - | + | + | + | - | - | - | - | - | + | - | - | - | + | + | - | - | + | + | + | + | + | - | + | + | + | + | - | - | - | + | - | + | + | + | - | - | - | - | - | - | + | - | + | - | + | + | + | - | + | + | - | + | - | - | - | + | - | + | + | + | + | + | + | + | + | + | + | - |
Isolation, sampling and environmental information
isolation
@ref | sample type |
---|---|
2931 | human wound |
53991 | Human wound |
120689 | Human, Wound |
isolation source categories
Cat1 | Cat2 | Cat3 |
---|---|---|
#Host | #Human | |
#Host Body-Site | #Other | #Wound |
taxonmaps
- @ref: 69479
- File name: preview.99_1236.png
- url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_23;96_224;97_842;98_978;99_1236&stattab=map
- Last taxonomy: Pseudomonas
- 16S sequence: D84002
- Sequence Identity:
- Total samples: 23564
- soil counts: 2524
- aquatic counts: 6287
- animal counts: 12446
- plant counts: 2307
Safety information
risk assessment
@ref | biosafety level | biosafety level comment |
---|---|---|
2931 | 2 | Risk group (German classification) |
120689 | 1 | Risk group (French classification) |
Sequence information
16S sequences
@ref | description | accession | length | database | NCBI tax ID |
---|---|---|---|---|---|
20218 | Pseudomonas luteola gene for 16S rRNA, complete sequence, strain: IAM 13000 | D84002 | 1527 | ena | 47886 |
20218 | Pseudomonas luteola gene for 16S rRNA, partial sequence, strain: NBRC 103146 | AB681955 | 1462 | ena | 47886 |
Genome sequences
@ref | description | accession | assembly level | database | NCBI tax ID |
---|---|---|---|---|---|
66792 | Pseudomonas luteola NBRC 103146 | GCA_002091675 | contig | ncbi | 1215106 |
66792 | Pseudomonas luteola NBRC 103146 strain NBRC 103146 | 1215106.3 | wgs | patric | 1215106 |
66792 | Pseudomonas luteola NBRC 103146 | 2806311027 | draft | img | 1215106 |
66792 | Pseudomonas luteola JCM 3352 | 2663762783 | draft | img | 47886 |
GC content
- @ref: 2931
- GC-content: 55.4
- method: thermal denaturation, midpoint method (Tm)
Genome-based predictions
predictions
trait | prediction | confidence | training_data |
---|---|---|---|
spore-forming | no | 84 | no |
motile | yes | 85.943 | no |
gram-positive | no | 98.437 | no |
anaerobic | no | 98.296 | no |
aerobic | yes | 92.178 | no |
halophile | no | 92.522 | no |
spore-forming | no | 94.601 | no |
thermophile | no | 99.449 | yes |
glucose-util | yes | 94.942 | yes |
flagellated | no | 55.846 | no |
glucose-ferment | no | 88.917 | yes |
External links
@ref: 2931
culture collection no.: DSM 6975, ATCC 43273, IAM 1300, JCM 3352, CCUG 37974, LMG 7041, IAM 13000, CIP 102995, LMG 8814, NBRC 103146
straininfo link
- @ref: 82256
- straininfo: 1747
literature
topic | Pubmed-ID | title | authors | journal | DOI | year | mesh | topic2 |
---|---|---|---|---|---|---|---|---|
Phylogeny | 15774686 | Pseudomonas pachastrellae sp. nov., isolated from a marine sponge. | Romanenko LA, Uchino M, Falsen E, Frolova GM, Zhukova NV, Mikhailov VV | Int J Syst Evol Microbiol | 10.1099/ijs.0.63176-0 | 2005 | Animals, Bacterial Typing Techniques, DNA, Bacterial, DNA, Ribosomal/analysis, Genes, rRNA, Molecular Sequence Data, Phenotype, Phylogeny, Porifera/*microbiology, Pseudomonas/*classification/genetics/isolation & purification/physiology, RNA, Ribosomal, 16S/genetics, Seawater, Sequence Analysis, DNA, Species Specificity | Genetics |
Phylogeny | 18523186 | Pseudomonas duriflava sp. nov., isolated from a desert soil. | Liu R, Liu H, Feng H, Wang X, Zhang CX, Zhang KY, Lai R | Int J Syst Evol Microbiol | 10.1099/ijs.0.65716-0 | 2008 | Bacterial Typing Techniques, Base Composition, China, DNA, Bacterial, DNA, Ribosomal, *Desert Climate, Fatty Acids/analysis, Genes, rRNA, Molecular Sequence Data, Nucleic Acid Hybridization, Phenotype, Phylogeny, Pseudomonas/*classification/genetics/*isolation & purification/physiology, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, *Soil Microbiology, Species Specificity | Genetics |
Phylogeny | 22199212 | Pseudomonas zeshuii sp. nov., isolated from herbicide-contaminated soil. | Feng Z, Zhang J, Huang X, Zhang J, Chen M, Li S | Int J Syst Evol Microbiol | 10.1099/ijs.0.037796-0 | 2011 | Bacterial Typing Techniques, Base Composition, China, DNA, Bacterial/genetics, Fatty Acids/analysis, Herbicides, Molecular Sequence Data, Nucleic Acid Hybridization, Phospholipids/analysis, *Phylogeny, Pseudomonas/*classification/genetics/isolation & purification, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, *Soil Microbiology, Soil Pollutants, Ubiquinone/analysis | Genetics |
Reference
@id | authors | catalogue | doi/url | title | journal | pubmed |
---|---|---|---|---|---|---|
2931 | Curators of the DSMZ | Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 6975) | https://www.dsmz.de/collection/catalogue/details/culture/DSM-6975 | |||
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 | |
33753 | Curators of the CIP | https://brclims.pasteur.fr/brcWeb/souche/detail/1/14742 | ||||
53991 | Curators of the CCUG | Culture Collection University of Gothenburg (CCUG) (CCUG 37974) | https://www.ccug.se/strain?id=37974 | |||
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 | |||||
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) | |||
82256 | Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J. | 10.60712/SI-ID1747.1 | StrainInfo: A central database for resolving microbial strain identifiers | |||
120689 | Curators of the CIP | Collection of Institut Pasteur (CIP 102995) | https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20102995 |