Strain identifier
BacDive ID: 17505
Type strain:
Species: Pseudoxanthomonas japonensis
Strain Designation: 12-3
Strain history: CIP <- 2002, H. Macarie, IRD, Marseille, France: strain 12-3 <- Takashi Iizuka, Ajonomoto Co., Japan
NCBI tax ID(s): 69284 (species)
General
@ref: 6763
BacDive-ID: 17505
DSM-Number: 17109
keywords: genome sequence, 16S sequence, Bacteria, aerobe, mesophilic, Gram-negative, motile, rod-shaped
description: Pseudoxanthomonas japonensis 12-3 is an aerobe, mesophilic, Gram-negative bacterium that was isolated from polluted urban soil.
NCBI tax id
- NCBI tax id: 69284
- Matching level: species
strain history
@ref | history |
---|---|
6763 | <- H. Macarie, IRD, Marseille; 12-3 <- T. Iizuka |
67770 | T. Iizuka 12-3. |
120311 | CIP <- 2002, H. Macarie, IRD, Marseille, France: strain 12-3 <- Takashi Iizuka, Ajonomoto Co., Japan |
doi: 10.13145/bacdive17505.20230509.8.1
Name and taxonomic classification
LPSN
- @ref: 20215
- description: domain/bacteria
- keyword: phylum/pseudomonadota
- domain: Bacteria
- phylum: Pseudomonadota
- class: Gammaproteobacteria
- order: Lysobacterales
- family: Lysobacteraceae
- genus: Pseudoxanthomonas
- species: Pseudoxanthomonas japonensis
- full scientific name: Pseudoxanthomonas japonensis Thierry et al. 2004
@ref: 6763
domain: Bacteria
phylum: Proteobacteria
class: Gammaproteobacteria
order: Xanthomonadales
family: Lysobacteraceae
genus: Pseudoxanthomonas
species: Pseudoxanthomonas japonensis
full scientific name: Pseudoxanthomonas japonensis Thierry et al. 2004
strain designation: 12-3
type strain: yes
Morphology
cell morphology
@ref | gram stain | cell length | cell width | cell shape | motility | confidence |
---|---|---|---|---|---|---|
29999 | negative | 1.2 µm | 0.6 µm | rod-shaped | yes | |
69480 | yes | 97.1 | ||||
69480 | negative | 99.988 | ||||
120311 | negative | rod-shaped | yes |
pigmentation
- @ref: 120311
- production: no
- name: Pyocyanin
Culture and growth conditions
culture medium
@ref | name | growth | link | composition |
---|---|---|---|---|
6763 | CASO AGAR (MERCK 105458) (DSMZ Medium 220) | yes | https://mediadive.dsmz.de/medium/220 | Name: CASO AGAR (Merck 105458) (DSMZ Medium 220) Composition: Agar 15.0 g/l Casein peptone 15.0 g/l NaCl 5.0 g/l Soy peptone 5.0 g/l Distilled water |
38171 | MEDIUM 72- for trypto casein soja agar | yes | Distilled water make up to (1000.000 ml);Trypto casein soy agar (40.000 g) | |
120311 | CIP Medium 72 | yes | https://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=72 |
culture temp
@ref | growth | type | temperature | range |
---|---|---|---|---|
6763 | positive | growth | 30 | mesophilic |
29999 | positive | growth | 10-37 | |
29999 | positive | optimum | 33.5 | mesophilic |
38171 | positive | growth | 30 | mesophilic |
67770 | positive | growth | 30 | mesophilic |
120311 | positive | growth | 25-37 | mesophilic |
120311 | no | growth | 10 | psychrophilic |
120311 | no | growth | 41 | thermophilic |
culture pH
@ref | ability | type | pH | PH range |
---|---|---|---|---|
29999 | positive | growth | 6.2-9.5 | alkaliphile |
29999 | positive | optimum | 8 |
Physiology and metabolism
oxygen tolerance
@ref | oxygen tolerance |
---|---|
29999 | aerobe |
120311 | obligate aerobe |
spore formation
@ref | spore formation | confidence |
---|---|---|
29999 | no | |
69481 | no | 98 |
69480 | no | 99.995 |
halophily
@ref | salt | growth | tested relation | concentration |
---|---|---|---|---|
29999 | NaCl | positive | growth | 0-3 % |
120311 | NaCl | positive | growth | 0-2 % |
120311 | NaCl | no | growth | 4 % |
120311 | NaCl | no | growth | 6 % |
120311 | NaCl | no | growth | 8 % |
120311 | NaCl | no | growth | 10 % |
observation
- @ref: 67770
- observation: quinones: Q-8
metabolite utilization
@ref | Chebi-ID | metabolite | utilization activity | kind of utilization tested |
---|---|---|---|---|
29999 | 35391 | aspartate | + | carbon source |
29999 | 17057 | cellobiose | + | carbon source |
29999 | 28260 | galactose | + | carbon source |
29999 | 17234 | glucose | + | carbon source |
29999 | 29987 | glutamate | + | carbon source |
29999 | 27570 | histidine | + | carbon source |
29999 | 17306 | maltose | + | carbon source |
29999 | 17822 | serine | + | carbon source |
29999 | 27082 | trehalose | + | carbon source |
29999 | 18222 | xylose | + | carbon source |
29999 | 4853 | esculin | + | hydrolysis |
120311 | 4853 | esculin | + | hydrolysis |
120311 | 17632 | nitrate | - | reduction |
120311 | 16301 | nitrite | + | reduction |
120311 | 17632 | nitrate | - | respiration |
antibiotic resistance
- @ref: 120311
- metabolite: 0129 (2,4-Diamino-6,7-di-iso-propylpteridine phosphate)
- is antibiotic: yes
- is sensitive: no
- is resistant: yes
metabolite production
- @ref: 120311
- Chebi-ID: 35581
- metabolite: indole
- production: no
enzymes
@ref | value | activity | ec |
---|---|---|---|
29999 | catalase | + | 1.11.1.6 |
29999 | cytochrome oxidase | + | 1.9.3.1 |
120311 | oxidase | - | |
120311 | beta-galactosidase | + | 3.2.1.23 |
120311 | alcohol dehydrogenase | - | 1.1.1.1 |
120311 | gelatinase | + | |
120311 | amylase | - | |
120311 | DNase | + | |
120311 | caseinase | + | 3.4.21.50 |
120311 | catalase | - | 1.11.1.6 |
120311 | tween esterase | + | |
120311 | lecithinase | - | |
120311 | lipase | - | |
120311 | lysine decarboxylase | - | 4.1.1.18 |
120311 | ornithine decarboxylase | - | 4.1.1.17 |
120311 | tryptophan deaminase | - | |
120311 | 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 |
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 |
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
120311 | - | + | + | + | - | + | - | - | + | + | - | + | - | - | + | - | + | - | - | - |
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 |
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
120311 | + | - | + | + | - | - | - | - | - | + | + | - | + | - | - | + | - | - | + | - | - | + | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | + | - | - | - | - | - | - | - | - | - | + | - | - | + | - | - | + | - | - | - | - | - | - | - | + | - | + | - | - | - | + | + | - | - | - | - | - | + | - | + | + | + | - | - | - | + | - | + | + | - |
Isolation, sampling and environmental information
isolation
@ref | sample type | geographic location | country | origin.country | continent | isolation date |
---|---|---|---|---|---|---|
6763 | polluted urban soil | Tokyo area | Japan | JPN | Asia | |
58048 | Soil,urban,polluted | Japan | JPN | Asia | ||
67770 | Polluted urban soil, collected at the riverside of the Tamagawa River | Tokyo metropolitan area | Japan | JPN | Asia | |
120311 | Environment, Polluted urban soil | Tokyo | Japan | JPN | Asia | 1994 |
isolation source categories
Cat1 | Cat2 | Cat3 |
---|---|---|
#Engineered | #Contamination | |
#Environmental | #Terrestrial | #Soil |
taxonmaps
- @ref: 69479
- File name: preview.99_4236.png
- url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_17;96_856;97_2573;98_3190;99_4236&stattab=map
- Last taxonomy: Pseudoxanthomonas
- 16S sequence: AB008507
- Sequence Identity:
- Total samples: 20716
- soil counts: 5760
- aquatic counts: 7508
- animal counts: 5790
- plant counts: 1658
Safety information
risk assessment
@ref | biosafety level | biosafety level comment |
---|---|---|
6763 | 1 | Risk group (German classification) |
120311 | 1 | Risk group (French classification) |
Sequence information
16S sequences
- @ref: 6763
- description: Pseudoxanthomonas japonensis gene for 16S rRNA, partial sequence, strain: 12-3
- accession: AB008507
- length: 1464
- database: ena
- NCBI tax ID: 69284
Genome sequences
@ref | description | accession | assembly level | database | NCBI tax ID |
---|---|---|---|---|---|
66792 | Pseudoxanthomonas japonensis strain DSM 17109 | 69284.4 | wgs | patric | 69284 |
67770 | Pseudoxanthomonas japonensis DSM 17109 | GCA_010093445 | contig | ncbi | 69284 |
GC content
@ref | GC-content | method |
---|---|---|
29999 | 65.2 | |
67770 | 64.2-66.2 | high performance liquid chromatography (HPLC) |
Genome-based predictions
predictions
trait | prediction | confidence | training_data |
---|---|---|---|
spore-forming | no | 98 | no |
gram-positive | no | 98.691 | no |
anaerobic | no | 97.998 | yes |
halophile | no | 95.943 | no |
spore-forming | no | 96.001 | yes |
glucose-util | yes | 91.073 | yes |
thermophile | no | 99.143 | yes |
flagellated | no | 79.842 | no |
aerobic | yes | 94.299 | no |
glucose-ferment | no | 90.729 | no |
motile | yes | 88.057 | yes |
External links
@ref: 6763
culture collection no.: DSM 17109, CCUG 48231, CIP 107388, JCM 11525, AJ 13070
straininfo link
- @ref: 86502
- straininfo: 134448
literature
topic | Pubmed-ID | title | authors | journal | DOI | year | mesh | topic2 |
---|---|---|---|---|---|---|---|---|
Phylogeny | 15545466 | Pseudoxanthomonas mexicana sp. nov. and Pseudoxanthomonas japonensis sp. nov., isolated from diverse environments, and emended descriptions of the genus Pseudoxanthomonas Finkmann et al. 2000 and of its type species. | Thierry S, Macarie H, Iizuka T, Geissdorfer W, Assih EA, Spanevello M, Verhe F, Thomas P, Fudou R, Monroy O, Labat M, Ouattara AS | Int J Syst Evol Microbiol | 10.1099/ijs.0.02810-0 | 2004 | Aerobiosis, Anti-Bacterial Agents/pharmacology, Bacterial Typing Techniques, Base Composition, Bioreactors/*microbiology, Carbohydrate Metabolism, DNA, Bacterial/chemistry/isolation & purification, DNA, Ribosomal/chemistry/isolation & purification, Fatty Acids/analysis/isolation & purification, Flagella, Genes, rRNA, Gentian Violet, Humans, Molecular Sequence Data, Movement, Nitrites/metabolism, Nucleic Acid Hybridization, Oxygen/metabolism, Phenazines, Phylogeny, RNA, Bacterial/genetics, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, *Soil Microbiology, Spores, Bacterial/cytology, Stenotrophomonas/genetics, Ubiquinone/analysis/isolation & purification, Urine/*microbiology, Xanthomonadaceae/*classification/cytology/*isolation & purification/physiology, Xanthomonas/genetics | Enzymology |
Phylogeny | 15774663 | Pseudoxanthomonas koreensis sp. nov. and Pseudoxanthomonas daejeonensis sp. nov. | Yang DC, Im WT, Kim MK, Lee ST | Int J Syst Evol Microbiol | 10.1099/ijs.0.63210-0 | 2005 | Bacterial Typing Techniques, DNA, Bacterial/analysis, DNA, Ribosomal/analysis, Fatty Acids/analysis, Genes, rRNA, Korea, Molecular Sequence Data, Panax/growth & development, Phenotype, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, *Soil Microbiology, Species Specificity, Xanthomonadaceae/chemistry/*classification/genetics/isolation & purification | Genetics |
Phylogeny | 20870889 | Pseudoxanthomonas indica sp. nov., isolated from a hexachlorocyclohexane dumpsite. | Kumari K, Sharma P, Tyagi K, Lal R | Int J Syst Evol Microbiol | 10.1099/ijs.0.017624-0 | 2010 | Bacterial Typing Techniques, Base Composition, Cluster Analysis, DNA, Bacterial/chemistry/genetics, DNA, Ribosomal/chemistry/genetics, Environmental Pollutants/*metabolism, Fatty Acids/analysis, Hexachlorocyclohexane/*metabolism, Molecular Sequence Data, Nucleic Acid Hybridization, Phospholipids/analysis, Phylogeny, Quinones/analysis, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Soil Microbiology, Xanthomonadaceae/*classification/*isolation & purification/metabolism | Metabolism |
Phylogeny | 28598308 | Pseudoxanthomonas putridarboris sp. nov. isolated from rotten tree. | Lee JK, Oh JS, Cho WD, Roh DH | Int J Syst Evol Microbiol | 10.1099/ijsem.0.001867 | 2017 | Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, Fatty Acids/chemistry, Nucleic Acid Hybridization, Phospholipids/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, Republic of Korea, Sequence Analysis, DNA, Ubiquinone/chemistry, Wood/*microbiology, Xanthomonadaceae/*classification/genetics/isolation & purification | Transcriptome |
Reference
@id | authors | catalogue | doi/url | title | ID_cross_reference | pubmed |
---|---|---|---|---|---|---|
6763 | Curators of the DSMZ | Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 17109) | https://www.dsmz.de/collection/catalogue/details/culture/DSM-17109 | |||
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 | |||
29999 | 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 | 26364 | 28776041 | |
38171 | Curators of the CIP | https://brclims.pasteur.fr/brcWeb/souche/detail/1/4818 | ||||
58048 | Curators of the CCUG | Culture Collection University of Gothenburg (CCUG) (CCUG 48231) | https://www.ccug.se/strain?id=48231 | |||
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 | |||
86502 | Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J. | 10.60712/SI-ID134448.1 | StrainInfo: A central database for resolving microbial strain identifiers | |||
120311 | Curators of the CIP | Collection of Institut Pasteur (CIP 107388) | https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20107388 |