Strain identifier

BacDive ID: 17505

Type strain: Yes

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)

For citation purpose refer to the digital object identifier (doi) of the current version.
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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

@refhistory
6763<- H. Macarie, IRD, Marseille; 12-3 <- T. Iizuka
67770T. Iizuka 12-3.
120311CIP <- 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

@refgram staincell lengthcell widthcell shapemotilityconfidence
29999negative1.2 µm0.6 µmrod-shapedyes
69480yes97.1
69480negative99.988
120311negativerod-shapedyes

pigmentation

  • @ref: 120311
  • production: no
  • name: Pyocyanin

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
6763CASO AGAR (MERCK 105458) (DSMZ Medium 220)yeshttps://mediadive.dsmz.de/medium/220Name: 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
38171MEDIUM 72- for trypto casein soja agaryesDistilled water make up to (1000.000 ml);Trypto casein soy agar (40.000 g)
120311CIP Medium 72yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=72

culture temp

@refgrowthtypetemperaturerange
6763positivegrowth30mesophilic
29999positivegrowth10-37
29999positiveoptimum33.5mesophilic
38171positivegrowth30mesophilic
67770positivegrowth30mesophilic
120311positivegrowth25-37mesophilic
120311nogrowth10psychrophilic
120311nogrowth41thermophilic

culture pH

@refabilitytypepHPH range
29999positivegrowth6.2-9.5alkaliphile
29999positiveoptimum8

Physiology and metabolism

oxygen tolerance

@refoxygen tolerance
29999aerobe
120311obligate aerobe

spore formation

@refspore formationconfidence
29999no
69481no98
69480no99.995

halophily

@refsaltgrowthtested relationconcentration
29999NaClpositivegrowth0-3 %
120311NaClpositivegrowth0-2 %
120311NaClnogrowth4 %
120311NaClnogrowth6 %
120311NaClnogrowth8 %
120311NaClnogrowth10 %

observation

  • @ref: 67770
  • observation: quinones: Q-8

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
2999935391aspartate+carbon source
2999917057cellobiose+carbon source
2999928260galactose+carbon source
2999917234glucose+carbon source
2999929987glutamate+carbon source
2999927570histidine+carbon source
2999917306maltose+carbon source
2999917822serine+carbon source
2999927082trehalose+carbon source
2999918222xylose+carbon source
299994853esculin+hydrolysis
1203114853esculin+hydrolysis
12031117632nitrate-reduction
12031116301nitrite+reduction
12031117632nitrate-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

@refvalueactivityec
29999catalase+1.11.1.6
29999cytochrome oxidase+1.9.3.1
120311oxidase-
120311beta-galactosidase+3.2.1.23
120311alcohol dehydrogenase-1.1.1.1
120311gelatinase+
120311amylase-
120311DNase+
120311caseinase+3.4.21.50
120311catalase-1.11.1.6
120311tween esterase+
120311lecithinase-
120311lipase-
120311lysine decarboxylase-4.1.1.18
120311ornithine decarboxylase-4.1.1.17
120311tryptophan deaminase-
120311urease-3.5.1.5
68382alkaline phosphatase+3.1.3.1
68382esterase (C 4)+
68382esterase lipase (C 8)+
68382lipase (C 14)-
68382leucine arylamidase+3.4.11.1
68382valine arylamidase-
68382cystine arylamidase-3.4.11.3
68382trypsin+3.4.21.4
68382alpha-chymotrypsin+3.4.21.1
68382acid phosphatase-3.1.3.2
68382naphthol-AS-BI-phosphohydrolase+
68382alpha-galactosidase-3.2.1.22
68382beta-galactosidase-3.2.1.23
68382beta-glucuronidase+3.2.1.31
68382alpha-glucosidase-3.2.1.20
68382beta-glucosidase+3.2.1.21
68382N-acetyl-beta-glucosaminidase-3.2.1.52
68382alpha-mannosidase-3.2.1.24
68382alpha-fucosidase-3.2.1.51

API zym

@refControlAlkaline phosphataseEsteraseEsterase LipaseLipaseLeucine arylamidaseValine arylamidaseCystine arylamidaseTrypsinalpha- ChymotrypsinAcid phosphataseNaphthol-AS-BI-phosphohydrolasealpha- Galactosidasebeta- Galactosidasebeta- Glucuronidasealpha- Glucosidasebeta- GlucosidaseN-acetyl-beta- glucosaminidasealpha- Mannosidasealpha- Fucosidase
120311-+++-+--++-+--+-+---

API biotype100

@refGLUFRUGALTREMNESBEMELSACRAFMTEMALLACLTEMbGaMaGaCELGENMbGuESCRIBARAXYLPLERHAFUCMLZDARLLARLXLTDULTAGGLYINOMANMTLTURSORADOHBGLYXERYMDG3MDGSATMUCLTATDTATMTATDMLTLMLTCATETATETTECITGRTGAT2KG5KGTRYNAGGNTPACPATpOBEQATGTEmOBEBATPPATCMTTGEBETPCEABTHINLATCAPCYTHISSUCFUMGREGYTAVTETNTTNGLNITA3OBUAPTGTTPRODALALALASERMNTPROPTYR2KT
120311+-++-----++-+--+--+--+---------------------------+---------+--+--+-------+-+---++-----+-+++---+-++-

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinentisolation date
6763polluted urban soilTokyo areaJapanJPNAsia
58048Soil,urban,pollutedJapanJPNAsia
67770Polluted urban soil, collected at the riverside of the Tamagawa RiverTokyo metropolitan areaJapanJPNAsia
120311Environment, Polluted urban soilTokyoJapanJPNAsia1994

isolation source categories

Cat1Cat2Cat3
#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

@refbiosafety levelbiosafety level comment
67631Risk group (German classification)
1203111Risk 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

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Pseudoxanthomonas japonensis strain DSM 1710969284.4wgspatric69284
67770Pseudoxanthomonas japonensis DSM 17109GCA_010093445contigncbi69284

GC content

@refGC-contentmethod
2999965.2
6777064.2-66.2high performance liquid chromatography (HPLC)

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno98no
gram-positiveno98.691no
anaerobicno97.998yes
halophileno95.943no
spore-formingno96.001yes
glucose-utilyes91.073yes
thermophileno99.143yes
flagellatedno79.842no
aerobicyes94.299no
glucose-fermentno90.729no
motileyes88.057yes

External links

@ref: 6763

culture collection no.: DSM 17109, CCUG 48231, CIP 107388, JCM 11525, AJ 13070

straininfo link

  • @ref: 86502
  • straininfo: 134448

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny15545466Pseudoxanthomonas 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 ASInt J Syst Evol Microbiol10.1099/ijs.0.02810-02004Aerobiosis, 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/geneticsEnzymology
Phylogeny15774663Pseudoxanthomonas koreensis sp. nov. and Pseudoxanthomonas daejeonensis sp. nov.Yang DC, Im WT, Kim MK, Lee STInt J Syst Evol Microbiol10.1099/ijs.0.63210-02005Bacterial 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 & purificationGenetics
Phylogeny20870889Pseudoxanthomonas indica sp. nov., isolated from a hexachlorocyclohexane dumpsite.Kumari K, Sharma P, Tyagi K, Lal RInt J Syst Evol Microbiol10.1099/ijs.0.017624-02010Bacterial 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/metabolismMetabolism
Phylogeny28598308Pseudoxanthomonas putridarboris sp. nov. isolated from rotten tree.Lee JK, Oh JS, Cho WD, Roh DHInt J Syst Evol Microbiol10.1099/ijsem.0.0018672017Bacterial 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 & purificationTranscriptome

Reference

@idauthorscataloguedoi/urltitleID_cross_referencepubmed
6763Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 17109)https://www.dsmz.de/collection/catalogue/details/culture/DSM-17109
20215Parte, A.C., Sardà Carbasse, J., Meier-Kolthoff, J.P., Reimer, L.C. and Göker, M.10.1099/ijsem.0.004332List of Prokaryotic names with Standing in Nomenclature (LPSN) moves to the DSMZ
29999Barberan A, Caceres Velazquez H, Jones S, Fierer N.10.1128/mSphere.00237-17Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information2636428776041
38171Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/4818
58048Curators of the CCUGCulture Collection University of Gothenburg (CCUG) (CCUG 48231)https://www.ccug.se/strain?id=48231
66792Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmannhttps://diaspora-project.de/progress.html#genomesAutomatically annotated for the DiASPora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information)
67770Curators of the JCMhttps://jcm.brc.riken.jp/en/
68382Automatically annotated from API zym
69479João 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
69480Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmannhttps://diaspora-project.de/progress.html#genomesPredictions based on genome sequence made in the Diaspora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information)
69481Xiao-Yin To, René Mreches, Martin Binder, Alice C. McHardy, Philipp C. Münch10.21203/rs.3.rs-2527258/v1Predictions based on the model GenomeNet Sporulation v. 1
86502Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID134448.1StrainInfo: A central database for resolving microbial strain identifiers
120311Curators of the CIPCollection of Institut Pasteur (CIP 107388)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20107388