Strain identifier

BacDive ID: 17628

Type strain: Yes

Species: Patulibacter minatonensis

Strain Designation: KV-614

Strain history: CIP <- 2006, JCM <- 2004, S. Omura, Kitasato Univ., Tokyo, Japan: strain KV-614

NCBI tax ID(s): 929712 (strain), 298163 (species)

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General

@ref: 7382

BacDive-ID: 17628

DSM-Number: 18081

keywords: genome sequence, 16S sequence, Bacteria, aerobe, mesophilic, Gram-positive, motile, rod-shaped

description: Patulibacter minatonensis KV-614 is an aerobe, mesophilic, Gram-positive bacterium that was isolated from soil.

NCBI tax id

NCBI tax idMatching level
298163species
929712strain

strain history

@refhistory
7382<- JCM <- S. Omura
67770S. ?mura KV-614.
120957CIP <- 2006, JCM <- 2004, S. Omura, Kitasato Univ., Tokyo, Japan: strain KV-614

doi: 10.13145/bacdive17628.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/actinomycetota
  • domain: Bacteria
  • phylum: Actinomycetota
  • class: Thermoleophilia
  • order: Solirubrobacterales
  • family: Patulibacteraceae
  • genus: Patulibacter
  • species: Patulibacter minatonensis
  • full scientific name: Patulibacter minatonensis Takahashi et al. 2006

@ref: 7382

domain: Bacteria

phylum: Actinobacteria

class: Thermoleophilia

order: Solirubrobacterales

family: Patulibacteraceae

genus: Patulibacter

species: Patulibacter minatonensis

full scientific name: Patulibacter minatonensis Takahashi et al. 2006 emend. Nouioui et al. 2018

strain designation: KV-614

type strain: yes

Morphology

cell morphology

@refgram staincell lengthcell widthcell shapemotilityconfidence
31552positive1.2-1.5 µm0.6-0.7 µmrod-shapedyes
69480positive97.71
120957positiverod-shapedno

colony morphology

@refcolony colorincubation periodmedium used
18411Colorless10-14 daysISP 2
18411Colorless10-14 daysISP 3
18411Colorless10-14 daysISP 4
18411Colorless10-14 daysISP 5
18411Colorless10-14 daysISP 7

multicellular morphology

@refforms multicellular complexmedium name
18411noISP 2
18411noISP 3
18411noISP 4
18411noISP 5
18411noISP 7

pigmentation

  • @ref: 31552
  • production: yes

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
7382R2A MEDIUM (DSMZ Medium 830)yeshttps://mediadive.dsmz.de/medium/830Name: R2A MEDIUM (DSMZ Medium 830) Composition: Agar 15.0 g/l Casamino acids 0.5 g/l Starch 0.5 g/l Glucose 0.5 g/l Proteose peptone 0.5 g/l Yeast extract 0.5 g/l K2HPO4 0.3 g/l Na-pyruvate 0.3 g/l MgSO4 x 7 H2O 0.05 g/l Distilled water
18411ISP 2yesName: ISP 2 / Yeast Malt Agar (5265); 5265 Composition Malt extract 10.0 g/l Yeast extract 4.0 g/l Glucose 4.0 g/l Agar 15.0 g/l Preparation: Sterilisation: 20 minutes at 121°C pH before sterilisation: 7.0 Usage: Maintenance and Taxonomy Organisms: All Actinomycetes
18411ISP 3yesName: ISP 3; 5315 Composition Dog oat flakes 20.0 g/l Trace element solution (5314) 2.5 ml/l Agar 18.0 g/l Preparation: Oat flakes are cooked for 20 minutes, trace element solution and agar are added (in the case of non rolled oat flakes the suspension has to bee filtrated). Sterilisation: 20 minutes at 121°C pH before sterilisation: 7.8 Usage: Maintenance and taxonomy (e.g. SEM As liquid medium for metabolite production) Organisms: All Actinomycetes Trace element solution 5314 Name: Trace element solution 5314; 5314 Composition CaCl2 x H2O 3.0 g/l Fe-III-citrate 1.0 g/l MnSO4 0.2 g/l ZnCl2 0.1 g/l CuSO4 x 5 H2O 0.025 g/l Sodium tetra borate 0.2 g/l CoCl2 x 6 H2O 0.004 g/l Sodium molybdate 0.01 g/l Preparation: Use double destillated water. Sterilisation: 20 minutes at 121°C pH before sterilisation: Usage: Trace element solution for different media Organisms:
18411ISP 4yesName: ISP 4; DSM 547 Solution I: Difco soluble starch, 10.0 g. Make a paste of the starch with a small amount of cold distilled water and bring to a volume of 500 ml. Solution II: CaCO3 2.0 g K2HPO4 (anhydrous) 1.0 g MgSO4 x 7 H2O 1.0 g NaCl 1.0 g (NH4)2SO4 2.0 g Distilled water 500.0 ml Trace salt solution (see below) 1.0 ml The pH should be between 7.0 and 7.4. Do not adjust if it is within this range. Mix solutions I and II together. Add 20.0 g agar. Liquify agar by steaming at 100°C for 10 to 20 min. Trace element solution: FeSO4 x 7 H2O 0.1 g MnCl2 x 4 H2O 0.1 g ZnSO4 x 7 H2O 0.1 g Distilled water 100.0 ml
18411ISP 5yesName: ISP 5 (5323) Composition L-Asparagine 1.0 g/l Glycerol 10.0 g/l K2HPO4 1.0 g/l Salt solution (see preparation) 1.0 ml/l Agar 20.0 g/l Preparation: Salt solution 1.0 g FeSO4 x 7 H2O 1.0 g MnCl2 x 4 H2O 1.0 g ZNSO4 x 7 H2O in 100 ml water Sterilisation: 20 minutes at 121°C pH before sterilisation: 7.2 Usage: Maintenance and taxonomy Organisms: All Actinomycetes
18411ISP 7yesName: ISP 7 (5322) Composition Glycerol 15.0 g/l L-Tyrosine 0.5 g/l L-Asparagine 1.0 g/l K2HPO4 0.5 g/l NaCl 0.5 g/l FeSO4 x 7 H2O 0.01 g/l Trace element solution 5343 1.0 ml/l Agar 20.0 Sterilisation: 20 minutes at 121°C pH before sterilisation: 7.3 Usage: Production of melanoid pigments Organisms: All Actinomycetes
37470MEDIUM 112 - for JanibacteryesDistilled water make up to (1000.000 ml);Magnesium sulphate heptahydrate (1.000 g);Agar (20.000 g);Yeast extract (5.000 g);Peptone (10.000 g);Tween 80 (50.000 mg);Glycerol (2.000 g);Malt extract (5.000 g);Beef extract (2.000 g);Casamino acids (5.000 g);Ca
120957CIP Medium 112yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=112

culture temp

@refgrowthtypetemperaturerange
7382positivegrowth25mesophilic
18411positiveoptimum28mesophilic
31552positivegrowth16-28
31552positiveoptimum24-27
37470positivegrowth25mesophilic
67770positivegrowth25mesophilic

culture pH

@refabilitytypepH
31552positivegrowth06-08
31552positiveoptimum7

Physiology and metabolism

oxygen tolerance

@refoxygen tolerance
31552aerobe
120957obligate aerobe

spore formation

@refspore formationconfidence
31552no
69480no99.986

halophily

@refsaltgrowthtested relationconcentration
31552NaClpositivegrowth0-1 %
31552NaClpositiveoptimum0-1 %

observation

@refobservation
31552aggregates in chains
67770quinones: DMK-7

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
3155222599arabinose+carbon source
3155218403L-arabitol+carbon source
3155217057cellobiose+carbon source
3155223652dextrin+carbon source
3155228757fructose+carbon source
3155233984fucose+carbon source
3155217234glucose+carbon source
3155224996lactate+carbon source
3155217306maltose+carbon source
3155237684mannose+carbon source
3155226546rhamnose+carbon source
3155217814salicin+carbon source
3155217632nitrate+reduction
12095717632nitrate-reduction
12095716301nitrite-reduction
6837917632nitrate-reduction
683794853esculin-hydrolysis
6837916199urea-hydrolysis
683795291gelatin-hydrolysis
6837917634D-glucose-fermentation
6837916988D-ribose-fermentation
6837965327D-xylose-fermentation
6837916899D-mannitol-fermentation
6837917306maltose-fermentation
6837917716lactose-fermentation
6837917992sucrose-fermentation
6837928087glycogen-fermentation

metabolite production

  • @ref: 120957
  • Chebi-ID: 35581
  • metabolite: indole
  • production: no

enzymes

@refvalueactivityec
31552catalase+1.11.1.6
68379gelatinase-
68379urease-3.5.1.5
68379beta-glucosidase-3.2.1.21
68379N-acetyl-beta-glucosaminidase-3.2.1.52
68379alpha-glucosidase-3.2.1.20
68379beta-galactosidase-3.2.1.23
68379beta-glucuronidase-3.2.1.31
68379alkaline phosphatase+3.1.3.1
68379pyrrolidonyl arylamidase-3.4.19.3
68379pyrazinamidase-3.5.1.B15
120957oxidase-
120957catalase+1.11.1.6
120957urease+3.5.1.5
68382esterase (C 4)+
68382esterase lipase (C 8)+
68382leucine arylamidase-3.4.11.1
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 coryne

@refNITPYZPYRAPALbeta GURbeta GALalpha GLUbeta NAGESCUREGELGLURIBXYLMANMALLACSACGLYG
18411---+---------------

API zym

@refAlkaline phosphataseEsteraseEsterase LipaseLipaseLeucine arylamidaseValine arylamidaseCystine arylamidaseTrypsinalpha- ChymotrypsinAcid phosphataseNaphthol-AS-BI-phosphohydrolasealpha- Galactosidasebeta- Galactosidasebeta- Glucuronidasealpha- Glucosidasebeta- GlucosidaseN-acetyl-beta- glucosaminidasealpha- Mannosidasealpha- FucosidaseControl
18411-+++-----++--------
120957+++--+---++---------

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinent
7382soilTokyo, Minatu-kuJapanJPNAsia
67770SoilMinato-ku, TokyoJapanJPNAsia
120957Environment, Soil sampleMinato, TokyoJapanJPNAsia

isolation source categories

  • Cat1: #Environmental
  • Cat2: #Terrestrial
  • Cat3: #Soil

taxonmaps

  • @ref: 69479
  • File name: preview.99_4083.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_373;96_1632;97_1954;98_3088;99_4083&stattab=map
  • Last taxonomy: Patulibacter
  • 16S sequence: AB193261
  • Sequence Identity:
  • Total samples: 18409
  • soil counts: 6270
  • aquatic counts: 3344
  • animal counts: 6085
  • plant counts: 2710

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
73821Risk group (German classification)
184111German classification
1209571Risk group (French classification)

Sequence information

16S sequences

  • @ref: 7382
  • description: Patulibacter minatonensis gene for 16S rRNA, partial sequence
  • accession: AB193261
  • length: 1528
  • database: ena
  • NCBI tax ID: 929712

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Patulibacter minatonensis DSM 18081929712.3wgspatric929712
66792Patulibacter minatonensis KV-614, DSM 180812510065083draftimg929712
67770Patulibacter minatonensis DSM 18081GCA_000519325scaffoldncbi929712

GC content

@refGC-contentmethod
738272
6777072high performance liquid chromatography (HPLC)
6777074.1genome sequence analysis

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno88no
motileyes73.785yes
flagellatedno90.188no
gram-positiveyes88.686yes
anaerobicno98.193no
halophileno94.007no
spore-formingno86.027no
thermophileno99.138yes
glucose-utilyes79.914no
aerobicyes88.44yes
glucose-fermentno88.592no

External links

@ref: 7382

culture collection no.: DSM 18081, CIP 109166, JCM 12834, NBRC 100761, NRRL B-24346, KCTC 19436, NCIMB 14347

straininfo link

  • @ref: 86620
  • straininfo: 289981

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny16449447Patulibacter minatonensis gen. nov., sp. nov., a novel actinobacterium isolated using an agar medium supplemented with superoxide dismutase, and proposal of Patulibacteraceae fam. nov.Takahashi Y, Matsumoto A, Morisaki K, Omura SInt J Syst Evol Microbiol10.1099/ijs.0.63796-02006Actinobacteria/*classification/genetics/*isolation & purification/physiology, *Agar, Bacterial Typing Techniques, Bacteriological Techniques, Base Composition, *Culture Media, DNA, Bacterial/analysis, DNA, Ribosomal/analysis, Genes, rRNA, Genotype, Molecular Sequence Data, Phenotype, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Soil Microbiology, Superoxide Dismutase/*metabolismGenetics
Phylogeny17625174Solirubrobacter soli sp. nov., isolated from soil of a ginseng field.Kim MK, Na JR, Lee TH, Im WT, Soung NK, Yang DCInt J Syst Evol Microbiol10.1099/ijs.0.64715-02007Actinobacteria/chemistry/*classification/*isolation & purification/physiology, Base Composition, DNA, Bacterial/chemistry/genetics, DNA, Ribosomal/chemistry/genetics, Fatty Acids/analysis, Genes, rRNA, Korea, Locomotion, Molecular Sequence Data, Panax, Phylogeny, RNA, Bacterial/genetics, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Sequence Homology, Nucleic Acid, *Soil Microbiology, Spores, Bacterial, Vitamin K 2/analysisGenetics
Phylogeny21515709Patulibacter ginsengiterrae sp. nov., isolated from soil of a ginseng field, and an emended description of the genus Patulibacter.Kim KK, Lee KC, Lee JSInt J Syst Evol Microbiol10.1099/ijs.0.032052-02011Actinobacteria/*classification/genetics/*isolation & purification/physiology, Bacterial Typing Techniques, Base Composition, Carbohydrates/analysis, Cell Wall/chemistry, Cluster Analysis, DNA, Bacterial/chemistry/genetics, DNA, Ribosomal/chemistry/genetics, Diaminopimelic Acid/analysis, Fatty Acids/analysis, Molecular Sequence Data, Nucleic Acid Hybridization, Panax/growth & development, Peptidoglycan/chemistry, Phospholipids/analysis, Phylogeny, Quinones/analysis, RNA, Ribosomal, 16S/genetics, Republic of Korea, Sequence Analysis, DNA, *Soil MicrobiologyGenetics
Phylogeny23264500Patulibacter medicamentivorans sp. nov., isolated from activated sludge of a wastewater treatment plant.Almeida B, Vaz-Moreira I, Schumann P, Nunes OC, Carvalho G, Crespo MTBInt J Syst Evol Microbiol10.1099/ijs.0.047522-02012Actinobacteria/*classification/genetics/isolation & purification, Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, Fatty Acids/analysis, Phosphatidylglycerols/analysis, *Phylogeny, Portugal, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Sewage/*microbiology, Vitamin K 2/analogs & derivatives/analysis, Waste WaterTranscriptome
Phylogeny27620694Patulibacter brassicae sp. nov., isolated from rhizosphere soil of Chinese cabbage (Brassica campestris).Jin D, Kong X, Li H, Luo L, Zhuang X, Zhuang G, Deng Y, Bai ZInt J Syst Evol Microbiol10.1099/ijsem.0.0014692016Bacterial Typing Techniques, Base Composition, Brassica/*microbiology, Cardiolipins/chemistry, DNA, Bacterial/genetics, Diaminopimelic Acid/chemistry, Fatty Acids/chemistry, Nucleic Acid Hybridization, Peptidoglycan/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, *Rhizosphere, Sequence Analysis, DNA, *Soil Microbiology, Vitamin K 2/analogs & derivatives/chemistryTranscriptome
Phylogeny29299847Baekduia soli gen. nov., sp. nov., a novel bacterium isolated from the soil of Baekdu Mountain and proposal of a novel family name, Baekduiaceae fam. nov.An DS, Siddiqi MZ, Kim KH, Yu HS, Im WTJ Microbiol10.1007/s12275-018-7107-62018Bacteria/*classification/genetics/*isolation & purification/metabolism, Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, Fatty Acids/chemistry/metabolism, Panax/growth & development, Phylogeny, RNA, Ribosomal, 16S/genetics, *Soil MicrobiologyMetabolism

Reference

@idauthorscataloguedoi/urltitleID_cross_referencepubmed
7382Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 18081)https://www.dsmz.de/collection/catalogue/details/culture/DSM-18081
18411Wink, J.http://www.dsmz.de/microorganisms/wink_pdf/DSM18081.pdfCompendium of Actinobacteria. HZI-Helmholtz-Centre for Infection Research, Braunschweig
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
31552Barberan A, Caceres Velazquez H, Jones S, Fierer N.10.1128/mSphere.00237-17Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information2784328776041
37470Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/6877
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/
68379Automatically annotated from API Coryne
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)
86620Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID289981.1StrainInfo: A central database for resolving microbial strain identifiers
120957Curators of the CIPCollection of Institut Pasteur (CIP 109166)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20109166