Strain identifier

BacDive ID: 16574

Type strain: Yes

Species: Planobispora longispora

Strain Designation: Pb-1075

Strain history: KCC A-0092 <-- J. E. Thiemann Pb 1075.

NCBI tax ID(s): 28887 (species)

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General

@ref: 10711

BacDive-ID: 16574

DSM-Number: 43041

keywords: genome sequence, 16S sequence, Bacteria, spore-forming, mesophilic

description: Planobispora longispora Pb-1075 is a spore-forming, mesophilic bacterium that was isolated from soil from the shore of Uramaco.

NCBI tax id

  • NCBI tax id: 28887
  • Matching level: species

strain history

@refhistory
10711<- KCC <- J.E. Thiemann, Pb-1075
67770KCC A-0092 <-- J. E. Thiemann Pb 1075.

doi: 10.13145/bacdive16574.20250331.9.3

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/actinomycetota
  • domain: Bacteria
  • phylum: Actinomycetota
  • class: Actinomycetes
  • order: Streptosporangiales
  • family: Streptosporangiaceae
  • genus: Planobispora
  • species: Planobispora longispora
  • full scientific name: Planobispora longispora Thiemann and Beretta 1968 (Approved Lists 1980)

@ref: 10711

domain: Bacteria

phylum: Actinobacteria

class: Actinobacteria

order: Actinomycetales

family: Streptosporangiaceae

genus: Planobispora

species: Planobispora longispora

full scientific name: Planobispora longispora Thiemann and Beretta 1968

strain designation: Pb-1075

type strain: yes

Morphology

cell morphology

  • @ref: 125439
  • gram stain: positive
  • confidence: 97.8

colony morphology

@refcolony colormedium used
69220Beige (1001)suter with tyrosine
69220Beige (1001)suter without tyrosine
69220Ivory (1014)ISP 2
69220Ivory (1014)ISP 6
69220Light ivory (1015)ISP 3
69220Light ivory (1015)ISP 4
69220Oyster white (1013)ISP 5
69220Oyster white (1013)ISP 7

multicellular morphology

@refforms multicellular complexcomplex namemedium name
69220noAerial myceliumISP 2
69220noAerial myceliumISP 3
69220noAerial myceliumISP 4
69220noAerial myceliumISP 5
69220noAerial myceliumISP 6
69220noAerial myceliumISP 7
69220noAerial myceliumsuter with tyrosine
69220noAerial myceliumsuter without tyrosine

pigmentation

@refproductionname
69220noMelanin
69220nosoluble pigment

multimedia

@refmultimedia contentcaptionintellectual property rights
69220DSM_43041_image3.jpegPlates (65, ISP2, ISP3, ISP4, ISP5, ISP7)Helmholtz-Zentrum für Infektionsforschung GmbH
69220DSM_43041_image4.jpegPlates (65, ISP2, ISP3, ISP4, ISP5, ISP7)Helmholtz-Zentrum für Infektionsforschung GmbH

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
10711ROLLED OATS MINERAL MEDIUM (DSMZ Medium 84)yeshttps://mediadive.dsmz.de/medium/84Name: ROLLED OATS MINERAL MEDIUM (DSMZ Medium 84) Composition: Agar 20.0 g/l Rolled oats 20.0 g/l ZnSO4 x 7 H2O 0.001 g/l MnCl2 x 4 H2O 0.001 g/l FeSO4 x 7 H2O 0.001 g/l Distilled water
10711GYM+S MEDIUM (DSMZ Medium 214)yeshttps://www.dsmz.de/microorganisms/medium/pdf/DSMZ_Medium214.pdf

culture temp

@refgrowthtypetemperature
10711positivegrowth28
19931positiveoptimum30
67770positivegrowth28

Physiology and metabolism

oxygen tolerance

  • @ref: 125439
  • oxygen tolerance: obligate aerobe
  • confidence: 97

spore formation

@refspore descriptionspore formationconfidence
19931Formation of spore chains (only spore pairs), spore surface smoothyes
125438yes91.382

halophily

  • @ref: 69220
  • salt: NaCl
  • growth: positive
  • tested relation: growth
  • concentration: 0 %

observation

  • @ref: 67770
  • observation: quinones: MK-9(III,VIII-H4), MK-9(H2), MK-9

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
6922022599arabinose+/-growth
6837928087glycogen-fermentation
6837917992sucrose-fermentation
6837917716lactose-fermentation
6837917306maltose-fermentation
6837916899D-mannitol-fermentation
6837965327D-xylose-fermentation
6837916988D-ribose-fermentation
6837917634D-glucose-fermentation
683795291gelatin+hydrolysis
6837916199urea-hydrolysis
683794853esculin+hydrolysis
6837917632nitrate+reduction
6922062968cellulose-growth
6922028757fructose+/-growth
6922017234glucose+growth
6922017268inositol+/-growth
6922037684mannose+/-growth
6922016634raffinose-growth
6922026546rhamnose-growth
6922017992sucrose-growth
6922018222xylose+/-growth
683685291gelatin+hydrolysis
6836827897tryptophan-energy source
6836816199urea-hydrolysis
6836816947citrate-assimilation
6836818257ornithine-degradation
6836825094lysine-degradation
6836829016arginine-hydrolysis

metabolite production

@refChebi-IDmetaboliteproduction
6836815688acetoinno
6836835581indoleno
6836816136hydrogen sulfideno

metabolite tests

@refChebi-IDmetabolitevoges-proskauer-testindole test
6836815688acetoin-
6836835581indole-

enzymes

@refvalueactivityec
68382alpha-fucosidase-3.2.1.51
68382alpha-mannosidase-3.2.1.24
68382N-acetyl-beta-glucosaminidase+3.2.1.52
68382alpha-glucosidase+3.2.1.20
68382beta-galactosidase+3.2.1.23
68382beta-glucuronidase-3.2.1.31
68382alpha-chymotrypsin+3.4.21.1
68382leucine arylamidase+3.4.11.1
68382valine arylamidase+
68382alkaline phosphatase+3.1.3.1
68382lipase (C 14)+
68379beta-glucosidase+3.2.1.21
68379alpha-glucosidase+3.2.1.20
68379beta-glucuronidase-3.2.1.31
68379alkaline phosphatase+3.1.3.1
68382beta-glucosidase+3.2.1.21
68382alpha-galactosidase-3.2.1.22
68382naphthol-AS-BI-phosphohydrolase+
68382acid phosphatase+3.1.3.2
68379gelatinase+
68379urease-3.5.1.5
68379N-acetyl-beta-glucosaminidase+3.2.1.52
68379pyrrolidonyl arylamidase-3.4.19.3
68379pyrazinamidase-3.5.1.B15
68368gelatinase+
68368tryptophan deaminase-4.1.99.1
68368urease-3.5.1.5
68368ornithine decarboxylase-4.1.1.17
68368lysine decarboxylase-4.1.1.18
68368arginine dihydrolase-3.5.3.6
68368beta-galactosidase+3.2.1.23

API coryne

@refNITPYZPYRAPALbeta GURbeta GALalpha GLUbeta NAGESCUREGELGLURIBXYLMANMALLACSACGLYG
69220+--+-+/-+++-+--------

API zym

@refAlkaline phosphataseEsteraseEsterase LipaseLipaseLeucine arylamidaseValine arylamidaseCystine arylamidaseTrypsinalpha- ChymotrypsinAcid phosphataseNaphthol-AS-BI-phosphohydrolasealpha- Galactosidasebeta- Galactosidasebeta- Glucuronidasealpha- Glucosidasebeta- GlucosidaseN-acetyl-beta- glucosaminidasealpha- Mannosidasealpha- Fucosidase
69220++/-+/-++++/-+/-+++-+-+++--

API 20E

@refONPGADH ArgLDC LysODCCITH2SURETDA TrpINDVPGEL
19931+---------+

Isolation, sampling and environmental information

isolation

@refsample typecountryorigin.countrycontinent
10711soil from the shore of UramacoVenezuelaVENMiddle and South America
67770SoilVenezuelaVENMiddle and South America

isolation source categories

Cat1Cat2Cat3
#Environmental#Terrestrial#Coast
#Environmental#Terrestrial#Soil

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
107111Risk group (German classification)
199311German classification

Sequence information

16S sequences

  • @ref: 20218
  • description: Planobispora longispora gene for 16S ribosomal RNA, partial sequence
  • accession: D85494
  • length: 1472
  • database: nuccore
  • NCBI tax ID: 28887

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Planobispora longispora NBRC 13918GCA_016863135contigncbi28887
66792Planobispora longispora strain NBRC 1391828887.3wgspatric28887

GC content

  • @ref: 67770
  • GC-content: 71
  • method: thermal denaturation, midpoint method (Tm)

Genome-based predictions

predictions

@refmodeltraitdescriptionpredictionconfidencetraining_data
125438gram-positivegram-positivePositive reaction to Gram-stainingyes85.224no
125438anaerobicanaerobicAbility to grow under anoxygenic conditions (including facultative anaerobes)no91.283no
125438spore-formingspore-formingAbility to form endo- or exosporesyes91.382yes
125438thermophilethermophilicAbility to grow at temperatures above or equal to 45°Cno94.409yes
125438aerobicaerobicAbility to grow under oxygenic conditions (including facultative aerobes)yes85.419no
125438motile2+flagellatedAbility to perform flagellated movementno58.933no
125439BacteriaNetspore_formationAbility to form endo- or exosporesyes65.2
125439BacteriaNetmotilityAbility to perform movementno78.8
125439BacteriaNetgram_stainReaction to gram-stainingpositive97.8
125439BacteriaNetoxygen_toleranceOxygenic conditions needed for growthobligate aerobe97

External links

@ref: 10711

culture collection no.: DSM 43041, ATCC 23867, CBS 115.69, IAM 14288, IFO 13879, IFO 13918, JCM 3092, KCC A-0092, NBRC 13879, NBRC 13918, NCIMB 13269, VKM Ac-700, BCRC 13637, CGMCC 4.1206, IMSNU 20108, KCTC 9176, MTCC 1070

straininfo link

  • @ref: 85601
  • straininfo: 38275

literature

  • topic: Phylogeny
  • Pubmed-ID: 24408527
  • title: Planobispora takensis sp. nov., isolated from soil.
  • authors: Ngaemthao W, Suriyachadkun C, Chunhametha S, Niemhom N, Thawai C, Sanglier JJ
  • journal: Int J Syst Evol Microbiol
  • DOI: 10.1099/ijs.0.057968-0
  • year: 2014
  • mesh: Actinomycetales/*classification/genetics/isolation & purification, Bacterial Typing Techniques, DNA, Bacterial/genetics, Diaminopimelic Acid/chemistry, Fatty Acids/chemistry, Molecular Sequence Data, Nucleic Acid Hybridization, Peptidoglycan/chemistry, Phospholipids/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, *Soil Microbiology, Thailand, Trees/microbiology, Vitamin K 2/analogs & derivatives/chemistry
  • topic2: Genetics

Reference

@idauthorscataloguedoi/urltitlejournalpubmed
10711Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 43041)https://www.dsmz.de/collection/catalogue/details/culture/DSM-43041
19931Wink, J.http://www.dsmz.de/microorganisms/wink_pdf/DSM43041.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
20218Verslyppe, B., De Smet, W., De Baets, B., De Vos, P., Dawyndt P.10.1016/j.syapm.2013.11.002StrainInfo introduces electronic passports for microorganisms.Syst Appl Microbiol. 37: 42-50 201424321274
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/
68368Automatically annotated from API 20E
68379Automatically annotated from API Coryne
68382Automatically annotated from API zym
69220Wink, J.https://cdn.dsmz.de/wink/DSM%2043041.pdfCompendium of Actinobacteria. HZI-Helmholtz-Centre for Infection Research, Braunschweig
85601Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID38275.1StrainInfo: A central database for resolving microbial strain identifiers
125438Julia Koblitz, Lorenz Christian Reimer, Rüdiger Pukall, Jörg Overmann10.1101/2024.08.12.607695Predicting bacterial phenotypic traits through improved machine learning using high-quality, curated datasets
125439Philipp Münch, René Mreches, Martin Binder, Hüseyin Anil Gündüz, Xiao-Yin To, Alice McHardyhttps://github.com/GenomeNet/deepGdeepG: Deep Learning for Genome Sequence Data. R package version 0.3.1