Strain identifier

BacDive ID: 14968

Type strain: Yes

Species: Streptomyces pathocidini

Strain Designation: B-28, BK-513

Strain history: CIP <- 1995, JCM <- KCC <- S. Suzuki: strain B-28

NCBI tax ID(s): 1650571 (species)

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General

@ref: 9805

BacDive-ID: 14968

DSM-Number: 40799

keywords: genome sequence, 16S sequence, Bacteria, obligate aerobe, spore-forming, mesophilic, antibiotic compound production

description: Streptomyces pathocidini B-28 is an obligate aerobe, spore-forming, mesophilic bacterium that produces antibiotic compounds and was isolated from Soil.

NCBI tax id

  • NCBI tax id: 1650571
  • Matching level: species

strain history

@refhistory
9805<- H.D. Tresner, BK-513
67770KCC S-0166 <-- S. Suzuki B-28.
121630CIP <- 1995, JCM <- KCC <- S. Suzuki: strain B-28

doi: 10.13145/bacdive14968.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/actinomycetota
  • domain: Bacteria
  • phylum: Actinomycetota
  • class: Actinomycetes
  • order: Kitasatosporales
  • family: Streptomycetaceae
  • genus: Streptomyces
  • species: Streptomyces pathocidini
  • full scientific name: Streptomyces pathocidini (Nagatsu et al. 1962) Labeda et al. 2014

  • synonyms

    • @ref: 20215
    • synonym: Streptomyces albus subsp. pathocidicus

@ref: 9805

domain: Bacteria

phylum: Actinobacteria

class: Actinobacteria

order: Actinomycetales

family: Streptomycetaceae

genus: Streptomyces

species: Streptomyces pathocidini

full scientific name: Streptomyces pathocidini (Nagatsu et al. 1962) Labeda et al. 2014

strain designation: B-28, BK-513

type strain: yes

Morphology

cell morphology

@refmotilityconfidencegram staincell shape
69480no95.837
69480100positive
121630nopositiverod-shaped

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
9805GYM STREPTOMYCES MEDIUM (DSMZ Medium 65)yeshttps://mediadive.dsmz.de/medium/65Name: GYM STREPTOMYCES MEDIUM (DSMZ Medium 65) Composition: Agar 18.0 g/l Malt extract 10.0 g/l Yeast extract 4.0 g/l Glucose 4.0 g/l CaCO3 2.0 g/l Distilled water
41379MEDIUM 122 - for StreptomycesyesDistilled water make up to (1000.000 ml);Agar (15.000 g);Yeast extract (2.000 g);Starch maize (10.000 g)
9805ROLLED OATS MINERAL MEDIUM (DSMZ Medium 84)yeshttps://www.dsmz.de/microorganisms/medium/pdf/DSMZ_Medium84.pdf
121630CIP Medium 122yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=122

culture temp

@refgrowthtypetemperaturerange
9805positivegrowth28mesophilic
41379positivegrowth30mesophilic
67770positivegrowth28mesophilic
121630positivegrowth30-45

Physiology and metabolism

oxygen tolerance

  • @ref: 121630
  • oxygen tolerance: obligate aerobe

spore formation

@refspore formationconfidence
69481yes100
69480yes99.111

compound production

@refcompound
9805blasticidin S
9805pathocidin-(8-azaguanine)
9805restriction endonuclease SpaI (XhoI)

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
1216304853esculin-hydrolysis
12163017234glucose+fermentation
12163017632nitrate-reduction
12163016301nitrite-reduction

metabolite production

@refChebi-IDmetaboliteproduction
67770634868-azaguanineyes
6777015353blasticidin Syes
12163035581indoleno

enzymes

@refvalueactivityec
121630oxidase-
121630beta-galactosidase+3.2.1.23
121630alcohol dehydrogenase-1.1.1.1
121630gelatinase+/-
121630amylase-
121630DNase+
121630caseinase-3.4.21.50
121630catalase+1.11.1.6
121630lecithinase+
121630lysine decarboxylase-4.1.1.18
121630ornithine decarboxylase-4.1.1.17
121630urease-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
121630-+---+--+-----------

API biotype100

@refGLUFRUGALTREMNESBEMELSACRAFMTEMALLACLTEMbGaMaGaCELGENMbGuESCRIBARAXYLPLERHAFUCMLZDARLLARLXLTDULTAGGLYINOMANMTLTURSORADOHBGLYXERYMDG3MDGSATMUCLTATDTATMTATDMLTLMLTCATETATETTECITGRTGAT2KG5KGTRYNAGGNTPACPATpOBEQATGTEmOBEBATPPATCMTTGEBETPCEABTHINLATCAPCYTHISSUCFUMGREGYTAVTETNTTNGLNITA3OBUAPTGTTPRODALALALASERMNTPROPTYR2KT
121630+----------------------+-----------------------------------+------------------------------+--------

Isolation, sampling and environmental information

isolation

@refsample type
67770Soil
121630Environment, Soil

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
98051Risk group (German classification)
1216301Risk group (French classification)

Sequence information

16S sequences

@refdescriptionaccessionlengthdatabaseNCBI tax ID
20218Streptomyces albus subsp. pathocidicus strain JCM 4166 16S ribosomal RNA gene, partial sequenceAY9998061431ena1650571
9805Streptomyces albus subsp. pathocidicus gene for 16S rRNA, partial sequence, strain: NBRC 13812AB1845011467ena1650571

Genome sequences

  • @ref: 67770
  • description: Streptomyces pathocidini NRRL B-24287
  • accession: GCA_001418495
  • assembly level: scaffold
  • database: ncbi
  • NCBI tax ID: 1650571

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingyes100no
flagellatedno98.206no
gram-positiveyes90.467no
anaerobicno99.297no
aerobicyes90.729no
halophileno90.511no
spore-formingyes89.617no
glucose-utilyes91.671no
thermophileno95.123yes
motileno92.397no
glucose-fermentno90.135no

External links

@ref: 9805

culture collection no.: DSM 40799, ATCC 14510, BCRC 12331, CCRC 12331, CGMCC 4.1633, CIP 104431, JCM 4166, KCTC 9671, NBRC 13812, NRRL B-24287, VKM Ac-598, KCC S-0166, IFO 13812

straininfo link

  • @ref: 84077
  • straininfo: 36101

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny24277863Taxonomic evaluation of Streptomyces albus and related species using multilocus sequence analysis and proposals to emend the description of Streptomyces albus and describe Streptomyces pathocidini sp. nov.Labeda DP, Doroghazi JR, Ju KS, Metcalf WWInt J Syst Evol Microbiol10.1099/ijs.0.058107-02013Algorithms, Bacterial Typing Techniques, DNA, Bacterial/genetics, Databases, Nucleic Acid, Genes, Bacterial, Likelihood Functions, Molecular Sequence Data, *Multilocus Sequence Typing, *Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Streptomyces/*classification/geneticsTranscriptome
Metabolism27055525Cell wall glycopolymers of Streptomyces albus, Streptomyces albidoflavus and Streptomyces pathocidini.Shashkov AS, Streshinskaya GM, Tul'skaya EM, Senchenkova SN, Baryshnikova LM, Dmitrenok AS, Ostash BE, Fedorenko VAAntonie Van Leeuwenhoek10.1007/s10482-016-0691-82016Cell Wall/metabolism, Lysine/metabolism, Magnetic Resonance Spectroscopy/methods, Phosphates/isolation & purification/metabolism, Polysaccharides, Bacterial/isolation & purification/*metabolism, Streptomyces/chemistry/*metabolism, Sugar Acids/isolation & purification/metabolism, Teichoic Acids/isolation & purification/metabolism, Uronic Acids/isolation & purification/metabolismEnzymology
Phylogeny27582375Streptomyces tremellae sp. nov., isolated from a culture of the mushroom Tremella fuciformis.Wen ZQ, Chen B, Li X, Li BB, Li CH, Huang QH, Zhang QH, Dai WH, Jiang YJInt J Syst Evol Microbiol10.1099/ijsem.0.0014642016*Agaricales, Bacterial Typing Techniques, Base Composition, *Basidiomycota, Cell Wall/chemistry, China, DNA, Bacterial/genetics, Diaminopimelic Acid/chemistry, Fatty Acids/chemistry, Nucleic Acid Hybridization, Phospholipids/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Soil Microbiology, Streptomyces/*classification/genetics/isolation & purification, Vitamin K 2/analogs & derivatives/chemistryTranscriptome

Reference

@idauthorscataloguedoi/urltitlejournalpubmed
9805Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 40799)https://www.dsmz.de/collection/catalogue/details/culture/DSM-40799
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
41379Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/16339
67770Curators of the JCMhttps://jcm.brc.riken.jp/en/
68382Automatically annotated from API zym
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
84077Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID36101.1StrainInfo: A central database for resolving microbial strain identifiers
121630Curators of the CIPCollection of Institut Pasteur (CIP 104431)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20104431