Strain identifier

BacDive ID: 16401

Type strain: Yes

Species: Embleya scabrispora

Strain Designation: KM-4927

Strain history: CIP <- 2004, JCM <- 2002, S. Omura: strain KM-4927

NCBI tax ID(s): 1123320 (strain), 159449 (species)

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General

@ref: 10637

BacDive-ID: 16401

DSM-Number: 41855

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

description: Embleya scabrispora KM-4927 is an aerobe, spore-forming, mesophilic bacterium that was isolated from soil.

NCBI tax id

NCBI tax idMatching level
1123320strain
159449species

strain history

@refhistory
10637<- JCM <- S. Omura; KM-4927
67770S. ?mura KM-4927.
122500CIP <- 2004, JCM <- 2002, S. Omura: strain KM-4927

doi: 10.13145/bacdive16401.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/actinomycetota
  • domain: Bacteria
  • phylum: Actinomycetota
  • class: Actinomycetes
  • order: Kitasatosporales
  • family: Streptomycetaceae
  • genus: Embleya
  • species: Embleya scabrispora
  • full scientific name: Embleya scabrispora (Ping et al. 2004) Nouioui et al. 2018

  • synonyms

    • @ref: 20215
    • synonym: Streptomyces scabrisporus

@ref: 10637

domain: Bacteria

phylum: Actinobacteria

class: Actinobacteria

order: Actinomycetales

family: Streptomycetaceae

genus: Embleya

species: Embleya scabrispora

full scientific name: Embleya scabrispora (Ping et al. 2004) Nouioui et al. 2018

strain designation: KM-4927

type strain: yes

Morphology

cell morphology

@refgram staincell lengthcell widthmotilityconfidencecell shape
29930positive1.4 µm0.7 µmno
69480no91.526
69480positive100
122500positivenorod-shaped

colony morphology

  • @ref: 122500

multimedia

  • @ref: 10637
  • multimedia content: https://www.dsmz.de/microorganisms/photos/DSM_41855.jpg
  • caption: Medium 65 28°C
  • intellectual property rights: © Leibniz-Institut DSMZ

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
10637GYM 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
33942MEDIUM 57 - for Streptomyces, Nocardioides, Lentzea albidocapillata and Streptoverticillium reticulumyesDistilled water make up to (1000.000 ml);Agar (15.000 g);Glucose (4.000g);Yeast extract (4.000 g);Malt extract (10.000 g);Calcium carbonate (2.000 g)
10637ROLLED 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
10637ISP2 MEDIUM (DSMZ Medium 987)yeshttps://mediadive.dsmz.de/medium/987Name: ISP 2 MEDIUM (DSMZ Medium 987) Composition: Agar 20.0 g/l Malt extract 10.0 g/l Dextrose 4.0 g/l Yeast extract 4.0 g/l Distilled water
122500CIP Medium 57yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=57
122500CIP Medium 116yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=116

culture temp

@refgrowthtypetemperaturerange
10637positivegrowth28mesophilic
29930positivegrowth18-36
33942positivegrowth30mesophilic
67770positivegrowth28mesophilic
122500positivegrowth25-37mesophilic
122500nogrowth10psychrophilic
122500nogrowth41thermophilic
122500nogrowth45thermophilic

culture pH

  • @ref: 29930
  • ability: positive
  • type: optimum
  • pH: 7

Physiology and metabolism

oxygen tolerance

@refoxygen tolerance
29930aerobe
122500obligate aerobe

spore formation

@refspore formationconfidence
29930yes
69481yes100
69480yes100

halophily

@refsaltgrowthtested relationconcentration
122500NaClpositivegrowth0-2 %
122500NaClnogrowth4 %
122500NaClnogrowth6 %
122500NaClnogrowth8 %
122500NaClnogrowth10 %

observation

@refobservation
29930aggregates in chains
67770quinones: MK-9(H4), MK-9(H2), MK-9(H6)

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
2993022599arabinose+carbon source
2993028757fructose+carbon source
2993017596inosine+carbon source
2993026546rhamnose+carbon source
2993017814salicin+carbon source
2993017992sucrose+carbon source
2993018222xylose+carbon source
2993017632nitrate+reduction
12250016947citrate-carbon source
1225004853esculin+hydrolysis
122500606565hippurate-hydrolysis
12250017632nitrate+reduction
12250016301nitrite-reduction
12250017632nitrate-respiration

antibiotic resistance

  • @ref: 122500
  • metabolite: 0129 (2,4-Diamino-6,7-di-iso-propylpteridine phosphate)
  • is antibiotic: yes
  • is sensitive: yes
  • is resistant: no

metabolite production

@refmetaboliteproductionChebi-ID
67770hitachimycinyes
122500indoleno35581

metabolite tests

@refChebi-IDmetabolitevoges-proskauer-testmethylred-test
12250015688acetoin-
12250017234glucose-

enzymes

@refvalueactivityec
122500oxidase-
122500beta-galactosidase+3.2.1.23
122500alcohol dehydrogenase-1.1.1.1
122500gelatinase-
122500amylase+
122500DNase-
122500caseinase-3.4.21.50
122500catalase+1.11.1.6
122500tween esterase+
122500gamma-glutamyltransferase+2.3.2.2
122500lecithinase-
122500lipase+
122500lysine decarboxylase-4.1.1.18
122500ornithine decarboxylase-4.1.1.17
122500phenylalanine ammonia-lyase-4.3.1.24
122500tryptophan deaminase-
122500urease-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
122500-+++++++-+++---+++--

API biotype100

@refGLUFRUGALTREMNESBEMELSACRAFMTEMALLACLTEMbGaMaGaCELGENMbGuESCRIBARAXYLPLERHAFUCMLZDARLLARLXLTDULTAGGLYINOMANMTLTURSORADOHBGLYXERYMDG3MDGSATMUCLTATDTATMTATDMLTLMLTCATETATETTECITGRTGAT2KG5KGTRYNAGGNTPACPATpOBEQATGTEmOBEBATPPATCMTTGEBETPCEABTHINLATCAPCYTHISSUCFUMGREGYTAVTETNTTNGLNITA3OBUAPTGTTPRODALALALASERMNTPROPTYR2KT
122500++--+----+---------------------++----------------+---------++-----------++-+---++---+-+---+---+--+-

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinent
10637soilIbaraki PrefectureJapanJPNAsia
67770SoilUshiku-cho, Ibaraki Pref.JapanJPNAsia
122500Environment, SoilUshikucho, IbarakiJapanJPNAsia

isolation source categories

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

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
106371Risk group (German classification)
1225001Risk group (French classification)

Sequence information

16S sequences

@refdescriptionaccessionlengthdatabaseNCBI tax ID
20218Streptomyces scabrisporus gene for 16S rRNA, partial sequence, strain: NBRC 100760AB2499461449ena159449
29930Streptomyces scabrisporus gene for 16S rRNA, partial sequenceAB0305851479nuccore159449

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Streptomyces scabrisporus DSM 418551123320.3wgspatric1123320
66792Embleya scabrispora DSM 418552515154197draftimg1123320
67770Embleya scabrispora DSM 41855GCA_000372745scaffoldncbi1123320

GC content

@refGC-contentmethod
1063770.6
6777070.6high performance liquid chromatography (HPLC)

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingyes100no
motileno93.503yes
flagellatedno98.225yes
gram-positiveyes89.785yes
anaerobicno99.068yes
aerobicyes90.4no
halophileno92.318no
spore-formingyes96.532yes
thermophileno98.168yes
glucose-utilyes89.726no
glucose-fermentno88.908no

External links

@ref: 10637

culture collection no.: DSM 41855, CIP 108319, JCM 11712, NRRL B-24202, NBRC 100760

straininfo link

  • @ref: 85448
  • straininfo: 131435

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny15023978Streptomyces scabrisporus sp. nov.Ping X, Takahashi Y, Seino A, Iwai Y, Omura SInt J Syst Evol Microbiol10.1099/ijs.0.02692-02004DNA, Bacterial/genetics, DNA, Ribosomal/genetics, Microscopy, Electron, Scanning, Molecular Sequence Data, Phenotype, Phylogeny, RNA, Bacterial/genetics, RNA, Ribosomal, 16S/genetics, Soil Microbiology, Spores, Bacterial/ultrastructure, Streptomyces/*classification/genetics/isolation & purification/physiologyGenetics
Phylogeny17610144Streptomyces serianimatus sp. nov., isolated from a rhizophere soil.Wang YX, Zhi XY, Chen HH, Zhang YQ, Tang SK, Jiang CL, Xu LH, Li WJAntonie Van Leeuwenhoek10.1007/s10482-007-9147-52007Bacterial Proteins/genetics, Gene Expression Regulation, Bacterial, Molecular Sequence Data, Phylogeny, Plant Roots/microbiology, *Soil Microbiology, Spores, Bacterial/cytology, Streptomyces/*classification/cytology/genetics/*isolation & purificationGenetics
Phylogeny20495021Streptomyces aomiensis sp. nov., isolated from a soil sample using the membrane-filter method.Nagai A, Khan ST, Tamura T, Takagi M, Shin-Ya KInt J Syst Evol Microbiol10.1099/ijs.0.020719-02010Base Composition, Cluster Analysis, DNA, Bacterial/chemistry/genetics, DNA, Ribosomal/chemistry/genetics, Diaminopimelic Acid/analysis, Filtration/methods, Molecular Sequence Data, Phylogeny, Quinones/analysis, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, *Soil Microbiology, Streptomyces/*classification/genetics/*isolation & purification, TokyoGenetics
Phylogeny24699065Streptomyces catbensis sp. nov., isolated from soil.Sakiyama Y, Giang NM, Miyadoh S, Luong DT, Van Hop D, Ando KInt J Syst Evol Microbiol10.1099/ijs.0.048264-02014Bacterial Typing Techniques, DNA, Bacterial/genetics, Diaminopimelic Acid/chemistry, Fatty Acids/chemistry, Molecular Sequence Data, Nucleic Acid Hybridization, *Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, *Soil Microbiology, Streptomyces/*classification/genetics/isolation & purification, Vietnam, Vitamin K 2/analogs & derivatives/chemistryGenetics
Phylogeny29119234Streptomyces lasii sp. nov., a Novel Actinomycete with Antifungal Activity Isolated from the Head of an Ant (Lasius flavus).Liu C, Han C, Jiang S, Zhao X, Tian Y, Yan K, Wang X, Xiang WCurr Microbiol10.1007/s00284-017-1388-62017Animals, Antifungal Agents/chemistry/metabolism/*pharmacology, Ants/*microbiology, DNA, Bacterial/genetics, DNA, Ribosomal/genetics, Head/microbiology, Phylogeny, RNA, Ribosomal, 16S/genetics, Streptomyces/*chemistry/classification/*isolation & purification/metabolismMetabolism
Phylogeny31935175Classification of 'Streptomyces hyalinum' Hamada and Yokoyama as Embleya hyalina sp. nov., the second species in the genus Embleya, and emendation of the genus Embleya.Komaki H, Hosoyama A, Kimura A, Ichikawa N, Igarashi Y, Tamura TInt J Syst Evol Microbiol10.1099/ijsem.0.0039412020Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, Diaminopimelic Acid/chemistry, Fatty Acids/chemistry, Nucleic Acid Hybridization, Phospholipids/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Streptomyces/*classification, Vitamin K 2/analogs & derivatives/chemistryTranscriptome
32244993Taxonomic Characterization and Secondary Metabolite Analysis of NEAU-wh3-1: An Embleya Strain with Antitumor and Antibacterial Activity.Wang H, Sun T, Song W, Guo X, Cao P, Xu X, Shen Y, Zhao JMicroorganisms10.3390/microorganisms80304412020
Phylogeny35403858Bioinformatic comparison of three Embleya species and description of steffimycins production by Embleya sp. NF3.Rodriguez-Pena K, Gomez-Roman MP, Macias-Rubalcava ML, Rocha-Zavaleta L, Rodriguez-Sanoja R, Sanchez SAppl Microbiol Biotechnol10.1007/s00253-022-11915-02022Anthracyclines, *Biological Products, Computational Biology, Humans, Multigene Family, Phylogeny, RNA, Ribosomal, 16S/genetics, *StreptomycetaceaePathogenicity

Reference

@idauthorscataloguedoi/urltitlejournalpubmedID_cross_reference
10637Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 41855)https://www.dsmz.de/collection/catalogue/details/culture/DSM-41855
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
29930Barberan A, Caceres Velazquez H, Jones S, Fierer N.10.1128/mSphere.00237-17Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information2877604126301
33942Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/5928
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)
66794Antje Chang, Lisa Jeske, Sandra Ulbrich, Julia Hofmann, Julia Koblitz, Ida Schomburg, Meina Neumann-Schaal, Dieter Jahn, Dietmar Schomburg10.1093/nar/gkaa1025BRENDA, the ELIXIR core data resource in 2021: new developments and updatesNucleic Acids Res. 49: D498-D508 202033211880
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
85448Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID131435.1StrainInfo: A central database for resolving microbial strain identifiers
122500Curators of the CIPCollection of Institut Pasteur (CIP 108319)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20108319