Strain identifier

BacDive ID: 16507

Type strain: Yes

Species: Herbidospora cretacea

Strain Designation: K-319

Strain history: T. Kudo K-319.

NCBI tax ID(s): 28444 (species)

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General

@ref: 11470

BacDive-ID: 16507

DSM-Number: 44071

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

description: Herbidospora cretacea K-319 is a spore-forming, mesophilic, Gram-positive bacterium that was isolated from soil collected in Saitama.

NCBI tax id

  • NCBI tax id: 28444
  • Matching level: species

strain history

@refhistory
11470<- IMET <- JCM, K-319
67770T. Kudo K-319.

doi: 10.13145/bacdive16507.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/actinomycetota
  • domain: Bacteria
  • phylum: Actinomycetota
  • class: Actinomycetes
  • order: Streptosporangiales
  • family: Streptosporangiaceae
  • genus: Herbidospora
  • species: Herbidospora cretacea
  • full scientific name: Herbidospora cretacea Kudo et al. 1993

  • synonyms

    @refsynonym
    20215Herbidospora osyris
    20215Streptosporangium claviforme

@ref: 11470

domain: Bacteria

phylum: Actinobacteria

class: Actinobacteria

order: Actinomycetales

family: Streptosporangiaceae

genus: Herbidospora

species: Herbidospora cretacea

full scientific name: Herbidospora cretacea Kudo et al. 1993 emend. Nouioui et al. 2018

strain designation: K-319

type strain: yes

Morphology

cell morphology

  • @ref: 69480
  • gram stain: positive
  • confidence: 100

multimedia

@refmultimedia contentintellectual property rightscaption
11470https://www.dsmz.de/microorganisms/photos/DSM_44071-1.jpg© Leibniz-Institut DSMZ
11470https://www.dsmz.de/microorganisms/photos/DSM_44071.jpg© Leibniz-Institut DSMZMedium 65 28°C

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
11470GYM 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
11470ROLLED 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

culture temp

@refgrowthtypetemperaturerange
11470positivegrowth28mesophilic
67770positivegrowth28mesophilic

Physiology and metabolism

spore formation

@refspore formationconfidence
69481yes97
69480yes100

observation

  • @ref: 67770
  • observation: quinones: MK-10(III,IX-H4), MK-10(H2), MK-10(H6)

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinent
11470soil collected in SaitamaSaitamaJapanJPNAsia
67770SoilSaitama Pref.JapanJPNAsia

isolation source categories

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

Safety information

risk assessment

  • @ref: 11470
  • biosafety level: 1
  • biosafety level comment: Risk group (German classification)

Sequence information

16S sequences

  • @ref: 11470
  • description: Herbidospora cretacea gene for 16S ribosomal RNA, partial sequence
  • accession: D85485
  • length: 1475
  • database: ena
  • NCBI tax ID: 28444

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Herbidospora cretacea strain NBRC 1547428444.4wgspatric28444
66792Herbidospora cretacea NBRC 154742724679244draftimg28444
67770Herbidospora cretacea NBRC 15474GCA_001570605scaffoldncbi28444

GC content

@refGC-contentmethod
6777070.7genome sequence analysis
6777070high performance liquid chromatography (HPLC)

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingyes97no
motileno92.021no
gram-positiveyes89.299no
anaerobicno99.168no
halophileno94.895no
spore-formingyes95.031no
glucose-utilyes88.454no
flagellatedno97.862no
aerobicyes93.925no
thermophileno98.611no
glucose-fermentno93.188no

External links

@ref: 11470

culture collection no.: DSM 44071, IAM 14284, IFO 15474, JCM 8553, NBRC 15474, ATCC 51904, BCRC 16356, IMSNU 21364, KCTC 9335, NCIMB 13372, VKM Ac-1997

straininfo link

  • @ref: 85540
  • straininfo: 46177

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny7684242Herbidospora gen. nov., a new genus of the family Streptosporangiaceae Goodfellow et al. 1990.Kudo T, Itoh T, Miyadoh S, Shomura T, Seino AInt J Syst Bacteriol10.1099/00207713-43-2-3191993Actinomycetales/*classification/*genetics/isolation & purification/ultrastructure, Bacterial Typing Techniques, Base Composition, Base Sequence, Cell Wall/chemistry, DNA, Bacterial/genetics, Fatty Acids/analysis, Japan, Molecular Sequence Data, Nucleic Acid Hybridization, Phylogeny, Plants/microbiology, RNA, Bacterial/classification/*genetics, RNA, Ribosomal, 5S/classification/*genetics, Sequence Homology, Nucleic Acid, Soil Microbiology, Spectrometry, Mass, Fast Atom Bombardment, Vitamin K/analysisGenetics
Phylogeny12139476Cell wall teichoic acids of actinomycetes of three genera of the order actinomycetales.Streshinskaya GM, Shashkov AS, Usov AI, Evtushenko LI, Naumova IBBiochemistry (Mosc)10.1023/a:10163487243082002Actinomycetales/*chemistry/*classification, Cell Wall/*chemistry, Magnetic Resonance Spectroscopy, Teichoic Acids/*analysis
Phylogeny19643877Herbidospora osyris sp. nov., isolated from surface-sterilized tissue of Osyris wightiana Wall. ex Wight.Li J, Zhao GZ, Qin S, Zhu WY, Xu LH, Li WJInt J Syst Evol Microbiol10.1099/ijs.0.010579-02009Actinomycetales/*classification/genetics/*isolation & purification/metabolism, China, DNA, Bacterial/genetics, DNA, Ribosomal/genetics, Fatty Acids/metabolism, Molecular Sequence Data, Phylogeny, RNA, Ribosomal, 16S/genetics, Santalaceae/*microbiologyMetabolism
Phylogeny19667396Herbidospora yilanensis sp. nov. and Herbidospora daliensis sp. nov., from sediment.Tseng M, Yang SF, Yuan GFInt J Syst Evol Microbiol10.1099/ijs.0.014803-02009Actinomycetales/*classification/genetics/*isolation & purification/physiology, Bacterial Typing Techniques, Base Composition, DNA, Bacterial/analysis, DNA, Ribosomal/analysis, Fatty Acids/analysis, Genes, rRNA, Genotype, Geologic Sediments/*microbiology, Molecular Sequence Data, Nucleic Acid Hybridization, Phenotype, Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Species Specificity, TaiwanGenetics
Phylogeny26452464Genome-based analysis of non-ribosomal peptide synthetase and type-I polyketide synthase gene clusters in all type strains of the genus Herbidospora.Komaki H, Ichikawa N, Oguchi A, Hamada M, Tamura T, Fujita NBMC Res Notes10.1186/s13104-015-1526-92015Base Sequence, Conserved Sequence/genetics, Evolution, Molecular, *Genome, Bacterial, *Multigene Family, Open Reading Frames/genetics, Peptide Synthases/*genetics, Phylogeny, Polyketide Synthases/*genetics, Polyketides/chemistry, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Species Specificity, Streptomyces/*enzymology/*geneticsGenetics

Reference

@idauthorscataloguedoi/urltitle
11470Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 44071)https://www.dsmz.de/collection/catalogue/details/culture/DSM-44071
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
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/
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
85540Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID46177.1StrainInfo: A central database for resolving microbial strain identifiers