Strain identifier
BacDive ID: 16507
Type strain: 
Species: Herbidospora cretacea
Strain Designation: K-319
Strain history: T. Kudo K-319.
NCBI tax ID(s): 28444 (species)
version 9.1 (current version)
General
@ref: 11470
BacDive-ID: 16507
DSM-Number: 44071
keywords: genome sequence, 16S sequence, Bacteria, spore-forming
description: Herbidospora cretacea K-319 is a spore-forming bacterium that was isolated from soil collected in Saitama.
NCBI tax id
- NCBI tax id: 28444
- Matching level: species
strain history
| @ref | history |
|---|---|
| 11470 | <- IMET <- JCM, K-319 |
| 67770 | T. Kudo K-319. |
doi: 10.13145/bacdive16507.20240916.9.1
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
@ref synonym 20215 Herbidospora osyris 20215 Streptosporangium 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: 90.508
multimedia
| @ref | multimedia content | intellectual property rights | caption |
|---|---|---|---|
| 11470 | https://www.dsmz.de/microorganisms/photos/DSM_44071-1.jpg | © Leibniz-Institut DSMZ | |
| 11470 | https://www.dsmz.de/microorganisms/photos/DSM_44071.jpg | © Leibniz-Institut DSMZ | Medium 65 28°C |
Culture and growth conditions
culture medium
| @ref | name | growth | link | composition |
|---|---|---|---|---|
| 11470 | GYM STREPTOMYCES MEDIUM (DSMZ Medium 65) | yes | https://mediadive.dsmz.de/medium/65 | Name: 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 |
| 11470 | ROLLED OATS MINERAL MEDIUM (DSMZ Medium 84) | yes | https://mediadive.dsmz.de/medium/84 | Name: 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
| @ref | growth | type | temperature |
|---|---|---|---|
| 11470 | positive | growth | 28 |
| 67770 | positive | growth | 28 |
Physiology and metabolism
spore formation
| @ref | spore formation | confidence |
|---|---|---|
| 69480 | yes | 91.475 |
| 69481 | yes | 97 |
observation
- @ref: 67770
- observation: quinones: MK-10(III,IX-H4), MK-10(H2), MK-10(H6)
Isolation, sampling and environmental information
isolation
| @ref | sample type | geographic location | country | origin.country | continent |
|---|---|---|---|---|---|
| 11470 | soil collected in Saitama | Saitama | Japan | JPN | Asia |
| 67770 | Soil | Saitama Pref. | Japan | JPN | Asia |
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: nuccore
- NCBI tax ID: 28444
Genome sequences
| @ref | description | accession | assembly level | database | NCBI tax ID |
|---|---|---|---|---|---|
| 66792 | Herbidospora cretacea strain NBRC 15474 | 28444.4 | wgs | patric | 28444 |
| 66792 | Herbidospora cretacea NBRC 15474 | 2724679244 | draft | img | 28444 |
| 67770 | Herbidospora cretacea NBRC 15474 | GCA_001570605 | scaffold | ncbi | 28444 |
GC content
| @ref | GC-content | method |
|---|---|---|
| 67770 | 70.7 | genome sequence analysis |
| 67770 | 70 | high performance liquid chromatography (HPLC) |
Genome-based predictions
predictions
| @ref | trait | model | description | prediction | confidence | training_data |
|---|---|---|---|---|---|---|
| 69481 | spore-forming | spore-forming | Ability to form endo- or exospores | yes | 97 | no |
| 69480 | gram-positive | gram-positive | Positive reaction to Gram-staining | yes | 90.508 | no |
| 69480 | anaerobic | anaerobic | Ability to grow under anoxygenic conditions (including facultative anaerobes) | no | 95.9 | no |
| 69480 | spore-forming | spore-forming | Ability to form endo- or exospores | yes | 91.475 | no |
| 69480 | aerobic | aerobic | Ability to grow under oxygenic conditions (including facultative aerobes) | yes | 89.453 | no |
| 69480 | thermophilic | thermophile | Ability to grow at temperatures above or equal to 45°C | no | 95.5 | yes |
| 69480 | flagellated | motile2+ | Ability to perform flagellated movement | no | 88 | no |
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
| topic | Pubmed-ID | title | authors | journal | DOI | year | mesh | topic2 |
|---|---|---|---|---|---|---|---|---|
| Phylogeny | 7684242 | Herbidospora gen. nov., a new genus of the family Streptosporangiaceae Goodfellow et al. 1990. | Kudo T, Itoh T, Miyadoh S, Shomura T, Seino A | Int J Syst Bacteriol | 10.1099/00207713-43-2-319 | 1993 | Actinomycetales/*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/analysis | Genetics |
| Phylogeny | 12139476 | Cell wall teichoic acids of actinomycetes of three genera of the order actinomycetales. | Streshinskaya GM, Shashkov AS, Usov AI, Evtushenko LI, Naumova IB | Biochemistry (Mosc) | 10.1023/a:1016348724308 | 2002 | Actinomycetales/*chemistry/*classification, Cell Wall/*chemistry, Magnetic Resonance Spectroscopy, Teichoic Acids/*analysis | |
| Phylogeny | 19643877 | Herbidospora 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 WJ | Int J Syst Evol Microbiol | 10.1099/ijs.0.010579-0 | 2009 | Actinomycetales/*classification/genetics/*isolation & purification/metabolism, China, DNA, Bacterial/genetics, DNA, Ribosomal/genetics, Fatty Acids/metabolism, Molecular Sequence Data, Phylogeny, RNA, Ribosomal, 16S/genetics, Santalaceae/*microbiology | Metabolism |
| Phylogeny | 19667396 | Herbidospora yilanensis sp. nov. and Herbidospora daliensis sp. nov., from sediment. | Tseng M, Yang SF, Yuan GF | Int J Syst Evol Microbiol | 10.1099/ijs.0.014803-0 | 2009 | Actinomycetales/*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, Taiwan | Genetics |
| Phylogeny | 26452464 | Genome-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 N | BMC Res Notes | 10.1186/s13104-015-1526-9 | 2015 | Base 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/*genetics | Genetics |
Reference
| @id | authors | catalogue | doi/url | title |
|---|---|---|---|---|
| 11470 | Curators of the DSMZ | Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 44071) | https://www.dsmz.de/collection/catalogue/details/culture/DSM-44071 | |
| 20215 | Parte, A.C., Sardà Carbasse, J., Meier-Kolthoff, J.P., Reimer, L.C. and Göker, M. | 10.1099/ijsem.0.004332 | List of Prokaryotic names with Standing in Nomenclature (LPSN) moves to the DSMZ | |
| 66792 | Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmann | https://diaspora-project.de/progress.html#genomes | Automatically annotated for the DiASPora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information) | |
| 67770 | Curators of the JCM | https://jcm.brc.riken.jp/en/ | ||
| 69480 | Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmann | https://diaspora-project.de/progress.html#genomes | Predictions based on genome sequence made in the Diaspora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information) | |
| 69481 | Xiao-Yin To, René Mreches, Martin Binder, Alice C. McHardy, Philipp C. Münch | 10.21203/rs.3.rs-2527258/v1 | Predictions based on the model GenomeNet Sporulation v. 1 | |
| 85540 | Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J. | 10.60712/SI-ID46177.1 | StrainInfo: A central database for resolving microbial strain identifiers |