Strain identifier
BacDive ID: 23303
Type strain: 
Species: Streptomyces harbinensis
Strain Designation: NEAU-Da3
Strain history: <- C. Liu,School of Science, Harbin, China; NEAU-Da3
NCBI tax ID(s): 1176198 (species)
version 8.1 (current version)
General
@ref: 18930
BacDive-ID: 23303
DSM-Number: 42076
keywords: genome sequence, 16S sequence, Bacteria, aerobe, spore-forming, mesophilic, Gram-positive, antibiotic compound production
description: Streptomyces harbinensis NEAU-Da3 is an aerobe, spore-forming, mesophilic bacterium that produces antibiotic compounds and was isolated from surface sterilized root of a soybean Merr).
NCBI tax id
- NCBI tax id: 1176198
- Matching level: species
strain history
- @ref: 18930
- history: <- C. Liu,School of Science, Harbin, China; NEAU-Da3
doi: 10.13145/bacdive23303.20230509.8.1
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 harbinensis
- full scientific name: Streptomyces harbinensis Liu et al. 2013
@ref: 18930
domain: Bacteria
phylum: Actinobacteria
class: Actinobacteria
order: Actinomycetales
family: Streptomycetaceae
genus: Streptomyces
species: Streptomyces harbinensis
full scientific name: Streptomyces harbinensis Liu et al. 2013
strain designation: NEAU-Da3
type strain: yes
Morphology
cell morphology
- @ref: 31027
- gram stain: positive
- cell length: 0.65 µm
- cell width: 0.39 µm
- motility: no
pigmentation
- @ref: 31027
- production: yes
Culture and growth conditions
culture medium
| @ref | name | growth | link | composition |
|---|---|---|---|---|
| 18930 | STARCH - MINERAL SALT - AGAR (STMS) (DSMZ Medium 252) | yes | https://www.dsmz.de/microorganisms/medium/pdf/DSMZ_Medium252.pdf | |
| 18930 | ROLLED OATS MINERAL MEDIUM (DSMZ Medium 84) | yes | https://www.dsmz.de/microorganisms/medium/pdf/DSMZ_Medium84.pdf | |
| 18930 | 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 |
culture temp
| @ref | growth | type | temperature | range |
|---|---|---|---|---|
| 18930 | positive | growth | 28 | mesophilic |
| 31027 | positive | growth | 18-40 | |
| 31027 | positive | optimum | 30 | mesophilic |
culture pH
| @ref | ability | type | pH | PH range |
|---|---|---|---|---|
| 31027 | positive | growth | 07-11 | alkaliphile |
| 31027 | positive | optimum | 8 |
Physiology and metabolism
oxygen tolerance
- @ref: 31027
- oxygen tolerance: aerobe
spore formation
- @ref: 31027
- spore formation: yes
compound production
- @ref: 18930
- compound: ikarugamycin
halophily
- @ref: 31027
- salt: NaCl
- growth: positive
- tested relation: growth
- concentration: 0-5 %
metabolite utilization
| @ref | Chebi-ID | metabolite | utilization activity | kind of utilization tested |
|---|---|---|---|---|
| 31027 | 16449 | alanine | + | carbon source |
| 31027 | 22599 | arabinose | + | carbon source |
| 31027 | 29016 | arginine | + | carbon source |
| 31027 | 28757 | fructose | + | carbon source |
| 31027 | 28260 | galactose | + | carbon source |
| 31027 | 17234 | glucose | + | carbon source |
| 31027 | 15428 | glycine | + | carbon source |
| 31027 | 17716 | lactose | + | carbon source |
| 31027 | 17306 | maltose | + | carbon source |
| 31027 | 37684 | mannose | + | carbon source |
| 31027 | 26546 | rhamnose | + | carbon source |
| 31027 | 17822 | serine | + | carbon source |
| 31027 | 26986 | threonine | + | carbon source |
| 31027 | 18222 | xylose | + | carbon source |
| 31027 | 4853 | esculin | + | hydrolysis |
enzymes
- @ref: 31027
- value: urease
- activity: +
- ec: 3.5.1.5
Isolation, sampling and environmental information
isolation
- @ref: 18930
- sample type: surface sterilized root of a soybean (Glycine max (L.) Merr)
- host species: Glycine max
- geographic location: Heilongjiang province, Harbin (45° 45' N 126° 41' E)
- country: China
- origin.country: CHN
- continent: Asia
- latitude: 45.75
- longitude: 126.683
isolation source categories
| Cat1 | Cat2 | Cat3 |
|---|---|---|
| #Host | #Plants | #Herbaceous plants (Grass,Crops) |
| #Host Body-Site | #Plant | #Root (Rhizome) |
| #Host Body-Site | #Plant | #Sterilized plant part |
taxonmaps
- @ref: 69479
- File name: preview.99_6878.png
- url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_15;96_2607;97_3968;98_5064;99_6878&stattab=map
- Last taxonomy: Streptomyces
- 16S sequence: JQ750974
- Sequence Identity:
- Total samples: 6887
- soil counts: 3388
- aquatic counts: 717
- animal counts: 1265
- plant counts: 1517
Safety information
risk assessment
- @ref: 18930
- biosafety level: 1
- biosafety level comment: Risk group (German classification)
Sequence information
16S sequences
- @ref: 18930
- description: Streptomyces harbinensis strain NEAU-Da3 16S ribosomal RNA gene, partial sequence
- accession: JQ750974
- length: 1521
- database: ena
- NCBI tax ID: 1176198
Genome sequences
| @ref | description | accession | assembly level | database | NCBI tax ID |
|---|---|---|---|---|---|
| 66792 | Streptomyces harbinensis CGMCC 4.7047 | GCA_900116145 | scaffold | ncbi | 1176198 |
| 66792 | Streptomyces harbinensis strain CGMCC 4.7047 | 1176198.3 | wgs | patric | 1176198 |
| 66792 | Streptomyces harbinensis CGMCC 4.7047 | 2675903139 | draft | img | 1176198 |
GC content
| @ref | GC-content | method |
|---|---|---|
| 18930 | 73.2 | thermal denaturation, midpoint method (Tm) |
| 31027 | 73.2 |
Genome-based predictions
predictions
| trait | prediction | confidence | training_data |
|---|---|---|---|
| motile | no | 92.518 | yes |
| flagellated | no | 97.531 | yes |
| gram-positive | yes | 91.465 | no |
| anaerobic | no | 99.421 | yes |
| aerobic | yes | 92.472 | yes |
| halophile | no | 72.16 | no |
| spore-forming | yes | 94.523 | yes |
| glucose-ferment | no | 87.458 | no |
| thermophile | no | 96.925 | no |
| glucose-util | yes | 87.691 | no |
External links
@ref: 18930
culture collection no.: DSM 42076, CGMCC 4.7047
straininfo link
- @ref: 87521
- straininfo: 407167
literature
| topic | Pubmed-ID | title | authors | journal | DOI | year | mesh | topic2 |
|---|---|---|---|---|---|---|---|---|
| Phylogeny | 23584286 | Streptomyces harbinensis sp. nov., an endophytic, ikarugamycin-producing actinomycete isolated from soybean root [Glycine max (L.) Merr]. | Liu C, Wang X, Zhao J, Liu Q, Wang L, Guan X, He H, Xiang W | Int J Syst Evol Microbiol | 10.1099/ijs.0.050088-0 | 2013 | Bacterial Typing Techniques, China, DNA, Bacterial/genetics, Fatty Acids/analysis, Lactams/*metabolism, Likelihood Functions, Molecular Sequence Data, Nucleic Acid Hybridization, Phospholipids/analysis, *Phylogeny, Plant Roots/microbiology, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Soybeans/*microbiology, Streptomyces/*classification/genetics/isolation & purification, Vitamin K 2/analogs & derivatives/analysis | Genetics |
| Phylogeny | 29177601 | Streptomyces ginkgonis sp. nov., an endophyte from Ginkgo biloba. | Yan X, Li Y, Wang N, Chen Y, Huang LL | Antonie Van Leeuwenhoek | 10.1007/s10482-017-0987-3 | 2017 | Base Composition/genetics, Endophytes/*genetics/physiology, Ginkgo biloba/*microbiology, Phylogeny, RNA, Ribosomal, 16S/genetics, Streptomyces/*genetics/physiology |
Reference
| @id | authors | catalogue | doi/url | title | ID_cross_reference | pubmed |
|---|---|---|---|---|---|---|
| 18930 | Curators of the DSMZ | Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 42076) | https://www.dsmz.de/collection/catalogue/details/culture/DSM-42076 | |||
| 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 | |||
| 31027 | Barberan A, Caceres Velazquez H, Jones S, Fierer N. | 10.1128/mSphere.00237-17 | Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information | 27357 | 28776041 | |
| 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) | |||
| 69479 | João F Matias Rodrigues, Janko Tackmann,Gregor Rot, Thomas SB Schmidt, Lukas Malfertheiner, Mihai Danaila,Marija Dmitrijeva, Daniela Gaio, Nicolas Näpflin and Christian von Mering. University of Zurich. | https://microbeatlas.org/ | MicrobeAtlas 1.0 beta | |||
| 87521 | Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J. | 10.60712/SI-ID407167.1 | StrainInfo: A central database for resolving microbial strain identifiers |