Strain identifier
BacDive ID: 16401
Type strain:
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)
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 id | Matching level |
---|---|
1123320 | strain |
159449 | species |
strain history
@ref | history |
---|---|
10637 | <- JCM <- S. Omura; KM-4927 |
67770 | S. ?mura KM-4927. |
122500 | CIP <- 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
@ref | gram stain | cell length | cell width | motility | confidence | cell shape |
---|---|---|---|---|---|---|
29930 | positive | 1.4 µm | 0.7 µm | no | ||
69480 | no | 91.526 | ||||
69480 | positive | 100 | ||||
122500 | positive | no | rod-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
@ref | name | growth | link | composition |
---|---|---|---|---|
10637 | 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 |
33942 | MEDIUM 57 - for Streptomyces, Nocardioides, Lentzea albidocapillata and Streptoverticillium reticulum | yes | Distilled 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) | |
10637 | 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 |
10637 | ISP2 MEDIUM (DSMZ Medium 987) | yes | https://mediadive.dsmz.de/medium/987 | Name: 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 |
122500 | CIP Medium 57 | yes | https://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=57 | |
122500 | CIP Medium 116 | yes | https://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=116 |
culture temp
@ref | growth | type | temperature | range |
---|---|---|---|---|
10637 | positive | growth | 28 | mesophilic |
29930 | positive | growth | 18-36 | |
33942 | positive | growth | 30 | mesophilic |
67770 | positive | growth | 28 | mesophilic |
122500 | positive | growth | 25-37 | mesophilic |
122500 | no | growth | 10 | psychrophilic |
122500 | no | growth | 41 | thermophilic |
122500 | no | growth | 45 | thermophilic |
culture pH
- @ref: 29930
- ability: positive
- type: optimum
- pH: 7
Physiology and metabolism
oxygen tolerance
@ref | oxygen tolerance |
---|---|
29930 | aerobe |
122500 | obligate aerobe |
spore formation
@ref | spore formation | confidence |
---|---|---|
29930 | yes | |
69481 | yes | 100 |
69480 | yes | 100 |
halophily
@ref | salt | growth | tested relation | concentration |
---|---|---|---|---|
122500 | NaCl | positive | growth | 0-2 % |
122500 | NaCl | no | growth | 4 % |
122500 | NaCl | no | growth | 6 % |
122500 | NaCl | no | growth | 8 % |
122500 | NaCl | no | growth | 10 % |
observation
@ref | observation |
---|---|
29930 | aggregates in chains |
67770 | quinones: MK-9(H4), MK-9(H2), MK-9(H6) |
metabolite utilization
@ref | Chebi-ID | metabolite | utilization activity | kind of utilization tested |
---|---|---|---|---|
29930 | 22599 | arabinose | + | carbon source |
29930 | 28757 | fructose | + | carbon source |
29930 | 17596 | inosine | + | carbon source |
29930 | 26546 | rhamnose | + | carbon source |
29930 | 17814 | salicin | + | carbon source |
29930 | 17992 | sucrose | + | carbon source |
29930 | 18222 | xylose | + | carbon source |
29930 | 17632 | nitrate | + | reduction |
122500 | 16947 | citrate | - | carbon source |
122500 | 4853 | esculin | + | hydrolysis |
122500 | 606565 | hippurate | - | hydrolysis |
122500 | 17632 | nitrate | + | reduction |
122500 | 16301 | nitrite | - | reduction |
122500 | 17632 | nitrate | - | 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
@ref | metabolite | production | Chebi-ID |
---|---|---|---|
67770 | hitachimycin | yes | |
122500 | indole | no | 35581 |
metabolite tests
@ref | Chebi-ID | metabolite | voges-proskauer-test | methylred-test |
---|---|---|---|---|
122500 | 15688 | acetoin | - | |
122500 | 17234 | glucose | - |
enzymes
@ref | value | activity | ec |
---|---|---|---|
122500 | oxidase | - | |
122500 | beta-galactosidase | + | 3.2.1.23 |
122500 | alcohol dehydrogenase | - | 1.1.1.1 |
122500 | gelatinase | - | |
122500 | amylase | + | |
122500 | DNase | - | |
122500 | caseinase | - | 3.4.21.50 |
122500 | catalase | + | 1.11.1.6 |
122500 | tween esterase | + | |
122500 | gamma-glutamyltransferase | + | 2.3.2.2 |
122500 | lecithinase | - | |
122500 | lipase | + | |
122500 | lysine decarboxylase | - | 4.1.1.18 |
122500 | ornithine decarboxylase | - | 4.1.1.17 |
122500 | phenylalanine ammonia-lyase | - | 4.3.1.24 |
122500 | tryptophan deaminase | - | |
122500 | urease | - | 3.5.1.5 |
68382 | alkaline phosphatase | + | 3.1.3.1 |
68382 | esterase (C 4) | + | |
68382 | esterase lipase (C 8) | + | |
68382 | lipase (C 14) | + | |
68382 | leucine arylamidase | + | 3.4.11.1 |
68382 | valine arylamidase | + | |
68382 | cystine arylamidase | + | 3.4.11.3 |
68382 | trypsin | - | 3.4.21.4 |
68382 | alpha-chymotrypsin | + | 3.4.21.1 |
68382 | acid phosphatase | + | 3.1.3.2 |
68382 | naphthol-AS-BI-phosphohydrolase | + | |
68382 | alpha-galactosidase | - | 3.2.1.22 |
68382 | beta-galactosidase | - | 3.2.1.23 |
68382 | beta-glucuronidase | - | 3.2.1.31 |
68382 | alpha-glucosidase | + | 3.2.1.20 |
68382 | beta-glucosidase | + | 3.2.1.21 |
68382 | N-acetyl-beta-glucosaminidase | + | 3.2.1.52 |
68382 | alpha-mannosidase | - | 3.2.1.24 |
68382 | alpha-fucosidase | - | 3.2.1.51 |
API zym
@ref | Control | Alkaline phosphatase | Esterase | Esterase Lipase | Lipase | Leucine arylamidase | Valine arylamidase | Cystine arylamidase | Trypsin | alpha- Chymotrypsin | Acid phosphatase | Naphthol-AS-BI-phosphohydrolase | alpha- Galactosidase | beta- Galactosidase | beta- Glucuronidase | alpha- Glucosidase | beta- Glucosidase | N-acetyl-beta- glucosaminidase | alpha- Mannosidase | alpha- Fucosidase |
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
122500 | - | + | + | + | + | + | + | + | - | + | + | + | - | - | - | + | + | + | - | - |
API biotype100
@ref | GLU | FRU | GAL | TRE | MNE | SBE | MEL | SAC | RAF | MTE | MAL | LAC | LTE | MbGa | MaGa | CEL | GEN | MbGu | ESC | RIB | ARA | XYL | PLE | RHA | FUC | MLZ | DARL | LARL | XLT | DUL | TAG | GLY | INO | MAN | MTL | TUR | SOR | ADO | HBG | LYX | ERY | MDG | 3MDG | SAT | MUC | LTAT | DTAT | MTAT | DMLT | LMLT | CATE | TATE | TTE | CIT | GRT | GAT | 2KG | 5KG | TRY | NAG | GNT | PAC | PAT | pOBE | QAT | GTE | mOBE | BAT | PPAT | CMT | TGE | BET | PCE | ABT | HIN | LAT | CAP | CYT | HIS | SUC | FUM | GRE | GYT | AVT | ETN | TTN | GLN | ITA | 3OBU | APT | GTT | PRO | DALA | LALA | SER | MNT | PROP | TYR | 2KT |
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
122500 | + | + | - | - | + | - | - | - | - | + | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | + | + | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | + | - | - | - | - | - | - | - | - | - | + | + | - | - | - | - | - | - | - | - | - | - | - | + | + | - | + | - | - | - | + | + | - | - | - | + | - | + | - | - | - | + | - | - | - | + | - | - | + | - |
Isolation, sampling and environmental information
isolation
@ref | sample type | geographic location | country | origin.country | continent |
---|---|---|---|---|---|
10637 | soil | Ibaraki Prefecture | Japan | JPN | Asia |
67770 | Soil | Ushiku-cho, Ibaraki Pref. | Japan | JPN | Asia |
122500 | Environment, Soil | Ushikucho, Ibaraki | Japan | JPN | Asia |
isolation source categories
- Cat1: #Environmental
- Cat2: #Terrestrial
- Cat3: #Soil
Safety information
risk assessment
@ref | biosafety level | biosafety level comment |
---|---|---|
10637 | 1 | Risk group (German classification) |
122500 | 1 | Risk group (French classification) |
Sequence information
16S sequences
@ref | description | accession | length | database | NCBI tax ID |
---|---|---|---|---|---|
20218 | Streptomyces scabrisporus gene for 16S rRNA, partial sequence, strain: NBRC 100760 | AB249946 | 1449 | ena | 159449 |
29930 | Streptomyces scabrisporus gene for 16S rRNA, partial sequence | AB030585 | 1479 | nuccore | 159449 |
Genome sequences
@ref | description | accession | assembly level | database | NCBI tax ID |
---|---|---|---|---|---|
66792 | Streptomyces scabrisporus DSM 41855 | 1123320.3 | wgs | patric | 1123320 |
66792 | Embleya scabrispora DSM 41855 | 2515154197 | draft | img | 1123320 |
67770 | Embleya scabrispora DSM 41855 | GCA_000372745 | scaffold | ncbi | 1123320 |
GC content
@ref | GC-content | method |
---|---|---|
10637 | 70.6 | |
67770 | 70.6 | high performance liquid chromatography (HPLC) |
Genome-based predictions
predictions
trait | prediction | confidence | training_data |
---|---|---|---|
spore-forming | yes | 100 | no |
motile | no | 93.503 | yes |
flagellated | no | 98.225 | yes |
gram-positive | yes | 89.785 | yes |
anaerobic | no | 99.068 | yes |
aerobic | yes | 90.4 | no |
halophile | no | 92.318 | no |
spore-forming | yes | 96.532 | yes |
thermophile | no | 98.168 | yes |
glucose-util | yes | 89.726 | no |
glucose-ferment | no | 88.908 | no |
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
topic | Pubmed-ID | title | authors | journal | DOI | year | mesh | topic2 |
---|---|---|---|---|---|---|---|---|
Phylogeny | 15023978 | Streptomyces scabrisporus sp. nov. | Ping X, Takahashi Y, Seino A, Iwai Y, Omura S | Int J Syst Evol Microbiol | 10.1099/ijs.0.02692-0 | 2004 | DNA, 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/physiology | Genetics |
Phylogeny | 17610144 | Streptomyces serianimatus sp. nov., isolated from a rhizophere soil. | Wang YX, Zhi XY, Chen HH, Zhang YQ, Tang SK, Jiang CL, Xu LH, Li WJ | Antonie Van Leeuwenhoek | 10.1007/s10482-007-9147-5 | 2007 | Bacterial Proteins/genetics, Gene Expression Regulation, Bacterial, Molecular Sequence Data, Phylogeny, Plant Roots/microbiology, *Soil Microbiology, Spores, Bacterial/cytology, Streptomyces/*classification/cytology/genetics/*isolation & purification | Genetics |
Phylogeny | 20495021 | Streptomyces aomiensis sp. nov., isolated from a soil sample using the membrane-filter method. | Nagai A, Khan ST, Tamura T, Takagi M, Shin-Ya K | Int J Syst Evol Microbiol | 10.1099/ijs.0.020719-0 | 2010 | Base 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, Tokyo | Genetics |
Phylogeny | 24699065 | Streptomyces catbensis sp. nov., isolated from soil. | Sakiyama Y, Giang NM, Miyadoh S, Luong DT, Van Hop D, Ando K | Int J Syst Evol Microbiol | 10.1099/ijs.0.048264-0 | 2014 | Bacterial 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/chemistry | Genetics |
Phylogeny | 29119234 | Streptomyces 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 W | Curr Microbiol | 10.1007/s00284-017-1388-6 | 2017 | Animals, 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/metabolism | Metabolism |
Phylogeny | 31935175 | Classification 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 T | Int J Syst Evol Microbiol | 10.1099/ijsem.0.003941 | 2020 | Bacterial 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/chemistry | Transcriptome |
32244993 | Taxonomic 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 J | Microorganisms | 10.3390/microorganisms8030441 | 2020 | |||
Phylogeny | 35403858 | Bioinformatic 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 S | Appl Microbiol Biotechnol | 10.1007/s00253-022-11915-0 | 2022 | Anthracyclines, *Biological Products, Computational Biology, Humans, Multigene Family, Phylogeny, RNA, Ribosomal, 16S/genetics, *Streptomycetaceae | Pathogenicity |
Reference
@id | authors | catalogue | doi/url | title | journal | pubmed | ID_cross_reference |
---|---|---|---|---|---|---|---|
10637 | Curators of the DSMZ | Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 41855) | https://www.dsmz.de/collection/catalogue/details/culture/DSM-41855 | ||||
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 | ||||
20218 | Verslyppe, B., De Smet, W., De Baets, B., De Vos, P., Dawyndt P. | 10.1016/j.syapm.2013.11.002 | StrainInfo introduces electronic passports for microorganisms. | Syst Appl Microbiol. 37: 42-50 2014 | 24321274 | ||
29930 | 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 | 28776041 | 26301 | ||
33942 | Curators of the CIP | https://brclims.pasteur.fr/brcWeb/souche/detail/1/5928 | |||||
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) | ||||
66794 | Antje Chang, Lisa Jeske, Sandra Ulbrich, Julia Hofmann, Julia Koblitz, Ida Schomburg, Meina Neumann-Schaal, Dieter Jahn, Dietmar Schomburg | 10.1093/nar/gkaa1025 | BRENDA, the ELIXIR core data resource in 2021: new developments and updates | Nucleic Acids Res. 49: D498-D508 2020 | 33211880 | ||
67770 | Curators of the JCM | https://jcm.brc.riken.jp/en/ | |||||
68382 | Automatically annotated from API zym | ||||||
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 | ||||
85448 | Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J. | 10.60712/SI-ID131435.1 | StrainInfo: A central database for resolving microbial strain identifiers | ||||
122500 | Curators of the CIP | Collection of Institut Pasteur (CIP 108319) | https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20108319 |