Strain identifier
BacDive ID: 12601
Type strain: 
Species: Promicromonospora sukumoe
Strain history: S. ?mura SK-2049.
NCBI tax ID(s): 88382 (species)
version 9.1 (current version)
General
@ref: 11416
BacDive-ID: 12601
DSM-Number: 44121
keywords: genome sequence, 16S sequence, Bacteria, amino acid production
description: Promicromonospora sukumoe DSM 44121 is a bacterium that produces amino acids and was isolated from soil.
NCBI tax id
- NCBI tax id: 88382
- Matching level: species
strain history
| @ref | history |
|---|---|
| 11416 | <- JCM <- S. Omura, SK-2049 |
| 67770 | S. ?mura SK-2049. |
doi: 10.13145/bacdive12601.20240916.9.1
Name and taxonomic classification
LPSN
- @ref: 20215
- description: domain/bacteria
- keyword: phylum/actinomycetota
- domain: Bacteria
- phylum: Actinomycetota
- class: Actinomycetes
- order: Micrococcales
- family: Promicromonosporaceae
- genus: Promicromonospora
- species: Promicromonospora sukumoe
- full scientific name: Promicromonospora sukumoe Takahashi et al. 1988
@ref: 11416
domain: Bacteria
phylum: Actinobacteria
class: Actinobacteria
order: Actinomycetales
family: Promicromonosporaceae
genus: Promicromonospora
species: Promicromonospora sukumoe
full scientific name: Promicromonospora sukumoe Takahashi et al. 1988
type strain: yes
Morphology
cell morphology
- @ref: 69480
- motility: no
- confidence: 92.5
Culture and growth conditions
culture medium
| @ref | name | growth | link | composition |
|---|---|---|---|---|
| 11416 | 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 |
| 11416 | R2A MEDIUM (DSMZ Medium 830) | yes | https://mediadive.dsmz.de/medium/830 | Name: R2A MEDIUM (DSMZ Medium 830) Composition: Agar 15.0 g/l Casamino acids 0.5 g/l Starch 0.5 g/l Glucose 0.5 g/l Proteose peptone 0.5 g/l Yeast extract 0.5 g/l K2HPO4 0.3 g/l Na-pyruvate 0.3 g/l MgSO4 x 7 H2O 0.05 g/l Distilled water |
| 11416 | YEAST STARCH AGAR (A) (DSMZ Medium 1027) | yes | https://mediadive.dsmz.de/medium/1027 | Name: YEAST STARCH AGAR (A) (DSMZ Medium 1027) Composition: Agar 15.0 g/l Starch 10.0 g/l Yeast extract 2.0 g/l Distilled water |
culture temp
| @ref | growth | type | temperature |
|---|---|---|---|
| 11416 | positive | growth | 28 |
| 67770 | positive | growth | 28 |
Physiology and metabolism
compound production
- @ref: 11416
- compound: 7-hydro-8 methylpteroylglutamylglutamic acid
murein
- @ref: 11416
- murein short key: A11.59
- type: A4alpha L-Lys-L-Ala-D-Glu
observation
- @ref: 67770
- observation: quinones: MK-9(H4), MK-9, MK-9(H2), MK-9(H6)
metabolite production
- @ref: 67770
- metabolite: 7-Hydro-8-methylpteroylglutamylglutamic acid
- production: yes
Isolation, sampling and environmental information
isolation
| @ref | sample type | geographic location | country | origin.country | continent |
|---|---|---|---|---|---|
| 11416 | soil | Sukumo City, Kochi prefecture | Japan | JPN | Asia |
| 67770 | Soil | Sukumo City, Kochi Pref. | Japan | JPN | Asia |
isolation source categories
- Cat1: #Environmental
- Cat2: #Terrestrial
- Cat3: #Soil
Safety information
risk assessment
- @ref: 11416
- biosafety level: 1
- biosafety level comment: Risk group (German classification)
Sequence information
16S sequences
| @ref | description | accession | length | database | NCBI tax ID |
|---|---|---|---|---|---|
| 20218 | Promicromonospora sukumoe partial 16S rRNA gene for 16S ribosomal RNA, strain type DSM 44121 | AJ272024 | 1460 | nuccore | 88382 |
| 20218 | Promicromonospora sukumoe gene for 16S rRNA, strain:IFO 14650T | AB023375 | 1487 | nuccore | 88382 |
| 20218 | Promicromonospora sukumoe gene for 16S rRNA, partial sequence | AB056130 | 1488 | nuccore | 88382 |
Genome sequences
| @ref | description | accession | assembly level | database | NCBI tax ID |
|---|---|---|---|---|---|
| 66792 | Promicromonospora sukumoe DSM 44121 | GCA_014137995 | contig | ncbi | 88382 |
| 66792 | Promicromonospora sukumoe strain DSM 44121 | 88382.4 | wgs | patric | 88382 |
| 66792 | Promicromonospora sukumoe DSM 44121 | 2820964733 | draft | img | 88382 |
Genome-based predictions
predictions
| @ref | trait | model | description | prediction | confidence | training_data |
|---|---|---|---|---|---|---|
| 69480 | gram-positive | gram-positive | Positive reaction to Gram-staining | yes | 88.529 | no |
| 69480 | anaerobic | anaerobic | Ability to grow under anoxygenic conditions (including facultative anaerobes) | no | 96.919 | no |
| 69480 | aerobic | aerobic | Ability to grow under oxygenic conditions (including facultative aerobes) | yes | 89.584 | no |
| 69480 | spore-forming | spore-forming | Ability to form endo- or exospores | yes | 65.759 | no |
| 69480 | thermophilic | thermophile | Ability to grow at temperatures above or equal to 45°C | no | 98.5 | yes |
| 69480 | flagellated | motile2+ | Ability to perform flagellated movement | no | 92.5 | no |
External links
@ref: 11416
culture collection no.: DSM 44121, IFO 14650, JCM 6845, NBRC 14650, VKM Ac-1966
straininfo link
- @ref: 81815
- straininfo: 125938
literature
| topic | Pubmed-ID | title | authors | journal | DOI | year | mesh | topic2 |
|---|---|---|---|---|---|---|---|---|
| Phylogeny | 13130039 | Promicromonospora vindobonensis sp. nov. and Promicromonospora aerolata sp. nov., isolated from the air in the medieval 'Virgilkapelle' in Vienna. | Busse HJ, Zlamala C, Buczolits S, Lubitz W, Kampfer P, Takeuchi M | Int J Syst Evol Microbiol | 10.1099/ijs.0.02522-0 | 2003 | Actinobacteria/*classification/genetics/*isolation & purification/metabolism, Air Microbiology, Austria, DNA, Bacterial/genetics, DNA, Ribosomal/genetics, Fatty Acids/analysis, Molecular Sequence Data, Phenotype, Phylogeny, RNA, Bacterial/genetics, RNA, Ribosomal, 16S/genetics, Species Specificity | Genetics |
| Phylogeny | 18523198 | Promicromonospora kroppenstedtii sp. nov., isolated from sandy soil. | Alonso-Vega P, Santamaria RI, Martinez-Molina E, Trujillo ME | Int J Syst Evol Microbiol | 10.1099/ijs.0.65458-0 | 2008 | Actinomycetales/*classification/genetics/isolation & purification/physiology, Bacterial Typing Techniques, DNA, Bacterial/analysis, DNA, Ribosomal/analysis, Genes, rRNA, Molecular Sequence Data, Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, *Silicon Dioxide, *Soil Microbiology, Spain, Species Specificity | Genetics |
| Phylogeny | 19654362 | Promicromonospora umidemergens sp. nov., isolated from moisture from indoor wall material. | Martin K, Schafer J, Kampfer P | Int J Syst Evol Microbiol | 10.1099/ijs.0.014142-0 | 2009 | Actinomycetales/*classification/genetics/*isolation & purification/metabolism, DNA, Bacterial/genetics, DNA, Ribosomal/genetics, Fatty Acids/chemistry/metabolism, *Household Articles, Molecular Sequence Data, Phylogeny, RNA, Ribosomal, 16S/genetics | Metabolism |
| Phylogeny | 28866992 | Promicromonospora callitridis sp. nov., an endophytic actinobacterium isolated from the surface-sterilized root of an Australian native pine tree. | Kaewkla O, Franco CMM | Int J Syst Evol Microbiol | 10.1099/ijsem.0.002165 | 2017 | Actinomycetales/*classification/genetics/isolation & purification, Australia, Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, Fatty Acids/chemistry, Nucleic Acid Hybridization, *Phylogeny, Pinus/*microbiology, Plant Roots/*microbiology, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Vitamin K 2/chemistry | Transcriptome |
Reference
| @id | authors | catalogue | doi/url | title | journal | pubmed |
|---|---|---|---|---|---|---|
| 11416 | Curators of the DSMZ | Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 44121) | https://www.dsmz.de/collection/catalogue/details/culture/DSM-44121 | |||
| 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 | |
| 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) | |||
| 81815 | Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J. | 10.60712/SI-ID125938.1 | StrainInfo: A central database for resolving microbial strain identifiers |