Strain identifier

BacDive ID: 12601

Type strain: Yes

Species: Promicromonospora sukumoe

Strain history: S. ?mura SK-2049.

NCBI tax ID(s): 88382 (species)

For citation purpose refer to the digital object identifier (doi) of the current version.
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General

@ref: 11416

BacDive-ID: 12601

DSM-Number: 44121

keywords: genome sequence, 16S sequence, Bacteria, mesophilic, amino acid production

description: Promicromonospora sukumoe DSM 44121 is a mesophilic bacterium that produces amino acids and was isolated from soil.

NCBI tax id

  • NCBI tax id: 88382
  • Matching level: species

strain history

@refhistory
11416<- JCM <- S. Omura, SK-2049
67770S. ?mura SK-2049.

doi: 10.13145/bacdive12601.20230509.8.1

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

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
11416GYM 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
11416R2A MEDIUM (DSMZ Medium 830)yeshttps://mediadive.dsmz.de/medium/830Name: 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
11416YEAST STARCH AGAR (A) (DSMZ Medium 1027)yeshttps://mediadive.dsmz.de/medium/1027Name: 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

@refgrowthtypetemperaturerange
11416positivegrowth28mesophilic
67770positivegrowth28mesophilic

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

@refsample typegeographic locationcountryorigin.countrycontinent
11416soilSukumo City, Kochi prefectureJapanJPNAsia
67770SoilSukumo City, Kochi Pref.JapanJPNAsia

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

@refdescriptionaccessionlengthdatabaseNCBI tax ID
20218Promicromonospora sukumoe partial 16S rRNA gene for 16S ribosomal RNA, strain type DSM 44121AJ2720241460ena88382
20218Promicromonospora sukumoe gene for 16S rRNA, strain:IFO 14650TAB0233751487ena88382
20218Promicromonospora sukumoe gene for 16S rRNA, partial sequenceAB0561301488ena88382

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Promicromonospora sukumoe DSM 44121GCA_014137995contigncbi88382
66792Promicromonospora sukumoe strain DSM 4412188382.4wgspatric88382
66792Promicromonospora sukumoe DSM 441212820964733draftimg88382

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
motileno90.646no
flagellatedno98.279no
gram-positiveyes89.668no
anaerobicno99.521no
halophileno87.481no
spore-formingno55.326no
thermophileno99.412yes
glucose-utilyes86.822no
aerobicyes93.735no
glucose-fermentno84.581no

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

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny13130039Promicromonospora 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 MInt J Syst Evol Microbiol10.1099/ijs.0.02522-02003Actinobacteria/*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 SpecificityGenetics
Phylogeny18523198Promicromonospora kroppenstedtii sp. nov., isolated from sandy soil.Alonso-Vega P, Santamaria RI, Martinez-Molina E, Trujillo MEInt J Syst Evol Microbiol10.1099/ijs.0.65458-02008Actinomycetales/*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 SpecificityGenetics
Phylogeny19654362Promicromonospora umidemergens sp. nov., isolated from moisture from indoor wall material.Martin K, Schafer J, Kampfer PInt J Syst Evol Microbiol10.1099/ijs.0.014142-02009Actinomycetales/*classification/genetics/*isolation & purification/metabolism, DNA, Bacterial/genetics, DNA, Ribosomal/genetics, Fatty Acids/chemistry/metabolism, *Household Articles, Molecular Sequence Data, Phylogeny, RNA, Ribosomal, 16S/geneticsMetabolism
Phylogeny28866992Promicromonospora callitridis sp. nov., an endophytic actinobacterium isolated from the surface-sterilized root of an Australian native pine tree.Kaewkla O, Franco CMMInt J Syst Evol Microbiol10.1099/ijsem.0.0021652017Actinomycetales/*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/chemistryTranscriptome

Reference

@idauthorscataloguedoi/urltitlejournalpubmed
11416Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 44121)https://www.dsmz.de/collection/catalogue/details/culture/DSM-44121
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
20218Verslyppe, B., De Smet, W., De Baets, B., De Vos, P., Dawyndt P.10.1016/j.syapm.2013.11.002StrainInfo introduces electronic passports for microorganisms.Syst Appl Microbiol. 37: 42-50 201424321274
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/
81815Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID125938.1StrainInfo: A central database for resolving microbial strain identifiers