Strain identifier

BacDive ID: 17003

Type strain: Yes

Species: Actinomadura rupiterrae

Strain Designation: CS5-AC15

Strain history: <- SD Lee, Cheju Univ.

NCBI tax ID(s): 559627 (species)

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General

@ref: 15916

BacDive-ID: 17003

DSM-Number: 45251

keywords: genome sequence, 16S sequence, Bacteria, aerobe, spore-forming, mesophilic, Gram-positive

description: Actinomadura rupiterrae CS5-AC15 is an aerobe, spore-forming, mesophilic bacterium that was isolated from soil from a cliff.

NCBI tax id

  • NCBI tax id: 559627
  • Matching level: species

strain history

@refhistory
15916<- S. D. Lee, Cheju National Univ., Rep. of Korea; CS5-AC15
67771<- SD Lee, Cheju Univ.

doi: 10.13145/bacdive17003.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/actinomycetota
  • domain: Bacteria
  • phylum: Actinomycetota
  • class: Actinomycetes
  • order: Streptosporangiales
  • family: Thermomonosporaceae
  • genus: Actinomadura
  • species: Actinomadura rupiterrae
  • full scientific name: Actinomadura rupiterrae Lee 2012

@ref: 15916

domain: Bacteria

phylum: Actinobacteria

class: Actinobacteria

order: Actinomycetales

family: Thermomonosporaceae

genus: Actinomadura

species: Actinomadura rupiterrae

full scientific name: Actinomadura rupiterrae Lee 2012

strain designation: CS5-AC15

type strain: yes

Morphology

cell morphology

  • @ref: 67771
  • gram stain: positive

pigmentation

  • @ref: 30399
  • production: yes

multimedia

  • @ref: 15916
  • multimedia content: https://www.dsmz.de/microorganisms/photos/DSM_45251.jpg
  • caption: Medium 554 28°C
  • intellectual property rights: © Leibniz-Institut DSMZ

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
15916TRYPTICASE SOY BROTH AGAR (DSMZ Medium 535)yeshttps://www.dsmz.de/microorganisms/medium/pdf/DSMZ_Medium535.pdf
15916N-Z-AMINE-MEDIUM (DSMZ Medium 554)yeshttps://mediadive.dsmz.de/medium/554Name: N-Z-AMINE-MEDIUM (DSMZ Medium 554) Composition: Starch 20.0 g/l Agar 20.0 g/l Glucose 10.0 g/l N-Z amine 5.0 g/l Yeast extract 5.0 g/l CaCO3 1.0 g/l Distilled water
15916BHI MEDIUM (DSMZ Medium 215)yeshttps://mediadive.dsmz.de/medium/215Name: BHI MEDIUM (DSMZ Medium 215) Composition: Brain heart infusion 37.0 g/l Distilled water

culture temp

@refgrowthtypetemperaturerange
15916positivegrowth28mesophilic
30399positivegrowth20-42
30399positiveoptimum37-42
67771positivegrowth30mesophilic

culture pH

@refabilitytypepHPH range
30399positivegrowth05-11alkaliphile
30399positiveoptimum06-08

Physiology and metabolism

oxygen tolerance

  • @ref: 67771
  • oxygen tolerance: aerobe

spore formation

  • @ref: 30399
  • spore formation: yes

halophily

  • @ref: 30399
  • salt: NaCl
  • growth: positive
  • tested relation: growth
  • concentration: <1 %

observation

  • @ref: 67771
  • observation: quinones: MK-9(H6), MK-9(H8)

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
3039916947citrate+carbon source
3039917234glucose+carbon source
3039917716lactose+carbon source
3039929864mannitol+carbon source
3039917992sucrose+carbon source
303994853esculin+hydrolysis

enzymes

@refvalueactivityec
30399catalase+1.11.1.6
30399gelatinase+

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinent
15916soil from a cliffJeju, Mara IslandRepublic of KoreaKORAsia
67771From soil of cliffMara island, JejuRepublic of KoreaKORAsia

isolation source categories

Cat1Cat2Cat3
#Environmental#Terrestrial#Geologic
#Environmental#Terrestrial#Soil

Safety information

risk assessment

  • @ref: 15916
  • biosafety level: 1
  • biosafety level comment: Risk group (German classification)

Sequence information

16S sequences

  • @ref: 15916
  • description: Actinomadura rupiterrae CS5-AC15 partial 16S rRNA gene, strain CS5-AC15
  • accession: FM210337
  • length: 1437
  • database: ena
  • NCBI tax ID: 559627

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Actinomadura rupiterrae DSM 452512863206357draftimg559627
66792Actinomadura rupiterrae DSM 45251GCA_024172125contigncbi559627

GC content

@refGC-contentmethod
1591670.9high performance liquid chromatography (HPLC)
3039970.9

External links

@ref: 15916

culture collection no.: DSM 45251, KCTC 19559

straininfo link

  • @ref: 86005
  • straininfo: 402517

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny21685258Actinomadura rupiterrae sp. nov., isolated from cliff soil.Lee SDInt J Syst Evol Microbiol10.1099/ijs.0.035121-02011Actinomycetales/*classification/genetics/isolation & purification, Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, Diaminopimelic Acid/chemistry, Fatty Acids/chemistry, Islands, Molecular Sequence Data, Nucleic Acid Hybridization, Peptidoglycan/chemistry, Phospholipids/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, Republic of Korea, Sequence Analysis, DNA, *Soil Microbiology, Vitamin K 2/analogs & derivatives/chemistryGenetics
Phylogeny30063200Actinomadura rhizosphaerae sp. nov., isolated from rhizosphere soil of the plant Azadirachta indica.Malisorn K, Kanchanasin P, Phongsopitanun W, Tanasupawat SInt J Syst Evol Microbiol10.1099/ijsem.0.0029402018Actinomycetales/*classification/genetics/isolation & purification, Azadirachta/*microbiology, Bacterial Typing Techniques, Base Composition, Cell Wall/chemistry, DNA, Bacterial/genetics, Diaminopimelic Acid/chemistry, Fatty Acids/chemistry, Muramic Acids/chemistry, Nucleic Acid Hybridization, Phospholipids/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, *Rhizosphere, Sequence Analysis, DNA, *Soil Microbiology, Thailand, Vitamin K 2/analogs & derivatives/chemistryTranscriptome
Phylogeny31287395Actinomadura logoneensis sp. nov., a novel actinomycete isolated from the soil.Shi L, Han L, Guo X, Zhao J, Wang J, Wang H, Jiang S, Xiang W, Wang XInt J Syst Evol Microbiol10.1099/ijsem.0.0035792019Actinobacteria/*classification, Bacterial Typing Techniques, Base Composition, Chad, DNA, Bacterial/genetics, Fatty Acids/chemistry, Nucleic Acid Hybridization, Phospholipids/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, *Soil Microbiology, Vitamin K 2/analogs & derivatives/chemistryTranscriptome
Phylogeny31671050Actinomadura harenae sp. nov., a novel actinomycete isolated from sea sand in Sanya.Hu J, Han C, Yu B, Zhao J, Guo X, Shen Y, Wang X, Xiang WInt J Syst Evol Microbiol10.1099/ijsem.0.0038192020Actinomycetales/*classification/isolation & purification, Bacterial Typing Techniques, Base Composition, Cell Wall/chemistry, China, DNA, Bacterial/genetics, Diaminopimelic Acid/chemistry, Fatty Acids/chemistry, Nucleic Acid Hybridization, Phospholipids/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, Sand/*microbiology, Sequence Analysis, DNA, Vitamin K 2/chemistryTranscriptome

Reference

@idauthorscataloguedoi/urltitleID_cross_referencepubmed
15916Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 45251)https://www.dsmz.de/collection/catalogue/details/culture/DSM-45251
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
30399Barberan A, Caceres Velazquez H, Jones S, Fierer N.10.1128/mSphere.00237-17Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information2673628776041
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)
67771Curators of the KCTChttps://kctc.kribb.re.kr/En/Kctc
86005Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID402517.1StrainInfo: A central database for resolving microbial strain identifiers