Strain identifier

BacDive ID: 7797

Type strain: Yes

Species: Actinocatenispora rupis

Strain Designation: CS5-AC17

Strain history: DSM 45178 <-- S. D. Lee CS5-AC17.

NCBI tax ID(s): 519421 (species)

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General

@ref: 15642

BacDive-ID: 7797

DSM-Number: 45178

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

description: Actinocatenispora rupis CS5-AC17 is an aerobe, spore-forming, mesophilic bacterium that was isolated from soil of cliff.

NCBI tax id

  • NCBI tax id: 519421
  • Matching level: species

strain history

@refhistory
15642<- S. D. Lee; CS5-AC17
67770DSM 45178 <-- S. D. Lee CS5-AC17.

doi: 10.13145/bacdive7797.20250331.9.3

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/actinomycetota
  • domain: Bacteria
  • phylum: Actinomycetota
  • class: Actinomycetes
  • order: Micromonosporales
  • family: Micromonosporaceae
  • genus: Actinocatenispora
  • species: Actinocatenispora rupis
  • full scientific name: Actinocatenispora rupis Seo and Lee 2009

@ref: 15642

domain: Bacteria

phylum: Actinobacteria

class: Actinobacteria

order: Actinomycetales

family: Micromonosporaceae

genus: Actinocatenispora

species: Actinocatenispora rupis

full scientific name: Actinocatenispora rupis Seo and Lee 2009

strain designation: CS5-AC17

type strain: yes

Morphology

cell morphology

@refgram staincell lengthcell widthmotilityconfidence
29428positive1.25 µm0.45 µm
125438no92.5
125438positive90.957
125439positive99.9

colony morphology

@refcolony colorincubation periodmedium used
20175Light ivory (1015)10-14 daysISP 2
20175Cream (9001)10-14 daysISP 3
20175Light ivory (1015)10-14 daysISP 4
20175Light ivory (1015)10-14 daysISP 5
20175Ivory (1014)10-14 daysISP 6
20175Cream (9001)10-14 daysISP 7

multicellular morphology

@refforms multicellular complexmedium name
20175noISP 2
20175noISP 3
20175noISP 4
20175noISP 5
20175noISP 6
20175noISP 7

pigmentation

  • @ref: 29428
  • production: no

multimedia

  • @ref: 15642
  • multimedia content: https://www.dsmz.de/microorganisms/photos/DSM_45178.jpg
  • caption: Medium 65 28°C
  • intellectual property rights: © Leibniz-Institut DSMZ

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
15642ROLLED OATS MINERAL MEDIUM (DSMZ Medium 84)yeshttps://mediadive.dsmz.de/medium/84Name: 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
15642GYM 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
20175ISP 2yesName: ISP 2 / Yeast Malt Agar (5265); 5265 Composition Malt extract 10.0 g/l Yeast extract 4.0 g/l Glucose 4.0 g/l Agar 15.0 g/l Preparation: Sterilisation: 20 minutes at 121°C pH before sterilisation: 7.0 Usage: Maintenance and Taxonomy Organisms: All Actinomycetes
20175ISP 3yesName: ISP 3; 5315 Composition Dog oat flakes 20.0 g/l Trace element solution (5314) 2.5 ml/l Agar 18.0 g/l Preparation: Oat flakes are cooked for 20 minutes, trace element solution and agar are added (in the case of non rolled oat flakes the suspension has to bee filtrated). Sterilisation: 20 minutes at 121°C pH before sterilisation: 7.8 Usage: Maintenance and taxonomy (e.g. SEM As liquid medium for metabolite production) Organisms: All Actinomycetes Trace element solution 5314 Name: Trace element solution 5314; 5314 Composition CaCl2 x H2O 3.0 g/l Fe-III-citrate 1.0 g/l MnSO4 0.2 g/l ZnCl2 0.1 g/l CuSO4 x 5 H2O 0.025 g/l Sodium tetra borate 0.2 g/l CoCl2 x 6 H2O 0.004 g/l Sodium molybdate 0.01 g/l Preparation: Use double destillated water. Sterilisation: 20 minutes at 121°C pH before sterilisation: Usage: Trace element solution for different media Organisms:
20175ISP 4yesName: ISP 4; DSM 547 Solution I: Difco soluble starch, 10.0 g. Make a paste of the starch with a small amount of cold distilled water and bring to a volume of 500 ml. Solution II: CaCO3 2.0 g K2HPO4 (anhydrous) 1.0 g MgSO4 x 7 H2O 1.0 g NaCl 1.0 g (NH4)2SO4 2.0 g Distilled water 500.0 ml Trace salt solution (see below) 1.0 ml The pH should be between 7.0 and 7.4. Do not adjust if it is within this range. Mix solutions I and II together. Add 20.0 g agar. Liquify agar by steaming at 100°C for 10 to 20 min. Trace element solution: FeSO4 x 7 H2O 0.1 g MnCl2 x 4 H2O 0.1 g ZnSO4 x 7 H2O 0.1 g Distilled water 100.0 ml
20175ISP 5yesName: ISP 5 (5323) Composition L-Asparagine 1.0 g/l Glycerol 10.0 g/l K2HPO4 1.0 g/l Salt solution (see preparation) 1.0 ml/l Agar 20.0 g/l Preparation: Salt solution 1.0 g FeSO4 x 7 H2O 1.0 g MnCl2 x 4 H2O 1.0 g ZNSO4 x 7 H2O in 100 ml water Sterilisation: 20 minutes at 121°C pH before sterilisation: 7.2 Usage: Maintenance and taxonomy Organisms: All Actinomycetes
20175ISP 6yesName: ISP 6 (5318) Composition Peptone 15.0 g/l Proteose peptose 5.0 g/l Ferric ammonium citrate 0.5 g/l Sodium glycerophosphate 1.0 g/l Sodium thiosulfate 0.08 g/l Yeast extract 1.0 g/l Agar 15.0 g/l Sterilisation: 20 minutes at 121°C pH before sterilisation: Usage: Production of melanoid pigments Organisms: All Actinomycetes
20175ISP 7yesName: ISP 7 (5322) Composition Glycerol 15.0 g/l L-Tyrosine 0.5 g/l L-Asparagine 1.0 g/l K2HPO4 0.5 g/l NaCl 0.5 g/l FeSO4 x 7 H2O 0.01 g/l Trace element solution 5343 1.0 ml/l Agar 20.0 Sterilisation: 20 minutes at 121°C pH before sterilisation: 7.3 Usage: Production of melanoid pigments Organisms: All Actinomycetes
15642GPHF-MEDIUM (DSMZ Medium 553)yeshttps://mediadive.dsmz.de/medium/553Name: GPHF-MEDIUM (DSMZ Medium 553) Composition: Agar 20.0 g/l Glucose 10.0 g/l Beef extract 5.0 g/l Yeast extract 5.0 g/l Casein peptone 5.0 g/l CaCl2 x 2 H2O 0.74 g/l Distilled water
15642ISP2 MEDIUM (DSMZ Medium 987)yeshttps://mediadive.dsmz.de/medium/987Name: 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

culture temp

@refgrowthtypetemperature
15642positivegrowth28
20175positiveoptimum28
29428positivegrowth25-42
29428positiveoptimum37
67770positivegrowth28

culture pH

@refabilitytypepHPH range
29428positivegrowth5.1-12.1alkaliphile
29428positiveoptimum7.1

Physiology and metabolism

oxygen tolerance

@refoxygen toleranceconfidence
29428aerobe
125438aerobe90.925
125439obligate aerobe99.8

spore formation

@refspore formationconfidence
29428yes
125439yes94.9

halophily

@refsaltgrowthtested relationconcentration
29428NaClpositivegrowth0-4 %
29428NaClpositiveoptimum7.1 %

observation

@refobservation
29428aggregates in clumps
67770quinones: MK-9(H4), MK-9(H6), MK-9(H8)

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
2017517234glucose+
2017522599arabinose+/-
2017517992sucrose+
2017518222xylose+/-
2017517268myo-inositol+/-
2017529864mannitol+
2017528757fructose+
2017526546rhamnose+/-
2017516634raffinose-
2017562968cellulose-
2942815963ribitol+carbon source
2942822599arabinose+carbon source
2942817057cellobiose+carbon source
2942816947citrate+carbon source
2942828260galactose+carbon source
2942817754glycerol+carbon source
2942817716lactose+carbon source
2942817306maltose+carbon source
2942829864mannitol+carbon source
2942837684mannose+carbon source
2942826546rhamnose+carbon source
2942830911sorbitol+carbon source
2942817992sucrose+carbon source
2942827082trehalose+carbon source
2942853426tween 80+carbon source
294284853esculin+hydrolysis

enzymes

@refvalueactivityec
68382alpha-fucosidase+3.2.1.51
68382alpha-mannosidase+3.2.1.24
68382alpha-glucosidase+3.2.1.20
68382beta-glucuronidase+3.2.1.31
68382alpha-galactosidase+3.2.1.22
68382beta-galactosidase+3.2.1.23
68382naphthol-AS-BI-phosphohydrolase+
68382alpha-chymotrypsin-3.4.21.1
68382acid phosphatase+3.1.3.2
68382trypsin+3.4.21.4
68382cystine arylamidase-3.4.11.3
68382valine arylamidase+
68382leucine arylamidase+3.4.11.1
68382esterase lipase (C 8)+
68382alkaline phosphatase+3.1.3.1
68382esterase (C 4)+
68382N-acetyl-beta-glucosaminidase+3.2.1.52
68382beta-glucosidase+3.2.1.21
68382lipase (C 14)-

API zym

@refAlkaline phosphataseEsteraseEsterase LipaseLipaseLeucine arylamidaseValine arylamidaseCystine arylamidaseTrypsinalpha- ChymotrypsinAcid phosphataseNaphthol-AS-BI-phosphohydrolasealpha- Galactosidasebeta- Galactosidasebeta- Glucuronidasealpha- Glucosidasebeta- GlucosidaseN-acetyl-beta- glucosaminidasealpha- Mannosidasealpha- Fucosidase
20175+++-++-+-++++++++++

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinent
15642soil of cliffJeju, Mara IslandRepublic of KoreaKORAsia
67770Soil from a cliff on Mara IslandJejuRepublic of KoreaKORAsia

isolation source categories

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

taxonmaps

  • @ref: 69479
  • File name: preview.99_119412.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_94;96_2691;97_3305;98_80504;99_119412&stattab=map
  • Last taxonomy: Actinocatenispora rupis subclade
  • 16S sequence: AM980986
  • Sequence Identity:
  • Total samples: 2865
  • soil counts: 2086
  • aquatic counts: 83
  • animal counts: 242
  • plant counts: 454

Safety information

risk assessment

  • @ref: 15642
  • biosafety level: 1
  • biosafety level comment: Risk group (German classification)

Sequence information

16S sequences

  • @ref: 15642
  • description: Actinocatenispora rupis partial 16S rRNA gene, type strain CS5-AC17T
  • accession: AM980986
  • length: 1408
  • database: nuccore
  • NCBI tax ID: 519421

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Actinocatenispora rupis NBRC 107355GCA_016861975contigncbi519421
66792Actinocatenispora rupis strain NBRC 107355519421.3wgspatric519421

GC content

@refGC-contentmethod
1564274.3high performance liquid chromatography (HPLC)
2942874.3

Genome-based predictions

predictions

@refmodeltraitdescriptionpredictionconfidencetraining_data
125438gram-positivegram-positivePositive reaction to Gram-stainingyes90.957yes
125438anaerobicanaerobicAbility to grow under anoxygenic conditions (including facultative anaerobes)no94.42yes
125438spore-formingspore-formingAbility to form endo- or exosporesyes83.909no
125438aerobicaerobicAbility to grow under oxygenic conditions (including facultative aerobes)yes90.925no
125438thermophilethermophilicAbility to grow at temperatures above or equal to 45°Cno94.922yes
125438motile2+flagellatedAbility to perform flagellated movementno92.5no
125439BacteriaNetspore_formationAbility to form endo- or exosporesyes94.9
125439BacteriaNetmotilityAbility to perform movementno88.5
125439BacteriaNetgram_stainReaction to gram-stainingpositive99.9
125439BacteriaNetoxygen_toleranceOxygenic conditions needed for growthobligate aerobe99.8

External links

@ref: 15642

culture collection no.: DSM 45178, JCM 16894, NBRC 107355, NRRL B-24660

straininfo link

  • @ref: 77239
  • straininfo: 403338

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny19643893Actinocatenispora rupis sp. nov., isolated from cliff soil, and emended description of the genus Actinocatenispora.Seo SH, Lee SDInt J Syst Evol Microbiol10.1099/ijs.0.012922-02009DNA, Bacterial/genetics, DNA, Ribosomal/genetics, Micromonosporaceae/*classification/genetics/*isolation & purification, Molecular Sequence Data, Phylogeny, RNA, Ribosomal, 16S/genetics, Republic of Korea, *Soil MicrobiologyGenetics
Phylogeny34242158Actinocatenispora comari sp. nov., an endophytic actinomycete isolated from aerial parts of Comarum salesowianum.Oyunbileg N, Iizaka Y, Hamada M, Davaapurev BO, Fukumoto A, Tsetseg B, Kato F, Tamura T, Batkhuu J, Anzai YInt J Syst Evol Microbiol10.1099/ijsem.0.0048612021Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, Diaminopimelic Acid/chemistry, Endophytes/classification/isolation & purification, Fatty Acids/chemistry, Micromonosporaceae/*classification/isolation & purification, Mongolia, Nucleic Acid Hybridization, Phospholipids/chemistry, *Phylogeny, Plant Components, Aerial/*microbiology, RNA, Ribosomal, 16S/genetics, Rosacea/*microbiology, Sequence Analysis, DNA, Vitamin K 2/analogs & derivatives/chemistryEnzymology

Reference

@idauthorscataloguedoi/urltitleID_cross_referencepubmed
15642Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 45178)https://www.dsmz.de/collection/catalogue/details/culture/DSM-45178
20175Wink, J.http://www.dsmz.de/microorganisms/wink_pdf/DSM45178.pdfCompendium of Actinobacteria. HZI-Helmholtz-Centre for Infection Research, Braunschweig
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
29428Barberan A, Caceres Velazquez H, Jones S, Fierer N.10.1128/mSphere.00237-17Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information2583428776041
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/
68382Automatically annotated from API zym
69479João 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
77239Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID403338.1StrainInfo: A central database for resolving microbial strain identifiers
125438Julia Koblitz, Lorenz Christian Reimer, Rüdiger Pukall, Jörg Overmann10.1101/2024.08.12.607695Predicting bacterial phenotypic traits through improved machine learning using high-quality, curated datasets
125439Philipp Münch, René Mreches, Martin Binder, Hüseyin Anil Gündüz, Xiao-Yin To, Alice McHardyhttps://github.com/GenomeNet/deepGdeepG: Deep Learning for Genome Sequence Data. R package version 0.3.1