Strain identifier

BacDive ID: 158522

Type strain: Yes

Species: Rhodococcus subtropicus

Strain Designation: C9-28

Strain history: <- S. D. Lee, Jeju National Univ., Rep. of Korea; C9-28 <- S. D. Lee, Jeju National Univ., Rep. of Korea; C9-28

NCBI tax ID(s): 2545757 (species)

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General

@ref: 65199

BacDive-ID: 158522

DSM-Number: 107559

keywords: genome sequence, 16S sequence, aerobe, mesophilic, Gram-positive, rod-shaped

description: Rhodococcus subtropicus C9-28 is an aerobe, mesophilic, Gram-positive prokaryote that was isolated from soil inside a natural cave.

NCBI tax id

  • NCBI tax id: 2545757
  • Matching level: species

strain history

  • @ref: 65199
  • history: <- S. D. Lee, Jeju National Univ., Rep. of Korea; C9-28 <- S. D. Lee, Jeju National Univ., Rep. of Korea; C9-28

doi: 10.13145/bacdive158522.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • genus: Rhodococcus
  • species: Rhodococcus subtropicus
  • full scientific name: Rhodococcus subtropicus Lee et al. 2019

  • synonyms

    • @ref: 20215
    • synonym: Prescottella subtropica

@ref: 65199

domain: Bacteria

phylum: Actinobacteria

class: Actinobacteria

order: Actinomycetales

family: Nocardiaceae

genus: Rhodococcus

species: Rhodococcus subtropicus

full scientific name: Rhodococcus subtropicus Lee et al., 2019

strain designation: C9-28

type strain: yes

Morphology

cell morphology

@refgram staincell shapemotilityconfidence
68023positiverod-shaped
68023coccus-shaped
68023no
69480positive100

colony morphology

@refcolony colormedium usedcolony sizecolony shapeincubation period
69246ColourlessISP 3
69246Beige (1001), sand yellow (1002)ISP 6
69246Beige (1001), grey beige (1019)suter with tyrosine
68023cream1.0-1.5 mmcircular5 days
69246Ivory (1014)ISP 4
69246Ivory (1014), light ivory (1015)ISP 5
69246Ivory (1014), light ivory (1015)ISP 7
69246Ivory (1014), light ivory (1015)suter without tyrosine
69246Sand yellow (1002)ISP 2

multicellular morphology

@refforms multicellular complexcomplex namemedium name
69246noAerial myceliumISP 2
69246noAerial myceliumISP 3
69246noAerial myceliumISP 4
69246noAerial myceliumISP 5
69246noAerial myceliumISP 6
69246noAerial myceliumISP 7
69246noAerial myceliumsuter with tyrosine
69246noAerial myceliumsuter without tyrosine

pigmentation

@refproductionnamecolor
69246noMelanin
69246yessoluble pigmentBeige (1001)

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
65199TRYPTICASE SOY BROTH AGAR (DSMZ Medium 535)yeshttps://mediadive.dsmz.de/medium/535Name: TRYPTICASE SOY BROTH AGAR (DSMZ Medium 535) Composition: Trypticase soy broth 30.0 g/l Agar 15.0 g/l Distilled water
65199ISP2 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

@refgrowthtypetemperaturerange
65199positivegrowth30mesophilic
68023positivegrowth10-30
68023positiveoptimum30mesophilic

culture pH

@refabilitytypepHPH range
68023positivegrowth6.0-9.0alkaliphile
68023positiveoptimum7

Physiology and metabolism

oxygen tolerance

  • @ref: 68023
  • oxygen tolerance: aerobe

spore formation

@refspore formationconfidence
69480no99.695
69481yes100

halophily

@refsaltgrowthtested relationconcentration
68023NaClpositivegrowth0.0-3.0 %
68023NaClpositiveoptimum0 %
69246NaClpositivegrowth0-2.5 %

observation

@refobservation
68023a rod-coccus cycle during growth is observed
68023meso-Diaminopimelic acid, arabinose and galactose are the diagnostic diamino acid and wholecell sugars in the cell wall
68023The predominant menaquinone is MK-8(H2)
68023The polar lipids contain diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylglycerol, phosphatidylinositol, phosphatidylinositol mannoside, three unidentified glycolipids and two unidentified lipids

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
6802317632nitrate+reduction
680235291gelatin+degradation
680234853esculin+hydrolysis
6802316991dna+hydrolysis
6802385146carboxymethylcellulose-hydrolysis
68023casein-hydrolysis
6802328017starch-hydrolysis
6802317368hypoxanthine-degradation
6802318186tyrosine-degradation
6802315318xanthine-degradation
6802317924D-sorbitol+carbon source
6802317924D-sorbitol+energy source
6802318401phenylacetate-energy source
6802315963ribitol-energy source
6802317108D-arabinose-energy source
6802316150benzoate-energy source
6802317057cellobiose-energy source
6802316813galactitol-energy source
6802352071dextran-energy source
6802362965sodium formate-energy source
6802315824D-fructose-energy source
6802317754glycerol-energy source
6802312936D-galactose-energy source
6802317268myo-inositol-energy source
6802317716lactose-energy source
680236731melezitose-energy source
6802328053melibiose-energy source
6802337657methyl D-glucoside-energy source
6802343943methyl alpha-D-mannoside-energy source
6802316634raffinose-energy source
6802362345L-rhamnose-energy source
6802317266L-sorbose-energy source
6802317814salicin-energy source
6802330031succinate-energy source
6802317992sucrose-energy source
6802327082trehalose-energy source
6802330927D-tartrate-energy source
6802330924L-tartrate-energy source
6802317151xylitol-energy source
6802365327D-xylose-energy source
6802318401phenylacetate-carbon source
6802315963ribitol-carbon source
6802317108D-arabinose-carbon source
6802316150benzoate-carbon source
6802317057cellobiose-carbon source
6802316813galactitol-carbon source
6802352071dextran-carbon source
6802362965sodium formate-carbon source
6802315824D-fructose-carbon source
6802317754glycerol-carbon source
6802312936D-galactose-carbon source
6802317268myo-inositol-carbon source
6802317716lactose-carbon source
680236731melezitose-carbon source
6802328053melibiose-carbon source
6802337657methyl D-glucoside-carbon source
6802343943methyl alpha-D-mannoside-carbon source
6802316634raffinose-carbon source
6802362345L-rhamnose-carbon source
6802317266L-sorbose-carbon source
6802317814salicin-carbon source
6802330031succinate-carbon source
6802317992sucrose-carbon source
6802327082trehalose-carbon source
6802330927D-tartrate-carbon source
6802330924L-tartrate-carbon source
6802317151xylitol-carbon source
6802365327D-xylose-carbon source
6802317234glucose-builds acid from
6802317634D-glucose+/-assimilation
6802325115malate+assimilation
6802330849L-arabinose-assimilation
6802316024D-mannose-assimilation
6802316899D-mannitol-assimilation
68023506227N-acetyl-D-glucosamine-assimilation
6802317306maltose-assimilation
6802324265gluconate-assimilation
6802317120hexanoate-assimilation
6802317128adipate-assimilation
6802316947citrate-assimilation
6802318401phenylacetate-assimilation
6924622599arabinose+growth
6924662968cellulose+growth
6924628757fructose-growth
6924617234glucose+growth
6924617268inositol+growth
6924637684mannose-growth
6924616634raffinose+growth
6924626546rhamnose+growth
6924617992sucrose+growth
6924618222xylose+growth
6837917632nitrate+reduction
683794853esculin-hydrolysis
6837916199urea-hydrolysis
683795291gelatin-hydrolysis
6837917634D-glucose-fermentation
6837916988D-ribose-fermentation
6837965327D-xylose-fermentation
6837916899D-mannitol-fermentation
6837917306maltose-fermentation
6837917716lactose-fermentation
6837917992sucrose-fermentation
6837928087glycogen-fermentation

metabolite production

  • @ref: 68023
  • Chebi-ID: 35581
  • metabolite: indole
  • production: no

enzymes

@refvalueactivityec
68023urease-3.5.1.5
68023cytochrome oxidase-1.9.3.1
68023catalase+1.11.1.6
68023arginine dihydrolase-3.5.3.6
68023alkaline phosphatase+/-3.1.3.1
68023esterase (C 4)+
68023esterase Lipase (C 8)+
68023leucine arylamidase+3.4.11.1
68023valine arylamidase+
68023acid phosphatase+3.1.3.2
68023naphthol-AS-BI-phosphohydrolase+
68023lipase (C 14)-
68023cystine arylamidase-3.4.11.3
68023trypsin-3.4.21.4
68023alpha-chymotrypsin-3.4.21.1
68023alpha-galactosidase-3.2.1.22
68023beta-galactosidase-3.2.1.23
68023beta-glucuronidase-3.2.1.31
68023alpha-glucosidase-3.2.1.20
68023beta-glucosidase-3.2.1.21
68023N-acetyl-beta-glucosaminidase-3.2.1.52
68023alpha-mannosidase-3.2.1.24
68023alpha-fucosidase-3.2.1.51
68379gelatinase-
68379urease-3.5.1.5
68379beta-glucosidase-3.2.1.21
68379N-acetyl-beta-glucosaminidase-3.2.1.52
68379alpha-glucosidase-3.2.1.20
68379beta-galactosidase-3.2.1.23
68379beta-glucuronidase-3.2.1.31
68379alkaline phosphatase-3.1.3.1
68379pyrrolidonyl arylamidase-3.4.19.3
68379pyrazinamidase-3.5.1.B15
68382esterase (C 4)-
68382leucine arylamidase+3.4.11.1
68382trypsin-3.4.21.4
68382alpha-chymotrypsin-3.4.21.1
68382alpha-galactosidase-3.2.1.22
68382beta-galactosidase-3.2.1.23
68382beta-glucuronidase-3.2.1.31
68382alpha-glucosidase-3.2.1.20
68382beta-glucosidase-3.2.1.21
68382N-acetyl-beta-glucosaminidase-3.2.1.52
68382alpha-mannosidase-3.2.1.24
68382alpha-fucosidase-3.2.1.51

fatty acid profile

  • fatty acids

    @reffatty acidpercentage
    68023C14:010.8
    68023C16:026.6
    68023C17:02.8
    68023C18:01.7
    68023C15:0 anteiso1.3
    68023C17:1 w8c5
    68023C18:1 w9c13.5
    68023C16:0 10-ME2.6
    68023C17:0 10-methyl1.5
    68023TBSA 10Me18:06.6
    68023C16:1 w7c / C16:1 w6c20
    68023C19:1 w11c / C19:1 w9c1.5
    68023C19:0 cyclo / C19:1 w6c1.2
  • type of FA analysis: whole cell analysis
  • incubation medium: ISP 2
  • agar/liquid: liquid
  • incubation temperature: 30
  • incubation time: 3.5
  • software version: Sherlock 6.1
  • library/peak naming table: RTSBA6
  • system: MIS MIDI
  • method/protocol: Sasser, 1990
  • cutoff value:

API coryne

@refNITPYZPYRAPALbeta GURbeta GALalpha GLUbeta NAGESCUREGELControlGLURIBXYLMANMALLACSACGLYG
65199+-------------------
69246+------------------

API zym

@refControlAlkaline phosphataseEsteraseEsterase LipaseLipaseLeucine arylamidaseValine arylamidaseCystine arylamidaseTrypsinalpha- ChymotrypsinAcid phosphataseNaphthol-AS-BI-phosphohydrolasealpha- Galactosidasebeta- Galactosidasebeta- Glucuronidasealpha- Glucosidasebeta- GlucosidaseN-acetyl-beta- glucosaminidasealpha- Mannosidasealpha- Fucosidase
65199-----++/--------------
69246+/--+/-+/-+++/---+/-+/---------

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinentlatitudelongitude
65199soil inside a natural caveJeju (33° 18' 43'' N, 126° 18' 21'' E)Republic of KoreaKORAsia33.3119126.306
68023soil sampled inside a natural caveJeju IslandRepublic of KoreaKORAsia33.3119126.307

isolation source categories

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

Sequence information

16S sequences

@refdescriptionaccessionlengthdatabaseNCBI tax ID
65199Rhodococcus subtropicus 16S ribosomal RNA gene, partial sequenceMK6052851430ena2545757
68023Rhodococcus subtropicus strain C9-28 16S ribosomal RNA, partial sequenceNR_1694751430nuccore2545757

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Rhodococcus subtropicus C9-282906892708draftimg2545757
68023Prescottella subtropica C9-28GCA_005434945scaffoldncbi2545757

GC content

@refGC-contentmethod
6519969.3sequence analysis
6802369.1genome sequence analysis

Genome-based predictions

predictions

  • trait: spore-forming
  • prediction: yes
  • confidence: 100
  • training_data: no

External links

@ref: 65199

culture collection no.: DSM 107559, KACC 19823

straininfo link

  • @ref: 111317
  • straininfo: 407868

literature

  • topic: Phylogeny
  • Pubmed-ID: 31364963
  • title: Rhodococcus subtropicus sp. nov., a new actinobacterium isolated from a cave.
  • authors: Lee SD, Kim YJ, Kim IS
  • journal: Int J Syst Evol Microbiol
  • DOI: 10.1099/ijsem.0.003601
  • year: 2019
  • mesh: Bacterial Typing Techniques, Base Composition, Caves/*microbiology, DNA, Bacterial/genetics, Diaminopimelic Acid/chemistry, Fatty Acids/chemistry, Nucleic Acid Hybridization, Phospholipids/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, Republic of Korea, Rhodococcus/*classification/isolation & purification, Sequence Analysis, DNA, *Soil Microbiology, Vitamin K 2/analogs & derivatives/chemistry
  • topic2: Transcriptome

Reference

@idauthorstitledoi/urlcataloguejournal
20215Parte, A.C., Sardà Carbasse, J., Meier-Kolthoff, J.P., Reimer, L.C. and Göker, M.List of Prokaryotic names with Standing in Nomenclature (LPSN) moves to the DSMZ10.1099/ijsem.0.004332
65199Curators of the DSMZhttps://www.dsmz.de/collection/catalogue/details/culture/DSM-107559Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 107559)
66792Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg OvermannAutomatically annotated for the DiASPora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information)https://diaspora-project.de/progress.html#genomes
68023Soon Dong Lee, Young-Ju Kim, In Seop KimRhodococcus subtropicus sp. nov., a new actinobacterium isolated from a cave10.1099/ijsem.0.003601IJSEM 69: 3128-3134 2019
68379Automatically annotated from API Coryne
68382Automatically annotated from API zym
69246Wink, J.Compendium of Actinobacteria. HZI-Helmholtz-Centre for Infection Research, Braunschweighttps://cdn.dsmz.de/wink/DSM%20107559.pdf
69480Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg OvermannPredictions based on genome sequence made in the Diaspora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information)https://diaspora-project.de/progress.html#genomes
69481Xiao-Yin To, René Mreches, Martin Binder, Alice C. McHardy, Philipp C. MünchPredictions based on the model GenomeNet Sporulation v. 110.21203/rs.3.rs-2527258/v1
111317Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.StrainInfo: A central database for resolving microbial strain identifiers10.60712/SI-ID407868.1