Strain identifier

BacDive ID: 8043

Type strain: Yes

Species: Catelliglobosispora koreensis

Strain Designation: LM042, LM 042

Strain history: CIP <- 2001, JCM <- S.O. Kang: strain LM 042

NCBI tax ID(s): 1121272 (strain), 129052 (species)

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General

@ref: 11762

BacDive-ID: 8043

DSM-Number: 44566

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

description: Catelliglobosispora koreensis LM042 is a spore-forming, mesophilic bacterium that was isolated from soil of gold mine cave.

NCBI tax id

NCBI tax idMatching level
1121272strain
129052species

strain history

@refhistory
11762<- S. D. Lee, Univ. Minnesota; LM042 = IMSNU 50729
67770S.-O. Kang LM 042.
120472CIP <- 2001, JCM <- S.O. Kang: strain LM 042

doi: 10.13145/bacdive8043.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/actinomycetota
  • domain: Bacteria
  • phylum: Actinomycetota
  • class: Actinomycetes
  • order: Micromonosporales
  • family: Micromonosporaceae
  • genus: Catelliglobosispora
  • species: Catelliglobosispora koreensis
  • full scientific name: Catelliglobosispora koreensis (Lee et al. 2000) Ara et al. 2008

  • synonyms

    • @ref: 20215
    • synonym: Catellatospora koreensis

@ref: 11762

domain: Bacteria

phylum: Actinobacteria

class: Actinobacteria

order: Actinomycetales

family: Micromonosporaceae

genus: Catelliglobosispora

species: Catelliglobosispora koreensis

full scientific name: Catelliglobosispora koreensis (Lee et al. 2000) Ara et al. 2008 emend. Nouioui et al. 2018

strain designation: LM042, LM 042

type strain: yes

Morphology

cell morphology

@refmotilityconfidencegram staincell shape
69480no91.222
69480100positive
120472nofilament-shaped

multimedia

@refmultimedia contentcaptionintellectual property rights
11762https://www.dsmz.de/microorganisms/photos/DSM_44566.jpgMedium 65 28°C© Leibniz-Institut DSMZ
66793EM_DSM_44566_1.jpgelectron microscopic image© HZI/Manfred Rohde
66793EM_DSM_44566_2.jpgelectron microscopic image© HZI/Manfred Rohde
66793EM_DSM_44566_3.jpgelectron microscopic image© HZI/Manfred Rohde
66793EM_DSM_44566_4.jpgelectron microscopic image© HZI/Manfred Rohde
66793EM_DSM_44566_5.jpgelectron microscopic image© HZI/Manfred Rohde

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
11762STARCH - MINERAL SALT - AGAR (STMS) (DSMZ Medium 252)yeshttps://mediadive.dsmz.de/medium/252Name: STARCH - MINERAL SALT - AGAR (STMS) (DSMZ Medium 252) Composition: Agar 14.985 g/l Starch 9.99001 g/l (NH4)2SO4 1.998 g/l CaCO3 1.998 g/l K2HPO4 0.999001 g/l MgSO4 x 7 H2O 0.999001 g/l NaCl 0.999001 g/l FeSO4 x 7 H2O 0.000999001 g/l MnCl2 x 4 H2O 0.000999001 g/l ZnSO4 x 7 H2O 0.000999001 g/l Distilled water
11762GYM 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
40655MEDIUM 375 - for Catellospora koreensisyesDistilled water make up to (1000.000 ml);Magnesium sulphate heptahydrate (0.500 g);Agar (15.000 g);Yeast extract (4.000 g);Starch maize (15.000 g);Di Potassium monohydrogenophosphate (0.500 g)
11762ROLLED 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
120472CIP Medium 375yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=375

culture temp

@refgrowthtypetemperaturerange
40655positivegrowth30mesophilic
67770positivegrowth28mesophilic
11762positivegrowth28mesophilic
120472positivegrowth25-30mesophilic
120472nogrowth10psychrophilic
120472nogrowth37mesophilic
120472nogrowth41thermophilic
120472nogrowth45thermophilic

Physiology and metabolism

spore formation

  • @ref: 69480
  • spore formation: yes
  • confidence: 100

halophily

@refsaltgrowthtested relationconcentration
120472NaClpositivegrowth0 %
120472NaClnogrowth2 %
120472NaClnogrowth4 %
120472NaClnogrowth6 %
120472NaClnogrowth8 %
120472NaClnogrowth10 %

observation

  • @ref: 67770
  • observation: quinones: MK-10(H4), MK-10(H6), MK-9(H4)

metabolite utilization

@refmetaboliteutilization activitykind of utilization testedChebi-ID
68371Potassium 5-ketogluconate-builds acid from
68371Potassium 2-ketogluconate-builds acid from
68371gluconate-builds acid from24265
68371L-arabitol-builds acid from18403
68371D-arabitol-builds acid from18333
68371L-fucose-builds acid from18287
68371D-fucose-builds acid from28847
68371D-tagatose-builds acid from16443
68371D-lyxose-builds acid from62318
68371turanose-builds acid from32528
68371gentiobiose-builds acid from28066
68371xylitol-builds acid from17151
68371glycogen-builds acid from28087
68371starch-builds acid from28017
68371raffinose-builds acid from16634
68371melezitose-builds acid from6731
68371inulin-builds acid from15443
68371trehalose-builds acid from27082
68371sucrose-builds acid from17992
68371melibiose-builds acid from28053
68371lactose-builds acid from17716
68371maltose-builds acid from17306
68371cellobiose-builds acid from17057
68371salicin-builds acid from17814
68371arbutin-builds acid from18305
68371amygdalin-builds acid from27613
68371N-acetylglucosamine-builds acid from59640
68371methyl alpha-D-glucopyranoside-builds acid from320061
68371methyl alpha-D-mannoside-builds acid from43943
68371D-sorbitol-builds acid from17924
68371D-mannitol-builds acid from16899
68371myo-inositol-builds acid from17268
68371galactitol-builds acid from16813
68371L-rhamnose-builds acid from62345
68371L-sorbose-builds acid from17266
68371D-mannose-builds acid from16024
68371D-fructose-builds acid from15824
68371D-glucose-builds acid from17634
68371D-galactose-builds acid from12936
68371methyl beta-D-xylopyranoside-builds acid from74863
68371ribitol-builds acid from15963
68371L-xylose-builds acid from65328
68371D-xylose-builds acid from65327
68371D-ribose-builds acid from16988
68371L-arabinose-builds acid from30849
68371D-arabinose-builds acid from17108
68371erythritol-builds acid from17113
68371glycerol-builds acid from17754
120472esculin+hydrolysis4853
120472hippurate-hydrolysis606565
120472nitrate+reduction17632
120472nitrite-reduction16301

antibiotic resistance

  • @ref: 120472
  • metabolite: 0129 (2,4-Diamino-6,7-di-iso-propylpteridine phosphate)
  • is antibiotic: yes
  • is sensitive: yes
  • is resistant: no

metabolite production

  • @ref: 120472
  • Chebi-ID: 35581
  • metabolite: indole
  • production: no

metabolite tests

@refChebi-IDmetabolitevoges-proskauer-testmethylred-test
12047215688acetoin-
12047217234glucose-

enzymes

@refvalueactivityec
120472oxidase-
120472beta-galactosidase-3.2.1.23
120472alcohol dehydrogenase-1.1.1.1
120472gelatinase+
120472catalase+1.11.1.6
120472gamma-glutamyltransferase+2.3.2.2
120472lysine decarboxylase-4.1.1.18
120472ornithine decarboxylase-4.1.1.17
120472phenylalanine ammonia-lyase-4.3.1.24
120472tryptophan deaminase+
120472urease-3.5.1.5
68382alkaline phosphatase+3.1.3.1
68382esterase (C 4)+
68382esterase lipase (C 8)+
68382lipase (C 14)-
68382leucine arylamidase+3.4.11.1
68382valine arylamidase+
68382cystine arylamidase-3.4.11.3
68382trypsin+3.4.21.4
68382alpha-chymotrypsin-3.4.21.1
68382acid phosphatase+3.1.3.2
68382naphthol-AS-BI-phosphohydrolase+
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

API zym

@refControlAlkaline phosphataseEsteraseEsterase LipaseLipaseLeucine arylamidaseValine arylamidaseCystine arylamidaseTrypsinalpha- ChymotrypsinAcid phosphataseNaphthol-AS-BI-phosphohydrolasealpha- Galactosidasebeta- Galactosidasebeta- Glucuronidasealpha- Glucosidasebeta- GlucosidaseN-acetyl-beta- glucosaminidasealpha- Mannosidasealpha- Fucosidase
120472-+++-++-+-++---+++--

API 50CHac

@refGLYERYDARALARARIBDXYLLXYLADOMDXGALGLUFRUMNESBERHADULINOMANSORMDMMDGNAGAMYARBESCSALCELMALLACMELSACTREINUMLZRAFAMDGLYGXLTGENTURLYXTAGDFUCLFUCDARLLARLGNT2KG5KG
120472------------------------+/-------------------------

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinent
11762soil of gold mine caveKorea, KongjuRepublic of KoreaKORAsia
67770Soil at a gold-mine caveKongjuRepublic of KoreaKORAsia
120472Environment, Soil at a gold-mine caveKongjuRepublic of KoreaKORAsia

isolation source categories

Cat1Cat2Cat3
#Engineered#Other#Mine
#Environmental#Terrestrial#Soil

taxonmaps

  • @ref: 69479
  • File name: preview.99_4812.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_94;96_2375;97_2891;98_3602;99_4812&stattab=map
  • Last taxonomy: Catelliglobosispora koreensis subclade
  • 16S sequence: AF171700
  • Sequence Identity:
  • Total samples: 5126
  • soil counts: 3344
  • aquatic counts: 259
  • animal counts: 212
  • plant counts: 1311

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
117621Risk group (German classification)
1204721Risk group (French classification)

Sequence information

16S sequences

  • @ref: 11762
  • description: Catellatospora koreensis 16S ribosomal RNA gene, partial sequence
  • accession: AF171700
  • length: 1510
  • database: ena
  • NCBI tax ID: 1121272

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Catelliglobosispora koreensis DSM 445661121272.3wgspatric1121272
66792Catelliglobosispora koreensis DSM 445662515154016draftimg1121272
67770Catelliglobosispora koreensis DSM 44566GCA_000379685scaffoldncbi1121272

GC content

@refGC-contentmethod
1176270.4high performance liquid chromatography (HPLC)
6777064.4genome sequence analysis

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingyes70no
motileno93.626no
flagellatedno98.173no
gram-positiveyes89.095no
anaerobicno99.195no
aerobicyes91.302no
halophileno93.573no
spore-formingyes91.271no
thermophileno97.68no
glucose-utilyes86.583no
glucose-fermentno89.159no

External links

@ref: 11762

culture collection no.: DSM 44566, JCM 10976, IMSNU 50729, CGMCC 4.5570, CIP 107020, NBRC 105861

straininfo link

  • @ref: 77471
  • straininfo: 50681

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny10843051Catellatospora koreensis sp. nov., a novel actinomycete isolated from a gold-mine cave.Lee SD, Kang SO, Hah YCInt J Syst Evol Microbiol10.1099/00207713-50-3-11032000Actinomycetales/*classification/genetics/isolation & purification/physiology, Base Composition, DNA, Bacterial/chemistry/genetics, DNA, Ribosomal/chemistry/genetics, Fatty Acids/analysis, *Gold, *Mining, Molecular Sequence Data, Nucleic Acid Hybridization, Phenotype, Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, *Soil MicrobiologyGenetics
Phylogeny18676486Transfer of Catellatospora koreensis Lee et al. 2000 as Catelliglobosispora koreensis gen. nov., comb. nov. and Catellatospora tsunoense Asano et al. 1989 as Hamadaea tsunoensis gen. nov., comb. nov., and emended description of the genus Catellatospora Asano and Kawamoto 1986 emend. Lee and Hah 2002.Ara I, Bakir MA, Kudo TInt J Syst Evol Microbiol10.1099/ijs.0.65548-02008Bacterial Typing Techniques, DNA, Bacterial/analysis, DNA, Ribosomal/analysis, Fatty Acids/analysis, Genes, rRNA, Japan, Korea, Micromonosporaceae/chemistry/*classification/genetics/physiology, Molecular Sequence Data, Nucleic Acid Hybridization, Phenotype, Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, *Soil Microbiology, Species SpecificityGenetics
Phylogeny30444473Allorhizocola rhizosphaerae gen. nov., sp. nov., a new member of Micromonosporaceae isolated from rhizosphere soil of the plant Calligonum mongolicum.Sun Y, Jiang ZM, Zhao LL, Su J, Yu LY, Tian YQ, Zhang YQInt J Syst Evol Microbiol10.1099/ijsem.0.0031142018Bacterial Typing Techniques, Base Composition, Cell Wall/chemistry, China, DNA, Bacterial/genetics, Diaminopimelic Acid/chemistry, Fatty Acids/chemistry, Micromonosporaceae/*classification/isolation & purification, Peptidoglycan/chemistry, *Phylogeny, Polygonaceae/*microbiology, RNA, Ribosomal, 16S/genetics, *Rhizosphere, Sequence Analysis, DNA, *Soil Microbiology, Vitamin K 2/chemistryTranscriptome

Reference

@idauthorscataloguedoi/urltitlejournalpubmed
11762Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 44566)https://www.dsmz.de/collection/catalogue/details/culture/DSM-44566
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
40655Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/19215
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)
66793Mukherjee et al.10.1038/nbt.3886GEBA: 1,003 reference genomes of bacterial and archaeal isolates expand coverage of the tree of life 35: 676-683 201728604660
67770Curators of the JCMhttps://jcm.brc.riken.jp/en/
68371Automatically annotated from API 50CH acid
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
69480Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmannhttps://diaspora-project.de/progress.html#genomesPredictions based on genome sequence made in the Diaspora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information)
77471Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID50681.1StrainInfo: A central database for resolving microbial strain identifiers
120472Curators of the CIPCollection of Institut Pasteur (CIP 107020)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20107020