Strain identifier

BacDive ID: 13383

Type strain: Yes

Species: Pseudonocardia kongjuensis

Strain Designation: LM 157

Strain history: CIP <- 2003, KCTC <- S.D. Lee, Minnesota Univ., USA: strain LM 157

NCBI tax ID(s): 102227 (species)

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General

@ref: 11732

BacDive-ID: 13383

DSM-Number: 44525

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

description: Pseudonocardia kongjuensis LM 157 is an aerobe, mesophilic, Gram-positive bacterium that was isolated from gold mine cave.

NCBI tax id

  • NCBI tax id: 102227
  • Matching level: species

strain history

@refhistory
11732<- S. D. Lee, Univ. Minnesota; LM 157
67770IMSNU 50583 <-- S. D. Lee LM 157.
67771<- SD Lee, Seoul Natl Univ
120461CIP <- 2003, KCTC <- S.D. Lee, Minnesota Univ., USA: strain LM 157

doi: 10.13145/bacdive13383.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/actinomycetota
  • domain: Bacteria
  • phylum: Actinomycetota
  • class: Actinomycetes
  • order: Pseudonocardiales
  • family: Pseudonocardiaceae
  • genus: Pseudonocardia
  • species: Pseudonocardia kongjuensis
  • full scientific name: Pseudonocardia kongjuensis Lee et al. 2001

@ref: 11732

domain: Bacteria

phylum: Actinobacteria

class: Actinobacteria

order: Actinomycetales

family: Pseudonocardiaceae

genus: Pseudonocardia

species: Pseudonocardia kongjuensis

full scientific name: Pseudonocardia kongjuensis Lee et al. 2001

strain designation: LM 157

type strain: yes

Morphology

cell morphology

@refgram staincell shapemotility
67771positive
120461positiverod-shapedno

colony morphology

  • @ref: 120461

multimedia

  • @ref: 11732
  • multimedia content: https://www.dsmz.de/microorganisms/photos/DSM_44525.jpg
  • caption: Medium 83 28°C
  • intellectual property rights: © Leibniz-Institut DSMZ

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
11732GYM 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
11732CZAPEK PEPTONE AGAR (DSMZ Medium 83)yeshttps://mediadive.dsmz.de/medium/83Name: CZAPEK PEPTONE AGAR (DSMZ Medium 83) Composition: Sucrose 30.0 g/l Agar 20.0 g/l Peptone 5.0 g/l NaNO3 3.0 g/l Yeast extract 2.0 g/l K2HPO4 1.0 g/l MgSO4 x 7 H2O 0.5 g/l KCl 0.5 g/l FeSO4 x 7 H2O 0.01 g/l Distilled water
33875MEDIUM 57 - for Streptomyces, Nocardioides, Lentzea albidocapillata and Streptoverticillium reticulumyesDistilled water make up to (1000.000 ml);Agar (15.000 g);Glucose (4.000g);Yeast extract (4.000 g);Malt extract (10.000 g);Calcium carbonate (2.000 g)
120461CIP Medium 57yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=57

culture temp

@refgrowthtypetemperaturerange
11732positivegrowth28mesophilic
33875positivegrowth30mesophilic
67770positivegrowth28mesophilic
67771positivegrowth30mesophilic
120461positivegrowth25-41
120461nogrowth10psychrophilic
120461nogrowth45thermophilic

Physiology and metabolism

oxygen tolerance

@refoxygen tolerance
67771aerobe
120461obligate aerobe

halophily

@refsaltgrowthtested relationconcentration
120461NaClpositivegrowth0-6 %
120461NaClnogrowth8 %
120461NaClnogrowth10 %

observation

  • @ref: 67770
  • observation: quinones: MK-8(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
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
68371melibiose-builds acid from28053
68371lactose-builds acid from17716
68371cellobiose-builds acid from17057
68371salicin-builds acid from17814
68371esculin-builds acid from4853
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
120461citrate+carbon source16947
120461esculin+hydrolysis4853
120461nitrate-reduction17632
120461nitrite-reduction16301
120461nitrate-respiration17632

antibiotic resistance

  • @ref: 120461
  • metabolite: 0129 (2,4-Diamino-6,7-di-iso-propylpteridine phosphate)
  • is antibiotic: yes
  • is sensitive: no
  • is resistant: yes

metabolite production

  • @ref: 120461
  • Chebi-ID: 35581
  • metabolite: indole
  • production: no

metabolite tests

@refChebi-IDmetabolitevoges-proskauer-testmethylred-test
12046115688acetoin-
12046117234glucose-

enzymes

@refvalueactivityec
120461oxidase-
120461beta-galactosidase+3.2.1.23
120461alcohol dehydrogenase-1.1.1.1
120461gelatinase+
120461amylase+
120461DNase-
120461caseinase-3.4.21.50
120461catalase+1.11.1.6
120461tween esterase+
120461lecithinase-
120461lipase-
120461lysine decarboxylase-4.1.1.18
120461ornithine decarboxylase-4.1.1.17
120461phenylalanine ammonia-lyase-4.3.1.24
120461protease+
120461tryptophan deaminase-
120461urease+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
120461-+++-+--------------

API 50CHac

@refGLYERYDARALARARIBDXYLLXYLADOMDXGALGLUFRUMNESBERHADULINOMANSORMDMMDGNAGAMYARBESCSALCELMALLACMELSACTREINUMLZRAFAMDGLYGXLTGENTURLYXTAGDFUCLFUCDARLLARLGNT2KG5KG
120461---------------------------+/---+/---------+/----------

API biotype100

@refGLUFRUGALTREMNESBEMELSACRAFMTEMALLACLTEMbGaMaGaCELGENMbGuESCRIBARAXYLPLERHAFUCMLZDARLLARLXLTDULTAGGLYINOMANMTLTURSORADOHBGLYXERYMDG3MDGSATMUCLTATDTATMTATDMLTLMLTCATETATETTECITGRTGAT2KG5KGTRYNAGGNTPACPATpOBEQATGTEmOBEBATPPATCMTTGEBETPCEABTHINLATCAPCYTHISSUCFUMGREGYTAVTETNTTNGLNITA3OBUAPTGTTPRODALALALASERMNTPROPTYR2KT
120461++-++--+--+----+----++---++----+-+-+-+--+-------++------++-+++++++------+--+-+-++-------+-++----+++

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinent
11732gold mine caveKorea, KongjuRepublic of KoreaKORAsia
67770Soil at a gold mine caveKongjuRepublic of KoreaKORAsia
67771From a gold mine cave near KongjuRepublic of KoreaKORAsia
120461Environment, Soil, gold mine caveKongjuRepublic of KoreaKORAsia

isolation source categories

  • Cat1: #Engineered
  • Cat2: #Other
  • Cat3: #Mine

taxonmaps

  • @ref: 69479
  • File name: preview.99_32460.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_10;96_175;97_435;98_24033;99_32460&stattab=map
  • Last taxonomy: Pseudonocardia kongjuensis
  • 16S sequence: AJ252833
  • Sequence Identity:
  • Total samples: 247
  • soil counts: 63
  • aquatic counts: 58
  • animal counts: 119
  • plant counts: 7

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
117321Risk group (German classification)
1204612Risk group (French classification)

Sequence information

16S sequences

  • @ref: 20218
  • description: Soil bacterium strain LM 157 16S rRNA gene
  • accession: AJ252833
  • length: 1512
  • database: ena
  • NCBI tax ID: 102227

GC content

@refGC-contentmethod
1173271
6777071high performance liquid chromatography (HPLC)

External links

@ref: 11732

culture collection no.: DSM 44525, IMSNU 50583, KCTC 9990, NBRC 100380, JCM 11896, CGMCC 1.3640, CIP 108046, VKM Ac-2517

straininfo link

  • @ref: 82580
  • straininfo: 50672

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny11491352Pseudonocardia kongjuensis sp. nov., isolated from a gold mine cave.Lee SD, Kim ES, Min KL, Lee WY, Kang SO, Hah YCInt J Syst Evol Microbiol10.1099/00207713-51-4-15052001Actinomycetales/*classification/genetics/*isolation & purification/metabolism, Base Composition, DNA, Bacterial/chemistry/genetics, DNA, Ribosomal/genetics, Fatty Acids/analysis, Gold, Korea, Microscopy, Electron, Scanning, Mining, Molecular Sequence Data, Nucleic Acid Hybridization, Phospholipids/analysis, Phylogeny, Species SpecificityGenetics
Phylogeny19244441Pseudonocardia endophytica sp. nov., isolated from the pharmaceutical plant Lobelia clavata.Chen HH, Qin S, Li J, Zhang YQ, Xu LH, Jiang CL, Kim CJ, Li WJInt J Syst Evol Microbiol10.1099/ijs.0.64740-02009Actinomycetales/*classification/genetics/isolation & purification/physiology, Bacterial Typing Techniques, Base Composition, DNA, Bacterial/analysis/isolation & purification, DNA, Ribosomal/analysis, Genes, rRNA, Lobelia/*microbiology, Medicine, Chinese Traditional, Molecular Sequence Data, Nucleic Acid Hybridization, Phenotype, Phylogeny, Plants, Medicinal/*microbiology, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Species SpecificityEnzymology
Phylogeny22733061Pseudonocardia nantongensis sp. nov., a novel endophytic actinomycete isolated from the coastal halophyte Tamarix chinensis Lour.Xing K, Qin S, Bian GK, Zhang YJ, Zhang WD, Dai CC, Liu CH, Li WJ, Jiang JHAntonie Van Leeuwenhoek10.1007/s10482-012-9764-52012Actinomycetales/*classification/genetics/*isolation & purification/physiology, Bacterial Typing Techniques, Base Composition, China, Cluster Analysis, DNA, Bacterial/chemistry/genetics, DNA, Ribosomal/chemistry/genetics, Endophytes/*classification/genetics/*isolation & purification/physiology, Fatty Acids/analysis, Molecular Sequence Data, Nucleic Acid Hybridization, Phospholipids/analysis, Phylogeny, Plant Leaves/microbiology, RNA, Ribosomal, 16S/genetics, Salt-Tolerant Plants/microbiology, Sequence Analysis, DNA, Tamaricaceae/*microbiology, Ubiquinone/analysisEnzymology

Reference

@idauthorscataloguedoi/urltitlejournalpubmed
11732Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 44525)https://www.dsmz.de/collection/catalogue/details/culture/DSM-44525
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
33875Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/5625
67770Curators of the JCMhttps://jcm.brc.riken.jp/en/
67771Curators of the KCTChttps://kctc.kribb.re.kr/En/Kctc
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
82580Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID50672.1StrainInfo: A central database for resolving microbial strain identifiers
120461Curators of the CIPCollection of Institut Pasteur (CIP 108046)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20108046