Strain identifier

BacDive ID: 13293

Type strain: Yes

Species: Kutzneria albida

Strain Designation: MCRL-048

Strain history: KCC A-0240 <-- Tanabe Seiyaku Co., Ltd., Japan; MCRL 048.

NCBI tax ID(s): 1449976 (strain), 43357 (species)

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General

@ref: 11351

BacDive-ID: 13293

DSM-Number: 43870

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

description: Kutzneria albida MCRL-048 is a spore-forming, mesophilic bacterium that builds an aerial mycelium and was isolated from soil.

NCBI tax id

NCBI tax idMatching level
43357species
1449976strain

strain history

@refhistory
11351<- ATCC <- T. Okuda, MCRL, 048
67770KCC A-0240 <-- Tanabe Seiyaku Co., Ltd., Japan; MCRL 048.

doi: 10.13145/bacdive13293.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/actinomycetota
  • domain: Bacteria
  • phylum: Actinomycetota
  • class: Actinomycetes
  • order: Pseudonocardiales
  • family: Pseudonocardiaceae
  • genus: Kutzneria
  • species: Kutzneria albida
  • full scientific name: Kutzneria albida (Furumai et al. 1968) Stackebrandt et al. 1994

  • synonyms

    • @ref: 20215
    • synonym: Streptosporangium albidum

@ref: 11351

domain: Bacteria

phylum: Actinobacteria

class: Actinobacteria

order: Actinomycetales

family: Pseudonocardiaceae

genus: Kutzneria

species: Kutzneria albida

full scientific name: Kutzneria albida (Furumai et al. 1968) Stackebrandt et al. 1994

strain designation: MCRL-048

type strain: yes

Morphology

cell morphology

@refmotilityconfidencegram stain
69480no95.333
69480100positive

colony morphology

@refcolony colorincubation periodmedium used
19973Beige (1001)10-14 daysISP 2
19973Beige (1001)10-14 daysISP 3
19973Beige (1001)10-14 daysISP 4
19973Beige (1001)10-14 daysISP 5
19973Beige (1001)10-14 daysISP 6
19973Beige (1001)10-14 daysISP 7

multicellular morphology

@refforms multicellular complexcomplex namecomplex colormedium name
19973yesAerial MyceliumWhiteISP 2
19973yesAerial MyceliumWhiteISP 3
19973yesAerial MyceliumWhiteISP 4
19973yesAerial MyceliumWhiteISP 5
19973yesAerial MyceliumWhiteISP 6
19973yesAerial MyceliumWhiteISP 7

multimedia

@refmultimedia contentintellectual property rightscaption
11351https://www.dsmz.de/microorganisms/photos/DSM_43870-1.jpg© Leibniz-Institut DSMZ
11351https://www.dsmz.de/microorganisms/photos/DSM_43870.jpg© Leibniz-Institut DSMZMedium 65 28°C

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
11351GYM 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
19973ISP 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
19973ISP 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:
19973ISP 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
19973ISP 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
19973ISP 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
19973ISP 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

culture temp

@refgrowthtypetemperaturerange
19973positiveoptimum30mesophilic
11351positivegrowth28mesophilic
67770positivegrowth28mesophilic

Physiology and metabolism

spore formation

@refspore descriptionspore formationconfidence
19973Formation of spore chains (rectiflixibilis), spore surface smoothyes
69481yes100
69480yes100

compound production

@refcompound
11351sporaviridin-like antibiotic
19973Aculeximycin
67770Sporaviridin-like antibiotic

halophily

  • @ref: 19973
  • salt: NaCl
  • growth: positive
  • tested relation: maximum
  • concentration: 2.5 %

observation

  • @ref: 67770
  • observation: quinones: MK-9(II,III-H4)

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
1997317234glucose-
1997322599arabinose-
1997317992sucrose-
1997318222xylose-
1997317268myo-inositol+
1997329864mannitol+
1997328757fructose-
1997326546rhamnose-
1997316634raffinose-
1997362968cellulose-
6836817632nitrate-reduction
6836830849L-arabinose-fermentation
6836827613amygdalin-fermentation
6836828053melibiose-fermentation
6836817992sucrose-fermentation
6836862345L-rhamnose-fermentation
6836830911sorbitol-fermentation
6836817268myo-inositol-fermentation
6836816899D-mannitol-fermentation
6836817634D-glucose-fermentation
683685291gelatin+hydrolysis
6836827897tryptophan-energy source
6836816947citrate-assimilation
6836818257ornithine-degradation

metabolite production

@refChebi-IDmetaboliteproduction
6836817997dinitrogenno
6836816301nitriteno
6836815688acetoinyes
6836835581indoleno
6836816136hydrogen sulfideno

metabolite tests

@refChebi-IDmetabolitevoges-proskauer-testindole test
6836815688acetoin+
6836835581indole-

enzymes

@refvalueactivityec
68368gelatinase+
68368tryptophan deaminase-4.1.99.1
68368ornithine decarboxylase-4.1.1.17
68382alkaline phosphatase+3.1.3.1
68382esterase lipase (C 8)+
68382leucine arylamidase+3.4.11.1
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
68382beta-glucosidase+3.2.1.21
68382N-acetyl-beta-glucosaminidase+3.2.1.52
68382alpha-mannosidase+3.2.1.24

API zym

@refAlkaline phosphataseEsteraseEsterase LipaseLipaseLeucine arylamidaseValine arylamidaseCystine arylamidaseTrypsinalpha- ChymotrypsinAcid phosphataseNaphthol-AS-BI-phosphohydrolasealpha- Galactosidasebeta- Galactosidasebeta- Glucuronidasealpha- Glucosidasebeta- GlucosidaseN-acetyl-beta- glucosaminidasealpha- Mannosidasealpha- FucosidaseControl
19973+++++++++++-+-+++++
11351+-+-++/---+/-++-+--+++--

API 20E

@refONPGADH ArgLDC LysODCCITH2SURETDA TrpINDVPGELGLUMANINOSorRHASACMELAMYARANO2N2
19973-++---+--++
11351+--------++-----------

Isolation, sampling and environmental information

isolation

@refsample typecountryorigin.countrycontinentgeographic location
11351soilJapanJPNAsia
67770SoilJapanJPNAsiaMt. Tanigawa, Gunma Pref.

isolation source categories

  • Cat1: #Environmental
  • Cat2: #Terrestrial
  • Cat3: #Soil

taxonmaps

  • @ref: 69479
  • File name: preview.99_2765.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_10;96_549;97_1753;98_2145;99_2765&stattab=map
  • Last taxonomy: Kutzneria
  • 16S sequence: EF543522
  • Sequence Identity:
  • Total samples: 1769
  • soil counts: 1307
  • aquatic counts: 34
  • animal counts: 80
  • plant counts: 348

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
113511Risk group (German classification)
199731German classification

Sequence information

16S sequences

  • @ref: 67770
  • description: Kutzneria albida strain NRRL B-24060 16S ribosomal RNA gene, partial sequence
  • accession: EF543522
  • length: 1502
  • database: ena
  • NCBI tax ID: 43357

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Kutzneria albida DSM 43870GCA_000525635completencbi1449976
66792Kutzneria albida DSM 438701449976.3completepatric1449976
66792Kutzneria albida DSM 438702565956555completeimg1449976
67770Kutzneria albida NRRL B-24060GCA_000715805scaffoldncbi43357

GC content

  • @ref: 67770
  • GC-content: 70.7
  • method: high performance liquid chromatography (HPLC)

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingyes100no
motileno92.723no
flagellatedno97.307no
gram-positiveyes88.294no
anaerobicno99.162no
halophileno94.721no
spore-formingyes94.687no
thermophileno97.636yes
glucose-utilyes88.67yes
aerobicyes93.863no
glucose-fermentno91.155yes

External links

@ref: 11351

culture collection no.: DSM 43870, ATCC 25243, IFO 13901, NBRC 13901, JCM 3240, BCRC 13345, CGMCC 4.1347, CGMCC 4.1497, IFM 1281, IMSNU 20234, KCCM 40283, KCTC 9237, NRRL B-24060

straininfo link

  • @ref: 82494
  • straininfo: 38437

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Genetics25301375Complete genome sequence of producer of the glycopeptide antibiotic Aculeximycin Kutzneria albida DSM 43870T, a representative of minor genus of Pseudonocardiaceae.Rebets Y, Tokovenko B, Lushchyk I, Ruckert C, Zaburannyi N, Bechthold A, Kalinowski J, Luzhetskyy ABMC Genomics10.1186/1471-2164-15-8852014Actinomycetales/*genetics/*metabolism, Anti-Bacterial Agents/*biosynthesis, Genome, Bacterial/genetics, *Genomics, Glycopeptides/*biosynthesis, Macrolides/*metabolism, Multigene Family/genetics, Phylogeny, Sequence Homology, Nucleic AcidMetabolism
Phylogeny26354083Kutzneria chonburiensis sp. nov., isolated from soil.Chanama M, Thongkrachang N, Suriyachadkun C, Chanama SInt J Syst Evol Microbiol10.1099/ijsem.0.0005522015Actinomycetales/*classification/genetics/isolation & purification, Bacterial Typing Techniques, Base Composition, Cell Wall/chemistry, DNA, Bacterial/genetics, Diaminopimelic Acid/chemistry, Fatty Acids/analysis, *Forests, Nucleic Acid Hybridization, Peptidoglycan/chemistry, Phospholipids/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, *Soil Microbiology, Thailand, Vitamin K 2/analogs & derivatives/chemistryTranscriptome
Metabolism32708402Identification of a Biosynthetic Gene Cluster Responsible for the Production of a New Pyrrolopyrimidine Natural Product-Huimycin.Shuai H, Myronovskyi M, Nadmid S, Luzhetskyy ABiomolecules10.3390/biom100710742020Actinobacteria/*genetics/metabolism, Biological Products/*metabolism, *Biosynthetic Pathways, Gene Expression, Genes, Bacterial, *Multigene Family, Pyrimidines/*metabolism, Pyrroles/*metabolism, Streptomyces/genetics/metabolismBiotechnology
Metabolism34279911Discovery and Characterization of Epemicins A and B, New 30-Membered Macrolides from Kutzneria sp. CA-103260.Kontou EE, Gren T, Ortiz-Lopez FJ, Thomsen E, Oves-Costales D, Diaz C, de la Cruz M, Jiang X, Jorgensen TS, Blin K, Charusanti P, Reyes F, Genilloud O, Weber TACS Chem Biol10.1021/acschembio.1c003182021Actinobacteria/*chemistry/genetics/metabolism, Anti-Bacterial Agents/biosynthesis/chemistry/isolation & purification/*pharmacology, Bacterial Proteins/chemistry/genetics/metabolism, Drug Discovery, Macrolides/chemistry/isolation & purification/metabolism/*pharmacology, Methicillin-Resistant Staphylococcus aureus/drug effects, Microbial Sensitivity Tests, Multigene Family, Polyketide Synthases/chemistry/genetics/metabolism, Protein Domains, StereoisomerismEnzymology
Phylogeny35212620Solihabitans fulvus gen. nov., sp. nov., a member of the family Pseudonocardiaceae isolated from soil.Jin CZ, Jin L, Liu MJ, Lee JM, Park DJ, Kim CJInt J Syst Evol Microbiol10.1099/ijsem.0.0051102022Actinobacteria/*classification/isolation & purification, Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, Fatty Acids/chemistry, Phospholipids/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, Republic of Korea, Sequence Analysis, DNA, *Soil Microbiology, Vitamin K 2/chemistryTranscriptome

Reference

@idauthorscataloguedoi/urltitlejournalpubmed
11351Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 43870)https://www.dsmz.de/collection/catalogue/details/culture/DSM-43870
19973Wink, J.http://www.dsmz.de/microorganisms/wink_pdf/DSM43870.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
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)
66794Antje Chang, Lisa Jeske, Sandra Ulbrich, Julia Hofmann, Julia Koblitz, Ida Schomburg, Meina Neumann-Schaal, Dieter Jahn, Dietmar Schomburg10.1093/nar/gkaa1025BRENDA, the ELIXIR core data resource in 2021: new developments and updatesNucleic Acids Res. 49: D498-D508 202033211880
67770Curators of the JCMhttps://jcm.brc.riken.jp/en/
68368Automatically annotated from API 20E
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)
69481Xiao-Yin To, René Mreches, Martin Binder, Alice C. McHardy, Philipp C. Münch10.21203/rs.3.rs-2527258/v1Predictions based on the model GenomeNet Sporulation v. 1
82494Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID38437.1StrainInfo: A central database for resolving microbial strain identifiers