Strain identifier

BacDive ID: 11076

Type strain: Yes

Species: Kribbella flavida

Strain Designation: 65-N86

Strain history: CIP <- 2002, KCTC <- IFO <- J. Ruan: strain 65-N86

NCBI tax ID(s): 479435 (strain), 182640 (species)

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General

@ref: 7207

BacDive-ID: 11076

DSM-Number: 17836

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

description: Kribbella flavida 65-N86 is an obligate aerobe, mesophilic, Gram-positive bacterium that was isolated from soil.

NCBI tax id

NCBI tax idMatching level
182640species
479435strain

strain history

@refhistory
7207<- M. E. Trujillo
67770KCTC 9580 <-- IFO 14399 <-- J. Ruan 65-N86.
119374CIP <- 2002, KCTC <- IFO <- J. Ruan: strain 65-N86

doi: 10.13145/bacdive11076.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/actinomycetota
  • domain: Bacteria
  • phylum: Actinomycetota
  • class: Actinomycetes
  • order: Propionibacteriales
  • family: Kribbellaceae
  • genus: Kribbella
  • species: Kribbella flavida
  • full scientific name: Kribbella flavida Park et al. 1999

@ref: 7207

domain: Bacteria

phylum: Actinobacteria

class: Actinobacteria

order: Actinomycetales

family: Kribbellaceae

genus: Kribbella

species: Kribbella flavida

full scientific name: Kribbella flavida Park et al. 1999

strain designation: 65-N86

type strain: yes

Morphology

cell morphology

  • @ref: 119374
  • gram stain: positive
  • cell shape: rod-shaped
  • motility: no

colony morphology

  • @ref: 119374

multimedia

  • @ref: 66793
  • multimedia content: EM_DSM_17836_1.jpg
  • caption: electron microscopic image
  • intellectual property rights: © HZI/Manfred Rohde

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
7207R2A MEDIUM (DSMZ Medium 830)yeshttps://mediadive.dsmz.de/medium/830Name: R2A MEDIUM (DSMZ Medium 830) Composition: Agar 15.0 g/l Casamino acids 0.5 g/l Starch 0.5 g/l Glucose 0.5 g/l Proteose peptone 0.5 g/l Yeast extract 0.5 g/l K2HPO4 0.3 g/l Na-pyruvate 0.3 g/l MgSO4 x 7 H2O 0.05 g/l Distilled water
33808MEDIUM 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)
119374CIP Medium 57yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=57

culture temp

@refgrowthtypetemperaturerange
7207positivegrowth28mesophilic
33808positivegrowth30mesophilic
67770positivegrowth28mesophilic
119374positivegrowth25-41
119374nogrowth10psychrophilic
119374nogrowth45thermophilic

Physiology and metabolism

oxygen tolerance

  • @ref: 119374
  • oxygen tolerance: obligate aerobe

halophily

@refsaltgrowthtested relationconcentration
119374NaClpositivegrowth0-4 %
119374NaClnogrowth6 %
119374NaClnogrowth8 %
119374NaClnogrowth10 %

observation

  • @ref: 67770
  • observation: quinones: 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
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
119374citrate-carbon source16947
119374esculin+hydrolysis4853
119374hippurate-hydrolysis606565
119374nitrate+reduction17632
119374nitrite-reduction16301
119374nitrate-respiration17632

antibiotic resistance

  • @ref: 119374
  • metabolite: 0129 (2,4-Diamino-6,7-di-iso-propylpteridine phosphate)
  • is antibiotic: yes
  • is sensitive: yes
  • is resistant: no

metabolite production

  • @ref: 119374
  • Chebi-ID: 35581
  • metabolite: indole
  • production: no

metabolite tests

@refChebi-IDmetabolitevoges-proskauer-testmethylred-test
11937415688acetoin-
11937417234glucose-

enzymes

@refvalueactivityec
119374oxidase-
119374beta-galactosidase-3.2.1.23
119374alcohol dehydrogenase-1.1.1.1
119374gelatinase+/-
119374amylase+
119374DNase+
119374caseinase+3.4.21.50
119374catalase+1.11.1.6
119374tween esterase+
119374gamma-glutamyltransferase+2.3.2.2
119374lecithinase-
119374lipase-
119374lysine decarboxylase-4.1.1.18
119374ornithine decarboxylase-4.1.1.17
119374phenylalanine ammonia-lyase-4.3.1.24
119374protease+
119374tryptophan deaminase-
119374urease-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
119374-+++-++-++++++-+++++

API 50CHac

@refGLYERYDARALARARIBDXYLLXYLADOMDXGALGLUFRUMNESBERHADULINOMANSORMDMMDGNAGAMYARBESCSALCELMALLACMELSACTREINUMLZRAFAMDGLYGXLTGENTURLYXTAGDFUCLFUCDARLLARLGNT2KG5KG
119374-----------+-------------------------------------

API biotype100

@refGLUFRUGALTREMNESBEMELSACRAFMTEMALLACLTEMbGaMaGaCELGENMbGuESCRIBARAXYLPLERHAFUCMLZDARLLARLXLTDULTAGGLYINOMANMTLTURSORADOHBGLYXERYMDG3MDGSATMUCLTATDTATMTATDMLTLMLTCATETATETTECITGRTGAT2KG5KGTRYNAGGNTPACPATpOBEQATGTEmOBEBATPPATCMTTGEBETPCEABTHINLATCAPCYTHISSUCFUMGREGYTAVTETNTTNGLNITA3OBUAPTGTTPRODALALALASERMNTPROPTYR2KT
119374+-----++++++--+++-+--++++++----+++-+-+-----------+---------+---------------+---+++---------------+-

Isolation, sampling and environmental information

isolation

@refsample typecountryorigin.countrycontinentgeographic location
7207soilChinaCHNAsia
67770SoilChinaCHNAsianear Beijing
119374Environment, SoilChinaCHNAsia

isolation source categories

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

taxonmaps

  • @ref: 69479
  • File name: preview.99_721.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_142;96_440;97_503;98_578;99_721&stattab=map
  • Last taxonomy: Kribbella
  • 16S sequence: AF005017
  • Sequence Identity:
  • Total samples: 653
  • soil counts: 499
  • aquatic counts: 21
  • animal counts: 106
  • plant counts: 27

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
72071Risk group (German classification)
1193741Risk group (French classification)

Sequence information

16S sequences

@refdescriptionaccessionlengthdatabaseNCBI tax ID
20218Kribbella flavida gene for 16S ribosomal RNA, partial sequence, strain: DSM 17836AB821480837ena182640
20218Nocardioides fulvus strain IFO 14399 16S-23S internal transcribed spacer, complete sequenceAF017503473ena60448
7207Nocardioides fulvus strain IFO 14399 16S ribosomal RNA gene, partial sequenceAF0050171472ena60448
67770Kribbella flavida 16S ribosomal RNA gene, partial sequenceAY2538631510ena182640

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Kribbella flavida DSM 17836GCA_000024345completencbi479435
66792Kribbella flavida DSM 17836479435.6completepatric479435
66792Kribbella flavida IFO 14399, DSM 17836646311938completeimg479435

GC content

@refGC-contentmethod
720770
6777070high performance liquid chromatography (HPLC)

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
motileno93.973no
flagellatedno98.37no
gram-positiveyes89.128no
anaerobicno99.577no
aerobicyes92.988no
halophileno94.312no
spore-formingyes89.858no
thermophileno98.804yes
glucose-utilyes84.948no
glucose-fermentno88.466no

External links

@ref: 7207

culture collection no.: DSM 17836, IFO 14399, JCM 10339, KCTC 9580, NBRC 14399, KACC 20248, CIP 107494, IMSNU 22160, NCIMB 13631, NRRL B-16234

straininfo link

  • @ref: 80325
  • straininfo: 62448

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny10319498Classification of 'Nocardioides fulvus' IFO 14399 and Nocardioides sp. ATCC 39419 in Kribbella gen. nov., as Kribbella flavida sp. nov. and Kribbella sandramycini sp. nov.Park YH, Yoon JH, Shin YK, Suzuki K, Kudo T, Seino A, Kim HJ, Lee JS, Lee STInt J Syst Bacteriol10.1099/00207713-49-2-7431999Actinomycetales/chemistry/*classification/genetics/physiology, Base Composition, Cell Wall/*chemistry, DNA, Bacterial/chemistry/genetics, DNA, Ribosomal/chemistry/genetics, Diaminopimelic Acid/*analysis, Fatty Acids/analysis, Genes, rRNA, Molecular Sequence Data, Phylogeny, RNA, Ribosomal, 16S/geneticsGenetics
Phylogeny16627661Kribbella karoonensis sp. nov. and Kribbella swartbergensis sp. nov., isolated from soil from the Western Cape, South Africa.Kirby BM, Roes ML, Meyers PRInt J Syst Evol Microbiol10.1099/ijs.0.63951-02006Actinomycetales/chemistry/*classification/*isolation & purification/physiology, Anaerobiosis, Anti-Bacterial Agents/pharmacology, Bacterial Typing Techniques, Carbohydrates/analysis, DNA Fingerprinting, DNA Restriction Enzymes/metabolism, DNA, Bacterial/chemistry/genetics/metabolism, DNA, Ribosomal/chemistry/genetics, Diaminopimelic Acid/analysis, Genes, rRNA, Glycine/analysis, Growth Inhibitors/pharmacology, Molecular Sequence Data, Peptidoglycan/chemistry, Phylogeny, RNA, Bacterial/genetics, RNA, Ribosomal, 16S/genetics, Sodium Chloride/pharmacology, *Soil Microbiology, South AfricaEnzymology
Phylogeny18768610Kribbella catacumbae sp. nov. and Kribbella sancticallisti sp. nov., isolated from whitish-grey patinas in the catacombs of St Callistus in Rome, Italy.Urzi C, De Leo F, Schumann PInt J Syst Evol Microbiol10.1099/ijs.0.65613-02008Actinomycetales/chemistry/*classification/genetics/*isolation & purification, Bacterial Typing Techniques, Cell Wall/chemistry, Cluster Analysis, DNA, Bacterial/chemistry/genetics, DNA, Ribosomal/chemistry/genetics, DNA, Ribosomal Spacer/chemistry/genetics, Diaminopimelic Acid/analysis, *Environmental Microbiology, Fatty Acids/analysis, Genes, rRNA, Molecular Sequence Data, Phospholipids/analysis, Phylogeny, Pigments, Biological/biosynthesis, RNA, Bacterial/genetics, RNA, Ribosomal, 16S/genetics, Rome, Sequence Analysis, DNA, Sequence Homology, Nucleic Acid, Vitamin K 2/analysisGenetics
Phylogeny19651720Kribbella ginsengisoli sp. nov., isolated from soil of a ginseng field.Cui YS, Lee JS, Lee ST, Im WTInt J Syst Evol Microbiol10.1099/ijs.0.008516-02009Actinomycetales/*classification/genetics/physiology, Base Composition, Base Sequence, DNA, Bacterial/chemistry, Molecular Sequence Data, Panax/*microbiology, RNA, Bacterial/genetics, RNA, Ribosomal, 16S/genetics, Republic of Korea, Sequence Homology, Nucleic Acid, *Soil MicrobiologyGenetics
Genetics21304701Complete genome sequence of Kribbella flavida type strain (IFO 14399).Pukall R, Lapidus A, Glavina Del Rio T, Copeland A, Tice H, Cheng JF, Lucas S, Chen F, Nolan M, Labutti K, Pati A, Ivanova N, Mavromatis K, Mikhailova N, Pitluck S, Bruce D, Goodwin L, Land M, Hauser L, Chang YJ, Jeffries CD, Chen A, Palaniappan K, Chain P, Rohde M, Goker M, Bristow J, Eisen JA, Markowitz V, Hugenholtz P, Kyrpides NC, Klenk HP, Brettin TStand Genomic Sci10.4056/sigs.7313212010
Phylogeny21705443Kribbella amoyensis sp. nov., isolated from rhizosphere soil of a pharmaceutical plant, Typhonium giganteum Engl.Xu Z, Xu Q, Zheng Z, Huang YInt J Syst Evol Microbiol10.1099/ijs.0.033290-02011Actinomycetales/*classification/genetics/*isolation & purification, Araceae/*microbiology, Bacterial Typing Techniques, Carbohydrates/analysis, China, Cluster Analysis, Cytosol/chemistry, DNA Gyrase/genetics, DNA, Bacterial/chemistry/genetics, DNA, Ribosomal/chemistry/genetics, Diaminopimelic Acid/analysis, Fatty Acids/analysis, Molecular Sequence Data, Nucleic Acid Hybridization, Peptidoglycan/chemistry, Phospholipids/analysis, Phylogeny, Plants, Medicinal/microbiology, Quinones/analysis, RNA, Ribosomal, 16S/genetics, *Rhizosphere, Sequence Analysis, DNA, *Soil MicrobiologyGenetics
Enzymology26026381Cloning, expression and characterization of a novel GH5 exo/endoglucanase of Thermobi fi da halotolerans YIM 90462(T) by genome mining.Zhang F, Zhang XM, Yin YR, Li WJJ Biosci Bioeng10.1016/j.jbiosc.2015.04.0122015Actinomycetales/*enzymology/*genetics, Biotechnology, Catalytic Domain, Cellulase/chemistry/*genetics/*metabolism, Cellulose/metabolism, Cloning, Molecular, Genome, Bacterial/*genetics, Hydrogen-Ion Concentration, Hydrolysis, Kinetics, Solubility, Substrate Specificity, Temperature, Time FactorsBiotechnology
Metabolism27302067Two Novel Glycoside Hydrolases Responsible for the Catabolism of Cyclobis-(1-->6)-alpha-nigerosyl.Tagami T, Miyano E, Sadahiro J, Okuyama M, Iwasaki T, Kimura AJ Biol Chem10.1074/jbc.M116.7273052016*Actinobacteria/enzymology/genetics, *Bacterial Proteins/genetics/metabolism, Genome, Bacterial/*physiology, Glucans/genetics/*metabolism, *Glycoside Hydrolases/genetics/metabolism, Multigene Family/*physiologyGenetics

Reference

@idauthorscataloguedoi/urltitlejournalpubmed
7207Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 17836)https://www.dsmz.de/collection/catalogue/details/culture/DSM-17836
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
33808Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/4935
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
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/
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
80325Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID62448.1StrainInfo: A central database for resolving microbial strain identifiers
119374Curators of the CIPCollection of Institut Pasteur (CIP 107494)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20107494