Strain identifier

BacDive ID: 12605

Type strain: Yes

Species: Krasilnikoviella flava

Strain Designation: CC 0387

Strain history: DSM 21481 <-- C.-L. Jiang CC 0387 <-- Y. Jiang.

NCBI tax ID(s): 526729 (species)

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General

@ref: 15732

BacDive-ID: 12605

DSM-Number: 21481

keywords: genome sequence, 16S sequence, Bacteria, facultative anaerobe, mesophilic, Gram-positive

description: Krasilnikoviella flava CC 0387 is a facultative anaerobe, mesophilic, Gram-positive bacterium that builds substrate mycelia and was isolated from sediment.

NCBI tax id

  • NCBI tax id: 526729
  • Matching level: species

strain history

@refhistory
15732<- C.-L. Jiang, Yunnan University,YIM, China; CC 0387 <- Y. Jiang
67770DSM 21481 <-- C.-L. Jiang CC 0387 <-- Y. Jiang.

doi: 10.13145/bacdive12605.20250331.9.3

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/actinomycetota
  • domain: Bacteria
  • phylum: Actinomycetota
  • class: Actinomycetes
  • order: Micrococcales
  • family: Promicromonosporaceae
  • genus: Krasilnikoviella
  • species: Krasilnikoviella flava
  • full scientific name: Krasilnikoviella flava (Jiang et al. 2009) Nishijima et al. 2017

  • synonyms

    • @ref: 20215
    • synonym: Promicromonospora flava

@ref: 15732

domain: Bacteria

phylum: Actinobacteria

class: Actinobacteria

order: Actinomycetales

family: Promicromonosporaceae

genus: Krasilnikoviella

species: Krasilnikoviella flava

full scientific name: Krasilnikoviella flava (Jiang et al. 2009) Nishijima et al. 2017

strain designation: CC 0387

type strain: yes

Morphology

cell morphology

@refgram staincell shapemotilityconfidence
25188positive
29100positivecoccus-shapedno
125438no93
125438positive93.875
125439positive98.6

colony morphology

@refcolony colorincubation periodmedium used
19795Sulfur yellow10-14 daysISP 2
19795Pable brown10-14 daysISP 3
19795Beige10-14 daysISP 4
19795Grey white10-14 daysISP 5
19795Sulfur yellow10-14 daysISP 6
19795Grey white10-14 daysISP 7

multicellular morphology

@refforms multicellular complexmedium namecomplex namefurther description
19795noISP 2
19795noISP 3
19795noISP 4
19795noISP 5
19795noISP 6
19795noISP 7
25188yessubstrate mycelianon-motile, coccoid, V-shaped, Y-shaped and rod-like elements

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
15732BACTO MARINE BROTH (DIFCO 2216) (DSMZ Medium 514)yeshttps://mediadive.dsmz.de/medium/514Name: BACTO MARINE BROTH (DIFCO 2216) (DSMZ Medium 514) Composition: NaCl 19.45 g/l MgCl2 5.9 g/l Bacto peptone 5.0 g/l Na2SO4 3.24 g/l CaCl2 1.8 g/l Yeast extract 1.0 g/l KCl 0.55 g/l NaHCO3 0.16 g/l Fe(III) citrate 0.1 g/l KBr 0.08 g/l SrCl2 0.034 g/l H3BO3 0.022 g/l Na2HPO4 0.008 g/l Na-silicate 0.004 g/l NaF 0.0024 g/l (NH4)NO3 0.0016 g/l Distilled water
19795ISP 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
19795ISP 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:
19795ISP 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
19795ISP 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
19795ISP 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
19795ISP 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
25188ISP 2yes
25188ISP 3yes
25188ISP 4yes
25188ISP 5yes
25188nutrient agar (NA)yes
15732TRYPTICASE 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
15732ORGANIC MEDIUM 79 (DSMZ Medium 426)yeshttps://mediadive.dsmz.de/medium/426Name: ORGANIC MEDIUM 79 (DSMZ Medium 426) Composition: Agar 15.0 g/l Peptone 10.0 g/l Dextrose 10.0 g/l NaCl 6.0 g/l Yeast extract 2.0 g/l Casein peptone 2.0 g/l Distilled water
15732GYM 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

culture temp

@refgrowthtypetemperature
15732positivegrowth28
19795positiveoptimum28
25188positivegrowth10.0-40.0
25188positiveoptimum25.0-30.0
67770positivegrowth28

culture pH

@refabilitytypepHPH range
25188positivegrowth5.5-10.5alkaliphile
25188positiveoptimum6.0-7.5

Physiology and metabolism

oxygen tolerance

@refoxygen toleranceconfidence
25188facultative anaerobe
29100aerobe
125439obligate aerobe99.5

spore formation

  • @ref: 29100
  • spore formation: no

halophily

@refsalttested relationconcentrationgrowth
25188NaClmaximum15 %(w/v)
25188NaCloptimum1 %(w/v)
29100NaClgrowth02-05 %positive
29100NaCloptimum3.5 %positive

observation

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

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
25188168082-dehydro-D-gluconate-builds acid from
25188581435-dehydro-D-gluconate-builds acid from
2518817128adipate-assimilation
2518815963ribitol-builds acid from
2518817108D-arabinose-builds acid from
2518828847D-fucose-builds acid from
2518862318D-lyxose-builds acid from
2518816899D-mannitol-builds acid from
2518816988D-ribose-builds acid from
2518817924D-sorbitol-builds acid from
2518816443D-tagatose-builds acid from
2518827689decanoate-assimilation
2518817113erythritol-builds acid from
2518816813galactitol-builds acid from
2518828066gentiobiose-builds acid from
2518824265gluconate-builds acid from
2518817268myo-inositol-builds acid from
2518818403L-arabitol-builds acid from
2518818287L-fucose-builds acid from
2518817266L-sorbose-builds acid from
2518865328L-xylose-builds acid from
2518817716lactose-builds acid from
2518825115malate-assimilation
2518874863methyl beta-D-xylopyranoside-builds acid from
2518818401phenylacetate-assimilation
2518853258sodium citrate-assimilation
2518827082trehalose-builds acid from
2518827897tryptophan-energy source
2518817151xylitol-builds acid from
2518827613amygdalin+builds acid from
2518822599arabinose+assimilation
2518818305arbutin+builds acid from
25188casein+hydrolysis
2518817057cellobiose+builds acid from
2518818333D-arabitol+builds acid from
2518815824D-fructose+builds acid from
2518812936D-galactose+builds acid from
2518817634D-glucose+builds acid from
2518816024D-mannose+builds acid from
2518865327D-xylose+builds acid from
2518816991dna+hydrolysis
251884853esculin+hydrolysis
2518817234glucose+fermentation
2518817234glucose+builds acid from
2518817234glucose+assimilation
2518817754glycerol+builds acid from
2518828087glycogen+builds acid from
2518835581indole+assimilation
2518815443inulin+builds acid from
2518830849L-arabinose+builds acid from
2518817306maltose+assimilation
2518817306maltose+builds acid from
2518829864mannitol+assimilation
2518837684mannose+assimilation
251886731melezitose+builds acid from
2518828053melibiose+builds acid from
25188320061methyl alpha-D-glucopyranoside+builds acid from
2518843943methyl alpha-D-mannoside+builds acid from
25188506227N-acetylglucosamine+builds acid from
25188506227N-acetylglucosamine+assimilation
2518817632nitrate+reduction
2518832032potassium gluconate+assimilation
2518816634raffinose+builds acid from
2518817814salicin+builds acid from
2518828017starch+hydrolysis
2518828017starch+builds acid from
2518832528turanose+builds acid from
2518853426tween 80+hydrolysis
2910016449alanine+carbon source
2910017234glucose+carbon source
2910017716lactose+carbon source
2910017268myo-inositol+carbon source
2910033942ribose+carbon source
2910017992sucrose+carbon source
2910027082trehalose+carbon source
2910017151xylitol+carbon source
2910017632nitrate+reduction
6837917992sucrose+fermentation
6837917634D-glucose+fermentation
6837965327D-xylose+fermentation
683795291gelatin-hydrolysis
6837916199urea-hydrolysis
683794853esculin+hydrolysis
6837917306maltose+fermentation

metabolite production

  • @ref: 25188
  • Chebi-ID: 35581
  • metabolite: indole
  • production: no

metabolite tests

  • @ref: 25188
  • Chebi-ID: 35581
  • metabolite: indole
  • indole test: -

enzymes

@refvalueactivityec
25188acid phosphatase+3.1.3.2
25188alkaline phosphatase+3.1.3.1
25188alpha-chymotrypsin-3.4.21.1
25188alpha-fucosidase+3.2.1.51
25188alpha-galactosidase+3.2.1.22
25188alpha-glucosidase+3.2.1.20
25188alpha-mannosidase+3.2.1.24
25188arginine dihydrolase-3.5.3.6
25188beta-galactosidase+3.2.1.23
25188beta-glucosidase+3.2.1.21
25188beta-glucuronidase+3.2.1.31
25188cystine arylamidase+3.4.11.3
25188cytochrome oxidase-1.9.3.1
25188esterase (C 4)+
25188esterase Lipase (C 8)+
25188lecithinase-
25188leucine arylamidase+3.4.11.1
25188lipase (C 14)+
25188N-acetyl-beta-glucosaminidase+3.2.1.52
25188naphthol-AS-BI-phosphohydrolase+
25188pyrazinamidase-3.5.1.B15
25188pyrrolidonyl arylamidase-3.4.19.3
25188trypsin-3.4.21.4
25188tryptophan deaminase-4.1.99.1
25188urease-3.5.1.5
25188valine arylamidase+
68382alpha-fucosidase-3.2.1.51
68382alpha-mannosidase-3.2.1.24
68382N-acetyl-beta-glucosaminidase+3.2.1.52
68382beta-glucosidase+3.2.1.21
68382beta-glucuronidase-3.2.1.31
68382alpha-glucosidase+3.2.1.20
68382beta-galactosidase+3.2.1.23
68382alpha-galactosidase-3.2.1.22
68382naphthol-AS-BI-phosphohydrolase+
68382acid phosphatase+3.1.3.2
68382alpha-chymotrypsin-3.4.21.1
68382trypsin-3.4.21.4
68382cystine arylamidase+3.4.11.3
68382valine arylamidase+
68382leucine arylamidase+3.4.11.1
68382lipase (C 14)+
68382esterase (C 4)+
68382esterase lipase (C 8)+
68382alkaline phosphatase+3.1.3.1
68379alpha-glucosidase+3.2.1.20
68379beta-galactosidase+3.2.1.23
68379alkaline phosphatase+3.1.3.1
68379gelatinase-
68379urease-3.5.1.5
68379beta-glucosidase+3.2.1.21
68379N-acetyl-beta-glucosaminidase+3.2.1.52
68379beta-glucuronidase-3.2.1.31
68379pyrrolidonyl arylamidase-3.4.19.3
68379pyrazinamidase-3.5.1.B15

fatty acid profile

  • fatty acids

    @reffatty acidpercentage
    25188C15:0 anteiso58.5
    25188C17:0 anteiso8.4
    25188C14:01.2
    25188C16:02.8
    25188C17:00.2
    25188C18:00.1
    25188C14:0 iso0.7
    25188C15:0 iso21.5
    25188C16:0 iso5.8
    25188C17:0 iso0.8
  • type of FA analysis: whole cell analysis
  • incubation medium: SCD
  • agar/liquid: agar
  • incubation temperature: 30
  • incubation time: 3
  • software version: Sherlock 6.1
  • library/peak naming table: TSBA 6
  • system: MIS MIDI

API coryne

@refNITPYZPYRAPALbeta GURbeta GALalpha GLUbeta NAGESCUREGELGLURIBXYLMANMALLACSACGLYG
19795+/---+-++++--++/-++/-++/-++/-

API zym

@refAlkaline phosphataseEsteraseEsterase LipaseLipaseLeucine arylamidaseValine arylamidaseCystine arylamidaseTrypsinalpha- ChymotrypsinAcid phosphataseNaphthol-AS-BI-phosphohydrolasealpha- Galactosidasebeta- Galactosidasebeta- Glucuronidasealpha- Glucosidasebeta- GlucosidaseN-acetyl-beta- glucosaminidasealpha- Mannosidasealpha- Fucosidase
19795+++++++--++-+-+++--

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinent
15732sedimentKiel Bay, Baltic SeaGermanyDEUEurope
67770Sediment from the Baltic SeaGermanyDEUEurope

isolation source categories

Cat1Cat2Cat3
#Environmental#Aquatic#Sediment
#Environmental#Terrestrial#Sediment

taxonmaps

  • @ref: 69479
  • File name: preview.99_7502.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_9;96_179;97_4293;98_5496;99_7502&stattab=map
  • Last taxonomy: Krasilnikoviella
  • 16S sequence: AM992980
  • Sequence Identity:
  • Total samples: 139
  • soil counts: 61
  • aquatic counts: 11
  • animal counts: 20
  • plant counts: 47

Safety information

risk assessment

  • @ref: 15732
  • biosafety level: 1
  • biosafety level comment: Risk group (German classification)

Sequence information

16S sequences

  • @ref: 15732
  • description: Promicromonospora flava partial 16S rRNA gene, type strain CC 0387T
  • accession: AM992980
  • length: 1612
  • database: nuccore
  • NCBI tax ID: 526729

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Krasilnikoviella flava strain DSM 21481526729.3wgspatric526729
66792Krasilnikoviella flava DSM 214812596583702draftimg526729
67770Krasilnikoviella flava DSM 21481GCA_900167525scaffoldncbi526729

GC content

@refGC-contentmethod
1573271.87high performance liquid chromatography (HPLC)
2518874.6genome sequence analysis
2910071.87
1573274.6high performance liquid chromatography (HPLC)

Genome-based predictions

predictions

@refmodeltraitdescriptionpredictionconfidencetraining_data
125438gram-positivegram-positivePositive reaction to Gram-stainingyes93.875yes
125438anaerobicanaerobicAbility to grow under anoxygenic conditions (including facultative anaerobes)no97.411yes
125438spore-formingspore-formingAbility to form endo- or exosporesno64.041no
125438aerobicaerobicAbility to grow under oxygenic conditions (including facultative aerobes)yes83.528no
125438thermophilethermophilicAbility to grow at temperatures above or equal to 45°Cno97.5yes
125438motile2+flagellatedAbility to perform flagellated movementno93yes
125439BacteriaNetspore_formationAbility to form endo- or exosporesno76.7
125439BacteriaNetmotilityAbility to perform movementno65
125439BacteriaNetgram_stainReaction to gram-stainingpositive98.6
125439BacteriaNetoxygen_toleranceOxygenic conditions needed for growthobligate aerobe99.5

External links

@ref: 15732

culture collection no.: DSM 21481, CCTCC AA 208024, JCM 16551

straininfo link

  • @ref: 81819
  • straininfo: 401283

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny19542138Promicromonospora flava sp. nov., isolated from sediment of the Baltic Sea.Jiang Y, Wiese J, Cao YR, Xu LH, Imhoff JF, Jiang CLInt J Syst Evol Microbiol10.1099/ijs.0.006197-02009Actinomycetales/*classification/genetics/isolation & purification/physiology, Bacterial Typing Techniques, Base Composition, DNA, Bacterial/analysis, Fatty Acids/analysis, Genes, rRNA, Genotype, Geologic Sediments/*microbiology, Germany, Molecular Sequence Data, Phenotype, Phylogeny, RNA, Ribosomal, 16S/genetics, Seawater/*microbiology, Sequence Analysis, DNA, Species SpecificityGenetics
Phylogeny19654362Promicromonospora umidemergens sp. nov., isolated from moisture from indoor wall material.Martin K, Schafer J, Kampfer PInt J Syst Evol Microbiol10.1099/ijs.0.014142-02009Actinomycetales/*classification/genetics/*isolation & purification/metabolism, DNA, Bacterial/genetics, DNA, Ribosomal/genetics, Fatty Acids/chemistry/metabolism, *Household Articles, Molecular Sequence Data, Phylogeny, RNA, Ribosomal, 16S/geneticsMetabolism

Reference

@idauthorscataloguedoi/urltitlejournalpubmedID_cross_reference
15732Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 21481)https://www.dsmz.de/collection/catalogue/details/culture/DSM-21481
19795Wink, J.http://www.dsmz.de/microorganisms/wink_pdf/DSM21481.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
25188M. T. Nishijima, N.,Handa, Y.,Umekawa, N.,Kigawa, R.,Sano, C.,Sugiyama, J.10.1099/ijsem.0.001618Krasilnikoviella muralis gen. nov., sp. nov., a member of the family Promicromonosporaceae, isolated from the Takamatsuzuka Tumulus stone chamber interior and reclassification of Promicromonospora flava as Krasilnikoviella flava comb. novIJSEM 67: 294-300 201727902237
29100Barberan A, Caceres Velazquez H, Jones S, Fierer N.10.1128/mSphere.00237-17Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information2877604125529
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/
68379Automatically annotated from API Coryne
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
81819Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID401283.1StrainInfo: A central database for resolving microbial strain identifiers
125438Julia Koblitz, Lorenz Christian Reimer, Rüdiger Pukall, Jörg Overmann10.1101/2024.08.12.607695Predicting bacterial phenotypic traits through improved machine learning using high-quality, curated datasets
125439Philipp Münch, René Mreches, Martin Binder, Hüseyin Anil Gündüz, Xiao-Yin To, Alice McHardyhttps://github.com/GenomeNet/deepGdeepG: Deep Learning for Genome Sequence Data. R package version 0.3.1