Strain identifier

BacDive ID: 132668

Type strain: Yes

Species: Actinocrispum wychmicini

Strain Designation: MI503-A4

Strain history: <- M. Hatano, Inst. of Micrpbial Chemistry, Shinagawa-ku Tokyo; MI503-A4

NCBI tax ID(s): 1213861 (species)

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General

@ref: 24457

BacDive-ID: 132668

DSM-Number: 45934

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

description: Actinocrispum wychmicini MI503-A4 is an aerobe, Gram-positive bacterium that builds an aerial mycelium and was isolated from soil.

NCBI tax id

  • NCBI tax id: 1213861
  • Matching level: species

strain history

  • @ref: 24457
  • history: <- M. Hatano, Inst. of Micrpbial Chemistry, Shinagawa-ku Tokyo; MI503-A4

doi: 10.13145/bacdive132668.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/actinomycetota
  • domain: Bacteria
  • phylum: Actinomycetota
  • class: Actinomycetes
  • order: Pseudonocardiales
  • family: Pseudonocardiaceae
  • genus: Actinocrispum
  • species: Actinocrispum wychmicini
  • full scientific name: Actinocrispum wychmicini Hatano et al. 2016

@ref: 24457

domain: Bacteria

phylum: Actinobacteria

class: Actinobacteria

order: Actinomycetales

family: Pseudonocardiaceae

genus: Actinocrispum

species: Actinocrispum wychmicini

full scientific name: Actinocrispum wychmicini Hatano et al. 2016

strain designation: MI503-A4

type strain: yes

Morphology

cell morphology

@refgram stainmotilityconfidence
24979positiveno
69480no94.597
69480positive100

colony morphology

@refcolony colormedium used
69454Clay brown (8003, ochre brown (8001)ISP 2
69454Ivory (1014)ISP 4
69454Ivory (1014)suter without tyrosine
69454Sand yellow (1002)ISP 6
69454Sand yellow (1002), brown beige (1011)ISP 3
69454Sand yellow (1002),ochre yellow (1024)ISP 5
69454Sand yellow (1002),ochre yellow (1024)ISP 7
69454Sand yellow (1002),ochre yellow (1024)suter with tyrosine

multicellular morphology

@refforms multicellular complexcomplex namecomplex colormedium name
69454yesAerial myceliumCream (9001)ISP 2
69454yesAerial myceliumSignal white (9003)ISP 3
69454noAerial myceliumISP 4
69454yesAerial myceliumSignal white (9003)ISP 5
69454noAerial myceliumISP 6
69454yesAerial myceliumPure white (9010)ISP 7
69454noAerial myceliumsuter with tyrosine
69454noAerial myceliumsuter without tyrosine

pigmentation

@refproductionname
69454noMelanin
69454nosoluble pigment

multimedia

@refmultimedia contentcaptionintellectual property rights
69454DSM_45934_image3.jpegPlates (553, ISP2, ISP3, ISP4, ISP5, ISP7)Helmholtz-Zentrum für Infektionsforschung GmbH
69454DSM_45934_image4.jpegPlates (553, ISP2, ISP3, ISP4, ISP5, ISP7)Helmholtz-Zentrum für Infektionsforschung GmbH

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
24979Yeast extract-malt extract agar (ISP2)yes
24979Oatmeal agar (ISP3)yes
24979Inorganic salts-starch agar (ISP4)yes
24979Glycerol-asparagine agar (ISP5)yes
24979Tyrosine Agar (ISP7)yes
24979soil extract agaryes
24979water agaryes
24457GPHF-MEDIUM (DSMZ Medium 553)yeshttps://mediadive.dsmz.de/medium/553Name: GPHF-MEDIUM (DSMZ Medium 553) Composition: Agar 20.0 g/l Glucose 10.0 g/l Beef extract 5.0 g/l Yeast extract 5.0 g/l Casein peptone 5.0 g/l CaCl2 x 2 H2O 0.74 g/l Distilled water

culture temp

@refgrowthtypetemperaturerange
24979positivegrowth20.0-34.0
24979positiveoptimum27mesophilic
24457positivegrowth28mesophilic

culture pH

@refabilitytypepHPH range
24979positivegrowth5.0-9.0alkaliphile
24979positiveoptimum7

Physiology and metabolism

oxygen tolerance

  • @ref: 24979
  • oxygen tolerance: aerobe

spore formation

@refspore formationconfidence
24979no
69481no96
69480yes100

halophily

@refsaltgrowthtested relationconcentration
24979NaClpositivegrowth0.0-3.0 %(w/v)
24979NaCloptimum0 %(w/v)
69454NaClpositivegrowth0 %

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
2497916708adenine-hydrolysis
2497916150benzoate-assimilation
2497915318xanthine-hydrolysis
24979casein+hydrolysis
2497917057cellobiose+builds acid from
2497916947citrate+assimilation
2497915824D-fructose+builds acid from
2497912936D-galactose+builds acid from
2497917634D-glucose+assimilation
2497917634D-glucose+builds acid from
2497917716lactose+builds acid from
2497915824D-fructose+assimilation
2497917306maltose+builds acid from
2497916899D-mannitol+assimilation
2497916899D-mannitol+builds acid from
2497916024D-mannose+builds acid from
2497916988D-ribose+builds acid from
2497965327D-xylose+assimilation
2497965327D-xylose+builds acid from
249794853esculin+hydrolysis
2497917368hypoxanthine+hydrolysis
2497917268myo-inositol+assimilation
2497917268myo-inositol+builds acid from
2497962345L-rhamnose+assimilation
2497917895L-tyrosine+hydrolysis
2497928053melibiose+builds acid from
2497916634raffinose+assimilation
2497916634raffinose+builds acid from
2497926546rhamnose+builds acid from
2497928017starch+hydrolysis
2497930031succinate+assimilation
2497917992sucrose+builds acid from
2497917992sucrose+assimilation
2497927082trehalose+builds acid from
6945422599arabinose-growth
6945462968cellulose-growth
6945428757fructose+growth
6945417234glucose+growth
6945417268inositol+growth
6945437684mannose+growth
6945416634raffinose-growth
6945426546rhamnose+growth
6945417992sucrose+/-growth
6945418222xylose+/-growth
6837917632nitrate-reduction
683794853esculin-hydrolysis
6837916199urea-hydrolysis
683795291gelatin+hydrolysis
6837917634D-glucose-fermentation
6837916988D-ribose-fermentation
6837965327D-xylose-fermentation
6837916899D-mannitol-fermentation
6837917306maltose-fermentation
6837917716lactose-fermentation
6837917992sucrose-fermentation
6837928087glycogen-fermentation

enzymes

@refvalueactivityec
68379gelatinase+
68379urease-3.5.1.5
68379beta-glucosidase-3.2.1.21
68379N-acetyl-beta-glucosaminidase+3.2.1.52
68379alpha-glucosidase+3.2.1.20
68379beta-galactosidase+3.2.1.23
68379beta-glucuronidase-3.2.1.31
68379alkaline phosphatase+3.1.3.1
68379pyrrolidonyl arylamidase+3.4.19.3
68379pyrazinamidase+3.5.1.B15
68382alkaline phosphatase+3.1.3.1
68382esterase (C 4)+
68382esterase lipase (C 8)+
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
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

API coryne

@refNITPYZPYRAPALbeta GURbeta GALalpha GLUbeta NAGESCUREGELGLURIBXYLMANMALLACSACGLYG
69454-+++-+++--+--------

API zym

@refAlkaline phosphataseEsteraseEsterase LipaseLipaseLeucine arylamidaseValine arylamidaseCystine arylamidaseTrypsinalpha- ChymotrypsinAcid phosphataseNaphthol-AS-BI-phosphohydrolasealpha- Galactosidasebeta- Galactosidasebeta- Glucuronidasealpha- Glucosidasebeta- GlucosidaseN-acetyl-beta- glucosaminidasealpha- Mannosidasealpha- Fucosidase
69454++++/-+++++++/-++-+++++/-

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinentenrichment cultureenrichment culture compositionenrichment culture durationenrichment culture temperatureisolation procedure
24457soilAomori Prefecture, KuroishiJapanJPNAsia
24979agar platescontaining 12.5 g glycerol, 1.0 g arginine, 1.0 g K2HPO4 , 1.0 g NaCl, 0.5 g MgSO4.7H2O, 20 g agar (Becton & Dickinson) in 1 l deionized water (pH 7.0)14 days27dilution plating technique

isolation source categories

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

taxonmaps

  • @ref: 69479
  • File name: preview.99_24466.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_10;96_415;97_14873;98_18401;99_24466&stattab=map
  • Last taxonomy: Kibdelosporangium
  • 16S sequence: AB738044
  • Sequence Identity:
  • Total samples: 140
  • soil counts: 137
  • animal counts: 1
  • plant counts: 2

Safety information

risk assessment

  • @ref: 24457
  • biosafety level: 1
  • biosafety level comment: Risk group (German classification)

Sequence information

16S sequences

  • @ref: 24457
  • description: Kibdelosporangium sp. MI503-A4 gene for 16S ribosomal RNA, partial sequence
  • accession: AB738044
  • length: 1480
  • database: ena
  • NCBI tax ID: 1213861

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Actinocrispum wychmicini DSM 45934GCA_004345645scaffoldncbi1213861
66792Actinocrispum wychmicini strain DSM 459341213861.3wgspatric1213861
66792Actinocrispum wychmicini DSM 459342799112271draftimg1213861

GC content

@refGC-contentmethod
2497970.3-71.1high performance liquid chromatography (HPLC)
2445771±0.7high performance liquid chromatography (HPLC)

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno96no
motileno95.304no
flagellatedno98.159yes
gram-positiveyes84.318yes
anaerobicno98.714yes
aerobicyes90.794yes
halophileno93.963no
spore-formingyes87.54yes
glucose-utilyes87.94yes
thermophileno98.727no
glucose-fermentno92.75yes

External links

@ref: 24457

culture collection no.: DSM 45934, NBRC 109632

straininfo link

  • @ref: 90978
  • straininfo: 400580

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny27535579Actinocrispum wychmicini gen. nov., sp. nov., a novel member of the family Pseudonocardiaceae, isolated from soil.Hatano M, Kinoshita N, Igarashi M, Nomoto AInt J Syst Evol Microbiol10.1099/ijsem.0.0014292016Actinomycetales/*classification/genetics/isolation & purification, Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, Diaminopimelic Acid/chemistry, Fatty Acids/chemistry, Japan, Muramic Acids/chemistry, Phospholipids/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, *Soil Microbiology, Vitamin K 2/analogs & derivatives/chemistryTranscriptome
36071214Wychimicins, a new class of spirotetronate polyketides from Actinocrispum wychmicini MI503-A4.Kimura T, Umekita M, Hatano M, Hayashi C, Sawa R, Igarashi MJ Antibiot (Tokyo)10.1038/s41429-022-00560-42022*Actinobacteria, *Actinomycetales, Anti-Bacterial Agents/chemistry, *Methicillin-Resistant Staphylococcus aureus, Microbial Sensitivity Tests, *Polyketides

Reference

@idauthorstitledoi/urlcataloguejournalpubmed
20215Parte, A.C., Sardà Carbasse, J., Meier-Kolthoff, J.P., Reimer, L.C. and Göker, M.List of Prokaryotic names with Standing in Nomenclature (LPSN) moves to the DSMZ10.1099/ijsem.0.004332
24457Curators of the DSMZhttps://www.dsmz.de/collection/catalogue/details/culture/DSM-45934Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 45934)
24979M. K. Hatano, Naoko,Igarashi, Masayuki,Nomoto, AkioActinocrispum wychmicini gen. nov., sp. nov., a novel member of the family Pseudonocardiaceae, isolated from soil10.1099/ijsem.0.001429IJSEM 66: 4779-4784 201627535579
66792Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg OvermannAutomatically annotated for the DiASPora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information)https://diaspora-project.de/progress.html#genomes
66794Antje Chang, Lisa Jeske, Sandra Ulbrich, Julia Hofmann, Julia Koblitz, Ida Schomburg, Meina Neumann-Schaal, Dieter Jahn, Dietmar SchomburgBRENDA, the ELIXIR core data resource in 2021: new developments and updates10.1093/nar/gkaa1025Nucleic Acids Res. 49: D498-D508 202033211880
68379Automatically annotated from API Coryne
68382Automatically annotated from API zym
69454Wink, J.Compendium of Actinobacteria. HZI-Helmholtz-Centre for Infection Research, Braunschweighttps://cdn.dsmz.de/wink/DSM%2045934.pdf
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.MicrobeAtlas 1.0 betahttps://microbeatlas.org/
69480Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg OvermannPredictions based on genome sequence made in the Diaspora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information)https://diaspora-project.de/progress.html#genomes
69481Xiao-Yin To, René Mreches, Martin Binder, Alice C. McHardy, Philipp C. MünchPredictions based on the model GenomeNet Sporulation v. 110.21203/rs.3.rs-2527258/v1
90978Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.StrainInfo: A central database for resolving microbial strain identifiers10.60712/SI-ID400580.1