Strain identifier

BacDive ID: 16519

Type strain: Yes

Species: Microbispora rosea

Strain Designation: FYU M-20

Strain history: KCC A-0006 <-- NI 9096 <-- Y. Ohara M-20.

NCBI tax ID(s): 58117 (species)

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General

@ref: 11323

BacDive-ID: 16519

DSM-Number: 43839

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

description: Microbispora rosea FYU M-20 is a spore-forming, mesophilic, Gram-positive bacterium that was isolated from garden soil.

NCBI tax id

  • NCBI tax id: 58117
  • Matching level: species

strain history

@refhistory
11323<- JCM <- KCC <- K. Tubaki, NI 9096 <- Y. Ohara, FYU M-20
67770KCC A-0006 <-- NI 9096 <-- Y. Ohara M-20.

doi: 10.13145/bacdive16519.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/actinomycetota
  • domain: Bacteria
  • phylum: Actinomycetota
  • class: Actinomycetes
  • order: Streptosporangiales
  • family: Streptosporangiaceae
  • genus: Microbispora
  • species: Microbispora rosea
  • full scientific name: Microbispora rosea Nonomura and Ohara 1957 (Approved Lists 1980)

  • synonyms

    @refsynonym
    20215Microbispora parva
    20215Microbispora karnatakensis
    20215Microbispora chromogenes
    20215Microbispora indica
    20215Microbispora diastatica
    20215Microbispora amethystogenes

@ref: 11323

domain: Bacteria

phylum: Actinobacteria

class: Actinobacteria

order: Actinomycetales

family: Streptosporangiaceae

genus: Microbispora

species: Microbispora rosea subsp. rosea

full scientific name: Microbispora rosea subsp. rosea (Nonomura and Ohara 1957) Miyadoh et al. 1991

strain designation: FYU M-20

type strain: yes

Morphology

cell morphology

  • @ref: 69480
  • gram stain: positive
  • confidence: 100

colony morphology

@refcolony colorincubation periodmedium used
19964Orange brown (8023)10-14 daysISP 2
19964Orange brown (8023)10-14 daysISP 3
19964Orange brown (8023)10-14 daysISP 4
19964Beige (1001)10-14 daysISP 5
19964Beige (1001)10-14 daysISP 6
19964Orange brown (8023)10-14 daysISP 7

multimedia

  • @ref: 11323
  • multimedia content: https://www.dsmz.de/microorganisms/photos/DSM_43839.jpg
  • caption: Medium 553 28°C
  • intellectual property rights: © Leibniz-Institut DSMZ

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
11323GPHF-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
19964ISP 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
19964ISP 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:
19964ISP 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
19964ISP 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
19964ISP 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
19964ISP 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
11323N-Z-AMINE-MEDIUM (DSMZ Medium 554)yeshttps://www.dsmz.de/microorganisms/medium/pdf/DSMZ_Medium554.pdf

culture temp

@refgrowthtypetemperaturerange
19964positiveoptimum30mesophilic
11323positivegrowth28mesophilic
67770positivegrowth28mesophilic

Physiology and metabolism

spore formation

@refspore formationconfidence
69481yes99
69480yes100

halophily

  • @ref: 19964
  • salt: NaCl
  • growth: positive
  • tested relation: maximum
  • concentration: 2.5 %

observation

  • @ref: 67770
  • observation: quinones: MK-9(H2), MK-9(III,VIII-H4), MK-9

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
1996462968cellulose+
1996416634raffinose+
1996426546rhamnose+
1996428757fructose+
1996429864mannitol+
1996417268myo-inositol+
1996418222xylose+
1996417992sucrose+
1996422599arabinose+
1996417234glucose+
683685291gelatin-hydrolysis
6836827897tryptophan-energy source
6836816199urea-hydrolysis
6836816947citrate-assimilation
6836818257ornithine-degradation
6836825094lysine-degradation
6836829016arginine-hydrolysis

metabolite production

@refChebi-IDmetaboliteproduction
6836815688acetoinno
6836835581indoleno
6836816136hydrogen sulfideno

metabolite tests

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

enzymes

@refvalueactivityec
68368gelatinase-
68368tryptophan deaminase-4.1.99.1
68368urease-3.5.1.5
68368ornithine decarboxylase-4.1.1.17
68368lysine decarboxylase-4.1.1.18
68368arginine dihydrolase-3.5.3.6
68368beta-galactosidase+3.2.1.23
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

@refAlkaline phosphataseEsteraseEsterase LipaseLipaseLeucine arylamidaseValine arylamidaseCystine arylamidaseTrypsinalpha- ChymotrypsinAcid phosphataseNaphthol-AS-BI-phosphohydrolasealpha- Galactosidasebeta- Galactosidasebeta- Glucuronidasealpha- Glucosidasebeta- GlucosidaseN-acetyl-beta- glucosaminidasealpha- Mannosidasealpha- Fucosidase
19964+++-++-+-+----+-+--

API 20E

@refONPGADH ArgLDC LysODCCITH2SURETDA TrpINDVPGEL
19964+----------

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinent
11323garden soil
67770Garden soilKofu City, Yamanashi Pref.JapanJPNAsia

isolation source categories

Cat1Cat2Cat3
#Environmental#Terrestrial#Soil
#Engineered#Agriculture#Garden

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
199641German classification
113231Risk group (German classification)

Sequence information

16S sequences

@refdescriptionaccessionlengthdatabaseNCBI tax ID
20218Microbispora rosea strain ATCC12950 16S ribosomal RNA gene, partial sequenceAF051394192ena58117
20218Microbispora rosea gene for 16S ribosomal RNA, partial sequenceD869361473ena58117

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Microbispora rosea subsp. rosea NBRC 14044GCA_016863055contigncbi58118
66792Microbispora rosea strain ATCC 1295058117.3wgspatric58117
66792Microbispora rosea subsp. rosea strain NBRC 1404458118.5wgspatric58118
66792Microbispora rosea ATCC 129502681812892draftimg58117
67770Microbispora rosea ATCC 12950GCA_900156315scaffoldncbi58117

GC content

@refGC-contentmethod
6777071.2genome sequence analysis
6777069.9high performance liquid chromatography (HPLC)
6777071thermal denaturation, midpoint method (Tm)
6777071.1

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingyes99no
gram-positiveyes86.935no
anaerobicno98.903no
halophileno93.014no
spore-formingyes95.583no
glucose-utilyes89.429no
thermophileno98.443yes
flagellatedno98.024no
aerobicyes90.24no
motileno92.744no
glucose-fermentno92.771no

External links

@ref: 11323

culture collection no.: DSM 43839, ATCC 12950, CBS 189.57, CBS 307.61, IAM 0114, IFO 14044, IFO 3559, IMRU 3757, JCM 3006, KCC A-0006, NBRC 14044, NBRC 3559, NCIB 9560, RIA 477, RIA 763, BCRC 11622, CGMCC 4.1227, CGMCC 4.1339, CGMCC 4.5564, HUT 6622, IMET 9534, IMSNU 20075, KACC 20042, KCTC 9181, KCTC 9326, NCIMB 9560, NRRL B-2632, VKM Ac-634

straininfo link

  • @ref: 85552
  • straininfo: 37733

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny2283505A taxonomic review of the genus Microbispora and a proposal to transfer two species to the genus Actinomadura and to combine ten species into Microbispora rosea.Miyadoh S, Amano S, Tohyama H, Shomura TJ Gen Microbiol10.1099/00221287-136-9-19051990Actinomycetales/*classification/genetics/ultrastructure, DNA, Bacterial/analysis, Fatty Acids/analysis, Microscopy, Electron, Scanning, Spores, Bacterial/ultrastructure
Phylogeny25634944Microbispora bryophytorum sp. nov., an actinomycete isolated from moss (Bryophyta).Li C, Zhang Y, Liu C, Wang H, Zhao J, Li L, Zhang Z, Wang X, Xiang WInt J Syst Evol Microbiol10.1099/ijs.0.0000952015Actinobacteria/*classification/genetics/isolation & purification, Bacterial Typing Techniques, Bryophyta/*microbiology, China, DNA, Bacterial/genetics, Diaminopimelic Acid/chemistry, Fatty Acids/chemistry, Molecular Sequence Data, Nucleic Acid Hybridization, Peptidoglycan/chemistry, Phospholipids/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Spiro Compounds, Vitamin K 2/analogs & derivatives/chemistryGenetics
Phylogeny26589683Microbispora camponoti sp. nov., a novel actinomycete isolated from the cuticle of Camponotus japonicus Mayr.Han C, Liu C, Zhao J, Guo L, Lu C, Li J, Jia F, Wang X, Xiang WAntonie Van Leeuwenhoek10.1007/s10482-015-0625-x2015Actinomycetales/classification/genetics/*isolation & purification/metabolism, Animal Structures/*microbiology, Animals, Ants/*microbiology, China, DNA, Bacterial/genetics, DNA, Ribosomal/genetics, Fatty Acids/chemistry/metabolism, Molecular Sequence Data, PhylogenyMetabolism
Phylogeny30739286Microbispora tritici sp. nov., a novel actinomycete isolated from a root of wheat (Triticum aestivum L.).Han C, Zhao J, Yu B, Shi H, Zhang C, Guo X, Xiang W, Wang XAntonie Van Leeuwenhoek10.1007/s10482-019-01246-y2019Actinobacteria/*classification/genetics/*isolation & purification/physiology, Bacterial Typing Techniques, Cell Wall/chemistry, Cluster Analysis, Cytosol/chemistry, DNA, Bacterial/chemistry/genetics, DNA, Ribosomal/chemistry/genetics, Diaminopimelic Acid/analysis, Fatty Acids/analysis, Glycolipids/analysis, Nucleic Acid Hybridization, Phospholipids/analysis, Phylogeny, Plant Roots/*microbiology, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Triticum/*microbiology, Vitamin K 2/analysisTranscriptome
Phylogeny31622227Microbispora fusca sp. nov., a novel actinomycete isolated from the ear of wheat (Triticum aestivum L.).Zhao J, Yu B, Han C, Cao P, Yu Z, Ju H, Xiang W, Wang XInt J Syst Evol Microbiol10.1099/ijsem.0.0037252020Actinomycetales/*classification/isolation & purification, Bacterial Typing Techniques, Base Composition, China, DNA, Bacterial/genetics, Fatty Acids/chemistry, Genes, Bacterial, Nucleic Acid Hybridization, *Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Triticum/*microbiologyTranscriptome
Phylogeny33047275Microbispora cellulosiformans sp. nov., a novel actinomycete with cellulase activity isolated from soil in the cold region.Gong X, Xiang W, Cao X, Yu Y, Hao Y, Li L, Wang Q, Zou H, Qian CAntonie Van Leeuwenhoek10.1007/s10482-020-01477-42020*Actinobacteria/genetics, Bacterial Typing Techniques, *Cellulases, DNA, Bacterial/genetics, Fatty Acids, Nucleic Acid Hybridization, Phospholipids, Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Soil, Soil MicrobiologyTranscriptome
Phylogeny34489568Microbispora oryzae sp. nov., isolated from leaves of rice plant (Oryza sativa L.).Muangham S, Duangmal KJ Antibiot (Tokyo)10.1038/s41429-021-00470-x2021Actinobacteria/classification/*genetics/isolation & purification, Base Composition, DNA, Bacterial/*genetics, Genotype, Oryza/*microbiology, Phenotype, Plant Leaves, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, ThailandGenetics

Reference

@idauthorscataloguedoi/urltitlejournalpubmed
11323Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 43839)https://www.dsmz.de/collection/catalogue/details/culture/DSM-43839
19964Wink, J.http://www.dsmz.de/microorganisms/wink_pdf/DSM43839.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
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
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
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
85552Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID37733.1StrainInfo: A central database for resolving microbial strain identifiers