Strain identifier

BacDive ID: 7996

Type strain: Yes

Species: Micromonospora viridifaciens

Strain Designation: FD 23988

Strain history: CIP <- 2005, DSMZ <- JCM <- KCC <- KY 11078 <- ATCC <- Chas Pfizer & Co.: strain FD 23988

NCBI tax ID(s): 1881 (species)

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General

@ref: 11260

BacDive-ID: 7996

DSM-Number: 43909

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

description: Micromonospora viridifaciens FD 23988 is an obligate aerobe, spore-forming, mesophilic bacterium that was isolated from soil.

NCBI tax id

  • NCBI tax id: 1881
  • Matching level: species

strain history

@refhistory
11260<- JCM (Micromonospora viridifaciens) <- KCC <- KY 11078 <- ATCC <- Chas Pfizer & Co., FD 23988
67770KCC A-0267 <-- Kyowa Hakko Kogyo Co., Ltd.; KY 11078 <-- ATCC 31146 <-- Pfizer; FD 23988.
123864CIP <- 2005, DSMZ <- JCM <- KCC <- KY 11078 <- ATCC <- Chas Pfizer & Co.: strain FD 23988

doi: 10.13145/bacdive7996.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/actinomycetota
  • domain: Bacteria
  • phylum: Actinomycetota
  • class: Actinomycetes
  • order: Micromonosporales
  • family: Micromonosporaceae
  • genus: Micromonospora
  • species: Micromonospora viridifaciens
  • full scientific name: Micromonospora viridifaciens Kroppenstedt et al. 2005

@ref: 11260

domain: Bacteria

phylum: Actinobacteria

class: Actinobacteria

order: Actinomycetales

family: Micromonosporaceae

genus: Micromonospora

species: Micromonospora viridifaciens

full scientific name: Micromonospora viridifaciens Kroppenstedt et al. 2005

strain designation: FD 23988

type strain: yes

Morphology

cell morphology

@refmotilityconfidencegram staincell shape
69480no90.191
69480100positive
123864nopositiverod-shaped

colony morphology

@refcolony colorincubation periodmedium used
19977Pastel yellow (1034)/ nut brown (8011)10-14 daysISP 2
19977Beige red (3012)10-14 daysISP 3
19977Colourless10-14 daysISP 5
19977Pastel yellow (1034)10-14 daysISP 6
19977Colourless10-14 daysISP 7
123864

multicellular morphology

@refforms multicellular complexmedium name
19977noISP 2
19977noISP 3
19977noISP 4
19977noISP 5
19977noISP 6
19977noISP 7

multimedia

@refmultimedia contentintellectual property rightscaption
11260https://www.dsmz.de/microorganisms/photos/DSM_43909-1.jpg© Leibniz-Institut DSMZ
11260https://www.dsmz.de/microorganisms/photos/DSM_43909.jpg© Leibniz-Institut DSMZMedium 554 28°C

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
11260N-Z-AMINE-MEDIUM (DSMZ Medium 554)yeshttps://mediadive.dsmz.de/medium/554Name: N-Z-AMINE-MEDIUM (DSMZ Medium 554) Composition: Starch 20.0 g/l Agar 20.0 g/l Glucose 10.0 g/l N-Z amine 5.0 g/l Yeast extract 5.0 g/l CaCO3 1.0 g/l Distilled water
11260GYM 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
19977ISP 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
19977ISP 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:
19977ISP 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
19977ISP 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
19977ISP 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
123864CIP Medium 57yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=57

culture temp

@refgrowthtypetemperaturerange
11260positivegrowth28mesophilic
67770positivegrowth28mesophilic

Physiology and metabolism

oxygen tolerance

  • @ref: 123864
  • oxygen tolerance: obligate aerobe

spore formation

@refspore formationconfidence
69481yes100
69480yes100

compound production

@refcompound
11260antibiotic 37505
67770Antibiotic 37,504

observation

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

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
1997717234glucose+/-
1997722599arabinose+/-
1997717992sucrose+/-
1997718222xylose+/-
1997717268myo-inositol+/-
1997729864mannitol+/-
1997728757fructose+/-
1997726546rhamnose+/-
1997716634raffinose+/-
1997762968cellulose+/-
12386417632nitrate-reduction
12386416301nitrite-reduction

metabolite production

  • @ref: 123864
  • Chebi-ID: 35581
  • metabolite: indole
  • production: no

enzymes

@refvalueactivityec
123864oxidase+
123864alcohol dehydrogenase-1.1.1.1
123864catalase+1.11.1.6
123864lysine decarboxylase-4.1.1.18
123864ornithine decarboxylase-4.1.1.17
123864urease-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
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
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- FucosidaseControl
19977+++-+--++++---+----
123864+++-+--+-+----+-+---

Isolation, sampling and environmental information

isolation

@refsample typecountryorigin.countrycontinent
11260soil
67770SoilJapanJPNAsia
123864Environment, Soil

isolation source categories

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

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
112601Risk group (German classification)
199771German classification
1238641Risk group (French classification)

Sequence information

16S sequences

  • @ref: 11260
  • description: Micromonospora viridifaciens 16S rRNA gene, type strain DSM 43909
  • accession: X92623
  • length: 1479
  • database: ena
  • NCBI tax ID: 1881

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Micromonospora viridifaciens DSM 43909GCA_900091545chromosomencbi1881
66792Micromonospora viridifaciens strain DSM 439091881.4completepatric1881
66792Micromonospora viridifaciens DSM 439092636416073draftimg1881

GC content

  • @ref: 67770
  • GC-content: 72.1
  • method: genome sequence analysis

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingyes100no
motileno95.043no
gram-positiveyes90.254no
anaerobicno98.981no
aerobicyes91.298no
halophileno95.868no
spore-formingyes89.902no
glucose-utilyes87.204no
flagellatedno98.008no
thermophileno96.015yes
glucose-fermentno93.435no

External links

@ref: 11260

culture collection no.: DSM 43909, ATCC 31146, CIP 108949, JCM 3267, KCC A-0267, NBRC 101887, BCRC 13409

straininfo link

  • @ref: 77426
  • straininfo: 39907

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny15997706Eight new species of the genus Micromonospora, Micromonospora citrea sp. nov., Micromonospora echinaurantiaca sp. nov., Micromonospora echinofusca sp. nov. Micromonospora fulviviridis sp. nov., Micromonospora inyonensis sp. nov., Micromonospora peucetia sp. nov., Micromonospora sagamiensis sp. nov., and Micromonospora viridifaciens sp. nov.Kroppenstedt RM, Mayilraj S, Wink JM, Kallow W, Schumann P, Secondini C, Stackebrandt ESyst Appl Microbiol10.1016/j.syapm.2004.12.0112005Carbohydrates/analysis, Diaminopimelic Acid/analysis, Fatty Acids/analysis, Isomerism, Micromonospora/*classification/cytology/genetics/physiology, Nucleic Acid Hybridization, Phospholipids/analysis, Phylogeny, Ribotyping, Spectrometry, Mass, Matrix-Assisted Laser Desorption-Ionization, Vitamin K 2/analysis
Phylogeny22634700Micromonospora equina sp. nov., isolated from soil from a racecourse.Everest GJ, Meyers PRInt J Syst Evol Microbiol10.1099/ijs.0.042929-02012Animals, Bacterial Typing Techniques, DNA, Bacterial/genetics, Horses, Micromonospora/*classification/genetics/isolation & purification, Molecular Sequence Data, Nucleic Acid Hybridization, *Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, *Soil Microbiology, South AfricaGenetics

Reference

@idauthorscataloguedoi/urltitle
11260Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 43909)https://www.dsmz.de/collection/catalogue/details/culture/DSM-43909
19977Wink, J.http://www.dsmz.de/microorganisms/wink_pdf/DSM43909.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)
67770Curators of the JCMhttps://jcm.brc.riken.jp/en/
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
77426Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID39907.1StrainInfo: A central database for resolving microbial strain identifiers
123864Curators of the CIPCollection of Institut Pasteur (CIP 108949)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20108949