Strain identifier

BacDive ID: 7980

Type strain: Yes

Species: Micromonospora matsumotoensis

Strain Designation: 6393-C

Strain history: CIP <- 2000, IFO <- K. Asano, Kyowa Hakko Kogyo Co.:strain 6393-C

NCBI tax ID(s): 121616 (species)

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General

@ref: 11396

BacDive-ID: 7980

DSM-Number: 44100

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

description: Micromonospora matsumotoensis 6393-C is a spore-forming, mesophilic bacterium that was isolated from woodland soil.

NCBI tax id

  • NCBI tax id: 121616
  • Matching level: species

strain history

@refhistory
11396<- IFO <- K. Asano, Kyowa Hakko Co., 6393-C
67770IFO 14550 <-- K. Asano 6393-C.
120860CIP <- 2000, IFO <- K. Asano, Kyowa Hakko Kogyo Co.:strain 6393-C

doi: 10.13145/bacdive7980.20230509.8.1

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 matsumotoensis
  • full scientific name: Micromonospora matsumotoensis corrig. (Asano et al. 1989) Lee et al. 2000

  • synonyms

    @refsynonym
    20215Catellatospora matsumotoensis
    20215Catellatospora matsumotoense
    20215Micromonospora matsumotoense

@ref: 11396

domain: Bacteria

phylum: Actinobacteria

class: Actinobacteria

order: Actinomycetales

family: Micromonosporaceae

genus: Micromonospora

species: Micromonospora matsumotoense

full scientific name: Micromonospora matsumotoense (Asano et al. 1989) Lee et al. 2000

strain designation: 6393-C

type strain: yes

Morphology

cell morphology

@refmotilityconfidencegram staincell shape
69480no93.08
69480100positive
120860nopositiverod-shaped

multimedia

@refmultimedia contentintellectual property rightscaption
11396https://www.dsmz.de/microorganisms/photos/DSM_44100-1.jpg© Leibniz-Institut DSMZ
11396https://www.dsmz.de/microorganisms/photos/DSM_44100.jpg© Leibniz-Institut DSMZMedium 65 28°C

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
11396GYM 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
36433MEDIUM 116 - for Streptomyces, Nocardia, Streptosporangium and Mycobacterium chlorophenolicumyesDistilled water make up to (1000.000 ml);Agar (20.000 g);Glucose (4.000g);Yeast extract (4.000 g);Malt extract (10.000 g)
11396N-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
120860CIP Medium 116yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=116

culture temp

@refgrowthtypetemperaturerange
11396positivegrowth28mesophilic
36433positivegrowth30mesophilic
67770positivegrowth28mesophilic
120860positivegrowth25-30mesophilic
120860nogrowth10psychrophilic
120860nogrowth37mesophilic
120860nogrowth41thermophilic
120860nogrowth45thermophilic

Physiology and metabolism

spore formation

@refspore formationconfidence
69481yes100
69480yes99.999

halophily

@refsaltgrowthtested relationconcentration
120860NaClpositivegrowth0-2 %
120860NaClnogrowth4 %
120860NaClnogrowth6 %
120860NaClnogrowth8 %
120860NaClnogrowth10 %

observation

  • @ref: 67770
  • observation: quinones: MK-10(H6), MK-10(H8), MK-10(H4)

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
12086016947citrate-carbon source
1208604853esculin+hydrolysis
120860606565hippurate-hydrolysis
12086017632nitrate+reduction
12086016301nitrite-reduction

metabolite production

  • @ref: 120860
  • Chebi-ID: 35581
  • metabolite: indole
  • production: no

metabolite tests

@refChebi-IDmetabolitevoges-proskauer-testmethylred-test
12086015688acetoin-
12086017234glucose-

enzymes

@refvalueactivityec
120860oxidase-
120860beta-galactosidase+3.2.1.23
120860alcohol dehydrogenase-1.1.1.1
120860gelatinase+
120860catalase+1.11.1.6
120860gamma-glutamyltransferase-2.3.2.2
120860lysine decarboxylase-4.1.1.18
120860ornithine decarboxylase-4.1.1.17
120860phenylalanine ammonia-lyase-4.3.1.24
120860tryptophan deaminase-
120860urease+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
120860-++--+---------+----

API biotype100

@refGLUFRUGALTREMNESBEMELSACRAFMTEMALLACLTEMbGaMaGaCELGENMbGuESCRIBARAXYLPLERHAFUCMLZDARLLARLXLTDULTAGGLYINOMANMTLTURSORADOHBGLYXERYMDG3MDGSATMUCLTATDTATMTATDMLTLMLTCATETATETTECITGRTGAT2KG5KGTRYNAGGNTPACPATpOBEQATGTEmOBEBATPPATCMTTGEBETPCEABTHINLATCAPCYTHISSUCFUMGREGYTAVTETNTTNGLNITA3OBUAPTGTTPRODALALALASERMNTPROPTYR2KT
120860+++++-++-+++---++-+-+--------------+------------------------+-------------------------+----------++

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinentisolation date
11396woodland soilNagano, MatsumotoJapanJPNAsia
67770SoilMatsumoto, Nagano Pref.JapanJPNAsia
120860Environment, Woodland soilMatsumoto, NaganoJapanJPNAsia1985

isolation source categories

Cat1Cat2Cat3
#Environmental#Terrestrial#Forest
#Environmental#Terrestrial#Soil

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
113961Risk group (German classification)
1208601Risk group (French classification)

Sequence information

16S sequences

@refdescriptionaccessionlengthdatabaseNCBI tax ID
20218Micromonospora matsumotoense strain IMSNU 22003T 16S ribosomal RNA gene, partial sequenceAF1521091506ena121616
20218Micromonospora matsumotoense axC10 16S ribosomal RNA gene, partial sequenceAF311998455ena121616

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Micromonospora matsumotoense strain DSM 44100121616.4wgspatric121616
66792Micromonospora matsumotoense DSM 441002622736591draftimg121616
67770Micromonospora matsumotoense DSM 44100GCA_900091525scaffoldncbi121616

GC content

@refGC-contentmethod
6777071thermal denaturation, midpoint method (Tm)
6777072.27genome sequence analysis
6777072.9high performance liquid chromatography (HPLC)

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingyes100no
motileno94.812no
gram-positiveyes91.168no
anaerobicno99.481no
aerobicyes96.071no
halophileno94.243no
spore-formingyes96.968no
thermophileno98.423no
glucose-utilyes88.657no
flagellatedno97.817no
glucose-fermentno90.634no

External links

@ref: 11396

culture collection no.: DSM 44100, ATCC 49364, FERM BP-1196, IFO 14550, NBRC 14550, NRRL B-16490, JCM 9104, CGMCC 4.5527, CIP 106812, IMSNU 22003, KCTC 9354, VKM Ac-2009

straininfo link

  • @ref: 77413
  • straininfo: 42440

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny23178730Micromonospora wenchangensis sp. nov., isolated from mangrove soil.Ren J, Li L, Wei B, Tang YL, Deng ZX, Sun M, Hong KInt J Syst Evol Microbiol10.1099/ijs.0.045476-02012Bacterial Typing Techniques, Base Composition, China, DNA, Bacterial/genetics, Fatty Acids/analysis, Genes, Bacterial, Micromonospora/*classification/genetics/isolation & purification, Molecular Sequence Data, Phospholipids/analysis, *Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, *Soil Microbiology, Vitamin K 2/analysisGenetics
Phylogeny24352533Micromonospora maoerensis sp. nov., isolated from a Chinese pine forest soil.Li C, Liu C, Zhao J, Zhang Y, Gao R, Zhang X, Yao M, Wang X, Xiang WAntonie Van Leeuwenhoek10.1007/s10482-013-0096-x2013Genes, Bacterial, Micromonospora/*classification/genetics/metabolism, Molecular Sequence Data, Phenotype, Phylogeny, Pinus, RNA, Ribosomal, 16S/genetics, *Soil Microbiology, TreesGenetics
Phylogeny26395026Micromonospora nickelidurans sp. nov., isolated from soil from a nickel-mining site.Lin YB, Fan MC, Guo YQ, Di XH, Dong DH, Zhang X, Wei GHInt J Syst Evol Microbiol10.1099/ijsem.0.0006232015Bacterial Typing Techniques, Base Composition, Cell Wall/chemistry, China, DNA, Bacterial/genetics, Diaminopimelic Acid/chemistry, Fatty Acids/chemistry, Micromonospora/*classification/genetics/isolation & purification, *Mining, Molecular Sequence Data, *Nickel, Nucleic Acid Hybridization, Phospholipids/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, *Soil Microbiology, Vitamin K 2/chemistryGenetics
Phylogeny26404428Micromonospora vulcania sp. nov., isolated from volcanic sediment.Jia F, Liu C, Zhou S, Li J, Shen Y, Guan X, Guo S, Gao M, Wang X, Xiang WAntonie Van Leeuwenhoek10.1007/s10482-015-0591-32015Bacterial Typing Techniques, China, Cluster Analysis, DNA Gyrase/genetics, DNA, Bacterial/chemistry/genetics, DNA, Ribosomal/chemistry/genetics, Geologic Sediments/*microbiology, Micromonospora/*classification/genetics/*isolation & purification/physiology, Molecular Sequence Data, Nucleic Acid Hybridization, Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Volcanic EruptionsGenetics
Phylogeny28629505Micromonospora fulva sp. nov., isolated from forest soil.Lee HJ, Whang KSInt J Syst Evol Microbiol10.1099/ijsem.0.0018582017Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, Diaminopimelic Acid/chemistry, Fatty Acids/chemistry, *Forests, Micromonospora/*classification/genetics/isolation & purification, Nucleic Acid Hybridization, Phospholipids/chemistry, *Phylogeny, Pigmentation, RNA, Ribosomal, 16S/genetics, Republic of Korea, Sequence Analysis, DNA, *Soil Microbiology, Ubiquinone/chemistry, Vitamin K 2/chemistryTranscriptome

Reference

@idauthorscataloguedoi/urltitlejournalpubmed
11396Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 44100)https://www.dsmz.de/collection/catalogue/details/culture/DSM-44100
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
36433Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/18984
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
77413Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID42440.1StrainInfo: A central database for resolving microbial strain identifiers
120860Curators of the CIPCollection of Institut Pasteur (CIP 106812)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20106812