Strain identifier

BacDive ID: 7985

Type strain: Yes

Species: Micromonospora mirobrigensis

Strain history: CIP <- 2005, M.E. Trujillo, Salamanca Univ., Salamanca, Spain: WA201

NCBI tax ID(s): 262898 (species)

For citation purpose refer to the digital object identifier (doi) of the current version.
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General

@ref: 12012

BacDive-ID: 7985

DSM-Number: 44830

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

description: Micromonospora mirobrigensis DSM 44830 is an aerobe, spore-forming, mesophilic bacterium that was isolated from water.

NCBI tax id

  • NCBI tax id: 262898
  • Matching level: species

strain history

@refhistory
12012<- M. E. Trujillo, Universidad de Salamanca, Spain; WA201
364162005, M.E. Trujillo, Salamanca Univ., Salamanca, Spain: WA201
67770DSM 44830 <-- M. E. Trujillo WA201.
120973CIP <- 2005, M.E. Trujillo, Salamanca Univ., Salamanca, Spain: WA201

doi: 10.13145/bacdive7985.20230509.8.1

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 mirobrigensis
  • full scientific name: Micromonospora mirobrigensis Trujillo et al. 2005

@ref: 12012

domain: Bacteria

phylum: Actinobacteria

class: Actinobacteria

order: Actinomycetales

family: Micromonosporaceae

genus: Micromonospora

species: Micromonospora mirobrigensis

full scientific name: Micromonospora mirobrigensis Trujillo et al. 2005

type strain: yes

Morphology

cell morphology

@refgram stainmotilityconfidencecell shape
31344positive
69480no92.839
69480positive100
120973positivenorod-shaped

colony morphology

@refcolony colorincubation periodmedium used
20129Deep orange (2011)10-14 daysISP 2
20129Yellow orange (2000)10-14 daysISP 3
20129Yellow orange (2000)10-14 daysISP 6
20129Yellow orange (2000)10-14 daysISP 7
120973

multicellular morphology

@refforms multicellular complexmedium name
20129noISP 2
20129noISP 3
20129noISP 4
20129noISP 5
20129noISP 6
20129noISP 7

pigmentation

  • @ref: 31344
  • production: yes

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
12012N-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
20129ISP 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
20129ISP 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:
20129ISP 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
20129ISP 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
36416MEDIUM 57 - for Streptomyces, Nocardioides, Lentzea albidocapillata and Streptoverticillium reticulumyesDistilled water make up to (1000.000 ml);Agar (15.000 g);Glucose (4.000g);Yeast extract (4.000 g);Malt extract (10.000 g);Calcium carbonate (2.000 g)
12012BENNETT'S AGAR (DSMZ Medium 548)yeshttps://mediadive.dsmz.de/medium/548Name: BENNETT'S AGAR (DSMZ Medium 548) Composition: Agar 15.0 g/l Glucose 10.0 g/l N-Z amine 2.0 g/l Yeast extract 1.0 g/l Beef extract 1.0 g/l Distilled water
12012GPHF-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
120973CIP Medium 57yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=57

culture temp

@refgrowthtypetemperaturerange
20129positiveoptimum28mesophilic
31344positivegrowth20-37
31344positiveoptimum28mesophilic
36416positivegrowth30mesophilic
67770positivegrowth28mesophilic
12012positivegrowth28mesophilic
120973positivegrowth25-41
120973nogrowth10psychrophilic
120973nogrowth45thermophilic

culture pH

  • @ref: 31344
  • ability: positive
  • type: optimum
  • pH: 7

Physiology and metabolism

oxygen tolerance

@refoxygen tolerance
31344aerobe
120973obligate aerobe

spore formation

@refspore formationconfidence
31344yes
69481yes100
69480yes100
120973no

halophily

@refsaltgrowthtested relationconcentration
31344NaClpositivegrowth<3 %
31344NaClpositiveoptimum1.5 %
120973NaClpositivegrowth0 %
120973NaClnogrowth2 %
120973NaClnogrowth4 %
120973NaClnogrowth6 %
120973NaClnogrowth8 %
120973NaClnogrowth10 %

observation

  • @ref: 67770
  • observation: quinones: MK-10(H4), MK-10(H6), MK-9(H4)

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
2012917234glucose+/-
2012922599arabinose+/-
2012917992sucrose+/-
2012918222xylose+/-
2012917268myo-inositol+/-
2012929864mannitol+/-
2012928757fructose-
2012926546rhamnose+/-
2012916634raffinose+/-
2012962968cellulose+/-
3134422599arabinose+carbon source
3134417057cellobiose+carbon source
3134428260galactose+carbon source
3134417234glucose+carbon source
3134427570histidine+carbon source
3134417306maltose+carbon source
3134437684mannose+carbon source
3134428053melibiose+carbon source
3134416634raffinose+carbon source
3134417992sucrose+carbon source
3134427082trehalose+carbon source
313444853esculin+hydrolysis
12097316947citrate-carbon source
1209734853esculin+hydrolysis
120973606565hippurate+hydrolysis
12097317632nitrate-reduction
12097316301nitrite-reduction
12097317632nitrate-respiration

metabolite production

  • @ref: 120973
  • Chebi-ID: 35581
  • metabolite: indole
  • production: no

metabolite tests

@refChebi-IDmetabolitevoges-proskauer-testmethylred-test
12097315688acetoin-
12097317234glucose-

enzymes

@refvalueactivityec
31344catalase+1.11.1.6
31344cytochrome oxidase+1.9.3.1
31344urease+3.5.1.5
120973oxidase+
120973beta-galactosidase-3.2.1.23
120973alcohol dehydrogenase-1.1.1.1
120973gelatinase+
120973amylase+
120973DNase+
120973caseinase+3.4.21.50
120973catalase+1.11.1.6
120973tween esterase-
120973gamma-glutamyltransferase-2.3.2.2
120973lecithinase-
120973lipase-
120973lysine decarboxylase-4.1.1.18
120973ornithine decarboxylase-4.1.1.17
120973phenylalanine ammonia-lyase-4.3.1.24
120973tryptophan deaminase-
120973urease-3.5.1.5
68382esterase (C 4)+
68382esterase lipase (C 8)+
68382lipase (C 14)-
68382leucine arylamidase+3.4.11.1
68382cystine arylamidase-3.4.11.3
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- FucosidaseControl
20129-++-+----++++-+++--
120973+++-++-+-++++-+++---

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinentisolation date
12012waterSalamaca, Ciudad RodrigoSpainESPEurope
67770Water of a pond located on a former uranium mineCiudad RodrigoSpainESPEurope
120973Environment, WaterCiudad Rodrigo, SalamancaSpainESPEurope2003

isolation source categories

  • Cat1: #Environmental
  • Cat2: #Aquatic

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
120121Risk group (German classification)
201291German classification
1209731Risk group (French classification)

Sequence information

16S sequences

  • @ref: 12012
  • description: Micromonospora mirobrigensis 16S rRNA gene, type strain WA201
  • accession: AJ626950
  • length: 1511
  • database: ena
  • NCBI tax ID: 262898

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Micromonospora mirobrigensis strain DSM 44830262898.5wgspatric262898
66792Micromonospora mirobrigensis DSM 448302619619047draftimg262898
67770Micromonospora mirobrigensis DSM 44830GCA_900091555scaffoldncbi262898

GC content

@refGC-contentmethod
3134468.6
6777068.6thermal denaturation, midpoint method (Tm)
6777073.34genome sequence analysis

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingyes100no
motileno94.3no
gram-positiveyes92.319yes
anaerobicno99.405yes
aerobicyes95.305yes
halophileno94.167yes
spore-formingyes92.737yes
glucose-utilyes87.585yes
flagellatedno97.683no
thermophileno98.917yes
glucose-fermentno93.71no

External links

@ref: 12012

culture collection no.: DSM 44830, LMG 22229, NBRC 101890, NRRL B-24769, WA 201, JCM 13240, CIP 108755

straininfo link

  • @ref: 77418
  • straininfo: 129610

literature

  • topic: Phylogeny
  • Pubmed-ID: 15774678
  • title: Micromonospora mirobrigensis sp. nov.
  • authors: Trujillo ME, Fernandez-Molinero C, Velazquez E, Kroppenstedt RM, Schumann P, Mateos PF, Martinez-Molina E
  • journal: Int J Syst Evol Microbiol
  • DOI: 10.1099/ijs.0.63361-0
  • year: 2005
  • mesh: Bacterial Typing Techniques, DNA, Bacterial/analysis, DNA, Ribosomal/analysis, Fresh Water/*microbiology, Genes, rRNA, Micromonospora/chemistry/*classification/genetics/isolation & purification, Molecular Sequence Data, Nucleic Acid Hybridization, Phenotype, RNA, Ribosomal, 16S/genetics, *Radon, Sequence Analysis, DNA, *Water Pollutants, Radioactive
  • topic2: Genetics

Reference

@idauthorscataloguedoi/urltitleID_cross_referencepubmed
12012Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 44830)https://www.dsmz.de/collection/catalogue/details/culture/DSM-44830
20129Wink, J.http://www.dsmz.de/microorganisms/wink_pdf/DSM44830.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
31344Barberan A, Caceres Velazquez H, Jones S, Fierer N.10.1128/mSphere.00237-17Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information2765828776041
36416Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/6419
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
77418Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID129610.1StrainInfo: A central database for resolving microbial strain identifiers
120973Curators of the CIPCollection of Institut Pasteur (CIP 108755)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20108755