Strain identifier

BacDive ID: 8021

Type strain: Yes

Species: Micromonospora cremea

Strain Designation: CR 30

Strain history: CECT 7891 <-- M. E. Trujillo, Univ. Salamanca, Spain; CR30.

NCBI tax ID(s): 709881 (species)

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General

@ref: 17740

BacDive-ID: 8021

DSM-Number: 45599

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

description: Micromonospora cremea CR 30 is an aerobe, spore-forming, mesophilic bacterium that was isolated from rhizosphere of Pisum sativum.

NCBI tax id

  • NCBI tax id: 709881
  • Matching level: species

strain history

@refhistory
17740<- M. E. Trujillo, Universidad de Salamanca, Spain; CR 30 <- L. Carro
67770CECT 7891 <-- M. E. Trujillo, Univ. Salamanca, Spain; CR30.

doi: 10.13145/bacdive8021.20250331.9.3

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 cremea
  • full scientific name: Micromonospora cremea Carro et al. 2012

@ref: 17740

domain: Bacteria

phylum: Actinobacteria

class: Actinobacteria

order: Actinomycetales

family: Micromonosporaceae

genus: Micromonospora

species: Micromonospora cremea

full scientific name: Micromonospora cremea Carro et al. 2012

strain designation: CR 30

type strain: yes

Morphology

cell morphology

@refgram staincell widthmotilityconfidence
30559positive0.4 µmno
125438positive90.567
125439positive99.6

colony morphology

@refcolony colormedium used
69410Dahlia yellow (1033)ISP 4
69410Dahlia yellow (1033)suter with tyrosine
69410Beige (1001)ISP 7
69410Ivory/ RAL 1007 daffodil yellow (1014)ISP 5
69410Ochre yellow (1024)suter without tyrosine
69410Pastel yellow (1034)ISP 3
69410Sun yellow (1037)ISP 6
69410Yellow orange (2000)ISP 2

multicellular morphology

@refforms multicellular complexcomplex namemedium name
69410noAerial myceliumISP 2
69410noAerial myceliumISP 3
69410noAerial myceliumISP 4
69410noAerial myceliumISP 5
69410noAerial myceliumISP 6
69410noAerial myceliumISP 7
69410noAerial myceliumsuter with tyrosine
69410noAerial myceliumsuter without tyrosine

pigmentation

@refproductioncolorname
30559yes
69410yesRal 8001 ochre brownsoluble pigment

multimedia

@refmultimedia contentcaptionintellectual property rights
69410DSM_45599_image3.jpegPlates (65, ISP2, ISP3, ISP4, ISP5, ISP7)Helmholtz-Zentrum für Infektionsforschung GmbH
69410DSM_45599_image4.jpegPlates (65, ISP2, ISP3, ISP4, ISP5, ISP7)Helmholtz-Zentrum für Infektionsforschung GmbH

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
17740GYM 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
17740N-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
17740GPHF-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
17740TRYPTICASE SOY BROTH AGAR (DSMZ Medium 535)yeshttps://mediadive.dsmz.de/medium/535Name: TRYPTICASE SOY BROTH AGAR (DSMZ Medium 535) Composition: Trypticase soy broth 30.0 g/l Agar 15.0 g/l Distilled water

culture temp

@refgrowthtypetemperature
17740positivegrowth28
30559positivegrowth10-37
67770positivegrowth28

culture pH

  • @ref: 30559
  • ability: positive
  • type: growth
  • pH: 07-08

Physiology and metabolism

oxygen tolerance

@refoxygen toleranceconfidence
30559aerobe
125438aerobe90.849
125439obligate aerobe99.7

spore formation

@refspore formationconfidence
30559yes
125438yes90.248

halophily

@refsaltgrowthtested relationconcentration
30559NaClpositivegrowth1 %
69410NaClpositivegrowth0 %

observation

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

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
3055922599arabinose+carbon source
3055929016arginine+carbon source
3055928757fructose+carbon source
3055917234glucose+carbon source
3055917306maltose+carbon source
3055937684mannose+carbon source
3055916634raffinose+carbon source
3055917814salicin+carbon source
3055917822serine+carbon source
3055917992sucrose+carbon source
3055917632nitrate+reduction
6837928087glycogen-fermentation
6837917992sucrose-fermentation
6837917716lactose-fermentation
6837917306maltose-fermentation
6837916899D-mannitol-fermentation
6837965327D-xylose-fermentation
6837916988D-ribose-fermentation
6837917634D-glucose-fermentation
683795291gelatin+hydrolysis
6837916199urea-hydrolysis
683794853esculin-hydrolysis
6837917632nitrate-reduction
6941022599arabinose+growth
6941062968cellulose-growth
6941028757fructose-growth
6941017234glucose+growth
6941017268inositol+growth
6941037684mannose-growth
6941016634raffinose-growth
6941026546rhamnose+growth
6941017992sucrose-growth
6941018222xylose-growth

enzymes

@refvalueactivityec
30559acid phosphatase+3.1.3.2
30559alkaline phosphatase+3.1.3.1
30559catalase+1.11.1.6
30559gelatinase+
30559cytochrome oxidase+1.9.3.1
30559pyrazinamidase+3.5.1.B15
68382alpha-fucosidase-3.2.1.51
68382alpha-mannosidase-3.2.1.24
68382alpha-galactosidase-3.2.1.22
68382beta-glucuronidase-3.2.1.31
68382naphthol-AS-BI-phosphohydrolase+
68382acid phosphatase+3.1.3.2
68382cystine arylamidase+3.4.11.3
68382trypsin-3.4.21.4
68382valine arylamidase+
68382leucine arylamidase+3.4.11.1
68382lipase (C 14)-
68382esterase lipase (C 8)+
68382alkaline phosphatase+3.1.3.1
68379N-acetyl-beta-glucosaminidase+3.2.1.52
68379alpha-glucosidase+3.2.1.20
68379pyrrolidonyl arylamidase-3.4.19.3
68382N-acetyl-beta-glucosaminidase+3.2.1.52
68382alpha-glucosidase+3.2.1.20
68382esterase (C 4)+
68379gelatinase+
68379urease-3.5.1.5
68379beta-glucosidase-3.2.1.21
68379beta-glucuronidase-3.2.1.31
68379alkaline phosphatase+3.1.3.1
68379pyrazinamidase-3.5.1.B15

API coryne

@refNITPYZPYRAPALbeta GURbeta GALalpha GLUbeta NAGESCUREGELGLURIBXYLMANMALLACSACGLYG
69410---+-+/-++--+--------

API zym

@refAlkaline phosphataseEsteraseEsterase LipaseLipaseLeucine arylamidaseValine arylamidaseCystine arylamidaseTrypsinalpha- ChymotrypsinAcid phosphataseNaphthol-AS-BI-phosphohydrolasealpha- Galactosidasebeta- Galactosidasebeta- Glucuronidasealpha- Glucosidasebeta- GlucosidaseN-acetyl-beta- glucosaminidasealpha- Mannosidasealpha- Fucosidase
69410+++-+++-+/-++-+/--++/-+--

Isolation, sampling and environmental information

isolation

@refsample typehost speciesgeographic locationcountryorigin.countrycontinentlatitudelongitude
17740rhizosphere of Pisum sativumPisum sativumZamora province, Canizal (41° 49' 00'' N 6° 13' 00'' W)SpainESPEurope41.8167-6.2167
67770Rhizosphere of a Pisum sativum plantPisum sativumZamoraSpainESPEurope

isolation source categories

Cat1Cat2Cat3
#Host#Plants#Herbaceous plants (Grass,Crops)
#Host Body-Site#Plant#Rhizosphere

Safety information

risk assessment

  • @ref: 17740
  • biosafety level: 1
  • biosafety level comment: Risk group (German classification)

Sequence information

16S sequences

  • @ref: 17740
  • description: Micromonospora cremea partial 16S rRNA gene, type strain CR30T
  • accession: FN658654
  • length: 1452
  • database: nuccore
  • NCBI tax ID: 709881

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Micromonospora cremea strain DSM 45599709881.3wgspatric709881
66792Micromonospora cremea DSM 455992630968262draftimg709881
67770Micromonospora cremea DSM 45599GCA_900143515contigncbi709881

GC content

@refGC-contentmethod
1774072.4thermal denaturation, midpoint method (Tm)
3055972.4
6777071.47genome sequence analysis

Genome-based predictions

predictions

@refmodeltraitdescriptionpredictionconfidencetraining_data
125438gram-positivegram-positivePositive reaction to Gram-stainingyes90.567no
125438anaerobicanaerobicAbility to grow under anoxygenic conditions (including facultative anaerobes)no95.871no
125438spore-formingspore-formingAbility to form endo- or exosporesyes90.248yes
125438aerobicaerobicAbility to grow under oxygenic conditions (including facultative aerobes)yes90.849yes
125438thermophilethermophilicAbility to grow at temperatures above or equal to 45°Cno95.5no
125438motile2+flagellatedAbility to perform flagellated movementno88yes
125439BacteriaNetspore_formationAbility to form endo- or exosporesyes69.9
125439BacteriaNetmotilityAbility to perform movementno83.1
125439BacteriaNetgram_stainReaction to gram-stainingpositive99.6
125439BacteriaNetoxygen_toleranceOxygenic conditions needed for growthobligate aerobe99.7

External links

@ref: 17740

culture collection no.: DSM 45599, CECT 7891, JCM 31700

straininfo link

  • @ref: 77451
  • straininfo: 382400

literature

  • topic: Phylogeny
  • Pubmed-ID: 22286910
  • title: Micromonospora cremea sp. nov. and Micromonospora zamorensis sp. nov., isolated from the rhizosphere of Pisum sativum.
  • authors: Carro L, Pukall R, Sproer C, Kroppenstedt RM, Trujillo ME
  • journal: Int J Syst Evol Microbiol
  • DOI: 10.1099/ijs.0.038695-0
  • year: 2012
  • mesh: Bacterial Typing Techniques, DNA, Bacterial/genetics, Fatty Acids/analysis, Micromonospora/*classification/genetics/isolation & purification, Molecular Sequence Data, Nucleic Acid Hybridization, Peas/*microbiology, Peptidoglycan/analysis, *Phylogeny, RNA, Ribosomal, 16S/genetics, *Rhizosphere, Sequence Analysis, DNA, *Soil Microbiology, Spain, Vitamin K 2/analysis
  • topic2: Genetics

Reference

@idauthorscataloguedoi/urltitleID_cross_referencepubmed
17740Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 45599)https://www.dsmz.de/collection/catalogue/details/culture/DSM-45599
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
30559Barberan A, Caceres Velazquez H, Jones S, Fierer N.10.1128/mSphere.00237-17Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information2689028776041
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/
68379Automatically annotated from API Coryne
68382Automatically annotated from API zym
69410Wink, J.https://cdn.dsmz.de/wink/DSM%2045599.pdfCompendium of Actinobacteria. HZI-Helmholtz-Centre for Infection Research, Braunschweig
77451Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID382400.1StrainInfo: A central database for resolving microbial strain identifiers
125438Julia Koblitz, Lorenz Christian Reimer, Rüdiger Pukall, Jörg Overmann10.1101/2024.08.12.607695Predicting bacterial phenotypic traits through improved machine learning using high-quality, curated datasets
125439Philipp Münch, René Mreches, Martin Binder, Hüseyin Anil Gündüz, Xiao-Yin To, Alice McHardyhttps://github.com/GenomeNet/deepGdeepG: Deep Learning for Genome Sequence Data. R package version 0.3.1