Strain identifier

BacDive ID: 8033

Type strain: Yes

Species: Micromonospora qiuiae

Strain Designation: RtIII47

Strain history: CGMCC 4.5826 <-- L. Xi et al. RtIII47.

NCBI tax ID(s): 502268 (species)

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General

@ref: 18199

BacDive-ID: 8033

DSM-Number: 45781

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

description: Micromonospora qiuiae RtIII47 is an aerobe, spore-forming, mesophilic bacterium that builds an aerial mycelium and was isolated from mangrove soil.

NCBI tax id

  • NCBI tax id: 502268
  • Matching level: species

strain history

@refhistory
18199<- J. Nakagawa, NBRC; NBRC 106684
67770CGMCC 4.5826 <-- L. Xi et al. RtIII47.

doi: 10.13145/bacdive8033.20230509.8.1

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 qiuiae
  • full scientific name: Micromonospora qiuiae (Xi et al. 2012) Nouioui et al. 2018

  • synonyms

    • @ref: 20215
    • synonym: Verrucosispora qiuiae

@ref: 18199

domain: Bacteria

phylum: Actinobacteria

class: Actinobacteria

order: Actinomycetales

family: Micromonosporaceae

genus: Micromonospora

species: Micromonospora qiuiae

full scientific name: Micromonospora qiuiae (Xi et al. 2012) Nouioui et al. 2018

strain designation: RtIII47

type strain: yes

Morphology

cell morphology

@refgram stainconfidence
30340positive
69480positive100

colony morphology

@refcolony colormedium used
69435Daffodil yellow (1007)ISP 2
69435Maize yellow (1006), signal orange (2010)suter with tyrosine
69435Maize yellow (1006), signal orange (2010)suter without tyrosine
69435Melon yellow (1028)ISP 4
69435Yellow orange (2000)ISP 3
69435Yellow orange (2000)ISP 5
69435Yellow orange (2000)ISP 6
69435Yellow orange (2000)ISP 7

multicellular morphology

@refforms multicellular complexcomplex namemedium name
69435noAerial myceliumISP 2
69435noAerial myceliumISP 3
69435noAerial myceliumISP 4
69435noAerial myceliumISP 5
69435noAerial myceliumISP 6
69435noAerial myceliumISP 7
69435yesAerial myceliumsuter with tyrosine
69435yesAerial myceliumsuter without tyrosine

pigmentation

@refproductioncolorname
30340no
69435yesSand yellow (1002)soluble pigment

multimedia

@refmultimedia contentcaptionintellectual property rights
18199https://www.dsmz.de/microorganisms/photos/DSM_45781.jpgMedium 553 28°C© Leibniz-Institut DSMZ
69435DSM_45781_image3.jpegPlates (65, ISP2, ISP3, ISP4, ISP5, ISP7)Helmholtz-Zentrum für Infektionsforschung GmbH
69435DSM_45781_image4.jpegPlates (65, ISP2, ISP3, ISP4, ISP5, ISP7)Helmholtz-Zentrum für Infektionsforschung GmbH

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
18199GYM STREPTOMYCES MEDIUM (DSMZ Medium 65)yeshttps://www.dsmz.de/microorganisms/medium/pdf/DSMZ_Medium65.pdf
18199TRYPTICASE SOY BROTH AGAR (DSMZ Medium 535)yeshttps://www.dsmz.de/microorganisms/medium/pdf/DSMZ_Medium535.pdf
18199GPHF-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

culture temp

@refgrowthtypetemperaturerange
18199positivegrowth28mesophilic
67770positivegrowth28mesophilic

Physiology and metabolism

oxygen tolerance

  • @ref: 30340
  • oxygen tolerance: aerobe

spore formation

@refspore formationconfidence
30340yes
69481yes100
69480yes100

halophily

@refsaltgrowthtested relationconcentration
30340NaClpositivegrowth0-10 %
30340NaClpositiveoptimum2.50 %
69435NaClpositivegrowth0-2.5 %

observation

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

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
3034022599arabinose+carbon source
3034028757fructose+carbon source
3034028260galactose+carbon source
3034017234glucose+carbon source
3034029864mannitol+carbon source
3034017268myo-inositol+carbon source
3034026546rhamnose+carbon source
3034033942ribose+carbon source
3034017992sucrose+carbon source
3034027082trehalose+carbon source
3034018222xylose+carbon source
6943522599arabinose+/-growth
6943562968cellulose-growth
6943528757fructose+/-growth
6943517234glucose+growth
6943517268inositol-growth
6943537684mannose-growth
6943516634raffinose-growth
6943526546rhamnose+/-growth
6943517992sucrose+/-growth
6943518222xylose+/-growth
6837917632nitrate-reduction
683794853esculin+hydrolysis
6837916199urea-hydrolysis
683795291gelatin+hydrolysis
6837917634D-glucose-fermentation
6837916988D-ribose-fermentation
6837965327D-xylose-fermentation
6837916899D-mannitol-fermentation
6837917306maltose-fermentation
6837917716lactose-fermentation
6837917992sucrose-fermentation
6837928087glycogen-fermentation

enzymes

@refvalueactivityec
68379gelatinase+
68379urease-3.5.1.5
68379beta-glucosidase+3.2.1.21
68379N-acetyl-beta-glucosaminidase-3.2.1.52
68379alpha-glucosidase+3.2.1.20
68379beta-galactosidase-3.2.1.23
68379beta-glucuronidase-3.2.1.31
68379alkaline phosphatase+3.1.3.1
68379pyrrolidonyl arylamidase-3.4.19.3
68382alkaline phosphatase+3.1.3.1
68382esterase lipase (C 8)+
68382lipase (C 14)-
68382leucine arylamidase+3.4.11.1
68382cystine arylamidase-3.4.11.3
68382trypsin+3.4.21.4
68382alpha-chymotrypsin+3.4.21.1
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
68382alpha-mannosidase-3.2.1.24
68382alpha-fucosidase-3.2.1.51

API coryne

@refNITPYZPYRAPALbeta GURbeta GALalpha GLUbeta NAGESCUREGELGLURIBXYLMANMALLACSACGLYG
69435-+/--+--+-+-+--------

API zym

@refAlkaline phosphataseEsteraseEsterase LipaseLipaseLeucine arylamidaseValine arylamidaseCystine arylamidaseTrypsinalpha- ChymotrypsinAcid phosphataseNaphthol-AS-BI-phosphohydrolasealpha- Galactosidasebeta- Galactosidasebeta- Glucuronidasealpha- Glucosidasebeta- GlucosidaseN-acetyl-beta- glucosaminidasealpha- Mannosidasealpha- Fucosidase
69435++/-+-++/--+++/-+---+++/---

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinent
18199mangrove soilHainan Province, SanyaChinaCHNAsia
67770Sediment from a mangrove swamp in SanyaHainan ProvinceChinaCHNAsia

isolation source categories

Cat1Cat2Cat3
#Environmental#Aquatic#Mangrove
#Environmental#Terrestrial#Soil

Safety information

risk assessment

  • @ref: 18199
  • biosafety level: 1
  • biosafety level comment: Risk group (German classification)

Sequence information

16S sequences

  • @ref: 18199
  • description: Verrucosispora qiuiae strain RtIII47 16S ribosomal RNA gene, partial sequence
  • accession: EU427445
  • length: 1457
  • database: ena
  • NCBI tax ID: 502268

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Micromonospora qiuiae NBRC 106684GCA_016863555contigncbi502268
66792Micromonospora qiuiae strain NBRC 106684502268.3wgspatric502268

GC content

@refGC-contentmethod
1819972.0
3034072
6777072thermal denaturation, midpoint method (Tm)

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingyes100no
gram-positiveyes90.494yes
anaerobicno99.28no
halophileno93.742no
spore-formingyes92.915yes
glucose-utilyes87.901yes
aerobicyes93.474yes
motileno93.947no
thermophileno96.797no
flagellatedno97.506no
glucose-fermentno89.997no

External links

@ref: 18199

culture collection no.: DSM 45781, CGMCC 4.5826, NBRC 106684, JCM 19682, BCC 51292

straininfo link

  • @ref: 77463
  • straininfo: 398955

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny21873512Description of Verrucosispora qiuiae sp. nov., isolated from mangrove swamp sediment, and emended description of the genus Verrucosispora.Xi L, Zhang L, Ruan J, Huang YInt J Syst Evol Microbiol10.1099/ijs.0.033787-02011Bacterial Typing Techniques, Base Composition, Carbohydrates/analysis, China, Cluster Analysis, DNA Gyrase/genetics, DNA, Bacterial/chemistry/genetics, DNA, Ribosomal/chemistry/genetics, *Environmental Microbiology, Micromonosporaceae/*classification/genetics/*isolation & purification, Molecular Sequence Data, Nucleic Acid Hybridization, Phospholipids/analysis, Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, WetlandsGenetics
Phylogeny23710052Verrucosispora andamanensis sp. nov., isolated from a marine sponge.Supong K, Suriyachadkun C, Suwanborirux K, Pittayakhajonwut P, Thawai CInt J Syst Evol Microbiol10.1099/ijs.0.050906-02013Animals, Bacterial Typing Techniques, Base Composition, Carbohydrates/chemistry, Cell Wall/chemistry, DNA, Bacterial/genetics, Diaminopimelic Acid/chemistry, Fatty Acids/chemistry, Micromonosporaceae/*classification/genetics/isolation & purification, Molecular Sequence Data, Nucleic Acid Hybridization, Peptidoglycan/chemistry, Phospholipids/chemistry, *Phylogeny, Porifera/*microbiology, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, ThailandGenetics
Phylogeny27707427Verrucosispora sonchi sp. nov., a novel endophytic actinobacterium isolated from the leaves of common sowthistle (Sonchus oleraceus L.).Ma Z, Zhao S, Cao T, Liu C, Huang Y, Gao Y, Yan K, Xiang W, Wang XInt J Syst Evol Microbiol10.1099/ijsem.0.0015372016Bacterial Typing Techniques, Base Composition, China, DNA, Bacterial/genetics, Diaminopimelic Acid/chemistry, Fatty Acids/chemistry, Micromonosporaceae/*classification/genetics/isolation & purification, Nucleic Acid Hybridization, *Phylogeny, Plant Leaves/*microbiology, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Sonchus/*microbiology, Vitamin K 2/analogs & derivatives/chemistryTranscriptome

Reference

@idauthorscataloguedoi/urltitleID_cross_referencepubmed
18199Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 45781)https://www.dsmz.de/collection/catalogue/details/culture/DSM-45781
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
30340Barberan A, Caceres Velazquez H, Jones S, Fierer N.10.1128/mSphere.00237-17Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information2668128776041
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
69435Wink, J.https://cdn.dsmz.de/wink/DSM%2045781.pdfCompendium of Actinobacteria. HZI-Helmholtz-Centre for Infection Research, Braunschweig
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
77463Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID398955.1StrainInfo: A central database for resolving microbial strain identifiers