Strain identifier

BacDive ID: 23120

Type strain: Yes

Species: Micromonospora wenchangensis

Strain Designation: 2602GPT1-05

Strain history: DSM 45709 <-- J. Ren; Wuhan Univ., China; 2602GPT1-05.

NCBI tax ID(s): 1185415 (species)

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General

@ref: 19374

BacDive-ID: 23120

DSM-Number: 45709

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

description: Micromonospora wenchangensis 2602GPT1-05 is an aerobe, spore-forming, mesophilic bacterium that was isolated from composite soil mangrove.

NCBI tax id

  • NCBI tax id: 1185415
  • Matching level: species

strain history

@refhistory
19374<- J. Ren, Wuhan Univ., School of Pharmaceutical Sciences, China; 2602GPT1-05
67770DSM 45709 <-- J. Ren; Wuhan Univ., China; 2602GPT1-05.

doi: 10.13145/bacdive23120.20230509.8.1

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 wenchangensis
  • full scientific name: Micromonospora wenchangensis Ren et al. 2013

@ref: 19374

domain: Bacteria

phylum: Actinobacteria

class: Actinobacteria

order: Actinomycetales

family: Micromonosporaceae

genus: Micromonospora

species: Micromonospora wenchangensis

full scientific name: Micromonospora wenchangensis Ren et al. 2013 emend. Nouioui et al. 2018

strain designation: 2602GPT1-05

type strain: yes

Morphology

cell morphology

@refgram stainmotilityconfidence
30829positiveno
69480no92.032
69480positive100

colony morphology

@refcolony colormedium used
69422Light ivory (1015), black brown (8022)ISP 5
69422Ochre brown (8001), black brown (8022)suter with tyrosine
69422Ochre brown (8001), black brown (8022)suter without tyrosine
69422Pastel yellow (1034)ISP 4
69422Pastel yellow (1034), black brown (8022)ISP 7
69422Yellow orange (2000), black brown (8022)ISP 2

multicellular morphology

@refforms multicellular complexcomplex namemedium name
69422noAerial myceliumISP 2
69422noAerial myceliumISP 4
69422noAerial myceliumISP 5
69422noAerial myceliumISP 7
69422noAerial myceliumsuter with tyrosine
69422noAerial myceliumsuter without tyrosine

pigmentation

@refproductionnamecolor
30829yes
69422noMelanin
69422yessoluble pigmentBrown beige (1011)

multimedia

@refmultimedia contentcaptionintellectual property rights
19374https://www.dsmz.de/microorganisms/photos/DSM_45709.jpgMedium 65 28°C© Leibniz-Institut DSMZ
69422DSM_45709_image3.jpegPlates (65, ISP2, ISP3, ISP4, ISP5, ISP7)Helmholtz-Zentrum für Infektionsforschung GmbH
69422DSM_45709_image4.jpegPlates (65, ISP2, ISP3, ISP4, ISP5, ISP7)Helmholtz-Zentrum für Infektionsforschung GmbH

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
19374N-Z-AMINE-MEDIUM (DSMZ Medium 554)yeshttps://www.dsmz.de/microorganisms/medium/pdf/DSMZ_Medium554.pdf
19374GPHF-MEDIUM (DSMZ Medium 553)yeshttps://www.dsmz.de/microorganisms/medium/pdf/DSMZ_Medium553.pdf
19374TRYPTICASE SOY BROTH AGAR (DSMZ Medium 535)yeshttps://www.dsmz.de/microorganisms/medium/pdf/DSMZ_Medium535.pdf
19374GYM 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

culture temp

@refgrowthtypetemperaturerange
19374positivegrowth28mesophilic
30829positivegrowth16-45
30829positiveoptimum32.5mesophilic
67770positivegrowth28mesophilic

culture pH

@refabilitytypepHPH range
30829positivegrowth5.0-9.0alkaliphile
30829positiveoptimum7.5

Physiology and metabolism

oxygen tolerance

  • @ref: 30829
  • oxygen tolerance: aerobe

spore formation

@refspore formationconfidence
30829yes
69481yes100
69480yes100

halophily

@refsaltgrowthtested relationconcentration
30829NaClpositivegrowth0-3 %
69422NaClpositivegrowth0-2.5 %

observation

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

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
6942222599arabinose+/-growth
3082917057cellobiose+carbon source
3082928757fructose+carbon source
3082928260galactose+carbon source
3082917234glucose+carbon source
3082917716lactose+carbon source
3082917306maltose+carbon source
3082937684mannose+carbon source
3082928053melibiose+carbon source
3082917992sucrose+carbon source
3082918222xylose+carbon source
308294853esculin+hydrolysis
3082917632nitrate+reduction
6942262968cellulose+/-growth
6942228757fructose+growth
6942217234glucose+growth
6942217268inositol-growth
6942237684mannose-growth
6942216634raffinose+growth
6942226546rhamnose-growth
6942217992sucrose+growth
6942218222xylose+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
30829catalase+1.11.1.6
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
68379pyrazinamidase-3.5.1.B15
68382alkaline phosphatase+3.1.3.1
68382esterase (C 4)+
68382esterase lipase (C 8)+
68382leucine arylamidase+3.4.11.1
68382trypsin-3.4.21.4
68382alpha-chymotrypsin-3.4.21.1
68382naphthol-AS-BI-phosphohydrolase-
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 coryne

@refNITPYZPYRAPALbeta GURbeta GALalpha GLUbeta NAGESCUREGELGLURIBXYLMANMALLACSACGLYG
69422---+-++---+--------

API zym

@refAlkaline phosphataseEsteraseEsterase LipaseLipaseLeucine arylamidaseValine arylamidaseCystine arylamidaseTrypsinalpha- ChymotrypsinAcid phosphataseNaphthol-AS-BI-phosphohydrolasealpha- Galactosidasebeta- Galactosidasebeta- Glucuronidasealpha- Glucosidasebeta- GlucosidaseN-acetyl-beta- glucosaminidasealpha- Mannosidasealpha- Fucosidase
69422++++/-++/-+/---+/--+/-+-+----

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinentlatitudelongitude
19374composite soil mangroveHainan Province, Wenchang, (19° 37.647' N, 110° 50.083' E)ChinaCHNAsia19.6275110.835
67770Mangrove soil from WenchangHainan ProvinceChinaCHNAsia

isolation source categories

Cat1Cat2Cat3
#Engineered#Biodegradation#Composting
#Environmental#Aquatic#Mangrove
#Environmental#Terrestrial#Soil

Safety information

risk assessment

  • @ref: 19374
  • biosafety level: 1
  • biosafety level comment: Risk group (German classification)

Sequence information

16S sequences

  • @ref: 19374
  • description: Micromonospora wenchangensis strain 2602GPT1-05 16S ribosomal RNA gene, partial sequence
  • accession: JQ768361
  • length: 1476
  • database: ena
  • NCBI tax ID: 1185415

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Micromonospora wenchangensis strain CCTCC AA 20120021185415.3wgspatric1185415
66792Micromonospora wenchangensis CCTCC AA 20120022788500614draftimg1185415
67770Micromonospora wenchangensis CCTCC AA 2012002GCA_002210435contigncbi1185415

GC content

@refGC-contentmethod
1937471.7high performance liquid chromatography (HPLC)
3082971.7
6777073genome sequence analysis

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingyes100no
motileno94.214yes
gram-positiveyes91.07yes
anaerobicno99.445no
aerobicyes95.739no
halophileno94.59no
spore-formingyes97.048yes
flagellatedno97.601yes
glucose-utilyes90.25yes
thermophileno98.384yes
glucose-fermentno91.426yes

External links

@ref: 19374

culture collection no.: DSM 45709, CCTCC AA 2012002, JCM 31038

straininfo link

  • @ref: 87356
  • straininfo: 400649

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
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
Phylogeny26942919Micromonospora mangrovi sp. nov., isolated from mangrove soil.Xie QY, Ren J, Li L, Li Y, Deng ZX, Hong KAntonie Van Leeuwenhoek10.1007/s10482-015-0641-x2016Base Composition, Base Sequence, China, DNA, Bacterial/genetics, Micromonospora/classification/genetics/*isolation & purification, Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Soil, *Soil Microbiology, *WetlandsTranscriptome
Phylogeny34913860Micromonospora humida sp. nov., exhibiting antimicrobial potential, isolated from riverside soil.Ra JS, Kim MJ, Lee DH, Jeong JW, Kim SBInt J Syst Evol Microbiol10.1099/ijsem.0.0051572021*Anti-Infective Agents, Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, Fatty Acids/chemistry, *Micromonospora/classification/isolation & purification, Nucleic Acid Hybridization, Phospholipids/chemistry, *Phylogeny, Pigmentation, RNA, Ribosomal, 16S/genetics, Rivers, Sequence Analysis, DNA, *Soil Microbiology, Vitamin K 2/chemistryTranscriptome
Phylogeny36223167Micromonospora antibiotica sp. nov. and Micromonospora humidisoli sp. nov., two new actinobacterial species exhibiting antimicrobial potential.Lee DH, Ra JS, Kim MJ, Kim SBInt J Syst Evol Microbiol10.1099/ijsem.0.0055222022*Anti-Infective Agents, Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, Fatty Acids/chemistry, *Micromonospora, Nucleotides, Phospholipids/chemistry, Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Sodium Chloride, SoilTranscriptome

Reference

@idauthorscataloguedoi/urltitleID_cross_referencepubmed
19374Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 45709)https://www.dsmz.de/collection/catalogue/details/culture/DSM-45709
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
30829Barberan A, Caceres Velazquez H, Jones S, Fierer N.10.1128/mSphere.00237-17Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information2715928776041
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
69422Wink, J.https://cdn.dsmz.de/wink/DSM%2045709.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
87356Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID400649.1StrainInfo: A central database for resolving microbial strain identifiers