Strain identifier

BacDive ID: 132666

Type strain: Yes

Species: Micromonospora profundi

Strain Designation: DS3010

Strain history: <- N. Sahin, Ondokuz Mayis Univ., Dept. of Biology, Kurupelit-Samsun, Turkey; DS3010 <- A. Veyisoglu

NCBI tax ID(s): 1420889 (species)

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General

@ref: 24455

BacDive-ID: 132666

DSM-Number: 45981

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

description: Micromonospora profundi DS3010 is an aerobe, spore-forming, Gram-positive bacterium that was isolated from deep marine sediment.

NCBI tax id

  • NCBI tax id: 1420889
  • Matching level: species

strain history

  • @ref: 24455
  • history: <- N. Sahin, Ondokuz Mayis Univ., Dept. of Biology, Kurupelit-Samsun, Turkey; DS3010 <- A. Veyisoglu

doi: 10.13145/bacdive132666.20230509.8.1

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 profundi
  • full scientific name: Micromonospora profundi Veyisoglu et al. 2016

@ref: 24455

domain: Bacteria

phylum: Actinobacteria

class: Actinobacteria

order: Actinomycetales

family: Micromonosporaceae

genus: Micromonospora

species: Micromonospora profundi

full scientific name: Micromonospora profundi Veyisoglu et al. 2016

strain designation: DS3010

type strain: yes

Morphology

cell morphology

@refgram stainmotilityconfidence
24976positiveno
69480positive100

colony morphology

@refcolony colormedium used
24976light brownYeast extract-malt extract agar (ISP2)
24976brownish blackOatmeal agar (ISP3)
24976strong orangeNA (Nutrient Agar)
24976strong orangeN-Z-Amine agar (DSMZ-medium 554)
24976strong orangeTSA (Trypticase soy agar)
24976light orangeCzapek’s agar
24976light orangeInorganic salts-starch agar (ISP4)
24976light orangeGlycerol-asparagine agar (ISP5)
24976light orangePeptone Yeast Extract Iron Agar (ISP6)
24976light orangeTyrosine Agar (ISP7)

multimedia

  • @ref: 24455
  • multimedia content: https://www.dsmz.de/microorganisms/photos/DSM_45981.jpg
  • caption: Medium 65 28°C
  • intellectual property rights: © Leibniz-Institut DSMZ

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
24976GPHF agar (DSMZ-medium 553)yes
24976Yeast extract-malt extract agar (ISP2)yes
24976Oatmeal agar (ISP3)yes
24976NA (Nutrient Agar)yes
24976N-Z-Amine agar (DSMZ-medium 554)yes
24976TSA (Trypticase soy agar)yes
24976Czapek’s agaryes
24976Inorganic salts-starch agar (ISP4)yes
24976Glycerol-asparagine agar (ISP5)yes
24976Peptone Yeast Extract Iron Agar (ISP6)yes
24976Tyrosine Agar (ISP7)yes
24455N-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
24455TRYPTICASE 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
24455GYM 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
24976positivegrowth28.0-40.0
24976positiveoptimum30mesophilic
24455positivegrowth28mesophilic

culture pH

@refabilitytypepHPH range
24976positivegrowth6.0-11.0alkaliphile
24976positiveoptimum7.0-8.0

Physiology and metabolism

oxygen tolerance

  • @ref: 24976
  • oxygen tolerance: aerobe

spore formation

@refspore descriptiontype of sporespore formationconfidence
24976elliptical to oval (0.6-0.9 0.8-1.2 µm) on well-developed branched substrate hyphaesporeyes
69481yes100
69480yes100

halophily

  • @ref: 24976
  • salt: NaCl
  • growth: positive
  • tested relation: growth
  • concentration: 3 %(w/v)

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
2497616708adenine-degradation
2497615963ribitol-carbon source
2497618305arbutin-hydrolysis
24976casein-degradation
2497617108D-arabinose-carbon source
2497616988D-ribose-carbon source
2497617924D-sorbitol-carbon source
2497652071dextran-carbon source
2497616235guanine-degradation
2497624741hydroxyproline-nitrogen source
2497617368hypoxanthine-degradation
2497615443inulin-carbon source
2497615971L-histidine-nitrogen source
2497662345L-rhamnose-carbon source
2497617266L-sorbose-carbon source
2497617632nitrate-reduction
2497653423tween 40-degradation
2497616199urea-hydrolysis
2497615318xanthine-degradation
2497637166xylan-degradation
2497615676allantoin+hydrolysis
2497617057cellobiose+carbon source
2497615824D-fructose+carbon source
2497612936D-galactose+carbon source
2497617306maltose+carbon source
2497616899D-mannitol+carbon source
2497616024D-mannose+carbon source
2497665327D-xylose+carbon source
2497623652dextrin+carbon source
2497615428glycine+nitrogen source
2497624898isoleucine+nitrogen source
2497616977L-alanine+nitrogen source
2497616467L-arginine+nitrogen source
2497617561L-cysteine+nitrogen source
2497616643L-methionine+nitrogen source
2497617295L-phenylalanine+nitrogen source
2497617203L-proline+nitrogen source
2497617115L-serine+nitrogen source
2497617895L-tyrosine+nitrogen source
2497616414L-valine+nitrogen source
2497617716lactose+carbon source
2497628017starch+degradation
2497617992sucrose+carbon source
2497653426tween 80+degradation

enzymes

@refvalueactivityec
24976alpha-chymotrypsin+3.4.21.1
24976alpha-fucosidase-3.2.1.51
24976alpha-galactosidase+3.2.1.22
24976alpha-glucosidase+3.2.1.20
24976alpha-mannosidase-3.2.1.24
24976beta-glucosidase-3.2.1.21
24976beta-glucuronidase-3.2.1.31
24976cystine arylamidase+3.4.11.3
24976esterase (C 4)-
24976esterase Lipase (C 8)-
24976leucine arylamidase-3.4.11.1
24976lipase (C 14)-
24976N-acetyl-beta-glucosaminidase+3.2.1.52
24976trypsin+3.4.21.4
24976valine arylamidase-

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinentlatitudelongitudeisolation procedure
24455deep marine sedimentBlack Sea, off the Yason Peninsula, near Ordu (41°00.353'N and 37°57.489'E) at a depth of 45 mTurkeyTURAsia41.005837.9581
24976standard dilution plate method,

isolation source categories

Cat1Cat2Cat3
#Environmental#Aquatic#Marine
#Environmental#Aquatic#Sediment

taxonmaps

  • @ref: 69479
  • File name: preview.99_3471.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_94;96_404;97_1111;98_1509;99_3471&stattab=map
  • Last taxonomy: Micromonospora
  • 16S sequence: KF494813
  • Sequence Identity:
  • Total samples: 1419
  • soil counts: 1017
  • aquatic counts: 161
  • animal counts: 219
  • plant counts: 22

Safety information

risk assessment

  • @ref: 24455
  • biosafety level: 1
  • biosafety level comment: Risk group (German classification)

Sequence information

16S sequences

  • @ref: 24455
  • description: Micromonospora profundi strain DS3010 16S ribosomal RNA gene, partial sequence
  • accession: KF494813
  • length: 1460
  • database: ena
  • NCBI tax ID: 1420889

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Micromonospora profundi DSM 45981GCA_011927785contigncbi1420889
66792Micromonospora profundi strain DSM 459811420889.3wgspatric1420889
66792Micromonospora profundi DSM 459812830928545draftimg1420889

GC content

@refGC-contentmethod
2497672.8-73.8thermal denaturation, midpoint method (Tm)
2445573.3thermal denaturation, midpoint method (Tm)

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingyes100no
motileno92.582yes
gram-positiveyes91.615yes
anaerobicno99.354yes
halophileno94.924no
spore-formingyes94.799yes
thermophileno98.975no
glucose-utilyes87.258no
aerobicyes96.109no
flagellatedno97.218yes
glucose-fermentno89.557no

External links

@ref: 24455

culture collection no.: DSM 45981, KCTC 29243

straininfo link

  • @ref: 90976
  • straininfo: 405643

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny27515497Micromonospora profundi sp. nov., isolated from deep marine sediment.Veyisoglu A, Carro L, Cetin D, Guven K, Sproer C, Potter G, Klenk HP, Sahin N, Goodfellow MInt J Syst Evol Microbiol10.1099/ijsem.0.0014192016Bacterial Typing Techniques, Base Composition, Black Sea, DNA, Bacterial/genetics, Genes, Bacterial, Geologic Sediments/*microbiology, Micromonospora/*classification/genetics/isolation & purification, Nucleic Acid Hybridization, *Phylogeny, RNA, Ribosomal, 16S/genetics, Seawater/*microbiology, Sequence Analysis, DNATranscriptome
Phylogeny27902235Micromonospora parathelypteridis sp. nov., an endophytic actinomycete with antifungal activity isolated from the root of Parathelypteris beddomei (Bak.) Ching.Zhao S, Liu C, Zheng W, Ma Z, Cao T, Zhao J, Yan K, Xiang W, Wang XInt J Syst Evol Microbiol10.1099/ijsem.0.0016142017Bacterial Typing Techniques, Base Composition, China, DNA, Bacterial/genetics, Fatty Acids/chemistry, Micromonospora/*classification/genetics/isolation & purification, Nucleic Acid Hybridization, *Phylogeny, Plant Roots/*microbiology, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Streptophyta/*microbiologyTranscriptome

Reference

@idauthorstitledoi/urlcataloguejournalpubmed
20215Parte, A.C., Sardà Carbasse, J., Meier-Kolthoff, J.P., Reimer, L.C. and Göker, M.List of Prokaryotic names with Standing in Nomenclature (LPSN) moves to the DSMZ10.1099/ijsem.0.004332
24455Curators of the DSMZhttps://www.dsmz.de/collection/catalogue/details/culture/DSM-45981Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 45981)
24976A. C. Veyisoglu, Lorena,Cetin, Demet,Guven, Kiymet,Spröer, Cathrin,Pötter, Gabriele,Klenk, Hans-Peter,Sahin, Nevzat,Goodfellow, MichaelMicromonospora profundi sp. nov., isolated from deep marine sediment10.1099/ijsem.0.001419IJSEM 66: 4735-4743 201627515497
66792Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg OvermannAutomatically annotated for the DiASPora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information)https://diaspora-project.de/progress.html#genomes
69479João F Matias Rodrigues, Janko Tackmann,Gregor Rot, Thomas SB Schmidt, Lukas Malfertheiner, Mihai Danaila,Marija Dmitrijeva, Daniela Gaio, Nicolas Näpflin and Christian von Mering. University of Zurich.MicrobeAtlas 1.0 betahttps://microbeatlas.org/
69480Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg OvermannPredictions based on genome sequence made in the Diaspora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information)https://diaspora-project.de/progress.html#genomes
69481Xiao-Yin To, René Mreches, Martin Binder, Alice C. McHardy, Philipp C. MünchPredictions based on the model GenomeNet Sporulation v. 110.21203/rs.3.rs-2527258/v1
90976Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.StrainInfo: A central database for resolving microbial strain identifiers10.60712/SI-ID405643.1