Strain identifier

BacDive ID: 11240

Type strain: Yes

Species: Nocardiopsis sinuspersici

Strain Designation: HM 7

Strain history: <- J. Hamedi; HM 7 <- F. Mohammadipanah

NCBI tax ID(s): 501010 (species)

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General

@ref: 16117

BacDive-ID: 11240

DSM-Number: 45278

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

description: Nocardiopsis sinuspersici HM 7 is an aerobe, spore-forming, mesophilic bacterium that builds an aerial mycelium and was isolated from sandy soil.

NCBI tax id

  • NCBI tax id: 501010
  • Matching level: species

strain history

  • @ref: 16117
  • history: <- J. Hamedi; HM 7 <- F. Mohammadipanah

doi: 10.13145/bacdive11240.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/actinomycetota
  • domain: Bacteria
  • phylum: Actinomycetota
  • class: Actinomycetes
  • order: Streptosporangiales
  • family: Nocardiopsidaceae
  • genus: Nocardiopsis
  • species: Nocardiopsis sinuspersici
  • full scientific name: Nocardiopsis sinuspersici Hamedi et al. 2010

  • synonyms

    • @ref: 20215
    • synonym: Nocardiopsis arvandica

@ref: 16117

domain: Bacteria

phylum: Actinobacteria

class: Actinobacteria

order: Actinomycetales

family: Nocardiopsaceae

genus: Nocardiopsis

species: Nocardiopsis arvandica

full scientific name: Nocardiopsis arvandica Hamedi et al. 2011

strain designation: HM 7

type strain: yes

Morphology

cell morphology

@refmotilityconfidencegram stain
69480no91.438
69480100positive

colony morphology

@refcolony colormedium usedincubation period
69380Beige (1001), Ochre yellow (1024)ISP 4
617635-7 days
69380Light ivory (1015)ISP 3
69380Light ivory (1015)ISP 5
69380Ochre brown (8001)ISP 7
69380Sand yellow (1002)ISP 2
69380Sand yellow (1002)ISP 6
69380Sand yellow (1002)suter without tyrosine

multicellular morphology

@refforms multicellular complexcomplex namemedium namecomplex color
69380noAerial myceliumISP 2
69380noAerial myceliumISP 3
69380yesAerial myceliumISP 4Cream (9001)
69380noAerial myceliumISP 5
69380noAerial myceliumISP 6
69380yesAerial myceliumISP 7

pigmentation

@refproductionnamecolor
69380noMelanin
69380yessoluble pigmentChocolate brown (8017)

multimedia

@refmultimedia contentcaptionintellectual property rights
69380DSM_45278_image3.jpegPlates (535, ISP2, ISP3, ISP4, ISP5, ISP7)Helmholtz-Zentrum für Infektionsforschung GmbH
69380DSM_45278_image4.jpegPlates (535, ISP2, ISP3, ISP4, ISP5, ISP7)Helmholtz-Zentrum für Infektionsforschung GmbH

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
16117GPHF-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
16117STARCH - MINERAL SALT - AGAR (STMS) (DSMZ Medium 252)yeshttps://www.dsmz.de/microorganisms/medium/pdf/DSMZ_Medium252.pdf
16117GYM STREPTOMYCES MEDIUM (DSMZ Medium 65)yeshttps://www.dsmz.de/microorganisms/medium/pdf/DSMZ_Medium65.pdf

culture temp

@refgrowthtypetemperaturerange
16117positivegrowth28mesophilic
61763positivegrowth30-37mesophilic

Physiology and metabolism

oxygen tolerance

  • @ref: 61763
  • oxygen tolerance: aerobe

spore formation

@refspore formationconfidence
69481yes100
69480yes100

halophily

  • @ref: 69380
  • salt: NaCl
  • growth: positive
  • tested relation: growth
  • concentration: 0-10 %

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
6938022599arabinose+growth
6938062968cellulose-growth
6938028757fructose+growth
6938017234glucose+growth
6938017268inositol-growth
6938037684mannose+growth
6938016634raffinose+/-growth
6938026546rhamnose+growth
6938017992sucrose-growth
6938018222xylose+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
68379pyrazinamidase-3.5.1.B15
68382alkaline phosphatase-3.1.3.1
68382esterase (C 4)-
68382esterase lipase (C 8)-
68382lipase (C 14)-
68382leucine arylamidase-3.4.11.1
68382valine arylamidase-
68382cystine arylamidase-3.4.11.3
68382trypsin-3.4.21.4
68382alpha-chymotrypsin-3.4.21.1
68382acid phosphatase-3.1.3.2
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 coryne

@refNITPYZPYRAPALbeta GURbeta GALalpha GLUbeta NAGESCUREGELGLURIBXYLMANMALLACSACGLYG
69380-------------------

API zym

@refAlkaline phosphataseEsteraseEsterase LipaseLipaseLeucine arylamidaseValine arylamidaseCystine arylamidaseTrypsinalpha- ChymotrypsinAcid phosphataseNaphthol-AS-BI-phosphohydrolasealpha- Galactosidasebeta- Galactosidasebeta- Glucuronidasealpha- Glucosidasebeta- GlucosidaseN-acetyl-beta- glucosaminidasealpha- Mannosidasealpha- Fucosidase
69380----------+/---------

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinentsampling date
16117sandy soilKhuzestan Province, Khoramshahr, banks of Arvand RiverIranIRNAsia
61763Sandy soil,seashoreKhozestan,Khoramshahr,Arvand riverIranIRNAsia2008

isolation source categories

Cat1Cat2Cat3
#Environmental#Terrestrial#Sandy
#Environmental#Terrestrial#Soil

taxonmaps

  • @ref: 69479
  • File name: preview.99_4414.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_152;96_659;97_762;98_3317;99_4414&stattab=map
  • Last taxonomy: Nocardiopsis
  • 16S sequence: EU410477
  • Sequence Identity:
  • Total samples: 22
  • soil counts: 7
  • animal counts: 14
  • plant counts: 1

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
161171Risk group (German classification)
21426L1German classification

Sequence information

16S sequences

  • @ref: 16117
  • description: Nocardiopsis arvandica strain HM7 16S ribosomal RNA gene, partial sequence
  • accession: EU410477
  • length: 1520
  • database: ena
  • NCBI tax ID: 501011

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Nocardiopsis sinuspersici DSM 45278GCA_013410445contigncbi501010
66792Nocardiopsis arvandica strain DSM 45278501011.3wgspatric501011
66792Nocardiopsis arvandica DSM 452782856499481draftimg501011

GC content

  • @ref: 16117
  • GC-content: 71.5
  • method: high performance liquid chromatography (HPLC)

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingyes100no
gram-positiveyes92.285no
anaerobicno98.972yes
halophileyes69.421no
spore-formingyes91.779no
glucose-utilyes87.882yes
thermophileno96.483no
motileno91.13no
aerobicyes93.478yes
flagellatedno97.921no
glucose-fermentno90.643no

External links

@ref: 16117

culture collection no.: DSM 45278, CCUG 58831, UTMC 00103

straininfo link

  • @ref: 80475
  • straininfo: 401661

literature

  • topic: Phylogeny
  • Pubmed-ID: 20562242
  • title: Nocardiopsis arvandica sp. nov., isolated from sandy soil.
  • authors: Hamedi J, Mohammadipanah F, Potter G, Sproer C, Schumann P, Goker M, Klenk HP
  • journal: Int J Syst Evol Microbiol
  • DOI: 10.1099/ijs.0.022756-0
  • year: 2010
  • mesh: Actinomycetales/*classification/genetics/*isolation & purification/metabolism, DNA, Bacterial/genetics, Fatty Acids/metabolism, Molecular Sequence Data, Phylogeny, RNA, Ribosomal, 16S/genetics, *Soil Microbiology
  • topic2: Metabolism

Reference

@idauthorscataloguedoi/urltitle
16117Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 45278)https://www.dsmz.de/collection/catalogue/details/culture/DSM-45278
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
21426Wink, J.http://www.dsmz.de/microorganisms/wink_pdf/DSM45278.pdfCompendium of Actinobacteria . HZI-Helmholtz-Centre for Infection Research, Braunschweig
61763Curators of the CCUGCulture Collection University of Gothenburg (CCUG) (CCUG 58831)https://www.ccug.se/strain?id=58831
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)
68379Automatically annotated from API Coryne
68382Automatically annotated from API zym
69380Wink, J.https://cdn.dsmz.de/wink/DSM%2045278.pdfCompendium of Actinobacteria. HZI-Helmholtz-Centre for Infection Research, Braunschweig
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.https://microbeatlas.org/MicrobeAtlas 1.0 beta
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
80475Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID401661.1StrainInfo: A central database for resolving microbial strain identifiers