Strain identifier

BacDive ID: 11215

Type strain: Yes

Species: Nocardiopsis aegyptia

Strain Designation: 49, SNG49

Strain history: CIP <- 2004, DSMZ <- H. Ghozhan: strain 49

NCBI tax ID(s): 220378 (species)

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General

@ref: 11769

BacDive-ID: 11215

DSM-Number: 44442

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

description: Nocardiopsis aegyptia 49 is an aerobe, spore-forming, mesophilic bacterium that builds an aerial mycelium and was isolated from marine sediments.

NCBI tax id

  • NCBI tax id: 220378
  • Matching level: species

strain history

@refhistory
11769<- H. Ghozhan; 49
67770DSM 44442 <-- H. Ghozhan 49.
116053CIP <- 2004, DSMZ <- H. Ghozhan: strain 49

doi: 10.13145/bacdive11215.20230509.8.1

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 aegyptia
  • full scientific name: Nocardiopsis aegyptia Sabry et al. 2004

@ref: 11769

domain: Bacteria

phylum: Actinobacteria

class: Actinobacteria

order: Actinomycetales

family: Nocardiopsaceae

genus: Nocardiopsis

species: Nocardiopsis aegyptia

full scientific name: Nocardiopsis aegyptia Sabry et al. 2004

strain designation: 49, SNG49

type strain: yes

Morphology

cell morphology

@refgram stainmotilityconfidencecell shape
30001positiveno
69480no93.945
69480positive100
116053positivenorod-shaped

colony morphology

@refcolony colorincubation periodmedium used
19667Pastel orange10-14 daysISP 2
19667Pastel orange10-14 daysISP 3
1966710-14 daysISP 4
1966710-14 daysISP 5
1966710-14 daysISP 6
1966710-14 daysISP 7
116053

multicellular morphology

@refforms multicellular complexmedium namecomplex namecomplex color
19667noISP 2
19667noISP 3
19667yesISP 4Aerial MyceliumWhite
19667yesISP 5Aerial MyceliumWhite
19667yesISP 6Aerial MyceliumWhite
19667yesISP 7Aerial MyceliumWhite

pigmentation

  • @ref: 30001
  • production: no

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
11769GYM + SEAWATER (DSMZ Medium 871)yeshttps://mediadive.dsmz.de/medium/871Name: GYM + SEAWATER (DSMZ Medium 871) Composition: Sea Salt 32.0 g/l Agar 15.0 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
19667ISP 2yesName: ISP 2 / Yeast Malt Agar (5265); 5265 Composition Malt extract 10.0 g/l Yeast extract 4.0 g/l Glucose 4.0 g/l Agar 15.0 g/l Preparation: Sterilisation: 20 minutes at 121°C pH before sterilisation: 7.0 Usage: Maintenance and Taxonomy Organisms: All Actinomycetes
19667ISP 3yesName: ISP 3; 5315 Composition Dog oat flakes 20.0 g/l Trace element solution (5314) 2.5 ml/l Agar 18.0 g/l Preparation: Oat flakes are cooked for 20 minutes, trace element solution and agar are added (in the case of non rolled oat flakes the suspension has to bee filtrated). Sterilisation: 20 minutes at 121°C pH before sterilisation: 7.8 Usage: Maintenance and taxonomy (e.g. SEM As liquid medium for metabolite production) Organisms: All Actinomycetes Trace element solution 5314 Name: Trace element solution 5314; 5314 Composition CaCl2 x H2O 3.0 g/l Fe-III-citrate 1.0 g/l MnSO4 0.2 g/l ZnCl2 0.1 g/l CuSO4 x 5 H2O 0.025 g/l Sodium tetra borate 0.2 g/l CoCl2 x 6 H2O 0.004 g/l Sodium molybdate 0.01 g/l Preparation: Use double destillated water. Sterilisation: 20 minutes at 121°C pH before sterilisation: Usage: Trace element solution for different media Organisms:
19667ISP 4yesName: ISP 4; DSM 547 Solution I: Difco soluble starch, 10.0 g. Make a paste of the starch with a small amount of cold distilled water and bring to a volume of 500 ml. Solution II: CaCO3 2.0 g K2HPO4 (anhydrous) 1.0 g MgSO4 x 7 H2O 1.0 g NaCl 1.0 g (NH4)2SO4 2.0 g Distilled water 500.0 ml Trace salt solution (see below) 1.0 ml The pH should be between 7.0 and 7.4. Do not adjust if it is within this range. Mix solutions I and II together. Add 20.0 g agar. Liquify agar by steaming at 100°C for 10 to 20 min. Trace element solution: FeSO4 x 7 H2O 0.1 g MnCl2 x 4 H2O 0.1 g ZnSO4 x 7 H2O 0.1 g Distilled water 100.0 ml
19667ISP 5yesName: ISP 5 (5323) Composition L-Asparagine 1.0 g/l Glycerol 10.0 g/l K2HPO4 1.0 g/l Salt solution (see preparation) 1.0 ml/l Agar 20.0 g/l Preparation: Salt solution 1.0 g FeSO4 x 7 H2O 1.0 g MnCl2 x 4 H2O 1.0 g ZNSO4 x 7 H2O in 100 ml water Sterilisation: 20 minutes at 121°C pH before sterilisation: 7.2 Usage: Maintenance and taxonomy Organisms: All Actinomycetes
19667ISP 6yesName: ISP 6 (5318) Composition Peptone 15.0 g/l Proteose peptose 5.0 g/l Ferric ammonium citrate 0.5 g/l Sodium glycerophosphate 1.0 g/l Sodium thiosulfate 0.08 g/l Yeast extract 1.0 g/l Agar 15.0 g/l Sterilisation: 20 minutes at 121°C pH before sterilisation: Usage: Production of melanoid pigments Organisms: All Actinomycetes
19667ISP 7yesName: ISP 7 (5322) Composition Glycerol 15.0 g/l L-Tyrosine 0.5 g/l L-Asparagine 1.0 g/l K2HPO4 0.5 g/l NaCl 0.5 g/l FeSO4 x 7 H2O 0.01 g/l Trace element solution 5343 1.0 ml/l Agar 20.0 Sterilisation: 20 minutes at 121°C pH before sterilisation: 7.3 Usage: Production of melanoid pigments Organisms: All Actinomycetes
33239MEDIUM 194 - for Nocardiopsis aegyptiayesAgar (15.000 g);Glucose (4.000 g);Yeast extract (4.000 g);Malt extract (10.000 g);Calcium carbonate (2.000 g);Synthetic sea solution - M01031 (1000.000 ml)
11769GYM STREPTOMYCES MEDIUM 10% NACL (DSMZ Medium 1159)yeshttps://mediadive.dsmz.de/medium/1159Name: GYM STREPTOMYCES MEDIUM 10% NACL (DSMZ Medium 1159) Composition: NaCl 100.0 g/l Agar 15.0 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
11769ISP2 MEDIUM (DSMZ Medium 987)yeshttps://mediadive.dsmz.de/medium/987Name: ISP 2 MEDIUM (DSMZ Medium 987; with strain-specific modifications) Composition: Agar 20.0 g/l Malt extract 10.0 g/l Dextrose 4.0 g/l Yeast extract 4.0 g/l Sea water Distilled water
116053CIP Medium 194yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=194

culture temp

@refgrowthtypetemperaturerange
11769positivegrowth28mesophilic
19667positiveoptimum28mesophilic
30001positivegrowth10-40
30001positiveoptimum25-28mesophilic
33239positivegrowth30mesophilic
67770positivegrowth28mesophilic
116053positivegrowth25-41
116053nogrowth10psychrophilic
116053nogrowth45thermophilic

Physiology and metabolism

oxygen tolerance

@refoxygen tolerance
30001aerobe
116053obligate aerobe

spore formation

@refspore formationconfidence
30001yes
69481yes100
69480yes100

halophily

@refsaltgrowthtested relationconcentration
19667NaClpositivemaximum10 %
30001NaClpositivegrowth05-09 %
30001NaClpositiveoptimum5 %
116053NaClpositivegrowth0-10 %

observation

  • @ref: 67770
  • observation: quinones: MK-10(H4), MK-10(H6), MK-10(H8)

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
1966717234glucose-
1966722599arabinose-
1966717992sucrose-
1966718222xylose-
1966717268myo-inositol-
1966729864mannitol-
1966728757fructose-
1966726546rhamnose-
1966716634raffinose+
1966762968cellulose-
3000122599arabinose+carbon source
3000128260galactose+carbon source
3000117754glycerol+carbon source
3000117716lactose+carbon source
3000129864mannitol+carbon source
3000137684mannose+carbon source
3000126546rhamnose+carbon source
3000117992sucrose+carbon source
3000118222xylose+carbon source
68371Potassium 5-ketogluconate-builds acid from
68371Potassium 2-ketogluconate-builds acid from
6837124265gluconate-builds acid from
6837118403L-arabitol-builds acid from
6837118333D-arabitol-builds acid from
6837118287L-fucose-builds acid from
6837128847D-fucose-builds acid from
6837116443D-tagatose-builds acid from
6837162318D-lyxose-builds acid from
6837132528turanose-builds acid from
6837128066gentiobiose-builds acid from
6837117151xylitol-builds acid from
6837128087glycogen-builds acid from
6837128017starch-builds acid from
6837116634raffinose-builds acid from
683716731melezitose-builds acid from
6837115443inulin-builds acid from
6837127082trehalose-builds acid from
6837117992sucrose-builds acid from
6837128053melibiose-builds acid from
6837117716lactose-builds acid from
6837117306maltose-builds acid from
6837117057cellobiose-builds acid from
6837117814salicin-builds acid from
683714853esculin+builds acid from
6837118305arbutin-builds acid from
6837127613amygdalin-builds acid from
6837159640N-acetylglucosamine-builds acid from
68371320061methyl alpha-D-glucopyranoside-builds acid from
6837143943methyl alpha-D-mannoside-builds acid from
6837117924D-sorbitol-builds acid from
6837116899D-mannitol-builds acid from
6837117268myo-inositol-builds acid from
6837116813galactitol-builds acid from
6837162345L-rhamnose-builds acid from
6837117266L-sorbose-builds acid from
6837116024D-mannose-builds acid from
6837115824D-fructose-builds acid from
6837117634D-glucose-builds acid from
6837112936D-galactose-builds acid from
6837174863methyl beta-D-xylopyranoside-builds acid from
6837115963ribitol-builds acid from
6837165328L-xylose-builds acid from
6837165327D-xylose-builds acid from
6837116988D-ribose-builds acid from
6837130849L-arabinose-builds acid from
6837117108D-arabinose-builds acid from
6837117113erythritol-builds acid from
6837117754glycerol-builds acid from
11605316947citrate-carbon source
1160534853esculin-hydrolysis
116053606565hippurate-hydrolysis
11605317632nitrate-reduction
11605316301nitrite-reduction
11605317632nitrate-respiration

metabolite production

  • @ref: 116053
  • Chebi-ID: 35581
  • metabolite: indole
  • production: no

metabolite tests

@refChebi-IDmetabolitevoges-proskauer-testmethylred-test
11605315688acetoin-
11605317234glucose-

enzymes

@refvalueactivityec
116053oxidase-
116053beta-galactosidase+3.2.1.23
116053alcohol dehydrogenase-1.1.1.1
116053gelatinase-
116053amylase+
116053DNase-
116053caseinase-3.4.21.50
116053catalase+1.11.1.6
116053tween esterase+
116053gamma-glutamyltransferase-2.3.2.2
116053lecithinase-
116053lipase-
116053lysine decarboxylase-4.1.1.18
116053ornithine decarboxylase-4.1.1.17
116053phenylalanine ammonia-lyase-4.3.1.24
116053protease-
116053tryptophan deaminase-
116053urease-3.5.1.5
68382alkaline phosphatase+3.1.3.1
68382esterase (C 4)+
68382esterase lipase (C 8)+
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
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 zym

@refAlkaline phosphataseEsteraseEsterase LipaseLipaseLeucine arylamidaseValine arylamidaseCystine arylamidaseTrypsinalpha- ChymotrypsinAcid phosphataseNaphthol-AS-BI-phosphohydrolasealpha- Galactosidasebeta- Galactosidasebeta- Glucuronidasealpha- Glucosidasebeta- GlucosidaseN-acetyl-beta- glucosaminidasealpha- Mannosidasealpha- FucosidaseControl
19667+++-++--+++++-+++--
116053++++++--+++-+-+++---

API 50CHac

@refGLYERYDARALARARIBDXYLLXYLADOMDXGALGLUFRUMNESBERHADULINOMANSORMDMMDGNAGAMYARBESCSALCELMALLACMELSACTREINUMLZRAFAMDGLYGXLTGENTURLYXTAGDFUCLFUCDARLLARLGNT2KG5KG
116053------------------------+------------------------

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinent
11769marine sedimentsAlexandria, Abu Air Bay
67770Marine sediment of Abu Qir Bay on the western seashore of AlexandriaEgyptEGYAfrica
116053Environment, Marine sediments

isolation source categories

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

taxonmaps

  • @ref: 69479
  • File name: preview.99_3419.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_152;96_659;97_762;98_2623;99_3419&stattab=map
  • Last taxonomy: Nocardiopsis
  • 16S sequence: AJ539401
  • Sequence Identity:
  • Total samples: 25
  • soil counts: 4
  • aquatic counts: 2
  • animal counts: 19

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
117691Risk group (German classification)
196671Risk group (German classification)
1160531Risk group (French classification)

Sequence information

16S sequences

  • @ref: 11769
  • description: Nocardiopsis aegyptica 16S rRNA gene, strain DSM 44442
  • accession: AJ539401
  • length: 1487
  • database: ena
  • NCBI tax ID: 220378

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Nocardiopsis aegyptia strain DSM 44442220378.3wgspatric220378
66792Nocardiopsis aegyptia DSM 444422856493217draftimg220378
67770Nocardiopsis aegyptia DSM 44442GCA_013410755contigncbi220378

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingyes100no
motileno91.9yes
gram-positiveyes88.964no
anaerobicno99.002yes
aerobicyes93.156yes
halophileyes75.136no
spore-formingyes92.353no
glucose-utilyes88.81no
flagellatedno97.995no
thermophileno98.063yes
glucose-fermentno90.686no

External links

@ref: 11769

culture collection no.: DSM 44442, JCM 13853, NRRL B-24244, CGMCC 4.2109, NBRC 104164, CIP 108419

straininfo link

  • @ref: 80459
  • straininfo: 97662

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny15023959Nocardiopsis aegyptia sp. nov., isolated from marine sediment.Sabry SA, Ghanem NB, Abu-Ella GA, Schumann P, Stackebrandt E, Kroppenstedt RMInt J Syst Evol Microbiol10.1099/ijs.0.02814-02004Base Composition, Carbohydrate Metabolism, DNA, Bacterial/genetics, DNA, Ribosomal/genetics, Egypt, Geologic Sediments/*microbiology, Molecular Sequence Data, Nocardiaceae/classification/genetics/growth & development/*isolation & purification, Nucleic Acid Hybridization, Phylogeny, RNA, Bacterial/genetics, RNA, Ribosomal, 16S/genetics, Seawater/*microbiologyGenetics
Phylogeny18319481Nocardiopsis quinghaiensis sp. nov., isolated from saline soil in China.Chen YG, Cui XL, Kroppenstedt RM, Stackebrandt E, Wen ML, Xu LH, Jiang CLInt J Syst Evol Microbiol10.1099/ijs.0.65441-02008Actinomycetales/*classification/genetics/isolation & purification/physiology, Bacterial Typing Techniques, Base Composition, China, DNA, Bacterial/analysis, DNA, Ribosomal/analysis, Fatty Acids/analysis, Genes, rRNA, Molecular Sequence Data, Nucleic Acid Hybridization, Phenotype, Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, *Sodium Chloride, Soil/*analysis, *Soil Microbiology, Species SpecificityGenetics
Phylogeny25380720Nocardiopsis algeriensis sp. nov., an alkalitolerant actinomycete isolated from Saharan soil.Bouras N, Meklat A, Zitouni A, Mathieu F, Schumann P, Sproer C, Sabaou N, Klenk HPAntonie Van Leeuwenhoek10.1007/s10482-014-0329-72014Actinobacteria/*classification/genetics/*isolation & purification/physiology, Africa, Northern, Bacterial Typing Techniques, Cell Wall/chemistry, Cluster Analysis, Cytosol/chemistry, DNA, Bacterial/chemistry/genetics, DNA, Ribosomal/chemistry/genetics, Diaminopimelic Acid/analysis, Fatty Acids/analysis, Hydrogen-Ion Concentration, Microscopy, Electron, Scanning, Molecular Sequence Data, Nucleic Acid Hybridization, Peptidoglycan/analysis, Phospholipids/analysis, Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Sodium Chloride/metabolism, *Soil Microbiology, Spores, Bacterial/cytology, Temperature, Vitamin K 2/analysisGenetics

Reference

@idauthorscataloguedoi/urltitleID_cross_referencepubmed
11769Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 44442)https://www.dsmz.de/collection/catalogue/details/culture/DSM-44442
19667Wink, J.http://www.dsmz.de/microorganisms/wink_pdf/DSM44442.pdfCompendium of Actinobacteria. HZI-Helmholtz-Centre for Infection Research, Braunschweig
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
30001Barberan A, Caceres Velazquez H, Jones S, Fierer N.10.1128/mSphere.00237-17Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information2636628776041
33239Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/6039
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/
68371Automatically annotated from API 50CH acid
68382Automatically annotated from API zym
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
80459Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID97662.1StrainInfo: A central database for resolving microbial strain identifiers
116053Curators of the CIPCollection of Institut Pasteur (CIP 108419)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20108419