Strain identifier

BacDive ID: 11194

Type strain: Yes

Species: Nocardiopsis synnemataformans

Strain history: DSM 44143 <-- A. F. Yassin IMMIB D-1215.

NCBI tax ID(s): 1245476 (strain), 61305 (species)

« back to strain detail view
For citation purpose refer to the digital object identifier (doi) of the current version.
Archive
version 8.1 (current version):
version 8:
version 7.1:
version 7:
version 6:
version 5:
version 4.1:
version 4:
version 3:
version 2.1:
version 2:
version 1:
version 8.1 (current version)

General

@ref: 11520

BacDive-ID: 11194

DSM-Number: 44143

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

description: Nocardiopsis synnemataformans DSM 44143 is a spore-forming, mesophilic human pathogen that builds an aerial mycelium and was isolated from sputum of a 35 year old man with kidney transplantation.

NCBI tax id

NCBI tax idMatching level
1245476strain
61305species

strain history

@refhistory
11520<- A.F. Yassin, IMMIB D-1215
67770DSM 44143 <-- A. F. Yassin IMMIB D-1215.

doi: 10.13145/bacdive11194.20230509.8.1

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 synnemataformans
  • full scientific name: Nocardiopsis synnemataformans Yassin et al. 1997

@ref: 11520

domain: Bacteria

phylum: Actinobacteria

class: Actinobacteria

order: Actinomycetales

family: Nocardiopsaceae

genus: Nocardiopsis

species: Nocardiopsis synnemataformans

full scientific name: Nocardiopsis synnemataformans Yassin et al. 1997 emend. Nouioui et al. 2018

type strain: yes

Morphology

cell morphology

@refmotilityconfidencegram stain
69480no91.495
69480100positive

colony morphology

@refcolony colorincubation periodmedium used
19634Ochre yellow10-14 daysISP 2
19634Ochre yellow10-14 daysISP 3
19634Ochre yellow10-14 daysISP 4
19634Ochre yellow10-14 daysISP 5
19634Ochre yellow10-14 daysISP 6
19634Ochre yellow10-14 daysISP 7

multicellular morphology

@refforms multicellular complexcomplex namemedium namecomplex color
19634yesAerial MyceliumISP 2
19634yesAerial MyceliumISP 3White
19634yesAerial MyceliumISP 4Ivory
19634noISP 5
19634yesAerial MyceliumISP 6
19634noISP 7

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
11520GYM 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
19634ISP 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
19634ISP 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:
19634ISP 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
19634ISP 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
19634ISP 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
19634ISP 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
11520TRYPTICASE 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

culture temp

@refgrowthtypetemperaturerange
19634positiveoptimum28mesophilic
11520positivegrowth28mesophilic
67770positivegrowth28mesophilic

Physiology and metabolism

spore formation

@refspore formationconfidence
69481yes96
69480yes100

halophily

  • @ref: 19634
  • salt: NaCl
  • growth: positive
  • tested relation: maximum
  • concentration: 10 %

observation

  • @ref: 67770
  • observation: quinones: MK-10, MK-10(H2)

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
1963417234glucose+/-
1963422599arabinose+/-
1963417992sucrose+/-
1963418222xylose+/-
1963417268myo-inositol+/-
1963429864mannitol+/-
1963428757fructose+/-
1963426546rhamnose+/-
1963416634raffinose+/-
1963462968cellulose+/-
683685291gelatin+hydrolysis
6836827897tryptophan-energy source
6836816199urea+hydrolysis
6836816947citrate-assimilation
6836818257ornithine+degradation
6836825094lysine+degradation
6836829016arginine+hydrolysis

metabolite production

@refChebi-IDmetaboliteproduction
6836815688acetoinyes
6836835581indoleno
6836816136hydrogen sulfideno

metabolite tests

@refChebi-IDmetabolitevoges-proskauer-testindole test
6836815688acetoin+
6836835581indole-

enzymes

@refvalueactivityec
68368gelatinase+
68368tryptophan deaminase-4.1.99.1
68368urease+3.5.1.5
68368ornithine decarboxylase+4.1.1.17
68368lysine decarboxylase+4.1.1.18
68368arginine dihydrolase+3.5.3.6
68368beta-galactosidase+3.2.1.23
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
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
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- Fucosidase
19634++++++--++++--++++-

API 20E

@refONPGADH ArgLDC LysODCCITH2SURETDA TrpINDVPGEL
19634++++--+--++

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.country
11520sputum of a 35 year old man with kidney transplantationIstanbulTurkeyTUR
67770Sputum of a 35-year-old Turkish patient who received a renal transplant

isolation source categories

Cat1Cat2Cat3
#Infection#Patient
#Host Body Product#Fluids#Sputum
#Host#Human#Male

taxonmaps

  • @ref: 69479
  • File name: preview.99_4184.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_152;96_659;97_762;98_2623;99_4184&stattab=map
  • Last taxonomy: Nocardiopsis
  • 16S sequence: Y13593
  • Sequence Identity:
  • Total samples: 98
  • soil counts: 18
  • aquatic counts: 7
  • animal counts: 51
  • plant counts: 22

Safety information

risk assessment

@refpathogenicity humanbiosafety levelbiosafety level comment
11520yes, in single cases1Risk group (German classification)
196341Risk group (German classification)

Sequence information

16S sequences

@refdescriptionaccessionlengthdatabaseNCBI tax ID
20218Nocardiopsis synnemataformans strain IMMIB D-1215 16S ribosomal RNA gene, partial sequenceJQ899230656ena1245476
20218Nocardiopsis synnemataformans 16S rRNA gene, strain IMMIB D-1215TY135931461ena1245476
20218Nocardiopsis synnemataformans gene for 16S rRNA, partial sequenceAB3687111487ena1245476

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Nocardiopsis synnemataformans DSM 441431245476.3wgspatric1245476
66792Nocardiopsis synnemataformans DSM 441432554235028draftimg1245476
67770Nocardiopsis synnemataformans DSM 44143GCA_000340945contigncbi1245476

GC content

@refGC-contentmethod
6777074.1high performance liquid chromatography (HPLC)
6777072.3genome sequence analysis

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingyes96no
motileno91.116no
gram-positiveyes90.969no
anaerobicno99.083no
aerobicyes94.552no
halophileyes67.275no
spore-formingyes93.842no
thermophileno98.223yes
glucose-utilyes90.193no
flagellatedno98.122no
glucose-fermentno92.713no

External links

@ref: 11520

culture collection no.: DSM 44143, JCM 10456, IMMIB D-1215, CGMCC 4.2091, NBRC 102581, VKM Ac-2518

straininfo link

  • @ref: 80443
  • straininfo: 50505

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny9336896Description of Nocardiopsis synnemataformans sp. nov., elevation of Nocardiopsis alba subsp. prasina to Nocardiopsis prasina comb. nov., and designation of Nocardiopsis antarctica and Nocardiopsis alborubida as later subjective synonyms of Nocardiopsis dassonvillei.Yassin AF, Rainey FA, Burghardt J, Gierth D, Ungerechts J, Lux I, Seifert P, Bal C, Schaal KPInt J Syst Bacteriol10.1099/00207713-47-4-9831997Base Composition, Culture Media, Conditioned/metabolism, DNA, Bacterial/*analysis, Humans, Microscopy, Electron, Molecular Sequence Data, Propionibacteriaceae/chemistry/*classification/genetics/growth & development/metabolism/ultrastructure, RNA, Ribosomal, 16S/*analysisCultivation
Enzymology25231460New structures and composition of cell wall teichoic acids from Nocardiopsis synnemataformans, Nocardiopsis halotolerans, Nocardiopsis composta and Nocardiopsis metallicus: a chemotaxonomic value.Tul'skaya EM, Shashkov AS, Streshinskaya GM, Potekhina NV, Evtushenko LIAntonie Van Leeuwenhoek10.1007/s10482-014-0280-72014Actinobacteria/*chemistry, Cell Wall/*chemistry, Magnetic Resonance Spectroscopy, Molecular Structure, Teichoic Acids/*chemistry/*isolation & purificationPhylogeny
Metabolism29981450Characterization of a new microbial Pictet-Spenglerase NscbB affording the beta-carboline skeletons from Nocardiopsis synnemataformans DSM 44143.Chen Q, Zhang S, Xie YJ Biotechnol10.1016/j.jbiotec.2018.07.0072018Actinobacteria/*enzymology, Bacterial Proteins/genetics/*metabolism, Carbolines/*metabolism, Escherichia coli/genetics/metabolismEnzymology

Reference

@idauthorscataloguedoi/urltitlejournalpubmed
11520Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 44143)https://www.dsmz.de/collection/catalogue/details/culture/DSM-44143
19634Wink, J.http://www.dsmz.de/microorganisms/wink_pdf/DSM44143.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
20218Verslyppe, B., De Smet, W., De Baets, B., De Vos, P., Dawyndt P.10.1016/j.syapm.2013.11.002StrainInfo introduces electronic passports for microorganisms.Syst Appl Microbiol. 37: 42-50 201424321274
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/
68368Automatically annotated from API 20E
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
80443Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID50505.1StrainInfo: A central database for resolving microbial strain identifiers