Strain identifier

BacDive ID: 11201

Type strain: Yes

Species: Nocardiopsis composta

Strain Designation: KS9

Strain history: CIP <- 2002, P. Kämpfer, Giessen Univ., Giessen, Germany: strain KS9

NCBI tax ID(s): 157465 (species)

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General

@ref: 11868

BacDive-ID: 11201

DSM-Number: 44551

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

description: Nocardiopsis composta KS9 is an obligate aerobe, spore-forming, mesophilic bacterium that builds an aerial mycelium and was isolated from atmosphere of a composting facility.

NCBI tax id

  • NCBI tax id: 157465
  • Matching level: species

strain history

@refhistory
11868<- P. Kämpfer, Univ. Giessen; KS9
338032002, P. Kämpfer, Univ., Giessen, Germany: strain KS9
67770DSM 44551 <-- P. Kämpfer KS9.
118714CIP <- 2002, P. Kämpfer, Giessen Univ., Giessen, Germany: strain KS9

doi: 10.13145/bacdive11201.20230509.8.1

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 composta
  • full scientific name: Nocardiopsis composta corrig. Kämpfer et al. 2002

  • synonyms

    • @ref: 20215
    • synonym: Nocardiopsis compostus

@ref: 11868

domain: Bacteria

phylum: Actinobacteria

class: Actinobacteria

order: Actinomycetales

family: Nocardiopsaceae

genus: Nocardiopsis

species: Nocardiopsis composta

full scientific name: Nocardiopsis composta Kämpfer et al. 2002

strain designation: KS9

type strain: yes

Morphology

cell morphology

@refgram stainconfidencecell shapemotility
69480positive100
118714positiverod-shapedno

colony morphology

@refcolony colorincubation periodmedium usedhemolysis ability
20073Beige (1001)10-14 daysISP 2
20073Beige (1001)10-14 daysISP 3
20073Saffron yellow (1017)10-14 daysISP 4
20073Beige (1001)10-14 daysISP 5
20073Beige (1001)10-14 daysISP 6
20073Saffron yellow (1017)10-14 daysISP 7
1187141

multicellular morphology

@refforms multicellular complexmedium namecomplex namecomplex color
20073noISP 2
20073noISP 3
20073yesISP 4Aerial MyceliumWhite
20073noISP 5
20073noISP 6
20073yesISP 7Aerial MyceliumWhite

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
11868CZAPEK PEPTONE AGAR (DSMZ Medium 83)yeshttps://mediadive.dsmz.de/medium/83Name: CZAPEK PEPTONE AGAR (DSMZ Medium 83) Composition: Sucrose 30.0 g/l Agar 20.0 g/l Peptone 5.0 g/l NaNO3 3.0 g/l Yeast extract 2.0 g/l K2HPO4 1.0 g/l MgSO4 x 7 H2O 0.5 g/l KCl 0.5 g/l FeSO4 x 7 H2O 0.01 g/l Distilled water
20073ISP 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
20073ISP 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:
20073ISP 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
20073ISP 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
20073ISP 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
20073ISP 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
33803MEDIUM 72- for trypto casein soja agaryesDistilled water make up to (1000.000 ml);Trypto casein soy agar (40.000 g)
11868TRYPTICASE 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
11868GPHF-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
118714CIP Medium 72yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=72

culture temp

@refgrowthtypetemperaturerange
20073positiveoptimum30mesophilic
11868positivegrowth28mesophilic
33803positivegrowth37mesophilic
67770positivegrowth28mesophilic
118714positivegrowth25-45
118714nogrowth10psychrophilic

Physiology and metabolism

oxygen tolerance

  • @ref: 118714
  • oxygen tolerance: obligate aerobe

spore formation

@refspore formationconfidence
69481yes100
69480yes100

halophily

@refsaltgrowthtested relationconcentration
118714NaClpositivegrowth0-4 %
118714NaClnogrowth6 %
118714NaClnogrowth8 %
118714NaClnogrowth10 %

observation

  • @ref: 67770
  • observation: quinones: MK-10(H8), MK-11(H8)

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
2007317234glucose+
2007322599arabinose+
2007317992sucrose+
2007318222xylose-
2007317268myo-inositol+
2007329864mannitol+
2007328757fructose+
2007326546rhamnose+
2007316634raffinose-
2007362968cellulose+
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
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
11871416947citrate+carbon source
1187144853esculin-hydrolysis
118714606565hippurate+hydrolysis
11871417632nitrate-reduction
11871416301nitrite-reduction
11871417632nitrate-respiration
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

antibiotic resistance

  • @ref: 118714
  • metabolite: 0129 (2,4-Diamino-6,7-di-iso-propylpteridine phosphate)
  • is antibiotic: yes
  • is sensitive: no
  • is resistant: yes

metabolite production

  • @ref: 118714
  • Chebi-ID: 35581
  • metabolite: indole
  • production: no

metabolite tests

  • @ref: 118714
  • Chebi-ID: 15688
  • metabolite: acetoin
  • voges-proskauer-test: -

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
118714oxidase+
118714beta-galactosidase+3.2.1.23
118714alcohol dehydrogenase-1.1.1.1
118714gelatinase+/-
118714amylase+
118714DNase+
118714caseinase-3.4.21.50
118714catalase+1.11.1.6
118714tween esterase+
118714gamma-glutamyltransferase-2.3.2.2
118714lecithinase-
118714lipase+
118714lysine decarboxylase-4.1.1.18
118714ornithine decarboxylase-4.1.1.17
118714phenylalanine ammonia-lyase-4.3.1.24
118714protease+
118714tryptophan deaminase-
118714urease+3.5.1.5
68382alkaline phosphatase+3.1.3.1
68382esterase (C 4)+
68382esterase lipase (C 8)+
68382leucine arylamidase+3.4.11.1
68382alpha-galactosidase-3.2.1.22
68382beta-glucuronidase-3.2.1.31
68382alpha-glucosidase+3.2.1.20
68382beta-glucosidase+3.2.1.21
68382alpha-fucosidase-3.2.1.51

API coryne

@refNITPYZPYRAPALbeta GURbeta GALalpha GLUbeta NAGESCUREGELGLURIBXYLMANMALLACSACGLYG
20073--++-+++++-------+-

API zym

@refAlkaline phosphataseEsteraseEsterase LipaseLipaseLeucine arylamidaseValine arylamidaseCystine arylamidaseTrypsinalpha- ChymotrypsinAcid phosphataseNaphthol-AS-BI-phosphohydrolasealpha- Galactosidasebeta- Galactosidasebeta- Glucuronidasealpha- Glucosidasebeta- GlucosidaseN-acetyl-beta- glucosaminidasealpha- Mannosidasealpha- FucosidaseControl
20073+++++++++++-+-++++-
118714+++-+---------++----

API 50CHac

@refGLYERYDARALARARIBDXYLLXYLADOMDXGALGLUFRUMNESBERHADULINOMANSORMDMMDGNAGAMYARBESCSALCELMALLACMELSACTREINUMLZRAFAMDGLYGXLTGENTURLYXTAGDFUCLFUCDARLLARLGNT2KG5KG
118714------------------------+/-------------------------

API biotype100

@refGLUFRUGALTREMNESBEMELSACRAFMTEMALLACLTEMbGaMaGaCELGENMbGuESCRIBARAXYLPLERHAFUCMLZDARLLARLXLTDULTAGGLYINOMANMTLTURSORADOHBGLYXERYMDG3MDGSATMUCLTATDTATMTATDMLTLMLTCATETATETTECITGRTGAT2KG5KGTRYNAGGNTPACPATpOBEQATGTEmOBEBATPPATCMTTGEBETPCEABTHINLATCAPCYTHISSUCFUMGREGYTAVTETNTTNGLNITA3OBUAPTGTTPRODALALALASERMNTPROPTYR2KT
118714+++++----+-----+-++++--+--+----+++-+-+--+--+----+++--+--+--++-+--+----+-++++--+++++++-+-+++++++-++-

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinentisolation date
11868atmosphere of a composting facilityKasselGermanyDEUEurope
67770Bioaerosol in the surroundings of a composting facilityKassel-NiederzwehrenGermanyDEUEurope
118714Plant, Bioaerosol generated in composting plantKasselGermanyDEUEurope1998

isolation source categories

Cat1Cat2Cat3
#Engineered#Biodegradation#Composting
#Environmental#Air

taxonmaps

  • @ref: 69479
  • File name: preview.99_8574.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_152;96_2754;97_3390;98_4514;99_8574&stattab=map
  • Last taxonomy: Nocardiopsis composta
  • 16S sequence: AF360734
  • Sequence Identity:
  • Total samples: 20
  • soil counts: 2
  • animal counts: 12
  • plant counts: 6

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
118681Risk group (German classification)
200731German classification
1187141Risk group (French classification)

Sequence information

16S sequences

  • @ref: 11868
  • description: Nocardiopsis compostus KS9 16S ribosomal RNA gene, partial sequence
  • accession: AF360734
  • length: 1454
  • database: ena
  • NCBI tax ID: 157465

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Nocardiopsis composta DSM 44551GCA_014200805contigncbi157465
66792Nocardiopsis composta strain DSM 44551157465.3wgspatric157465
66792Nocardiopsis composta DSM 445512852736999draftimg157465

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingyes100no
motileno91.584no
gram-positiveyes90.768no
anaerobicno99.298no
aerobicyes91.955no
halophileyes60.195no
spore-formingyes92.819no
glucose-utilyes86.131yes
flagellatedno97.974no
thermophileno97.506yes
glucose-fermentno88yes

External links

@ref: 11868

culture collection no.: DSM 44551, JCM 11768, NRRL B-24145, BCRC 16374, CGMCC 4.2090, CIP 107461, NBRC 100345, NCIMB 14354, VKM Ac-2521, VTT E-042201

straininfo link

  • @ref: 80448
  • straininfo: 100825

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny11931176Nocardiopsis compostus sp. nov., from the atmosphere of a composting facility.Kampfer P, Busse HJ, Rainey FAInt J Syst Evol Microbiol10.1099/00207713-52-2-6212002Actinomycetales/chemistry/*classification/physiology, Air Microbiology, Fertilizers/microbiology, Lipids/analysis, Molecular Sequence Data, Phylogeny, RNA, Bacterial/chemistry, RNA, Ribosomal, 16S/chemistry, Vitamin K 2/analysisGenetics
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

Reference

@idauthorscataloguedoi/urltitle
11868Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 44551)https://www.dsmz.de/collection/catalogue/details/culture/DSM-44551
20073Wink, J.http://www.dsmz.de/microorganisms/wink_pdf/DSM44551.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
33803Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/4899
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
68379Automatically annotated from API Coryne
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
80448Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID100825.1StrainInfo: A central database for resolving microbial strain identifiers
118714Curators of the CIPCollection of Institut Pasteur (CIP 107461)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20107461