Strain identifier

BacDive ID: 16558

Type strain: Yes

Species: Nonomuraea dietziae

Strain Designation: FH 2205, FH2205

Strain history: CIP <- 2001, DSMZ <- J. Wink: strain FH2205

NCBI tax ID(s): 65515 (species)

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General

@ref: 11668

BacDive-ID: 16558

DSM-Number: 44320

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

description: Nonomuraea dietziae FH 2205 is a spore-forming, mesophilic bacterium that builds an aerial mycelium and was isolated from soil.

NCBI tax id

  • NCBI tax id: 65515
  • Matching level: species

strain history

@refhistory
11668<- J. Wink, Hoechst AG, FH 2205 <- NRRL (Sebekia benihana)
67770A. Shimazu <-- IFO 14309 <-- Upjohn Co., USA; UC 5762.
118933CIP <- 2001, DSMZ <- J. Wink: strain FH2205

doi: 10.13145/bacdive16558.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/actinomycetota
  • domain: Bacteria
  • phylum: Actinomycetota
  • class: Actinomycetes
  • order: Streptosporangiales
  • family: Streptosporangiaceae
  • genus: Nonomuraea
  • species: Nonomuraea dietziae
  • full scientific name: Nonomuraea dietziae corrig. Stackebrandt et al. 2001

  • synonyms

    @refsynonym
    20215Sebekia benihana
    20215Nonomuraea dietzii

@ref: 11668

domain: Bacteria

phylum: Actinobacteria

class: Actinobacteria

order: Actinomycetales

family: Streptosporangiaceae

genus: Nonomuraea

species: Nonomuraea dietziae

full scientific name: Nonomuraea dietziae Stackebrandt et al. 2001

strain designation: FH 2205, FH2205

type strain: yes

Morphology

cell morphology

@refmotilityconfidencegram staincell shape
69480no91.588
69480100positive
118933nopositivefilament-shaped

colony morphology

@refcolony colorincubation periodmedium used
20044Brown10-14 daysISP 2
20044Beige10-14 daysISP 3
20044Pink10-14 daysISP 4
20044Rose10-14 daysISP 5
20044Rose10-14 daysISP 6
20044Pink10-14 daysISP 7

multicellular morphology

@refforms multicellular complexcomplex namecomplex colormedium name
20044yesAerial MyceliumRed brown (8012)ISP 2
20044yesAerial MyceliumBeige (1001)ISP 3
20044yesAerial MyceliumPinkISP 4
20044yesAerial MyceliumAntique rose (3014)ISP 5
20044yesAerial MyceliumWhiteISP 6
20044yesAerial MyceliumPinkISP 7

multimedia

  • @ref: 11668
  • multimedia content: https://www.dsmz.de/microorganisms/photos/DSM_44320.jpg
  • caption: Medium 65 28°C
  • intellectual property rights: © Leibniz-Institut DSMZ

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
11668GYM 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
20044ISP 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
20044ISP 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:
20044ISP 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
20044ISP 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
20044ISP 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
20044ISP 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
38196MEDIUM 57 - for Streptomyces, Nocardioides, Lentzea albidocapillata and Streptoverticillium reticulumyesDistilled water make up to (1000.000 ml);Agar (15.000 g);Glucose (4.000g);Yeast extract (4.000 g);Malt extract (10.000 g);Calcium carbonate (2.000 g)
11668N-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
118933CIP Medium 57yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=57

culture temp

@refgrowthtypetemperaturerange
11668positivegrowth28mesophilic
20044positiveoptimum30mesophilic
38196positivegrowth30mesophilic
67770positivegrowth28mesophilic
118933positivegrowth15-41
118933nogrowth5psychrophilic

Physiology and metabolism

spore formation

@refspore descriptionspore formationconfidence
20044Formation of spore chains (rectiflixibilis), spore surface wartyyes
69481yes95
69480yes100

compound production

  • @ref: 11668
  • compound: novobiocin

halophily

@refsaltgrowthtested relationconcentration
20044NaClpositivemaximum2.5 %
118933NaClpositivegrowth0-2 %
118933NaClnogrowth4 %
118933NaClnogrowth6 %
118933NaClnogrowth8 %
118933NaClnogrowth10 %

observation

@refobservation
67770Hydroxylation of novobiocins
67770quinones: MK-9(III,VIII-H4), MK-9(H2)

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
2004417234glucose+
2004422599arabinose+/-
2004417992sucrose-
2004418222xylose-
2004417268myo-inositol-
2004429864mannitol-
2004428757fructose+
2004426546rhamnose+
2004416634raffinose-
2004462968cellulose-
683685291gelatin+hydrolysis
6836827897tryptophan-energy source
6836816199urea+hydrolysis
6836816947citrate+assimilation
6836818257ornithine+degradation
6836825094lysine-degradation
6836829016arginine+hydrolysis
11893316947citrate-carbon source
1189334853esculin-hydrolysis
11893317632nitrate-reduction
11893316301nitrite-reduction
11893317632nitrate-respiration

metabolite production

@refChebi-IDmetaboliteproduction
6836815688acetoinyes
6836835581indoleno
6836816136hydrogen sulfideno
11893335581indoleno

metabolite tests

@refChebi-IDmetabolitevoges-proskauer-testindole testmethylred-test
6836815688acetoin+
6836835581indole-
11893315688acetoin+
11893317234glucose-

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
118933oxidase-
118933alcohol dehydrogenase-1.1.1.1
118933gelatinase+/-
118933amylase-
118933DNase-
118933caseinase-3.4.21.50
118933catalase+1.11.1.6
118933tween esterase-
118933gamma-glutamyltransferase+2.3.2.2
118933lysine decarboxylase-4.1.1.18
118933ornithine decarboxylase-4.1.1.17
118933phenylalanine ammonia-lyase-4.3.1.24
118933tryptophan deaminase-
118933urease-3.5.1.5
68382alkaline phosphatase+3.1.3.1
68382esterase lipase (C 8)-
68382lipase (C 14)-
68382valine arylamidase-
68382cystine arylamidase-3.4.11.3
68382trypsin-3.4.21.4
68382acid phosphatase+3.1.3.2
68382beta-galactosidase-3.2.1.23
68382beta-glucuronidase-3.2.1.31
68382beta-glucosidase-3.2.1.21
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
20044+--------+-+-----+-
118933++--+---+++---+-+---

API 20E

@refONPGADH ArgLDC LysODCCITH2SURETDA TrpINDVPGEL
20044++-++-+--++

Isolation, sampling and environmental information

isolation

@refsample typeisolation date
11668soil
118933Environment, Soil1997

isolation source categories

  • Cat1: #Environmental
  • Cat2: #Terrestrial
  • Cat3: #Soil

taxonmaps

  • @ref: 69479
  • File name: preview.99_45791.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_239;96_2032;97_14842;98_20307;99_45791&stattab=map
  • Last taxonomy: Nonomuraea
  • 16S sequence: AJ294350
  • Sequence Identity:
  • Total samples: 87
  • soil counts: 53
  • aquatic counts: 3
  • animal counts: 9
  • plant counts: 22

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
116681Risk group (German classification)
200441German classification
1189331Risk group (French classification)

Sequence information

16S sequences

@refdescriptionaccessionlengthdatabaseNCBI tax ID
20218Sebekia benihana 16S rRNA gene for 16S ribosomal RNA, strain DSM 44320AJ2782201447ena65515
20218Nonomuraea dietziae gene for 16S ribosomal RNA, partial sequenceAB0061561473ena65515
20218Sebekia benihana partial 16S rRNA gene, strain NRRL 11111AJ2943501450ena65515

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Nonomuraea dietziae DSM 44320GCA_014195505contigncbi65515
66792Nonomuraea dietziae strain DSM 4432065515.3wgspatric65515
66792Nonomuraea dietziae DSM 443202827618455draftimg65515

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingyes95no
gram-positiveyes85.137no
anaerobicno98.914no
halophileno93.333no
spore-formingyes94.992yes
glucose-utilyes91.237yes
flagellatedno97.219no
thermophileno95.417yes
motileno91.997no
aerobicyes92.775no
glucose-fermentno91.628no

External links

@ref: 11668

culture collection no.: DSM 44320, ATCC 35861, IFO 14309, NBRC 14309, NRRL 11111, JCM 3338, BCRC 13419, CGMCC 4.1204, CIP 107127, KCCM 12213, KCTC 9173, KCTC 9610

straininfo link

  • @ref: 85586
  • straininfo: 41341

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Metabolism3417565Microbial conversion of nigericin in three successive steps, by Sebekia benihana.Delort AM, Jeminet G, Sancelme M, Dauphin GJ Antibiot (Tokyo)10.7164/antibiotics.41.9161988Anti-Bacterial Agents/*metabolism, Bacteria/metabolism, Inactivation, Metabolic, Molecular Conformation, Nigericin/*metabolism, Oxidation-Reduction
Metabolism8823511Microbial biotransformation products of cyclosporin A.Kuhnt M, Bitsch F, France J, Hofmann H, Sanglier JJ, Traber RJ Antibiot (Tokyo)10.7164/antibiotics.49.7811996Bacteria/*metabolism, Biotransformation, Cyclosporine/*pharmacokinetics, Fungi/*metabolism, Humans, Immunosuppressive Agents/*pharmacokineticsEnzymology
Phylogeny11491343Nonomuraea dietzii sp. nov..Stackebrandt E, Wink J, Steiner U, Kroppenstedt RMInt J Syst Evol Microbiol10.1099/00207713-51-4-14372001Actinomycetales/*classification/*genetics/metabolism, DNA, Bacterial/genetics, DNA, Ribosomal/genetics, Molecular Sequence Data, Nucleic Acid Hybridization, Phylogeny, Species Specificity, Terminology as TopicGenetics
Phylogeny20889768Nonomuraea rhizophila sp. nov., an actinomycete isolated from rhizosphere soil.Zhao GZ, Li J, Huang HY, Zhu WY, Xu LH, Li WJInt J Syst Evol Microbiol10.1099/ijs.0.028050-02010Actinomycetales/*classification/genetics/*isolation & purification/physiology, Bacterial Typing Techniques, Base Composition, China, Cluster Analysis, DNA, Bacterial/chemistry/genetics, DNA, Ribosomal/chemistry/genetics, Fatty Acids/analysis, Molecular Sequence Data, Nucleic Acid Hybridization, Phylogeny, Quinones/analysis, RNA, Ribosomal, 16S/genetics, Rhizosphere, Sequence Analysis, DNA, Sodium Chloride/metabolism, *Soil Microbiology, Tripterygium/microbiologyGenetics
Phylogeny28853687Nonomuraea stahlianthi sp. nov., an endophytic actinomycete isolated from the stem of Stahlianthus campanulatus.Niemhom N, Chutrakul C, Suriyachadkun C, Thawai CInt J Syst Evol Microbiol10.1099/ijsem.0.0020452017Actinomycetales/*classification/genetics/isolation & purification, Bacterial Typing Techniques, Base Composition, Cell Wall/chemistry, DNA, Bacterial/genetics, Diaminopimelic Acid/chemistry, Fatty Acids/chemistry, Nucleic Acid Hybridization, Peptidoglycan/chemistry, Phospholipids/chemistry, *Phylogeny, Plant Stems/*microbiology, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, *Soil Microbiology, Thailand, Vitamin K 2/analogs & derivatives/chemistry, Zingiberaceae/*microbiologyTranscriptome
Phylogeny30179151Nonomuraea mangrovi sp. nov., an actinomycete isolated from mangrove soil.Huang H, Liu M, Zhong W, Mo K, Zhu J, Zou X, Hu Y, Bao SInt J Syst Evol Microbiol10.1099/ijsem.0.0029542018Actinomycetales/*classification/genetics/isolation & purification, Bacterial Typing Techniques, Base Composition, Cell Wall/chemistry, China, DNA, Bacterial/genetics, Diaminopimelic Acid/chemistry, Fatty Acids/chemistry, Nucleic Acid Hybridization, *Phylogeny, RNA, Ribosomal, 16S/genetics, Rhizophoraceae/*microbiology, Sequence Analysis, DNA, *Soil MicrobiologyTranscriptome

Reference

@idauthorscataloguedoi/urltitlejournalpubmed
11668Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 44320)https://www.dsmz.de/collection/catalogue/details/culture/DSM-44320
20044Wink, J.http://www.dsmz.de/microorganisms/wink_pdf/DSM44320.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
38196Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/4529
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
85586Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID41341.1StrainInfo: A central database for resolving microbial strain identifiers
118933Curators of the CIPCollection of Institut Pasteur (CIP 107127)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20107127