Strain identifier

BacDive ID: 16563

Type strain: Yes

Species: Nonomuraea bangladeshensis

Strain Designation: 5-10-10

Strain history: CIP <- 2007, JCM <- 2006, I. Ara, Kitasato Univ., Tokyo, Japan: strain 5-10-10

NCBI tax ID(s): 404385 (species)

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General

@ref: 12375

BacDive-ID: 16563

DSM-Number: 45128

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

description: Nonomuraea bangladeshensis 5-10-10 is an aerobe, spore-forming, mesophilic bacterium that builds an aerial mycelium and was isolated from sandy soil.

NCBI tax id

  • NCBI tax id: 404385
  • Matching level: species

strain history

@refhistory
12375<- JCM <- T. Kudo <- I. Ara; 5-10-10
67770T. Kudo <-- I. Ara 5-10-10.
116728CIP <- 2007, JCM <- 2006, I. Ara, Kitasato Univ., Tokyo, Japan: strain 5-10-10

doi: 10.13145/bacdive16563.20230509.8.1

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 bangladeshensis
  • full scientific name: Nonomuraea bangladeshensis Ara et al. 2007

@ref: 12375

domain: Bacteria

phylum: Actinobacteria

class: Actinobacteria

order: Actinomycetales

family: Streptosporangiaceae

genus: Nonomuraea

species: Nonomuraea bangladeshensis

full scientific name: Nonomuraea bangladeshensis Ara et al. 2007

strain designation: 5-10-10

type strain: yes

Morphology

cell morphology

@refgram stainmotilitycell shape
32160positiveno
116728positivenorod-shaped

colony morphology

@refcolony colorincubation periodmedium used
20167Oxide red (3009)10-14 daysISP 2
20167Rose (3017)10-14 daysISP 3
20167Light pink (3015)10-14 daysISP 4
20167Light pink (3015)10-14 daysISP 5
20167Brown beige (1011)10-14 daysISP 6
20167Light pink (3015)10-14 daysISP 7

multicellular morphology

@refforms multicellular complexmedium namecomplex namecomplex color
20167noISP 2
20167yesISP 3Aerial MyceliumCream
20167noISP 4
20167noISP 5
20167yesISP 6Aerial MyceliumBrown beige
20167noISP 7

multimedia

  • @ref: 12375
  • multimedia content: https://www.dsmz.de/microorganisms/photos/DSM_45128.jpg
  • caption: Medium 65 28°C
  • intellectual property rights: © Leibniz-Institut DSMZ

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
12375ROLLED OATS MINERAL MEDIUM (DSMZ Medium 84)yeshttps://mediadive.dsmz.de/medium/84Name: ROLLED OATS MINERAL MEDIUM (DSMZ Medium 84) Composition: Agar 20.0 g/l Rolled oats 20.0 g/l ZnSO4 x 7 H2O 0.001 g/l MnCl2 x 4 H2O 0.001 g/l FeSO4 x 7 H2O 0.001 g/l Distilled water
12375GYM 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
20167ISP 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
20167ISP 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:
20167ISP 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
20167ISP 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
20167ISP 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
20167ISP 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
37804MEDIUM 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)
12375TRYPTICASE 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
116728CIP Medium 57yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=57

culture temp

@refgrowthtypetemperaturerange
12375positivegrowth28mesophilic
20167positiveoptimum28mesophilic
32160positivegrowth15-45
32160positiveoptimum30mesophilic
37804positivegrowth30mesophilic
67770positivegrowth28mesophilic

culture pH

@refabilitytypepHPH range
32160positivegrowth5.0-9.0alkaliphile
32160positiveoptimum7

Physiology and metabolism

oxygen tolerance

  • @ref: 32160
  • oxygen tolerance: aerobe

spore formation

  • @ref: 32160
  • spore formation: yes

halophily

@refsaltgrowthtested relationconcentration
32160NaClpositivegrowth0.0-5.0 %
32160NaClpositiveoptimum2.5 %

observation

  • @ref: 67770
  • observation: quinones: MK-9(H4)

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
2016717234glucose+
2016722599arabinose+
2016717992sucrose+
2016718222xylose+
2016717268myo-inositol+
2016729864mannitol+
2016728757fructose+
2016726546rhamnose+
2016716634raffinose+
2016762968cellulose+
3216022599arabinose+carbon source
3216017057cellobiose+carbon source
3216028757fructose+carbon source
3216017754glycerol+carbon source
3216029864mannitol+carbon source
3216037684mannose+carbon source
3216017268myo-inositol+carbon source
3216016634raffinose+carbon source
3216026546rhamnose+carbon source
3216017992sucrose+carbon source
3216018222xylose+carbon source
11672817632nitrate+reduction
11672816301nitrite-reduction

metabolite production

  • @ref: 116728
  • Chebi-ID: 35581
  • metabolite: indole
  • production: no

enzymes

@refvalueactivityec
116728oxidase+
116728catalase+1.11.1.6
116728urease-3.5.1.5
68382alkaline phosphatase+3.1.3.1
68382esterase (C 4)+
68382esterase lipase (C 8)+
68382leucine arylamidase+3.4.11.1
68382cystine arylamidase-3.4.11.3
68382alpha-chymotrypsin+3.4.21.1
68382beta-glucuronidase-3.2.1.31
68382alpha-glucosidase+3.2.1.20
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
20167++++++--+++++-+++--
116728+++-+--++-----+-+---

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinent
12375sandy soilBangladesh, Cox's BazarBangladeshBGDAsia
67770Sandy soilCox's BazarBangladeshBGDAsia
116728Environment, Soil, sandCox's BazarBangladeshBGDAsia

isolation source categories

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

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
123751Risk group (German classification)
201671German classification
1167281Risk group (French classification)

Sequence information

16S sequences

  • @ref: 12375
  • description: Nonomuraea bangladeshensis gene for 16S rRNA
  • accession: AB274966
  • length: 1513
  • database: ena
  • NCBI tax ID: 404385

GC content

@refGC-contentmethod
1237572.7
6777072.7high performance liquid chromatography (HPLC)

External links

@ref: 12375

culture collection no.: DSM 45128, CIP 109648, JCM 13930, MTCC 8089, CIP 109647

straininfo link

  • @ref: 85590
  • straininfo: 309470

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny17625184Nonomuraea bangladeshensis sp. nov. and Nonomuraea coxensis sp. nov.Ara I, Kudo T, Matsumoto A, Takahashi Y, Omura SInt J Syst Evol Microbiol10.1099/ijs.0.65054-02007Actinomycetales/chemistry/*classification/*isolation & purification/physiology, Aerobiosis, Bacterial Typing Techniques, Bangladesh, DNA, Bacterial/chemistry/genetics, DNA, Ribosomal/chemistry/genetics, Fatty Acids/analysis, Genes, rRNA, Locomotion, Microscopy, Electron, Scanning, Molecular Sequence Data, Nucleic Acid Hybridization, Phospholipids/analysis, Phylogeny, RNA, Bacterial/genetics, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Sequence Homology, Nucleic Acid, *Soil Microbiology, Vitamin K 2/analysisGenetics
Phylogeny24368692Nonomuraea fuscirosea sp. nov., an actinomycete isolated from the rhizosphere soil of rehmannia (Rehmannia glutinosa Libosch).Zhang X, Zhang Y, Zhao J, Liu C, Wang S, Yang L, He H, Xiang W, Wang XInt J Syst Evol Microbiol10.1099/ijs.0.057877-02013Actinomycetales/*classification/genetics/isolation & purification, Bacterial Typing Techniques, Base Composition, China, DNA, Bacterial/genetics, Diaminopimelic Acid/chemistry, Fatty Acids/chemistry, Molecular Sequence Data, Nucleic Acid Hybridization, Phospholipids/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, Rehmannia/*microbiology, *Rhizosphere, Sequence Analysis, DNA, Soil Microbiology, Vitamin K 2/analogs & derivatives/chemistryGenetics

Reference

@idauthorscataloguedoi/urltitleID_cross_referencepubmed
12375Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 45128)https://www.dsmz.de/collection/catalogue/details/culture/DSM-45128
20167Wink, J.http://www.dsmz.de/microorganisms/wink_pdf/DSM45128.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
32160Barberan A, Caceres Velazquez H, Jones S, Fierer N.10.1128/mSphere.00237-17Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information2840328776041
37804Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/7413
67770Curators of the JCMhttps://jcm.brc.riken.jp/en/
68382Automatically annotated from API zym
85590Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID309470.1StrainInfo: A central database for resolving microbial strain identifiers
116728Curators of the CIPCollection of Institut Pasteur (CIP 109647)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20109647