Strain identifier

BacDive ID: 16537

Type strain: Yes

Species: Nonomuraea ferruginea

Strain history: CIP <- 2001, CCM <- IMET, Actinomadura ferruginea <- H. Prauser

NCBI tax ID(s): 46174 (species)

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General

@ref: 11140

BacDive-ID: 16537

DSM-Number: 43553

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

description: Nonomuraea ferruginea DSM 43553 is a spore-forming, mesophilic, Gram-positive bacterium that builds an aerial mycelium and was isolated from compost soil.

NCBI tax id

  • NCBI tax id: 46174
  • Matching level: species

strain history

@refhistory
11140<- IMET <- J. Meyer, 487-2
67770KCC A-0283 <-- IMET 9567 <-- J. Meyer 487-2.
119333CIP <- 2001, CCM <- IMET, Actinomadura ferruginea <- H. Prauser

doi: 10.13145/bacdive16537.20230509.8.1

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 ferruginea
  • full scientific name: Nonomuraea ferruginea corrig. (Meyer 1981) Zhang et al. 1998

  • synonyms

    @refsynonym
    20215Actinomadura ferruginea
    20215Nonomuria ferruginea
    20215Microtetraspora ferruginea

@ref: 11140

domain: Bacteria

phylum: Actinobacteria

class: Actinobacteria

order: Actinomycetales

family: Streptosporangiaceae

genus: Nonomuraea

species: Nonomuraea ferruginea

full scientific name: Nonomuraea ferruginea (Meyer 1981) Zhang et al. 1998

type strain: yes

Morphology

cell morphology

  • @ref: 119333
  • gram stain: positive
  • cell shape: filament-shaped
  • motility: no

colony morphology

@refcolony colorincubation periodmedium used
19574dark red10-14 daysISP 2
19574orange10-14 daysISP 3
19574orange10-14 daysISP 4
19574brown red10-14 daysISP 5
19574brown red10-14 daysISP 6
19574orange10-14 daysISP 7

multicellular morphology

@refforms multicellular complexcomplex namecomplex colormedium name
19574yesAerial MyceliumWhiteISP 2
19574yesAerial MyceliumWhiteISP 3
19574yesAerial MyceliumWhiteISP 4
19574yesAerial MyceliumWhiteISP 5
19574noISP 6
19574noISP 7

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
11140ROLLED 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
19574ISP 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
19574ISP 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:
19574ISP 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
19574ISP 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
19574ISP 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
19574ISP 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
37278MEDIUM 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)
11140GYM 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
119333CIP Medium 57yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=57

culture temp

@refgrowthtypetemperaturerange
19574positiveoptimum28mesophilic
37278positivegrowth30mesophilic
11140positivegrowth28mesophilic
67770positivegrowth28mesophilic
119333positivegrowth22-41
119333nogrowth5psychrophilic
119333nogrowth15psychrophilic

Physiology and metabolism

spore formation

  • @ref: 19574
  • spore description: Formation of spore chains (short spirals), spore surface smooth
  • type of spore: spore
  • spore formation: yes

halophily

@refsaltgrowthtested relationconcentration
19574NaClpositivemaximum2.5 %
119333NaClpositivegrowth0-4 %
119333NaClnogrowth6 %
119333NaClnogrowth8 %
119333NaClnogrowth10 %

observation

  • @ref: 67770
  • observation: quinones: MK-9(H4), MK-9(H2), MK-9

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
1957417234glucose+
1957422599arabinose+
1957417992sucrose+
1957418222xylose+
1957417268myo-inositol-
1957429864mannitol+
1957428757fructose+
1957426546rhamnose+
1957416634raffinose-
1957462968cellulose-
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
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
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
6837117108D-arabinose-builds acid from
6837117113erythritol-builds acid from
6837117754glycerol-builds acid from
683685291gelatin+hydrolysis
6836827897tryptophan-energy source
6836816199urea+hydrolysis
6836816947citrate+assimilation
6836818257ornithine+degradation
6836825094lysine+degradation
6836829016arginine+hydrolysis
1193334853esculin-hydrolysis
11933317632nitrate+reduction
11933316301nitrite-reduction
11933317632nitrate-respiration

antibiotic resistance

  • @ref: 119333
  • metabolite: 0129 (2,4-Diamino-6,7-di-iso-propylpteridine phosphate)
  • is antibiotic: yes
  • is sensitive: no
  • is resistant: yes

metabolite production

@refChebi-IDmetaboliteproduction
6836815688acetoinyes
6836835581indoleno
6836816136hydrogen sulfideno
11933335581indoleno

metabolite tests

@refChebi-IDmetabolitevoges-proskauer-testindole testmethylred-test
6836815688acetoin+
6836835581indole-
11933315688acetoin-
11933317234glucose-

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
119333oxidase-
119333beta-galactosidase+3.2.1.23
119333alcohol dehydrogenase-1.1.1.1
119333gelatinase+
119333amylase-
119333DNase-
119333caseinase-3.4.21.50
119333catalase+1.11.1.6
119333tween esterase-
119333gamma-glutamyltransferase+2.3.2.2
119333lysine decarboxylase-4.1.1.18
119333ornithine decarboxylase-4.1.1.17
119333phenylalanine ammonia-lyase-4.3.1.24
119333tryptophan deaminase-
119333urease-3.5.1.5
68382alkaline phosphatase+3.1.3.1
68382esterase (C 4)+
68382esterase lipase (C 8)+
68382lipase (C 14)-
68382leucine arylamidase+3.4.11.1
68382valine arylamidase+
68382trypsin+3.4.21.4
68382alpha-chymotrypsin+3.4.21.1
68382beta-galactosidase+3.2.1.23
68382beta-glucuronidase-3.2.1.31
68382alpha-glucosidase+3.2.1.20
68382N-acetyl-beta-glucosaminidase+3.2.1.52
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
19574+++-++++++-++-+++--
119333+++-++-++-+-+-+-++--

API 20E

@refONPGADH ArgLDC LysODCCITH2SURETDA TrpINDVPGEL
19574+++++-+--++

API 50CHac

@refGLYERYDARALARARIBDXYLLXYLADOMDXGALGLUFRUMNESBERHADULINOMANSORMDMMDGNAGAMYARBESCSALCELMALLACMELSACTREINUMLZRAFAMDGLYGXLTGENTURLYXTAGDFUCLFUCDARLLARLGNT2KG5KG
119333---+/---------------------+/-------+/------------+/------

API biotype100

@refGLUFRUGALTREMNESBEMELSACRAFMTEMALLACLTEMbGaMaGaCELGENMbGuESCRIBARAXYLPLERHAFUCMLZDARLLARLXLTDULTAGGLYINOMANMTLTURSORADOHBGLYXERYMDG3MDGSATMUCLTATDTATMTATDMLTLMLTCATETATETTECITGRTGAT2KG5KGTRYNAGGNTPACPATpOBEQATGTEmOBEBATPPATCMTTGEBETPCEABTHINLATCAPCYTHISSUCFUMGREGYTAVTETNTTNGLNITA3OBUAPTGTTPRODALALALASERMNTPROPTYR2KT
119333++--+----+--+-----++++-++-----+-++---------++--------------++---+------++-++-------+-------------++

Isolation, sampling and environmental information

isolation

@refsample typecountryorigin.countrycontinentisolation date
11140compost soil
67770Compost soil
119333Environment, Compost soilGermanyDEUEurope1965

isolation source categories

Cat1Cat2Cat3
#Engineered#Biodegradation#Composting
#Environmental#Terrestrial#Soil

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
111401Risk group (German classification)
195741Risk group (German classification)
1193331Risk group (French classification)

Sequence information

16S sequences

  • @ref: 20218
  • description: Microtetraspora ferruginea 16S rRNA gene
  • accession: U48845
  • length: 1415
  • database: ena
  • NCBI tax ID: 46174

Genome sequences

  • @ref: 66792
  • description: Nonomuraea ferruginea DSM 43553
  • accession: GCA_027620355
  • assembly level: contig
  • database: ncbi
  • NCBI tax ID: 46174

GC content

@refGC-contentmethod
6777068.1thermal denaturation, midpoint method (Tm)
6777068thermal denaturation, midpoint method (Tm)

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
motileno90.755no
flagellatedno97.691no
gram-positiveyes90.129no
anaerobicno99.172no
aerobicyes93.094no
halophileno88.852no
spore-formingyes95.63yes
glucose-fermentno90.668no
thermophileno98.375yes
glucose-utilyes87.554yes

External links

@ref: 11140

culture collection no.: DSM 43553, ATCC 35575, IFO 14094, IMET 9567, JCM 3283, NBRC 14094, NCIB 11630, NRRL B-16096, BCRC 12537, CCM 3424, CIP 106925, IMSNU 20090, KCTC 9269, MTCC 1059, NCIMB 11630, VKM Ac-854, CCRC 12537, KCC A-0283

straininfo link

  • @ref: 85567
  • straininfo: 41167

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny24179038Nonomuraea guangzhouensis sp. nov., and Nonomuraea harbinensis sp. nov., two novel actinomycetes isolated from soil.Wang S, Liu C, Zhang Y, Zhao J, Zhang X, Yang L, Wang X, Xiang WAntonie Van Leeuwenhoek10.1007/s10482-013-0058-32013Actinomycetales/*classification/genetics/*isolation & purification/metabolism, Bacterial Typing Techniques, Base Composition, China, DNA, Bacterial/genetics/metabolism, Fatty Acids/chemistry/metabolism, Molecular Sequence Data, Phylogeny, RNA, Ribosomal, 16S/genetics, Soil MicrobiologyMetabolism
Phylogeny26289724Nonomuraea flavida sp. nov., a novel species of soil actinomycete isolated from Aconitum napellus rhizosphere.Chen S, Shi J, Li D, Wu Y, Huang YInt J Syst Evol Microbiol10.1099/ijsem.0.0005382015Aconitum/*microbiology, Actinomycetales/*classification/genetics/isolation & purification, Bacterial Typing Techniques, Base Composition, China, DNA, Bacterial/genetics, Fatty Acids/chemistry, Nucleic Acid Hybridization, Peptidoglycan/chemistry, Phospholipids/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, *Rhizosphere, Sequence Analysis, DNA, *Soil Microbiology, Vitamin K 2/chemistryTranscriptome

Reference

@idauthorscataloguedoi/urltitlejournalpubmed
11140Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 43553)https://www.dsmz.de/collection/catalogue/details/culture/DSM-43553
19574Wink, J.http://www.dsmz.de/microorganisms/wink_pdf/DSM43553.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
37278Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/19109
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
68371Automatically annotated from API 50CH acid
68382Automatically annotated from API zym
85567Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID41167.1StrainInfo: A central database for resolving microbial strain identifiers
119333Curators of the CIPCollection of Institut Pasteur (CIP 106925)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20106925