Strain identifier

BacDive ID: 16548

Type strain: Yes

Species: Nonomuraea africana

Strain history: CIP <- 2002, JCM <- DSMZ <- INA : 1839

NCBI tax ID(s): 46171 (species)

For citation purpose refer to the digital object identifier (doi) of the current version.
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General

@ref: 11245

BacDive-ID: 16548

DSM-Number: 43748

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

description: Nonomuraea africana DSM 43748 is a spore-forming, mesophilic bacterium that was isolated from soil.

NCBI tax id

  • NCBI tax id: 46171
  • Matching level: species

strain history

@refhistory
11245<- N.S. Agre, INA
67770DSM 43748 <-- INA 1839.
116105CIP <- 2002, JCM <- DSMZ <- INA : 1839

doi: 10.13145/bacdive16548.20230509.8.1

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 africana
  • full scientific name: Nonomuraea africana corrig. (Preobrazhenskaya and Sveshnikova 1974) Zhang et al. 1998
  • synonyms

    @refsynonym
    20215Actinomadura africana
    20215Microtetraspora africana
    20215Nonomuria africana
    20215Nocardiopsis africana

@ref: 11245

domain: Bacteria

phylum: Actinobacteria

class: Actinobacteria

order: Actinomycetales

family: Streptosporangiaceae

genus: Nonomuraea

species: Nonomuraea africana

full scientific name: Nonomuraea africana (Preobrazhenskaya and Sveshnikova 1974) Zhang et al. 1998

type strain: yes

Morphology

cell morphology

@refmotilityconfidencegram staincell shape
69480no90.44
69480100positive
116105nopositiverod-shaped

colony morphology

@refcolony colorincubation periodmedium used
19582Salmon orange10-14 daysISP 2
19582Salmon orange10-14 daysISP 3
19582Salmon orange10-14 daysISP 4
19582Salmon orange10-14 daysISP 5
1958210-14 daysISP 6
19582Salmon orange10-14 daysISP 7

multicellular morphology

@refforms multicellular complexmedium name
19582noISP 2
19582noISP 3
19582noISP 4
19582noISP 5
19582noISP 6
19582noISP 7

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
11245GYM 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
19582ISP 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
19582ISP 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:
19582ISP 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
19582ISP 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
19582ISP 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
19582ISP 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
39772MEDIUM 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)
11245ROLLED OATS MINERAL MEDIUM (DSMZ Medium 84)yeshttps://www.dsmz.de/microorganisms/medium/pdf/DSMZ_Medium84.pdf
116105CIP Medium 57yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=57

culture temp

@refgrowthtypetemperaturerange
19582positiveoptimum30mesophilic
11245positivegrowth28mesophilic
39772positivegrowth30mesophilic
67770positivegrowth28mesophilic
116105positivegrowth30-37mesophilic
116105nogrowth5psychrophilic
116105nogrowth15psychrophilic

Physiology and metabolism

spore formation

@refspore formationconfidence
69481yes94
69480yes100

halophily

@refsaltgrowthtested relationconcentration
19582NaClpositivemaximum2.5 %
116105NaClpositivegrowth0-2 %
116105NaClnogrowth4 %
116105NaClnogrowth6 %
116105NaClnogrowth8 %
116105NaClnogrowth10 %

observation

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

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
1958217234glucose+
1958222599arabinose+
1958217992sucrose+
1958218222xylose+
1958217268myo-inositol+
1958229864mannitol+
1958228757fructose+
1958226546rhamnose+
1958216634raffinose+
1958262968cellulose+
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
683685291gelatin+hydrolysis
6836827897tryptophan-energy source
6836816199urea+hydrolysis
6836816947citrate+assimilation
6836818257ornithine+degradation
6836825094lysine+degradation
6836829016arginine+hydrolysis
1161054853esculin-hydrolysis
11610517632nitrate-reduction
11610516301nitrite-reduction
11610517632nitrate-respiration

antibiotic resistance

  • @ref: 116105
  • 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
11610535581indoleno

metabolite tests

@refChebi-IDmetabolitevoges-proskauer-testindole testmethylred-test
6836815688acetoin+
6836835581indole-
11610515688acetoin-
11610517234glucose-

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
116105oxidase-
116105alcohol dehydrogenase-1.1.1.1
116105gelatinase+/-
116105amylase-
116105caseinase-3.4.21.50
116105catalase+1.11.1.6
116105tween esterase-
116105gamma-glutamyltransferase+2.3.2.2
116105lecithinase-
116105lipase-
116105lysine decarboxylase-4.1.1.18
116105ornithine decarboxylase-4.1.1.17
116105phenylalanine ammonia-lyase-4.3.1.24
116105tryptophan deaminase-
116105urease+3.5.1.5
68382alkaline phosphatase+3.1.3.1
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
68382acid phosphatase+3.1.3.2
68382beta-glucuronidase-3.2.1.31
68382alpha-glucosidase+3.2.1.20
68382beta-glucosidase+3.2.1.21
68382alpha-mannosidase+3.2.1.24

API zym

@refAlkaline phosphataseEsteraseEsterase LipaseLipaseLeucine arylamidaseValine arylamidaseCystine arylamidaseTrypsinalpha- ChymotrypsinAcid phosphataseNaphthol-AS-BI-phosphohydrolasealpha- Galactosidasebeta- Galactosidasebeta- Glucuronidasealpha- Glucosidasebeta- GlucosidaseN-acetyl-beta- glucosaminidasealpha- Mannosidasealpha- FucosidaseControl
19582+-+-++-++++++-++-++
116105+++-++++++----++++--

API 20E

@refONPGADH ArgLDC LysODCCITH2SURETDA TrpINDVPGEL
19582-++++-+--++

API 50CHac

@refGLYERYDARALARARIBDXYLLXYLADOMDXGALGLUFRUMNESBERHADULINOMANSORMDMMDGNAGAMYARBESCSALCELMALLACMELSACTREINUMLZRAFAMDGLYGXLTGENTURLYXTAGDFUCLFUCDARLLARLGNT2KG5KG
116105------------------------+/-------------------------

API biotype100

@refGLUFRUGALTREMNESBEMELSACRAFMTEMALLACLTEMbGaMaGaCELGENMbGuESCRIBARAXYLPLERHAFUCMLZDARLLARLXLTDULTAGGLYINOMANMTLTURSORADOHBGLYXERYMDG3MDGSATMUCLTATDTATMTATDMLTLMLTCATETATETTECITGRTGAT2KG5KGTRYNAGGNTPACPATpOBEQATGTEmOBEBATPPATCMTTGEBETPCEABTHINLATCAPCYTHISSUCFUMGREGYTAVTETNTTNGLNITA3OBUAPTGTTPRODALALALASERMNTPROPTYR2KT
116105---------++----+--+-----+-------------------------------------+--+---------+----------+----+-----+-

Isolation, sampling and environmental information

isolation

@refsample type
11245soil
67770Soil

isolation source categories

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

taxonmaps

  • @ref: 69479
  • File name: preview.99_32461.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_239;96_2032;97_14842;98_20307;99_32461&stattab=map
  • Last taxonomy: Nonomuraea
  • 16S sequence: AJ269555
  • Sequence Identity:
  • Total samples: 17
  • soil counts: 16
  • plant counts: 1

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
112451Risk group (German classification)
195821Risk group (German classification)
1161051Risk group (French classification)

Sequence information

16S sequences

@refdescriptionaccessionlengthdatabaseNCBI tax ID
20218Nonomuraea africana 16S rRNA gene, strain DSM 43748AJ2695551448ena46171
20218Microtetraspora africana 16S-23S ribosomal RNA spacer regionAF004008340ena46171
20218Microtetraspora africana 16S rRNA geneU488421413ena46171

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Nonomuraea africana DSM 43748GCA_014873535contigncbi46171
66792Nonomuraea africana strain DSM 4374846171.3wgspatric46171
66792Nonomuraea africana DSM 437482873337989draftimg46171

GC content

  • @ref: 67770
  • GC-content: 64
  • method: thermal denaturation, midpoint method (Tm)

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingyes94no
gram-positiveyes83.025no
anaerobicno99.064no
halophileno93.945no
spore-formingyes92.798no
glucose-utilyes88.406yes
aerobicyes93.862no
flagellatedno97.662no
thermophileno97.749no
motileno91.812no
glucose-fermentno91.383no

External links

@ref: 11245

culture collection no.: DSM 43748, ATCC 35107, IFO 14745, INA 1839, NBRC 14745, RIA 1839, JCM 6240, BCRC 16334, CIP 107353, KCTC 9260, MTCC 1417, NRRL B-16114, VKM Ac-924

straininfo link

  • @ref: 85578
  • straininfo: 92766

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
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
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
11245Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 43748)https://www.dsmz.de/collection/catalogue/details/culture/DSM-43748
19582Wink, J.http://www.dsmz.de/microorganisms/wink_pdf/DSM43748.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
39772Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/4779
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
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
85578Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID92766.1StrainInfo: A central database for resolving microbial strain identifiers
116105Curators of the CIPCollection of Institut Pasteur (CIP 107353)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20107353