Strain identifier

BacDive ID: 16573

Type strain: Yes

Species: Nonomuraea jabiensis

Strain Designation: A4036

Strain history: <- Nevzat Sahin, Ondokuz Mayis Univ., Turkey

NCBI tax ID(s): 882448 (species)

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General

@ref: 17454

BacDive-ID: 16573

DSM-Number: 45507

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

description: Nonomuraea jabiensis A4036 is an aerobe, spore-forming, mesophilic bacterium that builds an aerial mycelium and was isolated from arid soil.

NCBI tax id

  • NCBI tax id: 882448
  • Matching level: species

strain history

@refhistory
17454<- N. Sahin. Ondokuz Mayis University; A4036
67771<- Nevzat Sahin, Ondokuz Mayis Univ., Turkey

doi: 10.13145/bacdive16573.20230509.8.1

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 jabiensis
  • full scientific name: Nonomuraea jabiensis Camas et al. 2013

@ref: 17454

domain: Bacteria

phylum: Actinobacteria

class: Actinobacteria

order: Actinomycetales

family: Streptosporangiaceae

genus: Nonomuraea

species: Nonomuraea jabiensis

full scientific name: Nonomuraea jabiensis Camas et al. 2013

strain designation: A4036

type strain: yes

Morphology

cell morphology

@refgram staincell shapemotilityconfidence
30589positivespiral-shapedno
67771positive
69480no92.586
69480positive100

colony morphology

@refcolony colormedium used
69399Honey yellow (1005)ISP 6
69399Ochre brown (8001)ISP 2
69399Ochre brown (8001)ISP 5
69399Sand yellow (1002)ISP 3
69399Sand yellow (1002)ISP 4
69399Sand yellow (1002)ISP 7
69399Sand yellow (1002)suter with tyrosine
69399Sand yellow (1002)suter without tyrosine

multicellular morphology

@refforms multicellular complexcomplex namemedium namecomplex color
69399noAerial myceliumISP 2
69399yesAerial myceliumISP 3Oyster white (1013)
69399yesAerial myceliumISP 4Oyster white (1013)
69399noAerial myceliumISP 5
69399noAerial myceliumISP 6
69399noAerial myceliumISP 7
69399noAerial myceliumsuter with tyrosine
69399noAerial myceliumsuter without tyrosine

pigmentation

@refproductionname
30589no
69399noMelanin
69399nosoluble pigment

multimedia

@refmultimedia contentcaptionintellectual property rights
69399DSM_45507_image3.jpegPlates (65, ISP2, ISP3, ISP4, ISP5, ISP7)Helmholtz-Zentrum für Infektionsforschung GmbH
69399DSM_45507_image4.jpegPlates (65, ISP2, ISP3, ISP4, ISP5, ISP7)Helmholtz-Zentrum für Infektionsforschung GmbH

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
17454ROLLED OATS MINERAL MEDIUM (DSMZ Medium 84)yeshttps://www.dsmz.de/microorganisms/medium/pdf/DSMZ_Medium84.pdf
17454GPHF-MEDIUM (DSMZ Medium 553)yeshttps://www.dsmz.de/microorganisms/medium/pdf/DSMZ_Medium553.pdf
17454CZAPEK PEPTONE AGAR (DSMZ Medium 83)yeshttps://www.dsmz.de/microorganisms/medium/pdf/DSMZ_Medium83.pdf
17454GYM 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

culture temp

@refgrowthtypetemperaturerange
17454positivegrowth28mesophilic
30589positivegrowth20-37
30589positiveoptimum28mesophilic
67771positivegrowth28mesophilic

culture pH

@refabilitytypepHPH range
30589positivegrowth05-10alkaliphile
30589positiveoptimum7

Physiology and metabolism

oxygen tolerance

@refoxygen tolerance
30589aerobe
67771aerobe

spore formation

@refspore formationconfidence
30589yes
69481yes99
69480yes100

halophily

@refsaltgrowthtested relationconcentration
30589NaClpositivegrowth0-2 %
30589NaClpositiveoptimum1 %
69399NaClpositivegrowth0-5 %

observation

  • @ref: 30589
  • observation: aggregates in chains

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
3058915963ribitol+carbon source
3058916449alanine+carbon source
3058923652dextrin+carbon source
3058928757fructose+carbon source
3058927570histidine+carbon source
30589182404-hydroxy-L-proline+carbon source
3058917716lactose+carbon source
3058925017leucine+carbon source
3058917306maltose+carbon source
3058929864mannitol+carbon source
3058937684mannose+carbon source
3058928053melibiose+carbon source
3058928044phenylalanine+carbon source
3058926271proline+carbon source
3058926546rhamnose+carbon source
3058917822serine+carbon source
3058930031succinate+carbon source
3058917992sucrose+carbon source
3058926986threonine+carbon source
3058918222xylose+carbon source
305894853esculin+hydrolysis
3058917632nitrate+reduction
6939922599arabinose+growth
6939962968cellulose+/-growth
6939928757fructose+growth
6939917234glucose+growth
6939917268inositol+/-growth
6939937684mannose+growth
6939916634raffinose+/-growth
6939926546rhamnose+growth
6939917992sucrose+growth
6939918222xylose+growth
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

enzymes

@refvalueactivityec
30589urease+3.5.1.5
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
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
68382naphthol-AS-BI-phosphohydrolase+
68382alpha-galactosidase+3.2.1.22
68382beta-galactosidase+3.2.1.23
68382beta-glucuronidase-3.2.1.31
68382alpha-glucosidase+3.2.1.20
68382beta-glucosidase+3.2.1.21
68382N-acetyl-beta-glucosaminidase+3.2.1.52
68382alpha-mannosidase+3.2.1.24

API coryne

@refNITPYZPYRAPALbeta GURbeta GALalpha GLUbeta NAGESCUREGELGLURIBXYLMANMALLACSACGLYG
69399---+-++++-+--------

API zym

@refAlkaline phosphataseEsteraseEsterase LipaseLipaseLeucine arylamidaseValine arylamidaseCystine arylamidaseTrypsinalpha- ChymotrypsinAcid phosphataseNaphthol-AS-BI-phosphohydrolasealpha- Galactosidasebeta- Galactosidasebeta- Glucuronidasealpha- Glucosidasebeta- GlucosidaseN-acetyl-beta- glucosaminidasealpha- Mannosidasealpha- Fucosidase
69399++/-+-+++/-++++++-+++++/-

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinent
17454arid soilHabuje, Jabi regionNigeriaNGAAfrica
67771From terrestial soilNigeriaNGAAfrica

isolation source categories

Cat1Cat2Cat3
#Environmental#Terrestrial#Soil
#Condition#Xerophilic

taxonmaps

  • @ref: 69479
  • File name: preview.99_14993.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_239;96_2032;97_2449;98_3030;99_14993&stattab=map
  • Last taxonomy: Nonomuraea
  • 16S sequence: HQ157186
  • Sequence Identity:
  • Total samples: 24
  • soil counts: 16
  • plant counts: 8

Safety information

risk assessment

  • @ref: 17454
  • biosafety level: 1
  • biosafety level comment: Risk group (German classification)

Sequence information

16S sequences

  • @ref: 17454
  • description: Nonomuraea jabiensis strain A4036 16S ribosomal RNA gene, partial sequence
  • accession: HQ157186
  • length: 1485
  • database: ena
  • NCBI tax ID: 882448

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Nonomuraea jabiensis DSM 45507GCA_014204795contigncbi882448
66792Nonomuraea jabiensis strain DSM 45507882448.3wgspatric882448
66792Nonomuraea jabiensis DSM 455072870526370draftimg882448

GC content

@refGC-contentmethod
1745469.6fluorimetric
3058969.6

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingyes99no
motileno91.467yes
flagellatedno97.589yes
gram-positiveyes87.186yes
anaerobicno98.94yes
halophileno91.895no
spore-formingyes94.122no
thermophileno98.863no
glucose-utilyes87.914yes
aerobicyes91.592no
glucose-fermentno91.822no

External links

@ref: 17454

culture collection no.: DSM 45507, KCTC 19870

straininfo link

  • @ref: 85600
  • straininfo: 396859

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny22389281Nonomuraea jabiensis sp. nov., isolated from arid soil.Camas M, Sazak A, Sproer C, Klenk HP, Cetin D, Guven K, Sahin NInt J Syst Evol Microbiol10.1099/ijs.0.039362-02012Actinomycetales/*classification/genetics/isolation & purification, Bacterial Typing Techniques, DNA, Bacterial/genetics, Fatty Acids/analysis, Molecular Sequence Data, Nigeria, Nucleic Acid Hybridization, *Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, *Soil Microbiology, Vitamin K 2/analogs & derivatives/analysisGenetics
Phylogeny25587565Characterization of antibiotic producing rare actinomycete Nonomuraea sp. JAJ18 derived from an Indian coastal solar saltern.Arul Jose P, Sivakala KK, Rajeswari P, Jebakumar SRScientificWorldJournal10.1155/2014/4560702014Acetates/chemistry, Actinomycetales/growth & development/*isolation & purification/*metabolism, Anti-Bacterial Agents/*biosynthesis/isolation & purification/pharmacology, Bacteria/drug effects, Chromatography, Thin Layer, Colony Count, Microbial, *Ecosystem, India, Microbial Sensitivity Tests, Phenotype, Phylogeny, Sodium Chloride/*isolation & purification, *Solar EnergyEnzymology
Phylogeny26944798Classification of Nonomuraea sp. ATCC 39727, an actinomycete that produces the glycopeptide antibiotic A40926, as Nonomuraea gerenzanensis sp. nov.Dalmastri C, Gastaldo L, Marcone GL, Binda E, Congiu T, Marinelli FInt J Syst Evol Microbiol10.1099/ijsem.0.0008102016Actinomycetales/*classification/genetics/isolation & purification, Anti-Bacterial Agents/biosynthesis, Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, Diaminopimelic Acid/chemistry, Fatty Acids/chemistry, Glycolipids/chemistry, India, Muramic Acids/chemistry, Nucleic Acid Hybridization, Phospholipids/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, *Soil Microbiology, Teicoplanin/*analogs & derivatives/biosynthesis, Vitamin K 2/analogs & derivatives/chemistryTranscriptome
Phylogeny26971302Nonomuraea zeae sp. nov., isolated from the rhizosphere of corn (Zea mays L.).Shen Y, Jia F, Liu C, Li J, Guo S, Zhou S, Wang X, Xiang WInt J Syst Evol Microbiol10.1099/ijsem.0.0010192016Actinomycetales/*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, Phospholipids/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, *Rhizosphere, Sequence Analysis, DNA, *Soil Microbiology, Vitamin K 2/analogs & derivatives/chemistry, Zea mays/*microbiologyTranscriptome
Phylogeny28073396Nonomuraea ceibae sp. nov., an actinobacterium isolated from Ceiba speciosa rhizosphere.Wang F, Shi J, Huang Y, Wu Y, Deng XInt J Syst Evol Microbiol10.1099/ijsem.0.0017822017Actinomycetales/*classification/genetics/isolation & purification, Bacterial Typing Techniques, Base Composition, Ceiba/*microbiology, China, DNA, Bacterial/genetics, Fatty Acids/chemistry, Nucleic Acid Hybridization, Peptidoglycan/chemistry, Phospholipids/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, *Rhizosphere, Sequence Analysis, DNA, *Soil MicrobiologyTranscriptome
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

Reference

@idauthorscataloguedoi/urltitleID_cross_referencepubmed
17454Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 45507)https://www.dsmz.de/collection/catalogue/details/culture/DSM-45507
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
30589Barberan A, Caceres Velazquez H, Jones S, Fierer N.10.1128/mSphere.00237-17Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information2692028776041
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)
67771Curators of the KCTChttps://kctc.kribb.re.kr/En/Kctc
68379Automatically annotated from API Coryne
68382Automatically annotated from API zym
69399Wink, J.https://cdn.dsmz.de/wink/DSM%2045507.pdfCompendium of Actinobacteria. HZI-Helmholtz-Centre for Infection Research, Braunschweig
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
85600Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID396859.1StrainInfo: A central database for resolving microbial strain identifiers