Strain identifier

BacDive ID: 16539

Type strain: Yes

Species: Nonomuraea pusilla

Strain Designation: A-118, A3, KCCA-0144

Strain history: CIP <- 2001, NCIMB <- ATCC <- H. Nonomura: strain A-118

NCBI tax ID(s): 46177 (species)

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General

@ref: 10977

BacDive-ID: 16539

DSM-Number: 43357

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

description: Nonomuraea pusilla A-118 is an obligate aerobe, spore-forming, mesophilic bacterium that was isolated from soil.

NCBI tax id

  • NCBI tax id: 46177
  • Matching level: species

strain history

@refhistory
10977<- M. Goodfellow, A3 <- H. Nonomura, A-118
67770KCC A-0144 <-- H. Nonomura A-118.
122064CIP <- 2001, NCIMB <- ATCC <- H. Nonomura: strain A-118

doi: 10.13145/bacdive16539.20230509.8.1

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 pusilla
  • full scientific name: Nonomuraea pusilla corrig. (Nonomura and Ohara 1971) Zhang et al. 1998

  • synonyms

    @refsynonym
    20215Actinomadura pusilla
    20215Nonomuria pusilla
    20215Microtetraspora pusilla

@ref: 10977

domain: Bacteria

phylum: Actinobacteria

class: Actinobacteria

order: Actinomycetales

family: Streptosporangiaceae

genus: Nonomuraea

species: Nonomuraea pusilla

full scientific name: Nonomuraea pusilla (Nonomura and Ohara 1971) Zhang et al. 1998 emend. Nouioui et al. 2018

strain designation: A-118, A3, KCCA-0144

type strain: yes

Morphology

cell morphology

@refgram stainconfidencecell shapemotility
69480positive100
122064positiverod-shapedno

multimedia

@refmultimedia contentcaptionintellectual property rights
10977https://www.dsmz.de/microorganisms/photos/DSM_43357.jpgMedium 65 37°C© Leibniz-Institut DSMZ
66793EM_DSM_43357_1.jpgelectron microscopic image© HZI/Manfred Rohde
66793EM_DSM_43357_2.jpgelectron microscopic image© HZI/Manfred Rohde
66793EM_DSM_43357_3.jpgelectron microscopic image© HZI/Manfred Rohde
66793EM_DSM_43357_4.jpgelectron microscopic image© HZI/Manfred Rohde
66793EM_DSM_43357_5.jpgelectron microscopic image© HZI/Manfred Rohde

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
10977CZAPEK PEPTONE AGAR (DSMZ Medium 83)yeshttps://mediadive.dsmz.de/medium/83Name: CZAPEK PEPTONE AGAR (DSMZ Medium 83) Composition: Sucrose 30.0 g/l Agar 20.0 g/l Peptone 5.0 g/l NaNO3 3.0 g/l Yeast extract 2.0 g/l K2HPO4 1.0 g/l MgSO4 x 7 H2O 0.5 g/l KCl 0.5 g/l FeSO4 x 7 H2O 0.01 g/l Distilled water
37279MEDIUM 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)
10977GYM 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
122064CIP Medium 57yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=57

culture temp

@refgrowthtypetemperaturerange
37279positivegrowth37mesophilic
10977positivegrowth37mesophilic
67770positivegrowth28mesophilic
122064positivegrowth22-41
122064nogrowth5psychrophilic
122064nogrowth15psychrophilic

Physiology and metabolism

oxygen tolerance

  • @ref: 122064
  • oxygen tolerance: obligate aerobe

spore formation

@refspore formationconfidence
69481yes100
69480yes100

compound production

@refcompound
10977actitiocin
20216Actinotiocin

halophily

@refsaltgrowthtested relationconcentration
122064NaClpositivegrowth0-2 %
122064NaClnogrowth4 %
122064NaClnogrowth6 %
122064NaClnogrowth8 %
122064NaClnogrowth10 %

observation

  • @ref: 67770
  • observation: quinones: MK-9(H4), MK-9(H6), MK-9(H4), MK-9(H2)

metabolite utilization

@refmetaboliteutilization activitykind of utilization testedChebi-ID
68371Potassium 2-ketogluconate-builds acid from
68371gluconate-builds acid from24265
68371L-arabitol-builds acid from18403
68371D-arabitol-builds acid from18333
68371D-tagatose-builds acid from16443
68371D-lyxose-builds acid from62318
68371turanose-builds acid from32528
68371gentiobiose-builds acid from28066
68371xylitol-builds acid from17151
68371glycogen-builds acid from28087
68371starch-builds acid from28017
68371raffinose-builds acid from16634
68371melezitose-builds acid from6731
68371inulin-builds acid from15443
68371melibiose-builds acid from28053
68371lactose-builds acid from17716
68371amygdalin-builds acid from27613
68371N-acetylglucosamine-builds acid from59640
68371methyl alpha-D-glucopyranoside-builds acid from320061
68371methyl alpha-D-mannoside-builds acid from43943
68371D-sorbitol-builds acid from17924
68371D-mannitol-builds acid from16899
68371myo-inositol-builds acid from17268
68371galactitol-builds acid from16813
68371L-sorbose-builds acid from17266
68371D-mannose-builds acid from16024
68371D-glucose-builds acid from17634
68371D-galactose-builds acid from12936
68371methyl beta-D-xylopyranoside-builds acid from74863
68371ribitol-builds acid from15963
68371L-xylose-builds acid from65328
68371glycerol-builds acid from17754
122064esculin-hydrolysis4853
122064nitrate+reduction17632
122064nitrite-reduction16301
122064nitrate-respiration17632

antibiotic resistance

  • @ref: 122064
  • metabolite: 0129 (2,4-Diamino-6,7-di-iso-propylpteridine phosphate)
  • is antibiotic: yes
  • is sensitive: no
  • is resistant: yes

metabolite production

@refmetaboliteproductionChebi-ID
67770actinotiocinyes
122064indoleno35581

metabolite tests

  • @ref: 122064
  • Chebi-ID: 17234
  • metabolite: glucose
  • methylred-test: -

enzymes

@refvalueactivityec
122064oxidase-
122064beta-galactosidase+3.2.1.23
122064alcohol dehydrogenase-1.1.1.1
122064gelatinase+/-
122064amylase-
122064DNase-
122064caseinase-3.4.21.50
122064catalase-1.11.1.6
122064tween esterase-
122064gamma-glutamyltransferase+2.3.2.2
122064lysine decarboxylase-4.1.1.18
122064ornithine decarboxylase-4.1.1.17
122064phenylalanine ammonia-lyase-4.3.1.24
122064tryptophan deaminase-
122064urease-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+
68382cystine arylamidase-3.4.11.3
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
68382alpha-fucosidase-3.2.1.51

API zym

@refControlAlkaline phosphataseEsteraseEsterase LipaseLipaseLeucine arylamidaseValine arylamidaseCystine arylamidaseTrypsinalpha- ChymotrypsinAcid phosphataseNaphthol-AS-BI-phosphohydrolasealpha- Galactosidasebeta- Galactosidasebeta- Glucuronidasealpha- Glucosidasebeta- GlucosidaseN-acetyl-beta- glucosaminidasealpha- Mannosidasealpha- Fucosidase
122064-++++++-++++-+-+-++-

API 50CHac

@refGLYERYDARALARARIBDXYLLXYLADOMDXGALGLUFRUMNESBERHADULINOMANSORMDMMDGNAGAMYARBESCSALCELMALLACMELSACTREINUMLZRAFAMDGLYGXLTGENTURLYXTAGDFUCLFUCDARLLARLGNT2KG5KG
122064-+/-+/-+/-+/-+/------+/---+/---------+/-+/-+/-+/-+/---+/-+/-----------+/-+/-----+/-

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinent
10977soil
67770Soil, dry-heatedYamanashi Pref.JapanJPNAsia
122064Environment, SoilJapanJPNAsia

isolation source categories

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

taxonmaps

  • @ref: 69479
  • File name: preview.99_6928.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_239;96_3254;97_3993;98_5096;99_6928&stattab=map
  • Last taxonomy: Nonomuraea pusilla subclade
  • 16S sequence: U48978
  • Sequence Identity:
  • Total samples: 1377
  • soil counts: 1122
  • aquatic counts: 31
  • animal counts: 43
  • plant counts: 181

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
109771Risk group (German classification)
1220641Risk group (French classification)

Sequence information

16S sequences

@refdescriptionaccessionlengthdatabaseNCBI tax ID
20218Microtetraspora pusilla strain ATCC27296 16S ribosomal RNA gene, partial sequenceAF05138477ena46177
20218Microtetraspora pusilla strain ATCC27296 16S ribosomal RNA gene, partial sequenceAF051391193ena46177
20218Nonomuraea pusilla gene for 16S ribosomal RNA, partial sequenceD854911471ena46177
20218Microtetraspora pusilla 16S rRNA geneU489781414ena46177

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Nonomuraea pusilla strain DSM 4335746177.4wgspatric46177
66792Nonomuraea pusilla DSM 433572599185218draftimg46177
67770Nonomuraea pusilla DSM 43357GCA_900109355scaffoldncbi46177

GC content

@refGC-contentmethod
6777072.4genome sequence analysis
6777068thermal denaturation, midpoint method (Tm)
6777068.3thermal denaturation, midpoint method (Tm)

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingyes100no
gram-positiveyes86.679no
anaerobicno98.993no
halophileno92.537no
spore-formingyes94.173no
glucose-utilyes86.405no
aerobicyes91.733no
flagellatedno98.033no
thermophileno97.634yes
motileno91.528no
glucose-fermentno91.504no

External links

@ref: 10977

culture collection no.: DSM 43357, ATCC 27296, CBS 262.72, IFO 14684, KCC A-0144, NBRC 14684, NCIMB 11116, JCM 3144, BCRC 11619, CECT 3284, CIP 106954, IMET 9586, IMSNU 20095, KCTC 9278, MTCC 1121, NBIMCC 1641, NRRL B-16126, VKM Ac-1508

straininfo link

  • @ref: 85569
  • straininfo: 389339

Reference

@idauthorscataloguedoi/urltitlejournalpubmed
10977Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 43357)https://www.dsmz.de/collection/catalogue/details/culture/DSM-43357
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
20216Curators of the HKIhttp://www.leibniz-hki.de/de/Collection Description Leibniz-Institut für Naturstoff-Forschung und Infektionsbiologie e. V. Hans-Knöll-Institut (HKI)
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
37279Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/19141
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)
66793Mukherjee et al.10.1038/nbt.3886GEBA: 1,003 reference genomes of bacterial and archaeal isolates expand coverage of the tree of life 35: 676-683 201728604660
66794Antje Chang, Lisa Jeske, Sandra Ulbrich, Julia Hofmann, Julia Koblitz, Ida Schomburg, Meina Neumann-Schaal, Dieter Jahn, Dietmar Schomburg10.1093/nar/gkaa1025BRENDA, the ELIXIR core data resource in 2021: new developments and updatesNucleic Acids Res. 49: D498-D508 202033211880
67770Curators of the JCMhttps://jcm.brc.riken.jp/en/
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
85569Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID389339.1StrainInfo: A central database for resolving microbial strain identifiers
122064Curators of the CIPCollection of Institut Pasteur (CIP 106954)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20106954