Strain identifier

BacDive ID: 17006

Type strain: Yes

Species: Actinoallomurus spadix

Strain Designation: FYU A 116, A-116

Strain history: CIP <- 1998, JCM <- KCC: strain A-0146 <- H. Nonomura: strain A-116

NCBI tax ID(s): 79912 (species)

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General

@ref: 11035

BacDive-ID: 17006

DSM-Number: 43459

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

description: Actinoallomurus spadix FYU A 116 is an aerobe, mesophilic, Gram-positive bacterium that was isolated from soil.

NCBI tax id

  • NCBI tax id: 79912
  • Matching level: species

strain history

@refhistory
11035<- M. Goodfellow <- KCC <- H. Nonomura, FYU, A 116
67770KCC A-0146 <-- H. Nonomura A-116.
67771<- NCIMB <- H Nonomura A-116
122686CIP <- 1998, JCM <- KCC: strain A-0146 <- H. Nonomura: strain A-116

doi: 10.13145/bacdive17006.20250331.9.3

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/actinomycetota
  • domain: Bacteria
  • phylum: Actinomycetota
  • class: Actinomycetes
  • order: Streptosporangiales
  • family: Thermomonosporaceae
  • genus: Actinoallomurus
  • species: Actinoallomurus spadix
  • full scientific name: Actinoallomurus spadix (Nonomura and Ohara 1971) Tamura et al. 2009

  • synonyms

    • @ref: 20215
    • synonym: Actinomadura spadix

@ref: 11035

domain: Bacteria

phylum: Actinobacteria

class: Actinobacteria

order: Actinomycetales

family: Thermomonosporaceae

genus: Actinoallomurus

species: Actinoallomurus spadix

full scientific name: Actinoallomurus spadix (Nonomura and Ohara 1971) Tamura et al. 2009

strain designation: FYU A 116, A-116

type strain: yes

Morphology

cell morphology

@refgram staincell shapemotility
67771positive
122686positiverod-shapedno

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
11035ISP2 MEDIUM (DSMZ Medium 987)yeshttps://mediadive.dsmz.de/medium/987Name: ISP 2 MEDIUM (DSMZ Medium 987) Composition: Agar 20.0 g/l Malt extract 10.0 g/l Dextrose 4.0 g/l Yeast extract 4.0 g/l Distilled water
32726MEDIUM 116 - for Streptomyces, Nocardia, Streptosporangium and Mycobacterium chlorophenolicumyesDistilled water make up to (1000.000 ml);Agar (20.000 g);Glucose (4.000g);Yeast extract (4.000 g);Malt extract (10.000 g)
11035GYM 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
122686CIP Medium 194yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=194
122686CIP Medium 116yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=116

culture temp

@refgrowthtypetemperature
18494positiveoptimum28
32726positivegrowth37
11035positivegrowth37
67770positivegrowth37
67771positivegrowth37
122686positivegrowth15-41
122686nogrowth5

Physiology and metabolism

oxygen tolerance

  • @ref: 67771
  • oxygen tolerance: aerobe

halophily

@refsaltgrowthtested relationconcentration
18494NaClpositivemaximum2.5 %
122686NaClpositivegrowth0 %
122686NaClnogrowth2 %
122686NaClnogrowth4 %
122686NaClnogrowth6 %
122686NaClnogrowth8 %
122686NaClnogrowth10 %

observation

@refobservation
67770quinones: MK-9(H8), MK-9(H6), MK-9(H4)
67771quinones: MK-9(H_8_), MK-9(H_6_), MK-9(H_4_)

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
1849417234glucose+
1849422599arabinose+/-
1849417992sucrose+/-
1849418222xylose+/-
1849417268myo-inositol+/-
1849429864mannitol+/-
1849428757fructose+/-
1849426546rhamnose+/-
1849416634raffinose+/-
1849462968cellulose+/-
1226864853esculin+hydrolysis
12268617632nitrate+reduction
12268616301nitrite-reduction
6837127613amygdalin-builds acid from
68371320061methyl alpha-D-glucopyranoside-builds acid from
6837117113erythritol-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
683716731melezitose-builds acid from
6837115443inulin-builds acid from
6837117814salicin-builds acid from
6837118305arbutin-builds acid from
6837159640N-acetylglucosamine-builds acid from
6837143943methyl alpha-D-mannoside-builds acid from
6837117924D-sorbitol-builds acid from
6837117268myo-inositol-builds acid from
6837116813galactitol-builds acid from
6837117266L-sorbose-builds acid from
6837174863methyl beta-D-xylopyranoside-builds acid from
6837165328L-xylose-builds acid from
683685291gelatin+hydrolysis
6836827897tryptophan-energy source
6836816199urea-hydrolysis
6836816947citrate-assimilation
6836818257ornithine-degradation
6836825094lysine-degradation
6836829016arginine-hydrolysis

antibiotic resistance

  • @ref: 122686
  • metabolite: 0129 (2,4-Diamino-6,7-di-iso-propylpteridine phosphate)
  • is antibiotic: yes
  • is sensitive: yes
  • is resistant: no

metabolite production

@refChebi-IDmetaboliteproduction
12268635581indoleno
6836815688acetoinyes
6836835581indoleno
6836816136hydrogen sulfideno

metabolite tests

@refChebi-IDmetabolitevoges-proskauer-testindole testmethylred-test
6836815688acetoin+
6836835581indole-
12268615688acetoin-
12268617234glucose-

enzymes

@refvalueactivityec
68382alpha-glucosidase+3.2.1.20
68382beta-glucuronidase-3.2.1.31
68382alpha-chymotrypsin-3.4.21.1
68382valine arylamidase-
68382lipase (C 14)-
68382leucine arylamidase+3.4.11.1
68382esterase (C 4)-
122686oxidase-
122686beta-galactosidase-3.2.1.23
122686alcohol dehydrogenase-1.1.1.1
122686gelatinase-
122686amylase-
122686caseinase+3.4.21.50
122686catalase+1.11.1.6
122686gamma-glutamyltransferase-2.3.2.2
122686lysine decarboxylase-4.1.1.18
122686ornithine decarboxylase-4.1.1.17
122686phenylalanine ammonia-lyase-4.3.1.24
122686tryptophan deaminase-
122686urease-3.5.1.5
68368lysine decarboxylase-4.1.1.18
68368arginine dihydrolase-3.5.3.6
68382alpha-fucosidase-3.2.1.51
68382alpha-mannosidase-3.2.1.24
68382N-acetyl-beta-glucosaminidase+3.2.1.52
68382beta-glucosidase-3.2.1.21
68382naphthol-AS-BI-phosphohydrolase+
68382acid phosphatase+3.1.3.2
68368gelatinase+
68368tryptophan deaminase-4.1.99.1
68368urease-3.5.1.5
68368ornithine decarboxylase-4.1.1.17
68368beta-galactosidase-3.2.1.23

API zym

@refAlkaline phosphataseEsteraseEsterase LipaseLipaseLeucine arylamidaseValine arylamidaseCystine arylamidaseTrypsinalpha- ChymotrypsinAcid phosphataseNaphthol-AS-BI-phosphohydrolasealpha- Galactosidasebeta- Galactosidasebeta- Glucuronidasealpha- Glucosidasebeta- GlucosidaseN-acetyl-beta- glucosaminidasealpha- Mannosidasealpha- FucosidaseControl
18494+-+-+-++-++++-+-+--
122686----+----++---+-+---

API 20E

@refONPGADH ArgLDC LysODCCITH2SURETDA TrpINDVPGEL
18494---------++

API 50CHac

@refGLYERYDARALARARIBDXYLLXYLADOMDXGALGLUFRUMNESBERHADULINOMANSORMDMMDGNAGAMYARBESCSALCELMALLACMELSACTREINUMLZRAFAMDGLYGXLTGENTURLYXTAGDFUCLFUCDARLLARLGNT2KG5KG
122686+/--+/-+/-+/-+/--+/--+/-+/-+/-+/--+/---+/-------+/--+/-+/-+/-+/-+/-+/---+/-+/-+/-+/-+/-+/-+/---+/-----+/-

Isolation, sampling and environmental information

isolation

@refsample typecountryorigin.countrycontinentgeographic location
11035soilJapanJPNAsia
67770Soil, dry-heatedJapanJPNAsiaYamanashi Pref.
67771From soil , dry-heatedJapanJPNAsiaYamanashi Pref.
122686Environment, SoilJapanJPNAsiaYamanashi

isolation source categories

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

taxonmaps

  • @ref: 69479
  • File name: preview.99_67778.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_239;96_5383;97_6498;98_47763;99_67778&stattab=map
  • Last taxonomy: Actinoallomurus spadix subclade
  • 16S sequence: AJ293712
  • Sequence Identity:
  • Total samples: 426
  • soil counts: 392
  • aquatic counts: 6
  • animal counts: 26
  • plant counts: 2

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
184941German classification
110351Risk group (German classification)
1226861Risk group (French classification)

Sequence information

16S sequences

@refdescriptionaccessionlengthdatabaseNCBI tax ID
20218Actinomadura spadix strain ATCC27298 16S ribosomal RNA gene, partial sequenceAF051380118nuccore79912
20218Actinomadura spadix 16S ribosomal RNA gene, partial sequenceAF1631201458nuccore79912
20218Actinomadura spadix 16S-23S ribosomal RNA intergenic spacer sequenceAF163131395nuccore79912
11035Actinoallomurus spadix gene for 16S rRNA, partial sequence, strain: NBRC 14099AB3645811449nuccore79912
67770Actinomadura spadix partial 16S rRNA gene, strain IMSNU 20015TAJ2937121488nuccore79912

Genome sequences

  • @ref: 66792
  • description: Actinoallomurus spadix KCTC 9252
  • accession: GCA_024055725
  • assembly level: contig
  • database: ncbi
  • NCBI tax ID: 79912

GC content

@refGC-contentmethod
1103574
6777166.4thermal denaturation, midpoint method (Tm)
6777074high performance liquid chromatography (HPLC)

Genome-based predictions

predictions

@refmodeltraitdescriptionpredictionconfidencetraining_data
125438gram-positivegram-positivePositive reaction to Gram-stainingyes89.252yes
125438anaerobicanaerobicAbility to grow under anoxygenic conditions (including facultative anaerobes)no90.312yes
125438aerobicaerobicAbility to grow under oxygenic conditions (including facultative aerobes)yes87.759yes
125438spore-formingspore-formingAbility to form endo- or exosporesyes89.334no
125438thermophilethermophilicAbility to grow at temperatures above or equal to 45°Cno96.25yes
125438motile2+flagellatedAbility to perform flagellated movementno88no

External links

@ref: 11035

culture collection no.: DSM 43459, ATCC 27298, BCRC 13386, CBS 261.72, CIP 105479, IFO 14099, IMET 9752, JCM 3146, KCC A-0146, KCTC 9252, NBRC 14099, NCIB 11118, NRRL B-16128, IMSNU 20015, MTCC 2556, NCIMB 11118, CCRC 13386, BRCC 13386

straininfo link

  • @ref: 86007
  • straininfo: 389340

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny19567582Transfer of Actinomadura spadix Nonomura and Ohara 1971 to Actinoallomurus spadix gen. nov., comb. nov., and description of Actinoallomurus amamiensis sp. nov., Actinoallomurus caesius sp. nov., Actinoallomurus coprocola sp. nov., Actinoallomurus fulvus sp. nov., Actinoallomurus iriomotensis sp. nov., Actinoallomurus luridus sp. nov., Actinoallomurus purpureus sp. nov. and Actinoallomurus yoronensis sp. nov.Tamura T, Ishida Y, Nozawa Y, Otoguro M, Suzuki KInt J Syst Evol Microbiol10.1099/ijs.0.006858-02009Actinomycetales/chemistry/*classification/genetics/*isolation & purification, Amino Acids/analysis, Bacterial Typing Techniques, Cluster Analysis, DNA, Bacterial/chemistry/genetics, DNA, Ribosomal/chemistry/genetics, Fatty Acids/analysis, Japan, Molecular Sequence Data, Peptidoglycan/chemistry, Phylogeny, Quinones/analysis, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, *Soil Microbiology, Spores, Bacterial/cytologyGenetics
Phylogeny23002049Actinoallomurus acanthiterrae sp. nov., an actinomycete isolated from rhizosphere soil of the mangrove plant Acanthus ilicifolius.Tang YL, Lin HP, Xie QY, Li L, Peng F, Deng Z, Hong KInt J Syst Evol Microbiol10.1099/ijs.0.043380-02012Acanthaceae/*microbiology, Actinomycetales/*classification/genetics/isolation & purification, Bacterial Typing Techniques, Base Composition, China, DNA, Bacterial/genetics, Diaminopimelic Acid/analysis, Fatty Acids/analysis, Molecular Sequence Data, Nucleic Acid Hybridization, Peptidoglycan, Phospholipids/analysis, *Phylogeny, Plant Roots/microbiology, RNA, Ribosomal, 16S/genetics, *Rhizosphere, Sequence Analysis, DNA, *Soil Microbiology, Vitamin K 2/analogs & derivatives/analysisGenetics

Reference

@idauthorscataloguedoi/urltitlejournalpubmed
11035Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 43459)https://www.dsmz.de/collection/catalogue/details/culture/DSM-43459
18494Wink, J.http://www.dsmz.de/microorganisms/wink_pdf/DSM43459.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
32726Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/17503
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/
67771Curators of the KCTChttps://kctc.kribb.re.kr/En/Kctc
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
86007Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID389340.1StrainInfo: A central database for resolving microbial strain identifiers
122686Curators of the CIPCollection of Institut Pasteur (CIP 105479)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20105479
125438Julia Koblitz, Lorenz Christian Reimer, Rüdiger Pukall, Jörg Overmann10.1101/2024.08.12.607695Predicting bacterial phenotypic traits through improved machine learning using high-quality, curated datasets