Strain identifier

BacDive ID: 8028

Type strain: Yes

Species: Spirilliplanes yamanashiensis

Strain Designation: YU 127-1

Strain history: IFO 15828 <-- M. Hayakawa YU127-1.

NCBI tax ID(s): 42233 (species)

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General

@ref: 11671

BacDive-ID: 8028

DSM-Number: 44325

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

description: Spirilliplanes yamanashiensis YU 127-1 is a spore-forming, mesophilic, Gram-positive bacterium that was isolated from soil sample.

NCBI tax id

  • NCBI tax id: 42233
  • Matching level: species

strain history

@refhistory
11671<- IFO
67770IFO 15828 <-- M. Hayakawa YU127-1.

doi: 10.13145/bacdive8028.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/actinomycetota
  • domain: Bacteria
  • phylum: Actinomycetota
  • class: Actinomycetes
  • order: Micromonosporales
  • family: Micromonosporaceae
  • genus: Spirilliplanes
  • species: Spirilliplanes yamanashiensis
  • full scientific name: Spirilliplanes yamanashiensis Tamura et al. 1997

@ref: 11671

domain: Bacteria

phylum: Actinobacteria

class: Actinobacteria

order: Actinomycetales

family: Micromonosporaceae

genus: Spirilliplanes

species: Spirilliplanes yamanashiensis

full scientific name: Spirilliplanes yamanashiensis Tamura et al. 1997

strain designation: YU 127-1

type strain: yes

Morphology

cell morphology

  • @ref: 69480
  • gram stain: positive
  • confidence: 100

colony morphology

@refcolony colorincubation periodmedium used
20045Yellow orange (2000)10-14 daysISP 2
20045Yellow orange (2000)10-14 daysISP 3
20045Yellow orange (2000)10-14 daysISP 4
20045Yellow orange (2000)10-14 daysISP 5
20045Yellow orange (2000)10-14 daysISP 6
20045Yellow orange (2000)10-14 daysISP 7

multicellular morphology

@refforms multicellular complexmedium name
20045noISP 2
20045noISP 3
20045noISP 4
20045noISP 5
20045noISP 6
20045noISP 7

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
11671GPHF-MEDIUM (DSMZ Medium 553)yeshttps://mediadive.dsmz.de/medium/553Name: GPHF-MEDIUM (DSMZ Medium 553) Composition: Agar 20.0 g/l Glucose 10.0 g/l Beef extract 5.0 g/l Yeast extract 5.0 g/l Casein peptone 5.0 g/l CaCl2 x 2 H2O 0.74 g/l Distilled water
11671GYM 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
20045ISP 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
20045ISP 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:
20045ISP 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
20045ISP 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
20045ISP 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
20045ISP 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

culture temp

@refgrowthtypetemperaturerange
20045positiveoptimum28mesophilic
11671positivegrowth28mesophilic
67770positivegrowth28mesophilic

Physiology and metabolism

spore formation

@refspore formationconfidence
69481yes92
69480yes99.525

halophily

  • @ref: 20045
  • salt: NaCl
  • growth: positive
  • tested relation: growth
  • concentration: 0 %

observation

  • @ref: 67770
  • observation: quinones: MK-10(H4), MK-10(H6), MK-10(H8)

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
2004517234glucose+
2004522599arabinose+/-
2004517992sucrose+
2004518222xylose+
2004517268myo-inositol-
2004529864mannitol+
2004528757fructose+
2004526546rhamnose+
2004516634raffinose+
2004562968cellulose+
683685291gelatin-hydrolysis
6836827897tryptophan-energy source
6836816199urea-hydrolysis
6836816947citrate-assimilation
6836818257ornithine-degradation
6836825094lysine-degradation
6836829016arginine-hydrolysis

metabolite production

@refChebi-IDmetaboliteproduction
6836815688acetoinyes
6836835581indoleno
6836816136hydrogen sulfideno

metabolite tests

@refChebi-IDmetabolitevoges-proskauer-testindole test
6836815688acetoin+
6836835581indole-

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
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

@refAlkaline phosphataseEsteraseEsterase LipaseLipaseLeucine arylamidaseValine arylamidaseCystine arylamidaseTrypsinalpha- ChymotrypsinAcid phosphataseNaphthol-AS-BI-phosphohydrolasealpha- Galactosidasebeta- Galactosidasebeta- Glucuronidasealpha- Glucosidasebeta- GlucosidaseN-acetyl-beta- glucosaminidasealpha- Mannosidasealpha- Fucosidase
20045+---+--+-+----+++--

API 20E

@refONPGADH ArgLDC LysODCCITH2SURETDA TrpINDVPGEL
20045---------+-

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinent
11671soil sampleYamanashi Prefecture, KofuJapanJPNAsia
67770SoilKofu, Yamanashi Pref.JapanJPNAsia

isolation source categories

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

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
116711Risk group (German classification)
200451German classification

Sequence information

16S sequences

@refdescriptionaccessionlengthdatabaseNCBI tax ID
20218Spirilliplanes yamanashiensis gene for 16S ribosomal RNA, partial sequenceD639121470ena42233
67770Spirilliplanes yamanashiensis gene for 16S ribosomal RNA, partial sequence, strain: JCM 10032LC0687791465ena42233

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Spirilliplanes yamanashiensis NBRC 15828GCA_016863475contigncbi42233
66792Spirilliplanes yamanashiensis strain NBRC 1582842233.3wgspatric42233
66792Spirilliplanes yamanashiensis DSM 443252923602881draftimg42233

GC content

@refGC-contentmethod
1167169
6777069high performance liquid chromatography (HPLC)

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingyes92no
gram-positiveyes88.464no
anaerobicno98.845no
halophileno95.574yes
spore-formingyes84.385no
glucose-utilyes88.971yes
aerobicyes92.144no
flagellatedno87.66no
thermophileno98.179yes
motileyes62.15no
glucose-fermentno90.478no

External links

@ref: 11671

culture collection no.: DSM 44325, IFO 15828, NBRC 15828, JCM 10032, CGMCC 4.5503, VKM Ac-1993

straininfo link

  • @ref: 77458
  • straininfo: 50567

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny8995810A new genus of the order Actinomycetales, Spirilliplanes gen. nov., with description of Spirilliplanes yamanashiensis sp. nov.Tamura T, Hayakawa M, Hatano KInt J Syst Bacteriol10.1099/00207713-47-1-971997Actinomyces/chemistry/*classification/genetics/ultrastructure, Alanine/analysis, Bacteriological Techniques, Base Composition, Cell Wall/chemistry, Culture Media/metabolism, Diaminopimelic Acid/analysis, Fatty Acids/analysis, Glucosamine/analysis, Glucose/analysis, Glutamic Acid/analysis, Glycine/analysis, Mannose/analysis, Methylmannosides/analysis, Microscopy, Electron, Scanning, Molecular Sequence Data, Mycolic Acids/analysis, Phospholipids/analysis, Phylogeny, Polymerase Chain Reaction, RNA, Ribosomal, 16S/genetics, Sequence Homology, Nucleic Acid, Soil Microbiology, Vitamin K/analysis, Xylose/analysisGenetics
11705473NMR-based identification of cell wall anionic polymers of Spirilliplanes yamanashiensis VKM Ac-1993(T).Shashkov AS, Streshinskaya GM, Evtushenko LI, Naumova IBCarbohydr Res10.1016/s0008-6215(01)00224-52001Actinomycetales/*chemistry, Cell Wall/*chemistry, Magnetic Resonance Spectroscopy, Micromonosporaceae/chemistry, Polysaccharides, Bacterial/*analysis/chemistry, Sugar Phosphates/chemistry, Teichoic Acids/chemistry

Reference

@idauthorscataloguedoi/urltitlejournalpubmed
11671Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 44325)https://www.dsmz.de/collection/catalogue/details/culture/DSM-44325
20045Wink, J.http://www.dsmz.de/microorganisms/wink_pdf/DSM44325.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
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
68382Automatically annotated from API zym
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
77458Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID50567.1StrainInfo: A central database for resolving microbial strain identifiers