Strain identifier

BacDive ID: 7808

Type strain: Yes

Species: Actinoplanes lobatus

Strain Designation: UNCC 72

Strain history: KCC A-0061 <-- CBS 192.64 <-- J. N. Couch UNCC 72.

NCBI tax ID(s): 113568 (species)

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

@ref: 10820

BacDive-ID: 7808

DSM-Number: 43150

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

description: Actinoplanes lobatus UNCC 72 is a spore-forming, mesophilic, Gram-positive bacterium that was isolated from soil.

NCBI tax id

  • NCBI tax id: 113568
  • Matching level: species

strain history

@refhistory
10820<- KCC <- CBS <- J.N. Couch, UNCC, 72
67770KCC A-0061 <-- CBS 192.64 <-- J. N. Couch UNCC 72.

doi: 10.13145/bacdive7808.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/actinomycetota
  • domain: Bacteria
  • phylum: Actinomycetota
  • class: Actinomycetes
  • order: Micromonosporales
  • family: Micromonosporaceae
  • genus: Actinoplanes
  • species: Actinoplanes lobatus
  • full scientific name: Actinoplanes lobatus (Couch 1963) Stackebrandt and Kroppenstedt 1988
  • synonyms

    @refsynonym
    20215Ampullaria lobata
    20215Ampullariella lobata

@ref: 10820

domain: Bacteria

phylum: Actinobacteria

class: Actinobacteria

order: Actinomycetales

family: Micromonosporaceae

genus: Actinoplanes

species: Actinoplanes lobatus

full scientific name: Actinoplanes lobatus (Couch 1963) Stackebrandt and Kroppenstedt 1988

strain designation: UNCC 72

type strain: yes

Morphology

cell morphology

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

colony morphology

@refcolony colorincubation periodmedium used
19548Yellow orange10-14 daysISP 2
19548Yellow orange10-14 daysISP 3
19548Yellow orange10-14 daysISP 4
19548Yellow orange10-14 daysISP 5
19548Yellow orange10-14 daysISP 6
19548Yellow orange10-14 daysISP 7

multicellular morphology

@refforms multicellular complexmedium name
19548noISP 2
19548noISP 3
19548noISP 4
19548noISP 5
19548noISP 6
19548noISP 7

Culture and growth conditions

culture medium

@refnamegrowthcompositionlink
19548ISP 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
19548ISP 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:
19548ISP 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
19548ISP 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
19548ISP 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
19548ISP 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
10820CZAPEK PEPTONE AGAR (DSMZ Medium 83)yesName: 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 waterhttps://mediadive.dsmz.de/medium/83
10820GYM STREPTOMYCES MEDIUM (DSMZ Medium 65)yesName: 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 waterhttps://mediadive.dsmz.de/medium/65

culture temp

@refgrowthtypetemperaturerange
19548positiveoptimum28mesophilic
10820positivegrowth28mesophilic
67770positivegrowth28mesophilic

Physiology and metabolism

spore formation

@refspore descriptiontype of sporespore formationconfidence
19548Spore surface: smooth, sporangia: +sporeyes
69481yes100
69480yes100

halophily

  • @ref: 19548
  • salt: NaCl
  • growth: positive
  • tested relation: maximum
  • concentration: 2.5 %

observation

  • @ref: 67770
  • observation: quinones: MK-9(H4), MK-10(H4) , MK-9(H4)

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
683685291gelatin-hydrolysis
6836827897tryptophan-energy source
6836816199urea-hydrolysis
6836816947citrate-assimilation
6836818257ornithine-degradation
6836825094lysine-degradation
6836829016arginine-hydrolysis

metabolite production

@refChebi-IDmetaboliteproduction
6836815688acetoinno
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

API 20E

@refONPGADH ArgLDC LysODCCITH2SURETDA TrpINDVPGEL
19548-----------

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinent
10820soil
67770SoilMadison, WIUSAUSANorth America

isolation source categories

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

taxonmaps

  • @ref: 69479
  • File name: preview.99_83982.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_94;96_240;97_16361;98_20282;99_83982&stattab=map
  • Last taxonomy: Actinoplanes
  • 16S sequence: AB037006
  • Sequence Identity:
  • Total samples: 17
  • soil counts: 8
  • aquatic counts: 2
  • animal counts: 2
  • plant counts: 5

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
108201Risk group (German classification)
195481Risk group (German classification)

Sequence information

16S sequences

  • @ref: 20218
  • description: Actinoplanes lobatus gene for 16S rRNA, partial sequence
  • accession: AB037006
  • length: 1472
  • database: ena
  • NCBI tax ID: 113568

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Actinoplanes lobatus NBRC 12513GCA_016862255contigncbi113568
66792Actinoplanes lobatus DSM 43150GCA_014205215contigncbi113568
66792Actinoplanes lobatus JCM 3061GCA_014647815scaffoldncbi113568
66792Actinoplanes lobatus strain DSM 43150113568.3wgspatric113568
66792Actinoplanes lobatus strain JCM 3061113568.4wgspatric113568
66792Actinoplanes lobatus strain NBRC 12513113568.5wgspatric113568
66792Actinoplanes lobatus DSM 431502873296955draftimg113568

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingyes100no
flagellatedno89.954no
gram-positiveyes86.999no
anaerobicno98.554no
aerobicyes92.873no
halophileno95.11no
spore-formingyes92.085yes
thermophileno99.019no
glucose-utilyes88.617no
motileyes58.795no
glucose-fermentno86.766no

External links

@ref: 10820

culture collection no.: DSM 43150, ATCC 15350, CBS 192.64, IFO 12513, KCC A-0061, NBRC 12513, JCM 3061, IFM 0126, IFM 1240, IMET 9246, IMSNU 22063, KCTC 9348, NCIMB 12888, NRRL B-3346, VKM Ac-676

straininfo link

  • @ref: 77250
  • straininfo: 36343

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny23114571Actinoplanes hulinensis sp. nov., a novel actinomycete isolated from soybean root (Glycine max (L.) Merr).Shen Y, Liu C, Wang X, Zhao J, Jia F, Zhang Y, Wang L, Yang D, Xiang WAntonie Van Leeuwenhoek10.1007/s10482-012-9809-92012Bacterial Typing Techniques, Cluster Analysis, DNA, Bacterial/chemistry/genetics, DNA, Ribosomal/chemistry/genetics, Micromonosporaceae/*classification/genetics/*isolation & purification/physiology, Microscopy, Electron, Scanning, Molecular Sequence Data, Nucleic Acid Hybridization, Phylogeny, Plant Roots/*microbiology, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Soybeans/*microbiologyGenetics
24531391A novel teichuronic acid, the major polymer from the cell wall of Actinoplanes lobatus VKM Ac-676(T.).Shashkov AS, Streshinskaya GM, Tul'skaya EM, Kozlova YI, Senchenkova SN, Evtushenko LICarbohydr Res10.1016/j.carres.2013.08.0312013Actinomycetales/chemistry, Anions/chemistry, Cell Wall/*chemistry, Magnetic Resonance Spectroscopy, Polymers/*chemistry, *Protein Conformation, Uronic Acids/*chemistry
Phylogeny34499595Actinoplanes flavus sp. nov., a novel cellulase-producing actinobacterium isolated from coconut palm rhizosphere soil.Luo X, Sun X, Huang Z, He C, Zhao J, Xiang W, Song J, Wang XInt J Syst Evol Microbiol10.1099/ijsem.0.0049902021*Actinoplanes/classification/isolation & purification, Bacterial Typing Techniques, Base Composition, Cellulase, China, Cocos/*microbiology, DNA, Bacterial/genetics, Fatty Acids/chemistry, Phospholipids/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, *Rhizosphere, Sequence Analysis, DNA, *Soil Microbiology, Vitamin K 2/analogs & derivatives/chemistryTranscriptome

Reference

@idauthorscataloguedoi/urltitlejournalpubmed
10820Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 43150)https://www.dsmz.de/collection/catalogue/details/culture/DSM-43150
19548Wink, J.http://www.dsmz.de/microorganisms/wink_pdf/DSM43150.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
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
77250Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID36343.1StrainInfo: A central database for resolving microbial strain identifiers