Strain identifier

BacDive ID: 7833

Type strain: Yes

Species: Actinoplanes humidus

Strain Designation: LA 6

Strain history: M. Goodfellow LA6.

NCBI tax ID(s): 113566 (species)

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General

@ref: 11388

BacDive-ID: 7833

DSM-Number: 43938

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

description: Actinoplanes humidus LA 6 is a spore-forming, mesophilic bacterium that was isolated from sediment.

NCBI tax id

  • NCBI tax id: 113566
  • Matching level: species

strain history

@refhistory
11388<- NCIMB <- M. Goodfellow, LA 6 <- L. J. Stanton
67770M. Goodfellow LA6.

doi: 10.13145/bacdive7833.20230509.8.1

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 humidus
  • full scientific name: Actinoplanes humidus Goodfellow et al. 1990

@ref: 11388

domain: Bacteria

phylum: Actinobacteria

class: Actinobacteria

order: Actinomycetales

family: Micromonosporaceae

genus: Actinoplanes

species: Actinoplanes humidus

full scientific name: Actinoplanes humidus Goodfellow et al. 1990

strain designation: LA 6

type strain: yes

Morphology

colony morphology

@refcolony colorincubation periodmedium used
19986Yellow orange (2000)10-14 daysISP 2
19986Yellow orange (2000)10-14 daysISP 3
19986Yellow orange (2000)10-14 daysISP 4
19986Yellow orange (2000)10-14 daysISP 5
19986Yellow orange (2000)10-14 daysISP 6
19986Yellow orange (2000)10-14 daysISP 7

multicellular morphology

@refforms multicellular complexmedium name
19986noISP 2
19986noISP 3
19986noISP 4
19986noISP 5
19986noISP 6
19986noISP 7

multimedia

  • @ref: 11388
  • multimedia content: https://www.dsmz.de/microorganisms/photos/DSM_43938.jpg
  • caption: Medium 83 28°C
  • intellectual property rights: © Leibniz-Institut DSMZ

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
11388CZAPEK 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
19986ISP 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
19986ISP 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:
19986ISP 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
19986ISP 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
19986ISP 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
19986ISP 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
11388BENNETT'S AGAR (DSMZ Medium 548)yeshttps://mediadive.dsmz.de/medium/548Name: BENNETT'S AGAR (DSMZ Medium 548) Composition: Agar 15.0 g/l Glucose 10.0 g/l N-Z amine 2.0 g/l Yeast extract 1.0 g/l Beef extract 1.0 g/l Distilled water
11388BENNETT'S MODIFIED MEDIUM (P. AGRAWAL, UNPUBLISHED) (DSMZ Medium 894)yeshttps://mediadive.dsmz.de/medium/894Name: BENNETT'S MODIFIED MEDIUM (P. AGRAWAL, UNPUBLISHED) (DSMZ Medium 894) Composition: Agar 15.0 g/l Lab-Lemco beef extract 10.0 g/l Glucose 10.0 g/l Tryptose 2.0 g/l Yeast extract 2.0 g/l CaCO3 0.1 g/l Starch 0.1 g/l CoCl2 Ferric ammonium citrate Distilled water
11388N-Z-AMINE-MEDIUM (DSMZ Medium 554)yeshttps://mediadive.dsmz.de/medium/554Name: N-Z-AMINE-MEDIUM (DSMZ Medium 554) Composition: Starch 20.0 g/l Agar 20.0 g/l Glucose 10.0 g/l N-Z amine 5.0 g/l Yeast extract 5.0 g/l CaCO3 1.0 g/l Distilled water

culture temp

@refgrowthtypetemperaturerange
11388positivegrowth28mesophilic
19986positiveoptimum28mesophilic
67770positivegrowth28mesophilic

Physiology and metabolism

spore formation

  • @ref: 19986
  • spore description: Formation of sporangia, spore surface smooth
  • spore formation: yes

observation

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

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
1998617234glucose+
1998622599arabinose+
1998617992sucrose+
1998618222xylose-
1998617268myo-inositol-
1998629864mannitol+
1998628757fructose+
1998626546rhamnose+
1998616634raffinose-
1998662968cellulose-
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
19986+++-++++++++++++++-

API 20E

@refONPGADH ArgLDC LysODCCITH2SURETDA TrpINDVPGEL
19986+++++----++

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinent
11388sedimentDerwent riverUnited KingdomGBREurope
67770River sediment

isolation source categories

Cat1Cat2Cat3
#Environmental#Aquatic#Sediment
#Environmental#Terrestrial#Sediment

taxonmaps

  • @ref: 69479
  • File name: preview.99_127621.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_94;96_404;97_1769;98_2163;99_127621&stattab=map
  • Last taxonomy: Actinoplanes
  • 16S sequence: AJ277571
  • Sequence Identity:
  • Total samples: 365
  • soil counts: 80
  • aquatic counts: 16
  • animal counts: 24
  • plant counts: 245

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
113881Risk group (German classification)
199861German classification

Sequence information

16S sequences

@refdescriptionaccessionlengthdatabaseNCBI tax ID
20218Actinoplanes humidus gene for 16S rRNA, complete sequenceAB0370041471ena113566
20218Actinoplanes humidus partial 16S rRNA gene, strain IMSNU 22051TAJ2775711470ena113566

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Actinoplanes humidus NBRC 14915GCA_016862215contigncbi113566
66792Actinoplanes humidus strain NBRC 14915113566.3wgspatric113566

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
motileyes51.522no
flagellatedno90.595no
gram-positiveyes89.316no
anaerobicno99.33no
aerobicyes93.988no
halophileno96.549no
spore-formingyes92.256no
thermophileno99.224yes
glucose-utilyes90.308yes
glucose-fermentno88.999no

External links

@ref: 11388

culture collection no.: DSM 43938, ATCC 49801, IFO 14915, NBRC 14915, NCIMB 20000, JCM 7555, BCRC 16344, IMSNU 20031, KCTC 9656, NRRL B-16690

straininfo link

  • @ref: 77272
  • straininfo: 88615

Reference

@idauthorscataloguedoi/urltitlejournalpubmed
11388Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 43938)https://www.dsmz.de/collection/catalogue/details/culture/DSM-43938
19986Wink, J.http://www.dsmz.de/microorganisms/wink_pdf/DSM43938.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
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
77272Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID88615.1StrainInfo: A central database for resolving microbial strain identifiers