Strain identifier

BacDive ID: 16991

Type strain: Yes

Species: Actinomadura rudentiformis

Strain Designation: HMC 1

Strain history: DSM 44962 <-- P. R. Meyers HMC1 <-- M. le Roes.

NCBI tax ID(s): 359158 (species)

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General

@ref: 12215

BacDive-ID: 16991

DSM-Number: 44962

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

description: Actinomadura rudentiformis HMC 1 is an aerobe, mesophilic, Gram-positive bacterium that was isolated from soil.

NCBI tax id

  • NCBI tax id: 359158
  • Matching level: species

strain history

@refhistory
12215<- P. R. Meyers; HMC 1 <- M. le Roes
67770DSM 44962 <-- P. R. Meyers HMC1 <-- M. le Roes.

doi: 10.13145/bacdive16991.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/actinomycetota
  • domain: Bacteria
  • phylum: Actinomycetota
  • class: Actinomycetes
  • order: Streptosporangiales
  • family: Thermomonosporaceae
  • genus: Actinomadura
  • species: Actinomadura rudentiformis
  • full scientific name: Actinomadura rudentiformis Le Roes and Meyers 2007

@ref: 12215

domain: Bacteria

phylum: Actinobacteria

class: Actinobacteria

order: Actinomycetales

family: Thermomonosporaceae

genus: Actinomadura

species: Actinomadura rudentiformis

full scientific name: Actinomadura rudentiformis le Roes and Meyers 2007

strain designation: HMC 1

type strain: yes

Morphology

cell morphology

  • @ref: 31825
  • gram stain: positive

colony morphology

@refcolony colorincubation periodmedium used
20146Brown beige (1011)10-14 daysISP 2
20146Beige (1001)10-14 daysISP 3
20146Beige (1001)10-14 daysISP 4
20146Beige (1001)10-14 daysISP 5
20146Beige (1001)10-14 daysISP 6
20146Beige (1001)10-14 daysISP 7

multicellular morphology

@refforms multicellular complexmedium name
20146noISP 2
20146noISP 3
20146noISP 4
20146noISP 5
20146noISP 6
20146noISP 7

pigmentation

  • @ref: 31825
  • production: no

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
12215N-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
12215GYM 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
12215GPHF-MEDIUM (DSMZ Medium 553)yeshttps://www.dsmz.de/microorganisms/medium/pdf/DSMZ_Medium553.pdf
20146ISP 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
20146ISP 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:
20146ISP 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
20146ISP 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
20146ISP 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
20146ISP 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
12215positivegrowth28mesophilic
20146positiveoptimum28mesophilic
31825positivegrowth30-45
31825positiveoptimum37.5mesophilic
67770positivegrowth28mesophilic

Physiology and metabolism

oxygen tolerance

  • @ref: 12215
  • oxygen tolerance: aerobe

spore formation

  • @ref: 31825
  • spore formation: no

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
3182530089acetate+carbon source
3182515963ribitol+carbon source
3182522599arabinose+carbon source
3182529016arginine+carbon source
3182517057cellobiose+carbon source
3182528757fructose+carbon source
3182528260galactose+carbon source
3182517234glucose+carbon source
3182527570histidine+carbon source
3182517716lactose+carbon source
3182529864mannitol+carbon source
3182537684mannose+carbon source
3182528053melibiose+carbon source
3182517268myo-inositol+carbon source
3182528044phenylalanine+carbon source
3182516634raffinose+carbon source
3182526546rhamnose+carbon source
3182533942ribose+carbon source
3182517814salicin+carbon source
3182517822serine+carbon source
3182517992sucrose+carbon source
3182526986threonine+carbon source
3182527082trehalose+carbon source
3182518222xylose+carbon source
318254853esculin+hydrolysis

enzymes

@refvalueactivityec
31825catalase+1.11.1.6
31825gelatinase+
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
20146+++-+++++++++--+++-

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinent
12215soilSwartberg nature reserveSouth AfricaZAFAfrica
67770Soil from the banks of the Gamka River in the Swartberg Nature ReserveWestern Cape ProvinceSouth AfricaZAFAfrica

isolation source categories

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

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
122151Risk group (German classification)
201461German classification

Sequence information

16S sequences

  • @ref: 12215
  • description: Actinomadura rudentiformis strain HMC1 16S ribosomal RNA gene, partial sequence
  • accession: DQ285420
  • length: 1433
  • database: ena
  • NCBI tax ID: 359158

External links

@ref: 12215

culture collection no.: DSM 44962, JCM 14907, NRRL B-24458

straininfo link

  • @ref: 85994
  • straininfo: 297112

literature

  • topic: Phylogeny
  • Pubmed-ID: 17220439
  • title: Actinomadura rudentiformis sp. nov., isolated from soil.
  • authors: le Roes M, Meyers PR
  • journal: Int J Syst Evol Microbiol
  • DOI: 10.1099/ijs.0.64438-0
  • year: 2007
  • mesh: Actinomycetales/*classification/genetics/isolation & purification/metabolism, Antibiosis, Bacterial Typing Techniques, DNA, Bacterial/analysis, DNA, Ribosomal/analysis, Enterococcus faecium/drug effects/growth & development, Escherichia coli/drug effects/growth & development, Genes, rRNA, Humans, Microbial Sensitivity Tests, Molecular Sequence Data, Mycobacterium/drug effects/growth & development, Phenotype, Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, *Soil Microbiology, South Africa
  • topic2: Pathogenicity

Reference

@idauthorscataloguedoi/urltitleID_cross_referencepubmed
12215Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 44962)https://www.dsmz.de/collection/catalogue/details/culture/DSM-44962
20146Wink, J.http://www.dsmz.de/microorganisms/wink_pdf/DSM44962.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
31825Barberan A, Caceres Velazquez H, Jones S, Fierer N.10.1128/mSphere.00237-17Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information2809128776041
67770Curators of the JCMhttps://jcm.brc.riken.jp/en/
68382Automatically annotated from API zym
85994Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID297112.1StrainInfo: A central database for resolving microbial strain identifiers