Strain identifier

BacDive ID: 11075

Type strain: Yes

Species: Kribbella swartbergensis

Strain Designation: HMC25

Strain history: CIP <- 2006, DSMZ <- P.R. Meyers, Cape Town Univ., Cape Town, South Africa: strain HMC25 <- M. Le Roes

NCBI tax ID(s): 324852 (species)

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General

@ref: 6909

BacDive-ID: 11075

DSM-Number: 17345

keywords: 16S sequence, Bacteria, aerobe, spore-forming, mesophilic, Gram-positive, rod-shaped

description: Kribbella swartbergensis HMC25 is an aerobe, spore-forming, mesophilic bacterium that builds an aerial mycelium and was isolated from soil.

NCBI tax id

  • NCBI tax id: 324852
  • Matching level: species

strain history

@refhistory
6909<- P. R. Meyers; HMC25 <- M. le Roes
67770DSM 17345 <-- P. R. Meyers HMC25.
123395CIP <- 2006, DSMZ <- P.R. Meyers, Cape Town Univ., Cape Town, South Africa: strain HMC25 <- M. Le Roes

doi: 10.13145/bacdive11075.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/actinomycetota
  • domain: Bacteria
  • phylum: Actinomycetota
  • class: Actinomycetes
  • order: Propionibacteriales
  • family: Kribbellaceae
  • genus: Kribbella
  • species: Kribbella swartbergensis
  • full scientific name: Kribbella swartbergensis Kirby et al. 2006

@ref: 6909

domain: Bacteria

phylum: Actinobacteria

class: Actinobacteria

order: Actinomycetales

family: Kribbellaceae

genus: Kribbella

species: Kribbella swartbergensis

full scientific name: Kribbella swartbergensis Kirby et al. 2006

strain designation: HMC25

type strain: yes

Morphology

cell morphology

  • @ref: 31641
  • gram stain: positive
  • cell shape: rod-shaped
  • motility: no

colony morphology

@refcolony colorincubation periodmedium used
19746Beige (1001)10-14 daysISP 2
19746Beige (1001)10-14 daysISP 3
19746Beige (1001)10-14 daysISP 4
19746Beige (1001)10-14 daysISP 5
19746Beige (1001)10-14 daysISP 6
19746Beige (1001)10-14 daysISP 7

multicellular morphology

@refforms multicellular complexcomplex namecomplex colormedium name
19746yesAerial MyceliumCreamISP 2
19746yesAerial MyceliumCreamISP 3
19746noISP 4
19746yesAerial MyceliumCreamISP 5
19746noISP 6
19746noISP 7

pigmentation

  • @ref: 31641
  • production: yes

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
6909R2A MEDIUM (DSMZ Medium 830)yeshttps://mediadive.dsmz.de/medium/830Name: R2A MEDIUM (DSMZ Medium 830) Composition: Agar 15.0 g/l Casamino acids 0.5 g/l Starch 0.5 g/l Glucose 0.5 g/l Proteose peptone 0.5 g/l Yeast extract 0.5 g/l K2HPO4 0.3 g/l Na-pyruvate 0.3 g/l MgSO4 x 7 H2O 0.05 g/l Distilled water
19746ISP 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
19746ISP 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:
19746ISP 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
19746ISP 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
19746ISP 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
19746ISP 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
123395CIP Medium 372yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=372

culture temp

@refgrowthtypetemperaturerange
6909positivegrowth28mesophilic
19746positiveoptimum28mesophilic
31641positivegrowth20-45
31641positiveoptimum30-45
67770positivegrowth28mesophilic

culture pH

@refabilitytypepHPH range
31641positivegrowth07-09alkaliphile
31641positiveoptimum07-09

Physiology and metabolism

oxygen tolerance

  • @ref: 31641
  • oxygen tolerance: aerobe

spore formation

  • @ref: 31641
  • spore formation: yes

halophily

@refsaltgrowthtested relationconcentration
31641NaClpositivegrowth02-04 %
31641NaClpositiveoptimum02-03 %

observation

  • @ref: 31641
  • observation: aggregates in chains

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
3164128757fructose+carbon source
3164117234glucose+carbon source
3164117306maltose+carbon source
3164128053melibiose+carbon source
3164130911sorbitol+carbon source
3164117992sucrose+carbon source
316414853esculin+hydrolysis
3164117632nitrate+reduction
6837917632nitrate-reduction
683794853esculin+hydrolysis
6837916199urea-hydrolysis
683795291gelatin+hydrolysis
6837917634D-glucose-fermentation
6837916988D-ribose-fermentation
6837965327D-xylose-fermentation
6837916899D-mannitol-fermentation
6837917306maltose-fermentation
6837917716lactose-fermentation
6837917992sucrose-fermentation
6837928087glycogen-fermentation

metabolite production

  • @ref: 31641
  • Chebi-ID: 16136
  • metabolite: hydrogen sulfide
  • production: yes

enzymes

@refvalueactivityec
31641catalase+1.11.1.6
68379gelatinase+
68379urease-3.5.1.5
68379beta-glucosidase+3.2.1.21
68379N-acetyl-beta-glucosaminidase+3.2.1.52
68379alpha-glucosidase-3.2.1.20
68379beta-galactosidase+3.2.1.23
68379beta-glucuronidase-3.2.1.31
68379alkaline phosphatase+3.1.3.1
68379pyrrolidonyl arylamidase+3.4.19.3
68379pyrazinamidase-3.5.1.B15
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 coryne

@refNITPYZPYRAPALbeta GURbeta GALalpha GLUbeta NAGESCUREGELGLURIBXYLMANMALLACSACGLYG
19746--++-+-++-+--------

API zym

@refAlkaline phosphataseEsteraseEsterase LipaseLipaseLeucine arylamidaseValine arylamidaseCystine arylamidaseTrypsinalpha- ChymotrypsinAcid phosphataseNaphthol-AS-BI-phosphohydrolasealpha- Galactosidasebeta- Galactosidasebeta- Glucuronidasealpha- Glucosidasebeta- GlucosidaseN-acetyl-beta- glucosaminidasealpha- Mannosidasealpha- Fucosidase
19746++++++----+-+-+++++

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinent
6909soilDie Hel,banks of the river GamkaSouth AfricaZAFAfrica
67770Soil from the banks of the River GamkaDie Hel in Groot Swartberg mountain range, Western Cape ProvinceSouth AfricaZAFAfrica
123395Environment, SoilThe banks of the River Gamka, Western Cape provinceSouth AfricaZAFAfrica

isolation source categories

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

taxonmaps

  • @ref: 69479
  • File name: preview.99_8461.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_142;96_440;97_503;98_578;99_8461&stattab=map
  • Last taxonomy: Kribbella
  • 16S sequence: AY995147
  • Sequence Identity:
  • Total samples: 3588
  • soil counts: 2798
  • aquatic counts: 101
  • animal counts: 158
  • plant counts: 531

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
69091Risk group (German classification)
197461Risk group (German classification)
1233951Risk group (French classification)

Sequence information

16S sequences

@refdescriptionaccessionlengthdatabaseNCBI tax ID
31641Kribbella swartbergensis strain HMC25 16S ribosomal RNA gene, partial sequenceAY9951471422nuccore324852
6909Kribbella swartbergensis partial 16S rRNA gene, strain DSM 17345FN6432231346ena324852

External links

@ref: 6909

culture collection no.: DSM 17345, CIP 109291, NBRC 101885, NRRL B-24426, JCM 14305, BCRC 16843

straininfo link

  • @ref: 80324
  • straininfo: 290980

literature

  • topic: Phylogeny
  • Pubmed-ID: 16627661
  • title: Kribbella karoonensis sp. nov. and Kribbella swartbergensis sp. nov., isolated from soil from the Western Cape, South Africa.
  • authors: Kirby BM, Roes ML, Meyers PR
  • journal: Int J Syst Evol Microbiol
  • DOI: 10.1099/ijs.0.63951-0
  • year: 2006
  • mesh: Actinomycetales/chemistry/*classification/*isolation & purification/physiology, Anaerobiosis, Anti-Bacterial Agents/pharmacology, Bacterial Typing Techniques, Carbohydrates/analysis, DNA Fingerprinting, DNA Restriction Enzymes/metabolism, DNA, Bacterial/chemistry/genetics/metabolism, DNA, Ribosomal/chemistry/genetics, Diaminopimelic Acid/analysis, Genes, rRNA, Glycine/analysis, Growth Inhibitors/pharmacology, Molecular Sequence Data, Peptidoglycan/chemistry, Phylogeny, RNA, Bacterial/genetics, RNA, Ribosomal, 16S/genetics, Sodium Chloride/pharmacology, *Soil Microbiology, South Africa
  • topic2: Enzymology

Reference

@idauthorscataloguedoi/urltitleID_cross_referencepubmed
6909Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 17345)https://www.dsmz.de/collection/catalogue/details/culture/DSM-17345
19746Wink, J.http://www.dsmz.de/microorganisms/wink_pdf/DSM17345.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
31641Barberan A, Caceres Velazquez H, Jones S, Fierer N.10.1128/mSphere.00237-17Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information2792428776041
67770Curators of the JCMhttps://jcm.brc.riken.jp/en/
68379Automatically annotated from API Coryne
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
80324Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID290980.1StrainInfo: A central database for resolving microbial strain identifiers
123395Curators of the CIPCollection of Institut Pasteur (CIP 109291)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20109291