Strain identifier

BacDive ID: 13292

Type strain: Yes

Species: Kibdelosporangium philippinense

Strain Designation: A80407

Strain history: ATCC 49844 <-- NRRL 18198 <-- F. P. Mertz A80407.

NCBI tax ID(s): 211113 (species)

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General

@ref: 11610

BacDive-ID: 13292

DSM-Number: 44226

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

description: Kibdelosporangium philippinense A80407 is a spore-forming, mesophilic bacterium that builds an aerial mycelium and was isolated from soil.

NCBI tax id

  • NCBI tax id: 211113
  • Matching level: species

strain history

@refhistory
11610<- NRRL <- F. P. Mertz, A 80407
67770ATCC 49844 <-- NRRL 18198 <-- F. P. Mertz A80407.

doi: 10.13145/bacdive13292.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/actinomycetota
  • domain: Bacteria
  • phylum: Actinomycetota
  • class: Actinomycetes
  • order: Pseudonocardiales
  • family: Pseudonocardiaceae
  • genus: Kibdelosporangium
  • species: Kibdelosporangium philippinense
  • full scientific name: Kibdelosporangium philippinense Mertz and Yao 1988

@ref: 11610

domain: Bacteria

phylum: Actinobacteria

class: Actinobacteria

order: Actinomycetales

family: Pseudonocardiaceae

genus: Kibdelosporangium

species: Kibdelosporangium philippinense

full scientific name: Kibdelosporangium philippinense Mertz and Yao 1988

strain designation: A80407

type strain: yes

Morphology

colony morphology

@refcolony colorincubation periodmedium used
19638Beige10-14 daysISP 2
19638Beige10-14 daysISP 3
19638Beige10-14 daysISP 4
19638Beige10-14 daysISP 5
19638Beige10-14 daysISP 6
19638Beige10-14 daysISP 7

multicellular morphology

@refforms multicellular complexcomplex namecomplex colormedium name
19638yesAerial MyceliumWhiteISP 2
19638yesAerial MyceliumWhiteISP 3
19638yesAerial MyceliumWhiteISP 4
19638noISP 5
19638noISP 6
19638noISP 7

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
11610GYM 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
19638ISP 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
19638ISP 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:
19638ISP 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
19638ISP 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
19638ISP 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
19638ISP 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
11610positivegrowth28mesophilic
19638positiveoptimum28mesophilic
67770positivegrowth28mesophilic

Physiology and metabolism

spore formation

  • @ref: 19638
  • spore description: Formation of spore chains (spirales), spore surface smooth, no fragmentation
  • type of spore: spore
  • spore formation: yes

halophily

  • @ref: 19638
  • salt: NaCl
  • growth: positive
  • tested relation: maximum
  • concentration: 2.5 %

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
1963817234glucose+
1963822599arabinose-
1963817992sucrose-
1963818222xylose-
1963817268myo-inositol+
1963829864mannitol+
1963828757fructose+
1963826546rhamnose-
1963816634raffinose-
1963862968cellulose-
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
19638+++++++++++++-++++-

API 20E

@refONPGADH ArgLDC LysODCCITH2SURETDA TrpINDVPGEL
19638+-----+--++

Isolation, sampling and environmental information

isolation

@refsample typecountryorigin.countrycontinent
11610soilPhilippinesPHLAsia
67770SoilPhilippinesPHLAsia

isolation source categories

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

taxonmaps

  • @ref: 69479
  • File name: preview.99_39378.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_10;96_415;97_470;98_28818;99_39378&stattab=map
  • Last taxonomy: Kibdelosporangium philippinense subclade
  • 16S sequence: AJ512464
  • Sequence Identity:
  • Total samples: 36
  • soil counts: 28
  • animal counts: 6
  • plant counts: 2

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
116101Risk group (German classification)
196381Risk group (German classification)

Sequence information

16S sequences

  • @ref: 20218
  • description: Kibdelosporangium philippinense 16S rRNA gene, type strain DSM 44226T
  • accession: AJ512464
  • length: 1490
  • database: ena
  • NCBI tax ID: 211113

Genome sequences

  • @ref: 66792
  • description: Kibdelosporangium philippinense ATCC 49844
  • accession: GCA_021390435
  • assembly level: contig
  • database: ncbi
  • NCBI tax ID: 211113

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
flagellatedno96.71no
flagellatedno96.71no
flagellatedno96.71no
gram-positiveyes82.393no
gram-positiveyes82.393no
gram-positiveyes82.393no
anaerobicno98.641no
anaerobicno98.641no
anaerobicno98.641no
aerobicyes88.029no
aerobicyes88.029no
aerobicyes88.029no
halophileno92.65no
halophileno92.65no
halophileno92.65no
spore-formingyes92.57no
spore-formingyes92.57no
spore-formingyes92.57no
motileno90.462no
motileno90.462no
motileno90.462no
glucose-fermentno91.269no
glucose-fermentno91.269no
glucose-fermentno91.269no
thermophileno99.089yes
thermophileno99.089yes
thermophileno99.089yes
glucose-utilyes90.044yes
glucose-utilyes90.044yes
glucose-utilyes90.044yes

External links

@ref: 11610

culture collection no.: DSM 44226, ATCC 49844, NRRL 18198, JCM 9918, IFO 14839, IFO 15154, KCTC 9838, NBRC 14839, NBRC 15154, NCIMB 13200

straininfo link

  • @ref: 82493
  • straininfo: 42714

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny21989686Kibdelosporangium phytohabitans sp. nov., a novel endophytic actinomycete isolated from oil-seed plant Jatropha curcas L. containing 1-aminocyclopropane-1-carboxylic acid deaminase.Xing K, Bian GK, Qin S, Klenk HP, Yuan B, Zhang YJ, Li WJ, Jiang JHAntonie Van Leeuwenhoek10.1007/s10482-011-9652-42011Actinomycetales/classification/*enzymology/genetics/*isolation & purification, Amino Acids, Cyclic/metabolism, Bacterial Proteins/genetics/*metabolism, Carbon-Carbon Lyases/genetics/*metabolism, China, Endophytes/classification/*enzymology/genetics/*isolation & purification, Fatty Acids/metabolism, Jatropha/metabolism/*microbiology, Molecular Sequence Data, Phylogeny, Plant Roots/metabolism/microbiologyMetabolism
Phylogeny25951859Kibdelosporangium lantanae sp. nov., isolated from the rhizosphere soil of an ornamental plant, Lantana camara L.Li D, Huang Y, Song S, Xue C, Wu Y, Deng XInt J Syst Evol Microbiol10.1099/ijs.0.0003022015Actinomycetales/*classification/genetics/isolation & purification, Bacterial Typing Techniques, Base Composition, China, DNA, Bacterial/genetics, Diaminopimelic Acid/chemistry, Fatty Acids/chemistry, Lantana/*microbiology, Molecular Sequence Data, Peptidoglycan/chemistry, Phospholipids/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, *Rhizosphere, Sequence Analysis, DNA, *Soil Microbiology, Vitamin K 2/analogs & derivatives/chemistryGenetics
Genetics35377176High-Quality Draft Genome Sequence of Kibdelosporangium philippinense, Generated by Hybrid Assembly of Short and Long Sequencing Reads.Fedorov EA, Omeragic M, Shalygina KF, Farwell AC, MacLea KSMicrobiol Resour Announc10.1128/mra.00020-222022

Reference

@idauthorscataloguedoi/urltitlejournalpubmed
11610Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 44226)https://www.dsmz.de/collection/catalogue/details/culture/DSM-44226
19638Wink, J.http://www.dsmz.de/microorganisms/wink_pdf/DSM44226.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
82493Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID42714.1StrainInfo: A central database for resolving microbial strain identifiers