Strain identifier

BacDive ID: 6242

Type strain: Yes

Species: Intrasporangium calvum

Strain Designation: No.7 KIP

Variant: Isotype of BacDive ID 6244

Strain history: KCC A-0097 <-- CUB 430 <-- H. A. Lechevalier <-- L. V. Kalakoutskii 7 KIP.

NCBI tax ID(s): 710696 (strain), 53358 (species)

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General

@ref: 10713

BacDive-ID: 6242

DSM-Number: 43043

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

description: Intrasporangium calvum No.7 KIP is a mesophilic, Gram-positive bacterium that was isolated from air in a school dining room.

NCBI tax id

NCBI tax idMatching level
53358species
710696strain

strain history

@refhistory
10713<- KCC <- T. Cross, CUB <- H. Lechevalier, IMRU <- L.V. Kalakoutskii, No.7 KIP
67770KCC A-0097 <-- CUB 430 <-- H. A. Lechevalier <-- L. V. Kalakoutskii 7 KIP.

doi: 10.13145/bacdive6242.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/actinomycetota
  • domain: Bacteria
  • phylum: Actinomycetota
  • class: Actinomycetes
  • order: Micrococcales
  • family: Intrasporangiaceae
  • genus: Intrasporangium
  • species: Intrasporangium calvum
  • full scientific name: Intrasporangium calvum Kalakoutskii et al. 1967 (Approved Lists 1980)

@ref: 10713

domain: Bacteria

phylum: Actinobacteria

class: Actinobacteria

order: Actinomycetales

family: Intrasporangiaceae

genus: Intrasporangium

species: Intrasporangium calvum

full scientific name: Intrasporangium calvum Kalakoutskii et al. 1967 emend. Yang et al. 2012 emend. Nouioui et al. 2018

strain designation: No.7 KIP

variant: Isotype of BacDive ID 6244

type strain: yes

Morphology

cell morphology

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

colony morphology

@refcolony colorincubation periodmedium used
19932Light ivory (1015)10-14 daysISP 2
19932Light ivory (1015)10-14 daysISP 3
19932Light ivory (1015)10-14 daysISP 4
19932Light ivory (1015)10-14 daysISP 5
19932Light ivory (1015)10-14 daysISP 6
19932Light ivory (1015)10-14 daysISP 7

multicellular morphology

@refforms multicellular complexmedium name
19932noISP 2
19932noISP 3
19932noISP 4
19932noISP 5
19932noISP 6
19932noISP 7

multimedia

  • @ref: 66793
  • multimedia content: EM_DSM_43043_1.jpg
  • caption: electron microscopic image
  • intellectual property rights: © HZI/Manfred Rohde

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
10713GYM 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
19932ISP 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
19932ISP 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:
19932ISP 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
19932ISP 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
19932ISP 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
19932ISP 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
10713BHI MEDIUM (DSMZ Medium 215)yeshttps://mediadive.dsmz.de/medium/215Name: BHI MEDIUM (DSMZ Medium 215) Composition: Brain heart infusion 37.0 g/l Distilled water

culture temp

@refgrowthtypetemperaturerange
19932positiveoptimum28mesophilic
10713positivegrowth28mesophilic
67770positivegrowth28mesophilic

Physiology and metabolism

spore formation

@refspore formationconfidence
69481no100
69480no99.994

murein

  • @ref: 10713
  • murein short key: A41.02
  • type: A3gamma LL-Dpm-Gly3; alpha-carboxyl group of D-Glu substituted by Gly

observation

  • @ref: 67770
  • observation: quinones: MK-8, MK-8(H4)

enzymes

@refvalueactivityec
68382alpha-fucosidase-3.2.1.51
68382alpha-mannosidase-3.2.1.24
68382N-acetyl-beta-glucosaminidase-3.2.1.52
68382beta-glucosidase-3.2.1.21
68382alpha-glucosidase+3.2.1.20
68382beta-glucuronidase-3.2.1.31
68382beta-galactosidase-3.2.1.23
68382alpha-galactosidase+3.2.1.22
68382naphthol-AS-BI-phosphohydrolase+
68382acid phosphatase+3.1.3.2
68382alpha-chymotrypsin-3.4.21.1
68382trypsin-3.4.21.4
68382cystine arylamidase-3.4.11.3
68382valine arylamidase-
68382leucine arylamidase+3.4.11.1
68382lipase (C 14)-
68382esterase lipase (C 8)+
68382esterase (C 4)+
68382alkaline phosphatase+3.1.3.1

API zym

@refAlkaline phosphataseEsteraseEsterase LipaseLipaseLeucine arylamidaseValine arylamidaseCystine arylamidaseTrypsinalpha- ChymotrypsinAcid phosphataseNaphthol-AS-BI-phosphohydrolasealpha- Galactosidasebeta- Galactosidasebeta- Glucuronidasealpha- Glucosidasebeta- GlucosidaseN-acetyl-beta- glucosaminidasealpha- Mannosidasealpha- Fucosidase
19932+++-+----+++--+----

Isolation, sampling and environmental information

isolation

@refsample typegeographic location
10713air in a school dining roomRutgers
67770Air

isolation source categories

Cat1Cat2Cat3
#Environmental#Air#Indoor Air
#Engineered#Built environment#House

taxonmaps

  • @ref: 69479
  • File name: preview.99_5089.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_9;96_2431;97_2983;98_3800;99_5089&stattab=map
  • Last taxonomy: Intrasporangium calvum
  • 16S sequence: AJ566282
  • Sequence Identity:
  • Total samples: 3771
  • soil counts: 2412
  • aquatic counts: 443
  • animal counts: 694
  • plant counts: 222

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
199321German classification
107131Risk group (German classification)

Sequence information

16S sequences

@refdescriptionaccessionlengthdatabaseNCBI tax ID
20218Intrasporangium calvum 16S rRNA gene, type strain DSM 43043TAJ5662821469ena710696
20218Intrasporangium calvum gene for 16S ribosomal RNA, partial sequenceD854861475ena710696

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Intrasporangium calvum DSM 43043GCA_000184685completencbi710696
66792Intrasporangium calvum DSM 43043710696.3completepatric710696
66792Intrasporangium calvum 7KIP, DSM 43043649633057completeimg710696

GC content

@refGC-contentmethod
6777068.2high performance liquid chromatography (HPLC)
6777070.7genome sequence analysis
6777068.8high performance liquid chromatography (HPLC)

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno100no
motileno96.374no
flagellatedno98.363no
gram-positiveyes89.213no
anaerobicno98.466no
aerobicyes83.203no
halophileno94.836no
spore-formingno87.669no
glucose-utilyes84.996no
thermophileno93.815yes
glucose-fermentno90.331no

External links

@ref: 10713

culture collection no.: DSM 43043, ATCC 23552, CUB 430, IFO 12989, IMET 7816, JCM 3097, KCC A-0097, NBRC 12989, NCIB 10167, CGMCC 4.5633, IAM 14907, IMSNU 21320, IMSNU 22007, KACC 20040, KCTC 9122, KCTC 9796, MTCC 499, NCIMB 10167, NRRL B-3866, PCM 2332, RIA 920, VKM Ac-701

straininfo link

  • @ref: 75721
  • straininfo: 38085

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny17766892Humihabitans oryzae gen. nov., sp. nov.Kageyama A, Takahashi Y, Omura SInt J Syst Evol Microbiol10.1099/ijs.0.65069-02007Actinomycetales/*classification/genetics/*isolation & purification/metabolism, Aerobiosis, Base Composition, DNA, Bacterial/chemistry/genetics, DNA, Ribosomal/chemistry/genetics, Diaminopimelic Acid/analysis, Genes, rRNA, Japan, Molecular Sequence Data, Mycolic Acids/analysis, Peptidoglycan/chemistry, Phylogeny, RNA, Bacterial/genetics, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Sequence Homology, Nucleic Acid, *Soil Microbiology, Vitamin K 2/analysisGenetics
Phylogeny21441371Intrasporangium chromatireducens sp. nov., a chromate-reducing actinobacterium isolated from manganese mining soil, and emended description of the genus Intrasporangium.Liu H, Wang H, Wang GInt J Syst Evol Microbiol10.1099/ijs.0.030528-02011Actinomycetales/chemistry/*classification/genetics/*isolation & purification, Bacterial Typing Techniques, China, Chromates/*metabolism, DNA, Bacterial/analysis, DNA, Ribosomal/analysis, Fatty Acids/analysis, Genes, rRNA, Lipids/analysis, *Manganese, *Mining, Molecular Sequence Data, Oxidation-Reduction, Phenotype, Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, *Soil Microbiology, Species Specificity, Vitamin K 2/analysisGenetics
Phylogeny21685254Proposal of Intrasporangium mesophilum sp. nov., and reclassification of Humihabitans oryzae Kageyama et al. 2007 as Intrasporangium oryzae comb. nov.Yang LL, Ao T, Wang XH, He J, Klenk HP, Tang SK, Li WJInt J Syst Evol Microbiol10.1099/ijs.0.029934-02011Actinomycetales/*classification/genetics/*isolation & purification/physiology, Aerobiosis, Bacterial Typing Techniques, Base Composition, China, Cluster Analysis, Cytosol/chemistry, DNA, Bacterial/chemistry/genetics, DNA, Ribosomal/chemistry/genetics, Diaminopimelic Acid/analysis, Fatty Acids/analysis, Jatropha/*microbiology, Molecular Sequence Data, Nucleic Acid Hybridization, Peptidoglycan/chemistry, Phylogeny, RNA, Ribosomal, 16S/genetics, *Rhizosphere, Sequence Analysis, DNA, *Soil Microbiology, Vitamin K 2/analysisGenetics

Reference

@idauthorscataloguedoi/urltitlejournalpubmed
10713Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 43043)https://www.dsmz.de/collection/catalogue/details/culture/DSM-43043
19932Wink, J.http://www.dsmz.de/microorganisms/wink_pdf/DSM43043.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)
66793Mukherjee et al.10.1038/nbt.3886GEBA: 1,003 reference genomes of bacterial and archaeal isolates expand coverage of the tree of life 35: 676-683 201728604660
66794Antje Chang, Lisa Jeske, Sandra Ulbrich, Julia Hofmann, Julia Koblitz, Ida Schomburg, Meina Neumann-Schaal, Dieter Jahn, Dietmar Schomburg10.1093/nar/gkaa1025BRENDA, the ELIXIR core data resource in 2021: new developments and updatesNucleic Acids Res. 49: D498-D508 202033211880
67770Curators of the JCMhttps://jcm.brc.riken.jp/en/
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
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
75721Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID38085.1StrainInfo: A central database for resolving microbial strain identifiers