Strain identifier

BacDive ID: 1840

Type strain: Yes

Species: Brevibacterium iodinum

Strain history: NCDO 613 <-- J. G. Davis.

NCBI tax ID(s): 1255616 (strain), 31943 (species)

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General

@ref: 8974

BacDive-ID: 1840

DSM-Number: 20626

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

description: Brevibacterium iodinum DSM 20626 is a mesophilic, Gram-positive bacterium that was isolated from milk.

NCBI tax id

NCBI tax idMatching level
1255616strain
31943species

strain history

@refhistory
8974<- NCDO <- J.G. Davis (Chromobacterium iodinum)
67770NCDO 613 <-- J. G. Davis.

doi: 10.13145/bacdive1840.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/actinomycetota
  • domain: Bacteria
  • phylum: Actinomycetota
  • class: Actinomycetes
  • order: Micrococcales
  • family: Brevibacteriaceae
  • genus: Brevibacterium
  • species: Brevibacterium iodinum
  • full scientific name: Brevibacterium iodinum (ex Davis 1939) Collins et al. 1981

  • synonyms

    • @ref: 20215
    • synonym: Arthrobacter iodinum

@ref: 8974

domain: Bacteria

phylum: Actinobacteria

class: Actinobacteria

order: Actinomycetales

family: Brevibacteriaceae

genus: Brevibacterium

species: Brevibacterium iodinum

full scientific name: Brevibacterium iodinum (ex Davis 1939) Collins et al. 1981

type strain: yes

Morphology

cell morphology

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

colony morphology

@refcolony colorincubation periodmedium used
18764Chocolate brown10-14 daysISP 2
18764Mahagony brown10-14 daysISP 3
18764Olive grey10-14 daysISP 4
18764Reed green10-14 daysISP 5
18764Reed green10-14 daysISP 6
18764Black olive10-14 daysISP 7

multicellular morphology

@refforms multicellular complexmedium name
18764noISP 2
18764noISP 3
18764noISP 4
18764noISP 5
18764noISP 6
18764noISP 7

Culture and growth conditions

culture medium

@refnamegrowthcompositionlink
18764ISP 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
18764ISP 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:
18764ISP 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
18764ISP 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
18764ISP 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
18764ISP 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
8974CORYNEBACTERIUM AGAR (DSMZ Medium 53)yesName: CORYNEBACTERIUM AGAR (DSMZ Medium 53) Composition: Agar 15.0 g/l Casein peptone 10.0 g/l NaCl 5.0 g/l Glucose 5.0 g/l Yeast extract 5.0 g/l Distilled waterhttps://mediadive.dsmz.de/medium/53

culture temp

@refgrowthtypetemperaturerange
18764positiveoptimum28mesophilic
8974positivegrowth30mesophilic
67770positivegrowth30mesophilic

Physiology and metabolism

spore formation

@refspore formationconfidence
69481no92
69480no99.998

halophily

  • @ref: 18764
  • salt: NaCl
  • growth: positive
  • tested relation: maximum
  • concentration: 10 %

murein

  • @ref: 8974
  • murein short key: A31
  • type: A1gamma m-Dpm-direct

observation

  • @ref: 67770
  • observation: quinones: MK-8(H2)

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
1876462968cellulose+
1876416634raffinose+
1876426546rhamnose+
1876428757fructose-
1876429864mannitol-
1876417268myo-inositol-
1876418222xylose+
1876417992sucrose-
1876422599arabinose-
1876417234glucose+
683685291gelatin-hydrolysis
6836827897tryptophan-energy source
6836816199urea-hydrolysis
6836816947citrate-assimilation
6836818257ornithine-degradation
6836825094lysine-degradation
6836829016arginine-hydrolysis
6837917632nitrate-reduction
683794853esculin-hydrolysis
6837916199urea-hydrolysis
6837917634D-glucose-fermentation
6837916988D-ribose-fermentation
6837965327D-xylose-fermentation
6837916899D-mannitol-fermentation
6837917306maltose-fermentation
6837917716lactose-fermentation
6837917992sucrose+fermentation
6837928087glycogen-fermentation

metabolite production

@refChebi-IDmetaboliteproduction
6836815688acetoinno
6836835581indoleno
6836816136hydrogen sulfideno

metabolite tests

@refChebi-IDmetabolitevoges-proskauer-testindole test
6836815688acetoin-
6836835581indole-

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
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
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

API coryne

@refNITPYZPYRAPALbeta GURbeta GALalpha GLUbeta NAGESCUREGELGLURIBXYLMANMALLACSACGLYG
18764-++-+-----+/-------+-

API zym

@refAlkaline phosphataseEsteraseEsterase LipaseLipaseLeucine arylamidaseValine arylamidaseCystine arylamidaseTrypsinalpha- ChymotrypsinAcid phosphataseNaphthol-AS-BI-phosphohydrolasealpha- Galactosidasebeta- Galactosidasebeta- Glucuronidasealpha- Glucosidasebeta- GlucosidaseN-acetyl-beta- glucosaminidasealpha- Mannosidasealpha- Fucosidase
18764+++-+--------------

API 20E

@refONPGADH ArgLDC LysODCCITH2SURETDA TrpINDVPGEL
18764-----------

Isolation, sampling and environmental information

isolation

@refsample typecountryorigin.countrycontinent
8974milk
67770MilkUnited KingdomGBREurope

isolation source categories

Cat1Cat2Cat3
#Host Body Product#Fluids#Milk
#Engineered#Food production#Dairy product

taxonmaps

  • @ref: 69479
  • File name: preview.99_4584.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_15817;96_81;97_619;98_713;99_4584&stattab=map
  • Last taxonomy: Brevibacterium
  • 16S sequence: X83813
  • Sequence Identity:
  • Total samples: 2870
  • soil counts: 309
  • aquatic counts: 309
  • animal counts: 2183
  • plant counts: 69

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
187641Hazard group
89741Risk group (German classification)

Sequence information

16S sequences

@refdescriptionaccessionlengthdatabaseNCBI tax ID
20218B.iodinum 16S rRNA geneX838131485ena31943
20218B.iodinum (NCDO 613) gene for 16S ribosomal RNAX765671438ena31943

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Brevibacterium iodinum ATCC 495141255616.4wgspatric1255616
66792Brevibacterium iodinum ATCC 495142600255375draftimg1255616
67770Brevibacterium iodinum ATCC 49514GCA_900169265contigncbi1255616

GC content

@refGC-content
897463.0
6777063.4

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno92no
motileno92.117no
gram-positiveyes89.313no
anaerobicno99.57no
aerobicyes95.407no
halophileyes74.59no
spore-formingno92.409no
thermophileno99.146yes
glucose-utilyes87.18yes
flagellatedno97.538no
glucose-fermentno92.639yes

External links

@ref: 8974

culture collection no.: DSM 20626, ATCC 49514, NCDO 613, JCM 2591, BCRC 12216, CCM 4116, CCUG 23893, CCUG 757, CGMCC 1.1928, IFO 15230, IMET 10995, KCTC 3083, LMG 21453, NBRC 15230, NCIMB 700613, NRRL B-1717, VKM Ac-2106

straininfo link

  • @ref: 71485
  • straininfo: 7658

literature

Pubmed-IDtitleauthorsjournalDOIyearmeshtopictopic2
15627390Structures of cell wall teichoic acids of Brevibacterium iodinum VKM Ac-2106.Potekhina NV, Evtushenko LI, Senchenkova SN, Shashkov AS, Naumova IBBiochemistry (Mosc)10.1007/s10541-005-0080-92004Brevibacterium/*chemistry, Cell Wall/*chemistry, Glucose/analysis/chemistry, Glycerol/analysis/chemistry, Mannitol/analysis/chemistry, Molecular Structure, Nuclear Magnetic Resonance, Biomolecular, Stereoisomerism, Teichoic Acids/*chemistry
27654846Brevibacterium sediminis sp. nov., isolated from deep-sea sediments from the Carlsberg and Southwest Indian Ridges.Chen P, Zhang L, Wang J, Ruan J, Han X, Huang YInt J Syst Evol Microbiol10.1099/ijsem.0.0015062016Bacterial Typing Techniques, Base Composition, Brevibacterium/*classification/genetics/isolation & purification, DNA, Bacterial/genetics, Fatty Acids/chemistry, Geologic Sediments/microbiology, Indian Ocean, Nucleic Acid Hybridization, Phospholipids/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, Seawater/*microbiology, Sequence Analysis, DNA, Vitamin K 2/analogs & derivatives/chemistryPhylogenyTranscriptome

Reference

@idauthorscataloguedoi/urltitlejournalpubmed
8974Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 20626)https://www.dsmz.de/collection/catalogue/details/culture/DSM-20626
18764Wink, J.http://www.dsmz.de/microorganisms/wink_pdf/DSM20626.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
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
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
71485Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID7658.1StrainInfo: A central database for resolving microbial strain identifiers