Strain identifier

BacDive ID: 18103

Type strain: Yes

Species: Exiguobacterium acetylicum

Strain Designation: 1005

Strain history: CIP <- 1982, ATCC, Brevibacterium acetylicum <- M. Levine: strain 1005

For citation purpose refer to the digital object identifier (doi) of the current version.
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General

@ref: 8801

BacDive-ID: 18103

DSM-Number: 20416

keywords: genome sequence, 16S sequence, Bacteria, mesophilic

description: Exiguobacterium acetylicum 1005 is a mesophilic bacterium that was isolated from creamery waste.

NCBI tax id

NCBI tax idMatching level
41170species
1397697strain

strain history

@refhistory
8801<- H. Seiler <- ATCC <- M. Levine, 1005
67770ATCC 953 <-- M. Levine 1005.
115992CIP <- 1982, ATCC, Brevibacterium acetylicum <- M. Levine: strain 1005

doi: 10.13145/bacdive18103.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/bacillota
  • domain: Bacteria
  • phylum: Bacillota
  • class: Bacilli
  • order: Caryophanales
  • family: Bacillaceae
  • genus: Exiguobacterium
  • species: Exiguobacterium acetylicum
  • full scientific name: Exiguobacterium acetylicum (Levine and Soppeland 1926) Farrow et al. 1994
  • synonyms

    @refsynonym
    20215Brevibacterium acetylicum
    20215Flavobacterium acetylicum

@ref: 8801

domain: Bacteria

phylum: Firmicutes

class: Bacilli

order: Bacillales

family: Bacilli, not assigned to family

genus: Exiguobacterium

species: Exiguobacterium acetylicum

full scientific name: Exiguobacterium acetylicum (Levine and Soppeland 1926) Farrow et al. 1994

strain designation: 1005

type strain: yes

Morphology

colony morphology

@refcolony colorincubation periodmedium used
18440Daffodil yellow (1007)10-14 daysISP 2
18440Daffodil yellow (1007)10-14 daysISP 3
18440beige10-14 daysISP 4
18440beige10-14 daysISP 5
18440beige10-14 daysISP 6
18440beige10-14 daysISP 7

multicellular morphology

@refforms multicellular complexmedium name
18440noISP 2
18440noISP 3
18440noISP 4
18440noISP 5
18440noISP 6
18440noISP 7

Culture and growth conditions

culture medium

@refnamegrowthcompositionlink
18440ISP 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
18440ISP 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:
18440ISP 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
18440ISP 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
18440ISP 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
18440ISP 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
8801CORYNEBACTERIUM 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
34012MEDIUM 3 - Columbia agaryesColumbia agar (39.000 g);distilled water (1000.000 ml)
115992CIP Medium 3yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=3

culture temp

@refgrowthtypetemperaturerange
18440positiveoptimum28mesophilic
8801positivegrowth30mesophilic
34012positivegrowth30mesophilic
67770positivegrowth30mesophilic

Physiology and metabolism

murein

  • @ref: 8801
  • murein short key: A11.01
  • type: A3alpha L-Lys-Gly

observation

  • @ref: 67770
  • observation: quinones: MK-7

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
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

enzymes

@refvalueactivityec
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
18440-----++-+----------

API zym

@refAlkaline phosphataseEsteraseEsterase LipaseLipaseLeucine arylamidaseValine arylamidaseCystine arylamidaseTrypsinalpha- ChymotrypsinAcid phosphataseNaphthol-AS-BI-phosphohydrolasealpha- Galactosidasebeta- Galactosidasebeta- Glucuronidasealpha- Glucosidasebeta- GlucosidaseN-acetyl-beta- glucosaminidasealpha- Mannosidasealpha- Fucosidase
18440-++---------+-++---

Isolation, sampling and environmental information

isolation

@refsample type
8801creamery waste
67770Creamy waste
115992Food, Milk skimmed

isolation source categories

Cat1Cat2Cat3
#Engineered#Food production#Dairy product
#Engineered#Industrial#Industrial production
#Engineered#Waste#Industrial waste

taxonmaps

  • @ref: 69479
  • File name: preview.99_656.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_130;96_390;97_439;98_501;99_656&stattab=map
  • Last taxonomy: Exiguobacterium
  • 16S sequence: DQ019167
  • Sequence Identity:
  • Total samples: 63843
  • soil counts: 9088
  • aquatic counts: 18655
  • animal counts: 28214
  • plant counts: 7886

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
184401German classification
88011Risk group (German classification)
1159921Risk group (French classification)

Sequence information

16S sequences

@refdescriptionaccessionlengthdatabaseNCBI tax ID
20218Exiguobacterium acetylicum strain DSM 20416 16S ribosomal RNA gene, partial sequenceDQ0191671550ena41170
20218Exiguobacterium acetylicum 16S rRNA gene, partial sequenceD557301482ena41170
20218Exiguobacterium acetylicum gene for 16S rRNA, partial sequence, strain: NBRC 12146AB6802461487ena41170
20218B.acetylicum (NCIMB 9889) 16S rRNAX703131473ena41170

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Exiguobacterium acetylicum DSM 204161397697.3wgspatric1397697
66792Exiguobacterium acetylicum DSM 204162562617000draftimg1397697
67770Exiguobacterium acetylicum DSM 20416GCA_000702605contigncbi1397697

GC content

@refGC-contentmethod
880146.6
6777046.6thermal denaturation, midpoint method (Tm)

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
motileyes89.261no
gram-positiveyes86.789no
anaerobicno98.467no
halophileyes74.89no
spore-formingno75.958no
glucose-utilyes89.628no
thermophileno99.527no
aerobicyes89.657no
flagellatedyes72.524no
glucose-fermentno77.802yes

External links

@ref: 8801

culture collection no.: DSM 20416, ATCC 953, NCIB 9889, CCUG 32630, JCM 1968, BCRC 10378, BCRC 17390, CGMCC 1.1917, CIP 82.109, HAMBI 2009, IAM 1790, IFO 12146, IMET 11072, KCTC 3255, NBRC 12146, NCCB 70030, NCIMB 9889

straininfo link

  • @ref: 87091
  • straininfo: 45045

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Enzymology9357959Characterization of guanosine kinase from Brevibacterium acetylicum ATCC 953.Usuda Y, Kawasaki H, Shimaoka M, Utagawa TBiochim Biophys Acta10.1016/s0167-4838(97)00080-01997Adenosine Triphosphate/metabolism, Brevibacterium/*enzymology, Cations, Divalent/pharmacology, Dimerization, Electrophoresis, Polyacrylamide Gel, Enzyme Activation/drug effects, Enzyme Inhibitors/chemistry/pharmacology, Hydrogen-Ion Concentration, Kinetics, Molecular Weight, Nucleotides/pharmacology, Phosphotransferases (Alcohol Group Acceptor)/chemistry/*isolation & purification/*metabolism, Substrate Specificity, TemperatureMetabolism
Enzymology9371440Molecular cloning and transcriptional analysis of a guanosine kinase gene of Brevibacterium acetylicum ATCC 953.Usuda Y, Kawasaki H, Shimaoka M, Utagawa TJ Bacteriol10.1128/jb.179.22.6959-6964.19971997Amino Acid Sequence, Base Sequence, Blotting, Northern, Brevibacterium/*enzymology/*genetics/metabolism, Cloning, Molecular, DNA, Bacterial/analysis/genetics, Escherichia coli/genetics, Gene Expression, Molecular Sequence Data, Nucleic Acid Hybridization, Open Reading Frames, Phosphotransferases (Alcohol Group Acceptor)/*genetics/metabolism, Plasmids, Promoter Regions, Genetic, Recombination, Genetic, Sequence Alignment, Sequence Analysis, DNA, Sequence Homology, Amino Acid, Transcription, GeneticMetabolism
Metabolism10830490Development of an improved assay for purine nucleoside kinase activity in cell extracts and detection of inosine kinase activity in Brevibacterium acetylicum ATCC 953, related species, and Corynebacterium flaccumfaciens ATCC 6887.Kawasaki H, Usuda Y, Shimaoka M, Utagawa TBiosci Biotechnol Biochem10.1271/bbb.64.7612000Adenosine Triphosphate/metabolism, Brevibacterium/*enzymology, Corynebacterium/*enzymology, Magnesium, Pentosyltransferases/*metabolism, Phosphorylation, Phosphotransferases/*metabolism, Phosphotransferases (Alcohol Group Acceptor)/*metabolismEnzymology
Phylogeny12148624Exiguobacterium undae sp. nov. and Exiguobacterium antarcticum sp. nov.Fruhling A, Schumann P, Hippe H, Straubler B, Stackebrandt EInt J Syst Evol Microbiol10.1099/00207713-52-4-11712002Bacillaceae/chemistry/*classification/genetics/physiology, Bacterial Typing Techniques, DNA, Ribosomal, Fresh Water/*microbiology, Molecular Sequence Data, Nucleic Acid Hybridization, Phenotype, Pigments, Biological/metabolism, RNA, Ribosomal, 16S, Ribotyping, Sequence Analysis, DNA, Spectroscopy, Fourier Transform InfraredGenetics
Phylogeny17158975Exiguobacterium indicum sp. nov., a psychrophilic bacterium from the Hamta glacier of the Himalayan mountain ranges of India.Chaturvedi P, Shivaji SInt J Syst Evol Microbiol10.1099/ijs.0.64508-02006Bacillaceae/chemistry/*classification/genetics/isolation & purification, Bacterial Typing Techniques, *Cold Temperature, DNA, Bacterial/analysis, DNA, Ribosomal/analysis, Ice Cover/*microbiology, India, Molecular Sequence Data, Nucleic Acid Hybridization, Phenotype, Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNAGenetics
Phylogeny18842873Exiguobacterium soli sp. nov., a psychrophilic bacterium from the McMurdo Dry Valleys, Antarctica.Chaturvedi P, Prabahar V, Manorama R, Pindi PK, Bhadra B, Begum Z, Shivaji SInt J Syst Evol Microbiol10.1099/ijs.0.2008/000067-02008Antarctic Regions, Bacillaceae/chemistry/*classification/*genetics/isolation & purification, DNA, Bacterial/genetics, Fatty Acids/chemistry, Genes, Bacterial, Genes, rRNA, Geologic Sediments/*microbiology, Molecular Sequence Data, Phenotype, Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, *Soil MicrobiologyGenetics
Phylogeny25716950Exiguobacterium enclense sp. nov., isolated from sediment.Dastager SG, Mawlankar R, Sonalkar VV, Thorat MN, Mual P, Verma A, Krishnamurthi S, Tang SK, Li WJInt J Syst Evol Microbiol10.1099/ijs.0.0001492015Bacillaceae/*classification/genetics/isolation & purification, Base Composition, DNA, Bacterial/genetics, Fatty Acids/chemistry, Geologic Sediments/*microbiology, India, Islands, Molecular Sequence Data, Nucleic Acid Hybridization, Peptidoglycan/chemistry, Phenotype, Phospholipids/chemistry, *Phylogeny, Pigmentation, RNA, Ribosomal, 16S/genetics, Seawater/*microbiology, Sequence Analysis, DNA, Vitamin K 2/analogs & derivatives/chemistryGenetics

Reference

@idauthorscataloguedoi/urltitlejournalpubmed
8801Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 20416)https://www.dsmz.de/collection/catalogue/details/culture/DSM-20416
18440Wink, J.http://www.dsmz.de/microorganisms/wink_pdf/DSM20416.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
34012Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/11386
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/
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
87091Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID45045.1StrainInfo: A central database for resolving microbial strain identifiers
115992Curators of the CIPCollection of Institut Pasteur (CIP 82.109)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%2082.109