Strain identifier

BacDive ID: 2253

Type strain: Yes

Species: Carnobacterium divergens

Strain Designation: 66

Strain history: CIP <- 1984, DSM <- W.H. Holzapfel: strain 66, Lactobacillus divergens

NCBI tax ID(s): 1449336 (strain), 2748 (species)

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General

@ref: 8971

BacDive-ID: 2253

DSM-Number: 20623

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

description: Carnobacterium divergens 66 is a microaerophile bacterium that was isolated from vacuum-packaged minced beef.

NCBI tax id

NCBI tax idMatching level
1449336strain
2748species

strain history

@refhistory
8971<- W.H. Holzapfel, 66
67770DSM 20623 <-- W. H. Holzapfel 66.
118951CIP <- 1984, DSM <- W.H. Holzapfel: strain 66, Lactobacillus divergens

doi: 10.13145/bacdive2253.20240916.9.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/bacillota
  • domain: Bacteria
  • phylum: Bacillota
  • class: Bacilli
  • order: Lactobacillales
  • family: Carnobacteriaceae
  • genus: Carnobacterium
  • species: Carnobacterium divergens
  • full scientific name: Carnobacterium divergens (Holzapfel and Gerber 1984) Collins et al. 1987

  • synonyms

    • @ref: 20215
    • synonym: Lactobacillus divergens

@ref: 8971

domain: Bacteria

phylum: Firmicutes

class: Bacilli

order: Lactobacillales

family: Carnobacteriaceae

genus: Carnobacterium

species: Carnobacterium divergens

full scientific name: Carnobacterium divergens (Holzapfel and Gerber 1984) Collins et al. 1987

strain designation: 66

type strain: yes

Morphology

cell morphology

@refgram staincell shapemotilityconfidence
118951positiverod-shapedno
69480positive91.43

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
8971TRYPTICASE SOY YEAST EXTRACT MEDIUM (DSMZ Medium 92)yeshttps://mediadive.dsmz.de/medium/92Name: TRYPTICASE SOY YEAST EXTRACT MEDIUM (DSMZ Medium 92) Composition: Trypticase soy broth 30.0 g/l Agar 15.0 g/l Yeast extract 3.0 g/l Distilled water
41662MEDIUM 72- for trypto casein soja agaryesDistilled water make up to (1000.000 ml);Trypto casein soy agar (40.000 g)
118951CIP Medium 3yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=3
118951CIP Medium 72yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=72

culture temp

@refgrowthtypetemperature
8971positivegrowth30
41662positivegrowth30
49897positivegrowth30
67770positivegrowth25
118951positivegrowth15-45

Physiology and metabolism

oxygen tolerance

@refoxygen tolerance
49897microaerophile
118951facultative anaerobe

murein

  • @ref: 8971
  • murein short key: A31
  • type: A1gamma m-Dpm-direct

metabolite utilization

@refmetaboliteutilization activitykind of utilization testedChebi-ID
68371Potassium 5-ketogluconate-builds acid from
68371Potassium 2-ketogluconate-builds acid from
68371gluconate-builds acid from24265
68371L-arabitol-builds acid from18403
68371D-arabitol-builds acid from18333
68371L-fucose-builds acid from18287
68371D-fucose-builds acid from28847
68371D-tagatose-builds acid from16443
68371D-lyxose-builds acid from62318
68371turanose-builds acid from32528
68371gentiobiose+builds acid from28066
68371xylitol-builds acid from17151
68371glycogen-builds acid from28087
68371starch-builds acid from28017
68371raffinose-builds acid from16634
68371melezitose+builds acid from6731
68371inulin-builds acid from15443
68371trehalose+builds acid from27082
68371sucrose+builds acid from17992
68371melibiose-builds acid from28053
68371lactose-builds acid from17716
68371maltose+builds acid from17306
68371cellobiose+builds acid from17057
68371salicin+builds acid from17814
68371esculin+builds acid from4853
68371arbutin+builds acid from18305
68371amygdalin+builds acid from27613
68371N-acetylglucosamine+builds acid from59640
68371methyl alpha-D-glucopyranoside-builds acid from320061
68371methyl alpha-D-mannoside-builds acid from43943
68371D-sorbitol-builds acid from17924
68371D-mannitol-builds acid from16899
68371myo-inositol-builds acid from17268
68371galactitol-builds acid from16813
68371L-rhamnose-builds acid from62345
68371L-sorbose-builds acid from17266
68371D-mannose+builds acid from16024
68371D-fructose+builds acid from15824
68371D-glucose+builds acid from17634
68371D-galactose-builds acid from12936
68371methyl beta-D-xylopyranoside-builds acid from74863
68371ribitol-builds acid from15963
68371L-xylose-builds acid from65328
68371D-xylose-builds acid from65327
68371D-ribose+builds acid from16988
68371L-arabinose-builds acid from30849
68371D-arabinose-builds acid from17108
68371erythritol-builds acid from17113
68371glycerol-builds acid from17754
118951nitrate-reduction17632
118951nitrite-reduction16301
118951nitrate+respiration17632

metabolite tests

  • @ref: 118951
  • Chebi-ID: 15688
  • metabolite: acetoin
  • voges-proskauer-test: -

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
118951oxidase-
118951alcohol dehydrogenase+1.1.1.1
118951catalase-1.11.1.6
118951lysine decarboxylase-4.1.1.18
118951ornithine decarboxylase-4.1.1.17

API zym

@refControlAlkaline phosphataseEsteraseEsterase LipaseLipaseLeucine arylamidaseValine arylamidaseCystine arylamidaseTrypsinalpha- ChymotrypsinAcid phosphataseNaphthol-AS-BI-phosphohydrolasealpha- Galactosidasebeta- Galactosidasebeta- Glucuronidasealpha- Glucosidasebeta- GlucosidaseN-acetyl-beta- glucosaminidasealpha- Mannosidasealpha- Fucosidase
118951--++-----+++----+---

API 50CHac

@refQGLYERYDARALARARIBDXYLLXYLADOMDXGALGLUFRUMNESBERHADULINOMANSORMDMMDGNAGAMYARBESCSALCELMALLACMELSACTREINUMLZRAFAMDGLYGXLTGENTURLYXTAGDFUCLFUCDARLLARLGNT2KG5KG
8971-----+-----+++--------+++++++--++-+----+----------

Isolation, sampling and environmental information

isolation

@refsample typecountryorigin.countrycontinent
8971vacuum-packaged minced beef
49897Vacuum-packaged minced beefSouth AfricaZAFAfrica
67770Raw vacuum-packaged minced beef
118951Food, Vacuum packaged minced beef

isolation source categories

Cat1Cat2Cat3
#Engineered#Food production#Bottled, canned, packed food
#Engineered#Food production#Meat

taxonmaps

  • @ref: 69479
  • File name: preview.99_2591.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_13;96_41;97_1652;98_2007;99_2591&stattab=map
  • Last taxonomy: Carnobacterium divergens subclade
  • 16S sequence: LC097075
  • Sequence Identity:
  • Total samples: 6470
  • soil counts: 441
  • aquatic counts: 963
  • animal counts: 4851
  • plant counts: 215

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
89711Risk group (German classification)
1189511Risk group (French classification)

Sequence information

16S sequences

@refdescriptionaccessionlengthdatabaseNCBI tax ID
20218Carnobacterium divergens strain ATCC 35677 16S ribosomal RNA gene, partial sequenceGU460377809nuccore2748
20218Carnobacterium divergens strain DSM 20623 16S ribosomal RNA gene, partial sequenceM588161502nuccore2748
20218Carnobacterium divergens gene for 16S rRNA, partial sequence, strain: NBRC 15683AB6809401481nuccore2748
20218Carnobacterium divergens 16S ribosomal RNA gene, partial sequence; small 16S-23S ribosomal RNA intergenic spacer, complete sequence; and 23S ribosomal RNA gene, partial sequenceAF374292446nuccore2748
20218Carnobacterium divergens 16S ribosomal RNA gene, partial sequence; medium 16S-23S intergenic spacer and tRNA-Ala gene, complete sequence; and 23S ribosomal RNA gene, partial sequenceAF374293554nuccore2748
20218Carnobacterium divergens 16S ribosomal RNA gene, partial sequence; large 16S-23S intergenic spacer, tRNA-Ile and tRNA-Ala genes, complete sequence; and 23S ribosomal RNA gene, partial sequenceAF374294668nuccore2748
20218Carnobacterium divergens partial 16S RNAX542701492nuccore2748
67770Carnobacterium divergens gene for 16S ribosomal RNA, partial sequence, strain: JCM 9133LC0970751494nuccore2748
67770Carnobacterium divergens gene for 16S ribosomal RNA, partial sequence, strain: JCM 5816LC1455561462nuccore2748

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Carnobacterium divergens DSM 20623 66GCA_000744255contigncbi1449336
66792Carnobacterium divergens DSM 20623GCA_001437085scaffoldncbi1449336
66792Carnobacterium divergens DSM 206231449336.4wgspatric1449336
66792Carnobacterium divergens DSM 20623 strain 661449336.3wgspatric1449336
66792Carnobacterium divergens 662574180433draftimg2748
66792Carnobacterium divergens DSM 206232700989267draftimg1449336

GC content

@refGC-contentmethod
897135.5
6777035.5thermal denaturation, midpoint method (Tm)
6777034.8thermal denaturation, midpoint method (Tm)

Genome-based predictions

predictions

@reftraitmodeldescriptionpredictionconfidencetraining_data
69480gram-positivegram-positivePositive reaction to Gram-stainingyes91.43no
69480anaerobicanaerobicAbility to grow under anoxygenic conditions (including facultative anaerobes)no90.719yes
69480aerobicaerobicAbility to grow under oxygenic conditions (including facultative aerobes)no93.973yes
69480spore-formingspore-formingAbility to form endo- or exosporesno73.686no
69480thermophilicthermophileAbility to grow at temperatures above or equal to 45°Cno95.971yes
69480flagellatedmotile2+Ability to perform flagellated movementno88.367no

External links

@ref: 8971

culture collection no.: DSM 20623, ATCC 35677, NCDO 2763, WDCM 00075, CCUG 30094, CCM 4117, JCM 5816, BCRC 14042, CECT 4016, CIP 101029, IFO 15683, JCM 9133, KCTC 3675, LMG 9199, NBRC 15683, NCIMB 11952, NRIC 1629, NRRL B-14830, VTT E-97850

straininfo link

  • @ref: 71812
  • straininfo: 1682

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny12406725Differentiation of closely related Carnobacterium food isolates based on 16S-23S ribosomal DNA intergenic spacer region polymorphism.Kabadjova P, Dousset X, Le Cam V, Prevost HAppl Environ Microbiol10.1128/AEM.68.11.5358-5366.20022002Bacteria/classification/genetics/*isolation & purification, Base Sequence, DNA, Bacterial/*analysis, DNA, Intergenic/analysis/*genetics, Molecular Sequence Data, Polymorphism, Genetic, RNA, Ribosomal/analysis/*genetics, Sequence Homology, Nucleic AcidGenetics
Enzymology18070972Genetic and biochemical characterization of CAD-1, a chromosomally encoded new class A penicillinase from Carnobacterium divergens.Meziane-Cherif D, Decre D, Hoiby EA, Courvalin P, Perichon BAntimicrob Agents Chemother10.1128/AAC.01145-072007Amino Acid Sequence, Chromosomes, Bacterial/*genetics, Cloning, Molecular, Electrophoresis, Gel, Pulsed-Field, Gram-Positive Bacteria/drug effects/*enzymology/genetics/isolation & purification, Gram-Positive Bacterial Infections/*microbiology, Humans, Infant, Newborn, Kinetics, Microbial Sensitivity Tests, Molecular Sequence Data, Penicillin Resistance, *Penicillinase/chemistry/genetics/metabolism, Sequence Alignment, Sequence Analysis, DNA, Substrate Specificity, beta-Lactams/pharmacologyPathogenicity
Metabolism19835762Comparison of different application strategies of divergicin M35 for inactivation of Listeria monocytogenes in cold-smoked wild salmon.Tahiri I, Desbiens M, Kheadr E, Lacroix C, Fliss IFood Microbiol10.1016/j.fm.2009.05.0032009Animals, Anti-Bacterial Agents/*pharmacology, *Antibiosis, Bacteriocins/*pharmacology, Biogenic Amines/analysis/metabolism, Carnobacterium/metabolism/*physiology, Cold Temperature, Colony Count, Microbial, Food Microbiology, Food Preservation/*methods, Listeria monocytogenes/drug effects/*growth & development, Odorants/analysis, Salmon/*microbiology, Seafood/*microbiology/standards, Smoke, Taste, Time FactorsBiotechnology

Reference

@idauthorscataloguedoi/urltitlejournalpubmed
8971Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 20623)https://www.dsmz.de/collection/catalogue/details/culture/DSM-20623
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
41662Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/12559
49897Curators of the CCUGCulture Collection University of Gothenburg (CCUG) (CCUG 30094)https://www.ccug.se/strain?id=30094
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)
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/
68371Automatically annotated from API 50CH acid
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)
71812Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID1682.1StrainInfo: A central database for resolving microbial strain identifiers
118951Curators of the CIPCollection of Institut Pasteur (CIP 101029)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20101029