Strain identifier

BacDive ID: 2264

Type strain: Yes

Species: Carnobacterium funditum

Strain Designation: pf3

Strain history: CIP <- 2000, CCUG <- B. Phillips, NCFB, Reading, UK <- DSMZ <- P.D. Franzmann: strain Pf3

NCBI tax ID(s): 1449337 (strain), 2752 (species)

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General

@ref: 2397

BacDive-ID: 2264

DSM-Number: 5970

keywords: genome sequence, 16S sequence, Bacteria, facultative anaerobe, Gram-positive

description: Carnobacterium funditum pf3 is a facultative anaerobe, Gram-positive bacterium that was isolated from water.

NCBI tax id

NCBI tax idMatching level
1449337strain
2752species

strain history

@refhistory
2397<- P.D. Franzmann, pf3
67770NBRC 15549 <-- IFO 15549 <-- NCFB 3002 <-- DSM 5970 <-- P. D. Franzmann pf3.
119490CIP <- 2000, CCUG <- B. Phillips, NCFB, Reading, UK <- DSMZ <- P.D. Franzmann: strain Pf3

doi: 10.13145/bacdive2264.20240916.9.1

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 funditum
  • full scientific name: Carnobacterium funditum Franzmann et al. 1993

@ref: 2397

domain: Bacteria

phylum: Firmicutes

class: Bacilli

order: Lactobacillales

family: Carnobacteriaceae

genus: Carnobacterium

species: Carnobacterium funditum

full scientific name: Carnobacterium funditum Franzmann et al. 1993

strain designation: pf3

type strain: yes

Morphology

cell morphology

  • @ref: 119490
  • gram stain: positive
  • cell shape: rod-shaped
  • motility: no

colony morphology

@refincubation period
522292-4 days
119490

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
2397TSBY SALT MEDIUM (DSMZ Medium 466)yeshttps://mediadive.dsmz.de/medium/466Name: TSBY SALT MEDIUM (DSMZ Medium 466) Composition: Trypticase soy broth 30.0 g/l NaCl 13.0 g/l MgCl2 x 6 H2O 4.0 g/l MgSO4 x 7 H2O 3.45 g/l Yeast extract 3.0 g/l KCl 0.34 g/l NH4Cl 0.25 g/l CaCl2 x 2 H2O 0.14 g/l Distilled water
39543MEDIUM 297 - for Carnobacterium alberfunditumyesDistilled water make up to (1000.000 ml);Sodium chloride (13.000 g);Potassium chloride (0.340 g);Magnesium chloride hexahydrate (4.000 g);Magnesium sulphate heptahydrate (3.450 g);Calcium chloride dihydrate (0.140 g);Agar (15.000 g);Yeast extract (3.000g)
119490CIP Medium 297yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=297

culture temp

@refgrowthtypetemperature
2397positivegrowth20
39543positivegrowth22
52229positivegrowth16-18
67770positivegrowth20
119490positivegrowth5-30
119490nogrowth37
119490nogrowth41

Physiology and metabolism

oxygen tolerance

  • @ref: 119490
  • oxygen tolerance: facultative anaerobe

halophily

@refsaltgrowthtested relationconcentration
119490NaClpositivegrowth2-4 %
119490NaClnogrowth0 %
119490NaClnogrowth6 %
119490NaClnogrowth8 %
119490NaClnogrowth10 %

murein

  • @ref: 2397
  • 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
119490citrate-carbon source16947
119490esculin+hydrolysis4853
119490hippurate-hydrolysis606565
119490nitrate-builds gas from17632
119490nitrate-reduction17632
119490nitrite-builds gas from16301
119490nitrite-reduction16301

metabolite production

  • @ref: 119490
  • Chebi-ID: 35581
  • metabolite: indole
  • production: no

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
119490oxidase-
119490beta-galactosidase-3.2.1.23
119490alcohol dehydrogenase-1.1.1.1
119490gelatinase-
119490amylase-
119490DNase-
119490caseinase-3.4.21.50
119490catalase-1.11.1.6
119490tween esterase-
119490gamma-glutamyltransferase-2.3.2.2
119490lysine decarboxylase-4.1.1.18
119490ornithine decarboxylase-4.1.1.17
119490phenylalanine ammonia-lyase-4.3.1.24
119490tryptophan deaminase-
119490urease-3.5.1.5

API zym

@refControlAlkaline phosphataseEsteraseEsterase LipaseLipaseLeucine arylamidaseValine arylamidaseCystine arylamidaseTrypsinalpha- ChymotrypsinAcid phosphataseNaphthol-AS-BI-phosphohydrolasealpha- Galactosidasebeta- Galactosidasebeta- Glucuronidasealpha- Glucosidasebeta- GlucosidaseN-acetyl-beta- glucosaminidasealpha- Mannosidasealpha- Fucosidase
119490-++--+---+++--------

API 50CHac

@refGLYERYDARALARARIBDXYLLXYLADOMDXGALGLUFRUMNESBERHADULINOMANSORMDMMDGNAGAMYARBESCSALCELMALLACMELSACTREINUMLZRAFAMDGLYGXLTGENTURLYXTAGDFUCLFUCDARLLARLGNT2KG5KG
119490----+-----+++----+---+----++--+----+--+----------

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcontinentcountryorigin.country
2397waterVestfold Hills, Ace Lake, depth 24 mAustralia and Oceania
52229WaterVestfold Hills,Ace LakeAustralia and OceaniaAntarcticaATA
67770WaterAce LakeAntarcticaAntarcticaATA
119490Environment, WaterAce lake, Vestfold hillsAntarcticaAntarcticaATA

isolation source categories

  • Cat1: #Environmental
  • Cat2: #Aquatic

taxonmaps

  • @ref: 69479
  • File name: preview.99_557.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_13;96_41;97_395;98_453;99_557&stattab=map
  • Last taxonomy: Carnobacterium
  • 16S sequence: LC145584
  • Sequence Identity:
  • Total samples: 451
  • soil counts: 45
  • aquatic counts: 90
  • animal counts: 304
  • plant counts: 12

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
23971Risk group (German classification)
1194901Risk group (French classification)

Sequence information

16S sequences

@refdescriptionaccessionlengthdatabaseNCBI tax ID
20218Carnobacterium funditum large 16S-23S rRNA intergenic spacer, tRNA-Ile and tRNA-Ala genes, complete sequenceAY170831427nuccore2752
20218Carnobacterium funditum medium 16S-23S rRNA intergenic spacer and tRNA-Ala gene, complete sequenceAY170832310nuccore2752
20218Carnobacterium funditum small 16S-23S rRNA intergenic spacer, complete sequenceAY170833204nuccore2752
20218Carnobacterium funditum strain pf3 16S ribosomal RNA gene, partial sequenceS861701521nuccore2752
20218Carnobacterium funditum gene for 16S rRNA, partial sequence, strain: NBRC 15549AB6808991484nuccore2752
67770Carnobacterium funditum gene for 16S ribosomal RNA, partial sequence, strain: JCM 12499LC1455841505nuccore2752

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Carnobacterium funditum DSM 5970 pf3GCA_000744185contigncbi1449337
66792Carnobacterium funditum DSM 5970 strain pf31449337.3wgspatric1449337
66792Carnobacterium funditum pf3, DSM 59702574179782draftimg2752

GC content

  • @ref: 2397
  • GC-content: 33.8
  • method: thermal denaturation, midpoint method (Tm)

Genome-based predictions

predictions

@reftraitmodeldescriptionpredictionconfidencetraining_data
69480gram-positivegram-positivePositive reaction to Gram-stainingyes86.975no
69480anaerobicanaerobicAbility to grow under anoxygenic conditions (including facultative anaerobes)no89.157yes
69480spore-formingspore-formingAbility to form endo- or exosporesno71.005no
69480aerobicaerobicAbility to grow under oxygenic conditions (including facultative aerobes)no93.517yes
69480thermophilicthermophileAbility to grow at temperatures above or equal to 45°Cno93.857yes
69480flagellatedmotile2+Ability to perform flagellated movementyes62.077no

External links

@ref: 2397

culture collection no.: CCUG 34644, IFO 15549, DSM 5970, ACAM 312, ATCC 49836, JCM 12499, CIP 106503, LMG 13519, LMG 14461, NBRC 15549, NCFB 3002, NCIMB 13247

straininfo link

  • @ref: 71823
  • straininfo: 8235

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny1793333Psychrotrophic, lactic acid-producing bacteria from anoxic waters in Ace Lake, Antarctica; Carnobacterium funditum sp. nov. and Carnobacterium alterfunditum sp. nov.Franzmann PD, Hopfl P, Weiss N, Tindall BJArch Microbiol10.1007/BF002629941991Anaerobiosis, Antarctic Regions, Base Sequence, Culture Media, Gram-Positive Asporogenous Rods/*classification/genetics/physiology, Lactates/biosynthesis, Lactic Acid, Molecular Sequence Data, Phenotype, Phylogeny, RNA, Ribosomal, 16S/*chemistry/genetics, Sequence Homology, Nucleic Acid, Temperature, *Water MicrobiologyCultivation
Phylogeny22798642Carnobacterium iners sp. nov., a psychrophilic, lactic acid-producing bacterium from the littoral zone of an Antarctic pond.Snauwaert I, Hoste B, De Bruyne K, Peeters K, De Vuyst L, Willems A, Vandamme PInt J Syst Evol Microbiol10.1099/ijs.0.042861-02012Antarctic Regions, Bacterial Typing Techniques, Base Composition, Carnobacterium/*classification/genetics/isolation & purification, DNA, Bacterial/genetics, Genes, Bacterial, Molecular Sequence Data, Multilocus Sequence Typing, Nucleic Acid Hybridization, Peptidoglycan/analysis, *Phylogeny, Ponds/*microbiology, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Water MicrobiologyGenetics

Reference

@idauthorscataloguedoi/urltitlejournalpubmed
2397Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 5970)https://www.dsmz.de/collection/catalogue/details/culture/DSM-5970
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
39543Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/18640
52229Curators of the CCUGCulture Collection University of Gothenburg (CCUG) (CCUG 34644)https://www.ccug.se/strain?id=34644
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/
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)
71823Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID8235.1StrainInfo: A central database for resolving microbial strain identifiers
119490Curators of the CIPCollection of Institut Pasteur (CIP 106503)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20106503