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)

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

@ref: 2397

BacDive-ID: 2264

DSM-Number: 5970

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

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

NCBI tax id

NCBI tax idMatching level
2752species
1449337strain

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/bacdive2264.20230509.8.1

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

@refgrowthtypetemperaturerange
2397positivegrowth20psychrophilic
39543positivegrowth22psychrophilic
52229positivegrowth16-18psychrophilic
67770positivegrowth20psychrophilic
119490positivegrowth5-30
119490nogrowth37mesophilic
119490nogrowth41thermophilic

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 sequenceAY170831427ena2752
20218Carnobacterium funditum medium 16S-23S rRNA intergenic spacer and tRNA-Ala gene, complete sequenceAY170832310ena2752
20218Carnobacterium funditum small 16S-23S rRNA intergenic spacer, complete sequenceAY170833204ena2752
20218Carnobacterium funditum strain pf3 16S ribosomal RNA gene, partial sequenceS861701521ena2752
20218Carnobacterium funditum gene for 16S rRNA, partial sequence, strain: NBRC 15549AB6808991484ena2752
67770Carnobacterium funditum gene for 16S ribosomal RNA, partial sequence, strain: JCM 12499LC1455841505ena2752

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

traitpredictionconfidencetraining_data
motileyes55.019no
gram-positiveyes90.952no
anaerobicno93.463no
halophileyes86.16no
spore-formingno83.516no
glucose-utilyes89.286no
thermophileno98.826yes
aerobicno94.444no
flagellatedno90.685no
glucose-fermentyes86.035no

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
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