Strain identifier

BacDive ID: 2266

Type strain: Yes

Species: Carnobacterium alterfunditum

Strain Designation: pf4

Strain history: CIP <- 1998, ATCC <- N. Weiss <- P. Franzmann: strain Pf4

NCBI tax ID(s): 1449335 (strain), 28230 (species)

« back to strain detail view
For citation purpose refer to the digital object identifier (doi) of the current version.
Archive
version 9.1 (current version):
version 9:
version 8.1:
version 8:
version 7.1:
version 7:
version 6:
version 5:
version 4.1:
version 4:
version 3:
version 2.1:
version 2:
version 1:
version 9.1 (current version)

General

@ref: 2399

BacDive-ID: 2266

DSM-Number: 5972

keywords: genome sequence, 16S sequence, Bacteria, aerobe, Gram-positive, motile, rod-shaped

description: Carnobacterium alterfunditum pf4 is an aerobe, Gram-positive, motile bacterium that was isolated from water.

NCBI tax id

NCBI tax idMatching level
28230species
1449335strain

strain history

@refhistory
2399<- P.D. Franzmann, pf4
116268CIP <- 1998, ATCC <- N. Weiss <- P. Franzmann: strain Pf4

doi: 10.13145/bacdive2266.20240916.9.1

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

@ref: 2399

domain: Bacteria

phylum: Firmicutes

class: Bacilli

order: Lactobacillales

family: Carnobacteriaceae

genus: Carnobacterium

species: Carnobacterium alterfunditum

full scientific name: Carnobacterium alterfunditum Franzmann et al. 1993

strain designation: pf4

type strain: yes

Morphology

cell morphology

  • @ref: 116268
  • gram stain: positive
  • cell shape: rod-shaped
  • motility: yes

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
2399TSBY 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
40197MEDIUM 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)
116268CIP Medium 297yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=297

culture temp

@refgrowthtypetemperature
2399positivegrowth20
40197positivegrowth20
52228positivegrowth16-22
116268positivegrowth5-30
116268nogrowth37
116268nogrowth41

Physiology and metabolism

oxygen tolerance

@refoxygen tolerance
52228aerobe
116268facultative anaerobe

halophily

@refsaltgrowthtested relationconcentration
116268NaClnogrowth0 %
116268NaClnogrowth2 %
116268NaClnogrowth4 %
116268NaClnogrowth6 %
116268NaClnogrowth8 %
116268NaClnogrowth10 %

murein

  • @ref: 2399
  • 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
68371salicin+builds acid from17814
68371esculin+builds acid from4853
68371arbutin+builds acid from18305
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
68371L-arabinose-builds acid from30849
68371D-arabinose-builds acid from17108
68371erythritol-builds acid from17113
68371glycerol-builds acid from17754
116268citrate-carbon source16947
116268esculin+hydrolysis4853
116268hippurate+hydrolysis606565
116268nitrate-builds gas from17632
116268nitrate-reduction17632
116268nitrite-builds gas from16301
116268nitrite-reduction16301

metabolite production

  • @ref: 116268
  • 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
116268oxidase-
116268beta-galactosidase-3.2.1.23
116268alcohol dehydrogenase-1.1.1.1
116268gelatinase-
116268amylase-
116268caseinase-3.4.21.50
116268catalase-1.11.1.6
116268tween esterase-
116268gamma-glutamyltransferase-2.3.2.2
116268lysine decarboxylase-4.1.1.18
116268ornithine decarboxylase-4.1.1.17
116268tryptophan deaminase-
116268urease-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
116268-----+---+----------

API 50CHac

@refGLYERYDARALARARIBDXYLLXYLADOMDXGALGLUFRUMNESBERHADULINOMANSORMDMMDGNAGAMYARBESCSALCELMALLACMELSACTREINUMLZRAFAMDGLYGXLTGENTURLYXTAGDFUCLFUCDARLLARLGNT2KG5KG
116268----+/------+++--------++/-++++/-+--++---++------------

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcontinentcountryorigin.country
2399waterVestfold Hills, Ace Lake, depth 24 mAustralia and Oceania
52228WaterVestfold Hills,Ace LakeAustralia and OceaniaAntarcticaATA
116268Environment, Ace lakeVestfold hillsAntarcticaAntarcticaATA

isolation source categories

  • Cat1: #Environmental
  • Cat2: #Aquatic

taxonmaps

  • @ref: 69479
  • File name: preview.99_1671.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_13;96_41;97_43;98_47;99_1671&stattab=map
  • Last taxonomy: Carnobacterium
  • 16S sequence: AB680898
  • Sequence Identity:
  • Total samples: 1285
  • soil counts: 303
  • aquatic counts: 370
  • animal counts: 580
  • plant counts: 32

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
23991Risk group (German classification)
1162681Risk group (French classification)

Sequence information

16S sequences

@refdescriptionaccessionlengthdatabaseNCBI tax ID
20218Carnobacterium alterfunditum large 16S-23S rRNA intergenic spacer, tRNA-Ile and tRNA-Ala genes, complete sequenceAY170834448nuccore28230
20218Carnobacterium alterfunditum medium 16S-23S rRNA intergenic spacer and tRNA-Ala gene, complete sequenceAY170835337nuccore28230
20218Carnobacterium alterfunditum small 16S-23S rRNA intergenic spacer, complete sequenceAY170836225nuccore28230
20218Carnobacterium alterfunditum gene for 16S rRNA, partial sequence, strain: NBRC 15548AB6808981484nuccore28230

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Carnobacterium alterfunditum DSM 5972 pf4GCA_000744115contigncbi1449335
66792Carnobacterium alterfunditum DSM 5972 strain pf41449335.3wgspatric1449335
66792Carnobacterium alterfunditum pf42574179752draftimg28230

GC content

  • @ref: 2399
  • GC-content: 33.3
  • method: thermal denaturation, midpoint method (Tm)

Genome-based predictions

predictions

@reftraitmodeldescriptionpredictionconfidencetraining_data
69481spore-formingspore-formingAbility to form endo- or exosporesyes75no
69480gram-positivegram-positivePositive reaction to Gram-stainingyes87.844no
69480anaerobicanaerobicAbility to grow under anoxygenic conditions (including facultative anaerobes)no89.078yes
69480spore-formingspore-formingAbility to form endo- or exosporesno68.494no
69480aerobicaerobicAbility to grow under oxygenic conditions (including facultative aerobes)no89.744no
69480thermophilicthermophileAbility to grow at temperatures above or equal to 45°Cno92.833yes
69480flagellatedmotile2+Ability to perform flagellated movementyes61.07no

External links

@ref: 2399

culture collection no.: DSM 5972, ACAM 313, ATCC 49837, CCUG 34643, IFO 15548, CIP 105796

straininfo link

  • @ref: 71825
  • straininfo: 8234

literature

  • topic: Phylogeny
  • Pubmed-ID: 1793333
  • title: Psychrotrophic, lactic acid-producing bacteria from anoxic waters in Ace Lake, Antarctica; Carnobacterium funditum sp. nov. and Carnobacterium alterfunditum sp. nov.
  • authors: Franzmann PD, Hopfl P, Weiss N, Tindall BJ
  • journal: Arch Microbiol
  • DOI: 10.1007/BF00262994
  • year: 1991
  • mesh: Anaerobiosis, 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 Microbiology
  • topic2: Cultivation

Reference

@idauthorscataloguedoi/urltitlejournalpubmed
2399Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 5972)https://www.dsmz.de/collection/catalogue/details/culture/DSM-5972
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
40197Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/17854
52228Curators of the CCUGCulture Collection University of Gothenburg (CCUG) (CCUG 34643)https://www.ccug.se/strain?id=34643
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)
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)
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
71825Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID8234.1StrainInfo: A central database for resolving microbial strain identifiers
116268Curators of the CIPCollection of Institut Pasteur (CIP 105796)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20105796