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)

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General

@ref: 2399

BacDive-ID: 2266

DSM-Number: 5972

keywords: genome sequence, 16S sequence, Bacteria, aerobe, psychrophilic, Gram-positive

description: Carnobacterium alterfunditum pf4 is an aerobe, psychrophilic, Gram-positive 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/bacdive2266.20230509.8.1

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 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

@refgram stainconfidencecell shapemotility
69480positive100
116268positiverod-shapedyes

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

@refgrowthtypetemperaturerange
2399positivegrowth20psychrophilic
40197positivegrowth20psychrophilic
52228positivegrowth16-22psychrophilic
116268positivegrowth5-30
116268nogrowth37mesophilic
116268nogrowth41thermophilic

Physiology and metabolism

oxygen tolerance

@refoxygen tolerance
52228aerobe
116268facultative anaerobe

spore formation

  • @ref: 69480
  • spore formation: no
  • confidence: 99.97

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 sequenceAY170834448ena28230
20218Carnobacterium alterfunditum medium 16S-23S rRNA intergenic spacer and tRNA-Ala gene, complete sequenceAY170835337ena28230
20218Carnobacterium alterfunditum small 16S-23S rRNA intergenic spacer, complete sequenceAY170836225ena28230
20218Carnobacterium alterfunditum gene for 16S rRNA, partial sequence, strain: NBRC 15548AB6808981484ena28230

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

traitpredictionconfidencetraining_data
spore-formingyes75no
motileno55.223no
gram-positiveyes88.391no
anaerobicno97.144yes
halophileyes85.982no
spore-formingno86.965no
thermophileno98.487yes
glucose-utilyes89.587no
aerobicno91.686no
flagellatedno79.805no
glucose-fermentyes75.877no

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)
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