Strain identifier

BacDive ID: 2270

Type strain: Yes

Species: Carnobacterium pleistocenium

Strain Designation: FTR 1, FTR1

Strain history: CIP <- 2003, E. Pikuta, NSSTC/NASA, Hunstville, Alabama, USA: strain FTR1

NCBI tax ID(s): 181073 (species)

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General

@ref: 7157

BacDive-ID: 2270

DSM-Number: 17715

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

description: Carnobacterium pleistocenium FTR 1 is an anaerobe, psychrophilic, Gram-positive bacterium that was isolated from ice core sample, Pleistocene thermokarst pond.

NCBI tax id

  • NCBI tax id: 181073
  • Matching level: species

strain history

@refhistory
7157<- E.V. Pikuta, FTR1
338722003, E. Pikuta, NSSTC/NASA, Hunstville, Alabama, USA: strain FTR1
67770E. V. Pikuta FTR1.
121869CIP <- 2003, E. Pikuta, NSSTC/NASA, Hunstville, Alabama, USA: strain FTR1

doi: 10.13145/bacdive2270.20230509.8.1

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 pleistocenium
  • full scientific name: Carnobacterium pleistocenium Pikuta et al. 2005

@ref: 7157

domain: Bacteria

phylum: Firmicutes

class: Bacilli

order: Lactobacillales

family: Carnobacteriaceae

genus: Carnobacterium

species: Carnobacterium pleistocenium

full scientific name: Carnobacterium pleistocenium Pikuta et al. 2005

strain designation: FTR 1, FTR1

type strain: yes

Morphology

cell morphology

  • @ref: 121869
  • gram stain: positive
  • cell shape: rod-shaped
  • motility: no

colony morphology

  • @ref: 121869

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
7157PYG MEDIUM (MODIFIED) (DSMZ Medium 104)yeshttps://mediadive.dsmz.de/medium/104Name: PYG MEDIUM (modified) (DSMZ Medium 104) Composition: Yeast extract 10.0 g/l Peptone 5.0 g/l Trypticase peptone 5.0 g/l Beef extract 5.0 g/l Glucose 5.0 g/l L-Cysteine HCl x H2O 0.5 g/l NaHCO3 0.4 g/l NaCl 0.08 g/l K2HPO4 0.04 g/l KH2PO4 0.04 g/l MgSO4 x 7 H2O 0.02 g/l CaCl2 x 2 H2O 0.01 g/l Hemin 0.005 g/l Ethanol 0.0038 g/l Resazurin 0.001 g/l Tween 80 Vitamin K1 NaOH Distilled water
33872MEDIUM 6 - Columbia agar with 10 % horse bloodyesDistilled water make up to (1000.000 ml);Columbia agar (39.000 g);Horseblood (100.000 ml)
121869CIP Medium 6yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=6

culture temp

@refgrowthtypetemperaturerange
7157positivegrowth23psychrophilic
33872positivegrowth22psychrophilic
67770positivegrowth26mesophilic
121869positivegrowth5-25psychrophilic
121869nogrowth30mesophilic
121869nogrowth37mesophilic
121869nogrowth41thermophilic

Physiology and metabolism

oxygen tolerance

@refoxygen tolerance
7157anaerobe
121869facultative anaerobe

halophily

@refsaltgrowthtested relationconcentration
121869NaClpositivegrowth0-2 %
121869NaClnogrowth4 %
121869NaClnogrowth6 %
121869NaClnogrowth8 %
121869NaClnogrowth10 %

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
68371melibiose-builds acid from28053
68371lactose-builds acid from17716
68371amygdalin-builds acid from27613
68371methyl alpha-D-glucopyranoside-builds acid from320061
68371methyl alpha-D-mannoside-builds acid from43943
68371D-sorbitol-builds acid from17924
68371myo-inositol-builds acid from17268
68371galactitol-builds acid from16813
68371L-rhamnose-builds acid from62345
68371L-sorbose-builds acid from17266
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
68369malate-assimilation25115
68369adipate-assimilation17128
68369decanoate-assimilation27689
68369gluconate-assimilation24265
68369maltose-assimilation17306
68369N-acetylglucosamine-assimilation59640
68369D-mannitol-assimilation16899
68369D-mannose-assimilation16024
68369L-arabinose-assimilation30849
68369D-glucose-assimilation17634
68369gelatin-hydrolysis5291
68369esculin-hydrolysis4853
68369urea+hydrolysis16199
68369arginine-hydrolysis29016
68369D-glucose-fermentation17634
68369tryptophan-energy source27897
68369nitrate+reduction17632
68368nitrate-reduction17632
68368D-glucose-fermentation17634
68368gelatin-hydrolysis5291
68368tryptophan-energy source27897
68368urea-hydrolysis16199
68368citrate-assimilation16947
68368ornithine-degradation18257
68368lysine-degradation25094
68368arginine-hydrolysis29016
121869D-arabinose-degradation17108
121869D-fructose-degradation15824
121869D-glucose-degradation17634
121869D-mannose-degradation16024
121869D-xylose-degradation65327
121869cellobiose-degradation17057
121869lactose-degradation17716
121869maltose-degradation17306
121869salicin-degradation17814
121869sucrose-degradation17992
121869citrate-carbon source16947
121869esculin+hydrolysis4853
121869hippurate+hydrolysis606565
121869nitrate-builds gas from17632
121869nitrate-reduction17632
121869nitrite-builds gas from16301
121869nitrite-reduction16301

metabolite production

@refChebi-IDmetaboliteproduction
6836935581indoleno
6836817997dinitrogenno
6836816301nitriteno
6836815688acetoinno
6836835581indoleno
6836816136hydrogen sulfideno
12186935581indoleno

metabolite tests

@refChebi-IDmetaboliteindole testvoges-proskauer-test
6836935581indole-
6836815688acetoin-
6836835581indole-

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
68369cytochrome oxidase+1.9.3.1
68369gelatinase-
68369beta-glucosidase-3.2.1.21
68369urease+3.5.1.5
68369arginine dihydrolase-3.5.3.6
68368gelatinase-
68368tryptophan deaminase-4.1.99.1
68368urease-3.5.1.5
68368ornithine decarboxylase-4.1.1.17
68368lysine decarboxylase-4.1.1.18
68368arginine dihydrolase-3.5.3.6
68368beta-galactosidase-3.2.1.23
121869oxidase-
121869beta-galactosidase-3.2.1.23
121869alcohol dehydrogenase-1.1.1.1
121869gelatinase-
121869amylase-
121869DNase-
121869caseinase-3.4.21.50
121869catalase-1.11.1.6
121869tween esterase-
121869gamma-glutamyltransferase-2.3.2.2
121869lysine decarboxylase-4.1.1.18
121869ornithine decarboxylase-4.1.1.17
121869phenylalanine ammonia-lyase-4.3.1.24
121869tryptophan deaminase-
121869urease-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
121869--+-------++--------

API 20E

@refONPGADH ArgLDC LysODCCITH2SURETDA TrpINDVPGELGLUNO2N2
121869--------------

API 20NE

@refNO3TRPGLU_ FermADH ArgUREESCGELPNPGGLU_ AssimARAMNEMANNAGMALGNTCAPADIMLTCITPACOX
7157+---+---------------+

API 50CHac

@refGLYERYDARALARARIBDXYLLXYLADOMDXGALGLUFRUMNESBERHADULINOMANSORMDMMDGNAGAMYARBESCSALCELMALLACMELSACTREINUMLZRAFAMDGLYGXLTGENTURLYXTAGDFUCLFUCDARLLARLGNT2KG5KG
121869----------+/-+/-+/-----+/----+/--+/-+/-+/-+/-+/---+/-+/------------------

API biotype100

@refGLUFRUGALTREMNESBEMELSACRAFMTEMALLACLTEMbGaMaGaCELGENMbGuESCRIBARAXYLPLERHAFUCMLZDARLLARLXLTDULTAGGLYINOMANMTLTURSORADOHBGLYXERYMDG3MDGSATMUCLTATDTATMTATDMLTLMLTCATETATETTECITGRTGAT2KG5KGTRYNAGGNTPACPATpOBEQATGTEmOBEBATPPATCMTTGEBETPCEABTHINLATCAPCYTHISSUCFUMGREGYTAVTETNTTNGLNITA3OBUAPTGTTPRODALALALASERMNTPROPTYR2KT
121869------------------+--------------------------------------------------------------------------------

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinent
7157ice core sample, Pleistocene thermokarst pondFox Permafrost Tunnel, AlaskaUSAUSANorth America
67770Ice core sample of permafrost from Fox TunnelAlaskaUSAUSANorth America
121869Frozen pleistocene thermokarst pond in CRREL permafrost tunnelFox, AlaskaUnited States of AmericaUSANorth America

isolation source categories

Cat1Cat2Cat3
#Environmental#Aquatic#Ice
#Environmental#Aquatic#Pond (small)
#Environmental#Terrestrial#Core sample

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: AF450136
  • 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
71571Risk group (German classification)
1218691Risk group (French classification)

Sequence information

16S sequences

  • @ref: 7157
  • description: Carnobacterium pleistocenium strain FTR1 16S ribosomal RNA gene, partial sequence
  • accession: AF450136
  • length: 1486
  • database: ena
  • NCBI tax ID: 1449343

Genome sequences

  • @ref: 67770
  • description: Carnobacterium pleistocenium FTR1
  • accession: GCA_000744285
  • assembly level: contig
  • database: ncbi
  • NCBI tax ID: 1449343

GC content

  • @ref: 67770
  • GC-content: 62.2
  • method: thermal denaturation, midpoint method (Tm)

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
motileno59.311no
flagellatedno78.738no
gram-positiveyes84.779no
anaerobicno95.266no
aerobicno93.047yes
halophileyes85.831no
spore-formingno86.912no
glucose-utilyes88.316no
thermophileno98.821yes
glucose-fermentyes75.008no

External links

@ref: 7157

culture collection no.: DSM 17715, ATCC BAA 754, CIP 108033, JCM 12174

straininfo link

  • @ref: 71828
  • straininfo: 135106

literature

  • topic: Phylogeny
  • Pubmed-ID: 15653921
  • title: Carnobacterium pleistocenium sp. nov., a novel psychrotolerant, facultative anaerobe isolated from permafrost of the Fox Tunnel in Alaska.
  • authors: Pikuta EV, Marsic D, Bej A, Tang J, Krader P, Hoover RB
  • journal: Int J Syst Evol Microbiol
  • DOI: 10.1099/ijs.0.63384-0
  • year: 2005
  • mesh: Alaska, Anaerobiosis, Bacterial Typing Techniques, DNA, Bacterial/analysis, DNA, Ribosomal/analysis, *Fossils, Freezing, Genes, rRNA, Gram-Positive Asporogenous Rods/*classification/genetics/growth & development/isolation & purification, *Ice, Molecular Sequence Data, Nucleic Acid Hybridization, RNA, Ribosomal, 16S/genetics, *Soil Microbiology
  • topic2: Genetics

Reference

@idauthorscataloguedoi/urltitle
7157Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 17715)https://www.dsmz.de/collection/catalogue/details/culture/DSM-17715
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
33872Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/5611
67770Curators of the JCMhttps://jcm.brc.riken.jp/en/
68368Automatically annotated from API 20E
68369Automatically annotated from API 20NE
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
71828Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID135106.1StrainInfo: A central database for resolving microbial strain identifiers
121869Curators of the CIPCollection of Institut Pasteur (CIP 108033)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20108033