Strain identifier

BacDive ID: 6622

Type strain: Yes

Species: Lactobacillus kefiranofaciens

Strain Designation: WT-2B

Strain history: CIP <- 1989, ATCC <- T. Mitsuoka: strain WT-2B <- S. Adachi

NCBI tax ID(s): 1423827 (strain), 267818 (species)

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General

@ref: 1909

BacDive-ID: 6622

DSM-Number: 5016

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

description: Lactobacillus kefiranofaciens WT-2B is an anaerobe, mesophilic, Gram-positive bacterium that was isolated from kefir grains.

NCBI tax id

NCBI tax idMatching level
267818species
1423827strain

strain history

@refhistory
1909<- JCM <- S. Adachi et al., WT-2B
67770T. Fujisawa <-- S. Adachi WT-2B.
120396CIP <- 1989, ATCC <- T. Mitsuoka: strain WT-2B <- S. Adachi

doi: 10.13145/bacdive6622.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/bacillota
  • domain: Bacteria
  • phylum: Bacillota
  • class: Bacilli
  • order: Lactobacillales
  • family: Lactobacillaceae
  • genus: Lactobacillus
  • species: Lactobacillus kefiranofaciens
  • full scientific name: Lactobacillus kefiranofaciens Fujisawa et al. 1988

@ref: 1909

domain: Bacteria

phylum: Firmicutes

class: Bacilli

order: Lactobacillales

family: Lactobacillaceae

genus: Lactobacillus

species: Lactobacillus kefiranofaciens subsp. kefiranofaciens

full scientific name: Lactobacillus kefiranofaciens subsp. kefiranofaciens (Fujisawa et al. 1988) Vancanneyt et al. 2004

strain designation: WT-2B

type strain: yes

Morphology

cell morphology

  • @ref: 120396
  • gram stain: positive
  • cell shape: rod-shaped
  • motility: no

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
1909KPL MEDIUM (DSMZ Medium 456)yeshttps://mediadive.dsmz.de/medium/456Name: KPL MEDIUM (DSMZ Medium 456) Composition: Skim milk 87.6424 g/l Agar 13.1464 g/l Galactose 8.76424 g/l Glucose 8.76424 g/l White wine Tween 80
1909LACTOBACILLUS KEFIRANOFACIENS (DSMZ Medium 1253)yeshttps://mediadive.dsmz.de/medium/1253Name: LACTOBACILLUS KEFIRANOFACIENS (DSMZ Medium 1253) Composition: Man Rogosa Sharp broth 54.4016 g/l Maltose 9.8912 g/l Cysteine hydrochloride 0.098912 g/l Hemin 0.0049456 g/l White wine NaOH Distilled water
34032MEDIUM 184 - for Lactobacillus kefiranofaciensyesDistilled water make up to (900.000 ml);Maltose (10.000 g);Man Rogosa Sharp broth (55.000 g);White wine (100.000 ml);Hemin solution - M00149 (5.000 ml);Cysteinehydrochloride 10 % solution - M0177 (1.000 ml)
120396CIP Medium 41yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=41

culture temp

@refgrowthtypetemperaturerange
1909positivegrowth30mesophilic
1909positivegrowth28mesophilic
34032positivegrowth30mesophilic
50929positivegrowth30mesophilic
50929positivegrowth30-35mesophilic
67770positivegrowth30mesophilic
120396positivegrowth25-45
120396nogrowth15psychrophilic

culture pH

  • @ref: 50929
  • ability: positive
  • type: growth
  • pH: 5.3

Physiology and metabolism

oxygen tolerance

@refoxygen tolerance
1909anaerobe
50929anaerobe
50929microaerophile

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
68371melezitose-builds acid from6731
68371inulin-builds acid from15443
68371trehalose-builds acid from27082
68371sucrose+builds acid from17992
68371melibiose-builds acid from28053
68371cellobiose-builds acid from17057
68371salicin-builds acid from17814
68371esculin-builds acid from4853
68371arbutin-builds acid from18305
68371amygdalin-builds acid from27613
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-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
120396nitrate-reduction17632
120396nitrite-reduction16301
120396nitrate+respiration17632

metabolite production

  • @ref: 120396
  • Chebi-ID: 35581
  • metabolite: indole
  • production: no

metabolite tests

  • @ref: 120396
  • Chebi-ID: 15688
  • metabolite: acetoin
  • voges-proskauer-test: -

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
120396oxidase-
120396alcohol dehydrogenase-1.1.1.1
120396catalase-1.11.1.6
120396lysine decarboxylase-4.1.1.18
120396ornithine decarboxylase-4.1.1.17
120396urease-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
120396--++-+-+--++-+-+----

API 50CHac

@refQGLYERYDARALARARIBDXYLLXYLADOMDXGALGLUFRUMNESBERHADULINOMANSORMDMMDGNAGAMYARBESCSALCELMALLACMELSACTREINUMLZRAFAMDGLYGXLTGENTURLYXTAGDFUCLFUCDARLLARLGNT2KG5KG
1909-----+----++++/------------------+---+--------------
120396---------++++--------+-----++-+------------------

Isolation, sampling and environmental information

isolation

@refsample type
1909kefir grains
50929Kefir grains
67770Kefir grains
120396Food, Kefir grains

isolation source categories

  • Cat1: #Engineered
  • Cat2: #Food production

taxonmaps

  • @ref: 69479
  • File name: preview.99_4347.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_46;96_146;97_157;98_3269;99_4347&stattab=map
  • Last taxonomy: Lactobacillus kefiranofaciens subclade
  • 16S sequence: LC071845
  • Sequence Identity:
  • Total samples: 4633
  • soil counts: 80
  • aquatic counts: 146
  • animal counts: 4348
  • plant counts: 59

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
19091Risk group (German classification)
1203961Risk group (French classification)

Sequence information

16S sequences

@refdescriptionaccessionlengthdatabaseNCBI tax ID
20218Lactobacillus kefiranofaciens ATCC 43761 16S ribosomal RNA gene, partial sequenceAF429517487ena267818
20218Lactobacillus kefiranofaciens strain ATCC 43761 16S ribosomal RNA gene, partial sequence; 16S-23S intergenic spacer, complete sequence; and 23S ribosomal RNA gene, partial sequenceAF429604560ena267818
20218Lactobacillus kefiranofaciens subsp. kefiranofaciens partial 16S rRNA gene, type strain ATCC 43761TFR6830921549ena190905
20218Lactobacillus kefiranofaciens subsp. kefiranofaciens partial 16S rRNA gene, strain type strain:DSM 5016AM1137811552ena190905
20218Lactobacillus kefiranofaciens subsp. kefiranofaciens gene for 16S rRNA, partial sequence, strain: JCM 6985AB289182651ena190905
20218Lactobacillus kefiranofaciens subsp. kefiranofaciens 16S rRNA gene, strain LMG 19149AJ5752591516ena190905
67770Lactobacillus kefiranofaciens subsp. kefiranofaciens gene for 16S ribosomal RNA, partial sequence, strain: JCM 6985LC0718451497ena190905

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Lactobacillus kefiranofaciens ATCC 43761GCA_900103655scaffoldncbi267818
66792Lactobacillus kefiranofaciens subsp. kefiranofaciens DSM 5016 = JCM 6985GCA_000615685contigncbi1423827
66792Lactobacillus kefiranofaciens strain ATCC 43761267818.5wgspatric267818
66792Lactobacillus kefiranofaciens subsp. kefiranofaciens DSM 5016 = JCM 69851423827.3wgspatric1423827
66792Lactobacillus kefiranofaciens subsp. kefiranofaciens JCM 69851236946.3wgspatric1423827
66792Lactobacillus kefiranofaciens kefiranofaciens DSM 50162667528030draftimg1423827
66792Lactobacillus kefiranofaciens ATCC 437612597490363draftimg267818
66792Lactobacillus kefiranofaciens kefiranofaciens JCM 69852585427926draftimg1423827
67770Lactobacillus kefiranofaciens subsp. kefiranofaciens DSM 5016 = JCM 6985GCA_001435275scaffoldncbi1423827

GC content

@refGC-contentmethod
190934.3
6777037.2
6777034.3thermal denaturation, midpoint method (Tm)

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
motileno96.489no
gram-positiveyes95.242no
anaerobicyes82.869no
halophileyes78.643no
spore-formingno95.56no
glucose-utilyes92.328no
thermophileno97.06yes
aerobicno98.123yes
flagellatedno97.75no
glucose-fermentyes89.411no

External links

@ref: 1909

culture collection no.: CCUG 32248, LMG 9916, CIP 103307, DSM 5016, ATCC 43761, JCM 6985, BCRC 16059, CECT 5954, CGMCC 1.3402, KCTC 5075, LMG 19149, NCFB 2797, NCIMB 702797, NRIC 1718

straininfo link

  • @ref: 76096
  • straininfo: 3321

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Genetics15315396Structural characterization and biological activities of an exopolysaccharide kefiran produced by Lactobacillus kefiranofaciens WT-2B(T).Maeda H, Zhu X, Suzuki S, Suzuki K, Kitamura SJ Agric Food Chem10.1021/jf049617g2004Animals, Blood Pressure/drug effects, Carbohydrate Sequence, Chemical Phenomena, Chemistry, Physical, Edible Grain/microbiology, Gas Chromatography-Mass Spectrometry, Lactobacillus/*metabolism, Lipids/blood, Magnetic Resonance Spectroscopy, Male, Methylation, Molecular Sequence Data, Polysaccharides/*chemistry/*pharmacology, RatsPathogenicity
Biotechnology27822552Microbial Succession and Flavor Production in the Fermented Dairy Beverage Kefir.Walsh AM, Crispie F, Kilcawley K, O'Sullivan O, O'Sullivan MG, Claesson MJ, Cotter PDmSystems10.1128/mSystems.00052-162016

Reference

@idauthorscataloguedoi/urltitlejournalpubmed
1909Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 5016)https://www.dsmz.de/collection/catalogue/details/culture/DSM-5016
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
34032Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/15091
50929Curators of the CCUGCulture Collection University of Gothenburg (CCUG) (CCUG 32248)https://www.ccug.se/strain?id=32248
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
76096Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID3321.1StrainInfo: A central database for resolving microbial strain identifiers
120396Curators of the CIPCollection of Institut Pasteur (CIP 103307)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20103307