Strain identifier

BacDive ID: 6828

Type strain: Yes

Species: Leuconostoc citreum

Strain Designation: B2399

Strain history: CIP <- 1989, NCFB <- 1966, A.C. Hayward, Kew, UK: strain B2399

NCBI tax ID(s): 33964 (species)

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General

@ref: 2229

BacDive-ID: 6828

DSM-Number: 5577

keywords: genome sequence, 16S sequence, Bacteria, facultative anaerobe, mesophilic, human pathogen

description: Leuconostoc citreum B2399 is a facultative anaerobe, mesophilic human pathogen that was isolated from honey dew of rye ear.

NCBI tax id

  • NCBI tax id: 33964
  • Matching level: species

strain history

@refhistory
2229<- NCFB <- A.C. Hayward, B2399
67770NRIC 1776 <-- NCFB 1837 <-- A. C. Hayward B2399.
118298CIP <- 1989, NCFB <- 1966, A.C. Hayward, Kew, UK: strain B2399

doi: 10.13145/bacdive6828.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/bacillota
  • domain: Bacteria
  • phylum: Bacillota
  • class: Bacilli
  • order: Lactobacillales
  • family: Lactobacillaceae
  • genus: Leuconostoc
  • species: Leuconostoc citreum
  • full scientific name: Leuconostoc citreum Farrow et al. 1989

  • synonyms

    • @ref: 20215
    • synonym: Leuconostoc amelibiosum

@ref: 2229

domain: Bacteria

phylum: Firmicutes

class: Bacilli

order: Lactobacillales

family: Leuconostocaceae

genus: Leuconostoc

species: Leuconostoc citreum

full scientific name: Leuconostoc citreum Farrow et al. 1989

strain designation: B2399

type strain: yes

Morphology

cell morphology

@refmotilityconfidencegram staincell shape
69480no95.613
69480100positive
118298nopositiveovoid-shaped

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
2229MRS MEDIUM (DSMZ Medium 11)yeshttps://mediadive.dsmz.de/medium/11Name: MRS MEDIUM (DSMZ Medium 11) Composition: Glucose 20.0 g/l Casein peptone 10.0 g/l Meat extract 10.0 g/l Na-acetate 5.0 g/l Yeast extract 5.0 g/l (NH4)3 citrate 2.0 g/l K2HPO4 2.0 g/l Tween 80 1.0 g/l MgSO4 x 7 H2O 0.2 g/l MnSO4 x H2O 0.05 g/l Distilled water
34244MEDIUM 40- for Lactobacillus and LeuconostocyesDistilled water make up to (1000.000 ml);Man Rogosa Sharp agar (68.000 g)
118298CIP Medium 40yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=40

culture temp

@refgrowthtypetemperaturerange
2229positivegrowth28mesophilic
34244positivegrowth30
49880positivegrowth30
67770positivegrowth30mesophilic
118298positivegrowth10-37
118298nogrowth45thermophilic

Physiology and metabolism

oxygen tolerance

  • @ref: 118298
  • oxygen tolerance: facultative anaerobe

spore formation

@refspore formationconfidence
69481no100
69480no99.999

halophily

@refsaltgrowthtested relationconcentration
118298NaClpositivegrowth0-4 %
118298NaClnogrowth6 %
118298NaClnogrowth8 %
118298NaClnogrowth10 %

murein

  • @ref: 2229
  • murein short key: A11.05
  • type: A3alpha L-Lys-L-Ala2

metabolite utilization

@refmetaboliteutilization activitykind of utilization testedChebi-ID
68371Potassium 5-ketogluconate-builds acid from
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
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
68371D-ribose-builds acid from16988
68371L-arabinose+builds acid from30849
68371D-arabinose-builds acid from17108
68371erythritol-builds acid from17113
68371glycerol-builds acid from17754
118298citrate-carbon source16947
118298nitrate-reduction17632
118298nitrite-reduction16301
118298nitrate+respiration17632

antibiotic resistance

  • @ref: 118298
  • metabolite: 0129 (2,4-Diamino-6,7-di-iso-propylpteridine phosphate)
  • is antibiotic: yes
  • is sensitive: no
  • is resistant: yes

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
118298oxidase-
118298alcohol dehydrogenase-1.1.1.1
118298gelatinase-
118298caseinase-3.4.21.50
118298catalase-1.11.1.6
118298lysine decarboxylase-4.1.1.18
118298ornithine decarboxylase-4.1.1.17

fatty acid profile

  • fatty acids

    @reffatty acidpercentageECL
    49880C14:02.314
    49880C16:038.616
    49880C16:1 ω7c8.515.819
    49880C17:0 CYCLO2.716.888
    49880C18:1 ω7c /12t/9t7.517.824
    49880C18:2 ω6,9c/C18:0 ANTE12.517.724
    49880C19:0 CYCLO ω8c27.918.9
  • type of FA analysis: whole cell analysis
  • method/protocol: CCUG

API zym

@refControlAlkaline phosphataseEsteraseEsterase LipaseLipaseLeucine arylamidaseValine arylamidaseCystine arylamidaseTrypsinalpha- ChymotrypsinAcid phosphataseNaphthol-AS-BI-phosphohydrolasealpha- Galactosidasebeta- Galactosidasebeta- Glucuronidasealpha- Glucosidasebeta- GlucosidaseN-acetyl-beta- glucosaminidasealpha- Mannosidasealpha- Fucosidase
118298--+-------++---+----

API 50CHac

@refQGLYERYDARALARARIBDXYLLXYLADOMDXGALGLUFRUMNESBERHADULINOMANSORMDMMDGNAGAMYARBESCSALCELMALLACMELSACTREINUMLZRAFAMDGLYGXLTGENTURLYXTAGDFUCLFUCDARLLARLGNT2KG5KG
2229----+------+++-------++++++++--++-------+---------
118298---+------+++-------++-+++-+--++------+/-+------++-

Isolation, sampling and environmental information

isolation

@refsample type
2229honey dew of rye ear
49880Honey-dew of rye ear
67770Honeydew of rye ear
118298Plant, Honey-dew of rye ear

isolation source categories

Cat1Cat2Cat3
#Host#Plants#Herbaceous plants (Grass,Crops)
#Host Body-Site#Plant#Fruit (Seed)
#Host Body Product#Plant#Plant exudate (Resin)

taxonmaps

  • @ref: 69479
  • File name: preview.99_476.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_22;96_35;97_348;98_393;99_476&stattab=map
  • Last taxonomy: Leuconostoc
  • 16S sequence: LC096222
  • Sequence Identity:
  • Total samples: 25424
  • soil counts: 1568
  • aquatic counts: 3075
  • animal counts: 19457
  • plant counts: 1324

Safety information

risk assessment

@refpathogenicity humanbiosafety levelbiosafety level comment
2229yes, in single cases1Risk group (German classification)
1182981Risk group (French classification)

Sequence information

16S sequences

@refdescriptionaccessionlengthdatabaseNCBI tax ID
20218Leuconostoc citreum 16S ribosomal RNA gene, partial sequenceAF1119481505ena33964
20218Leuconostoc citreum gene for 16S rRNA, strain:NRIC 1776AB0229231448ena33964
20218Leuconostoc citreum DNA, 16S-23S rRNA intergenic spacer region, strain: NRIC 1776AB290437377ena33964
67770Leuconostoc citreum gene for 16S ribosomal RNA, partial sequence, strain: JCM 9698LC0962221491ena33964

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Leuconostoc citreum NRIC 1776GCA_008326545scaffoldncbi33964
66792Leuconostoc citreum strain ATCC 4937033964.176wgspatric33964
66792Leuconostoc citreum strain NRIC 177633964.186wgspatric33964
67770Leuconostoc citreum ATCC 49370GCA_004354555contigncbi33964

GC content

@refGC-contentmethod
222939.8
6777039.8thermal denaturation, midpoint method (Tm)

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno100no
motileno96.303no
flagellatedno98.029no
gram-positiveyes96.509no
anaerobicno85.219no
aerobicno96.355no
halophileyes94.243no
spore-formingno94.944no
glucose-utilyes89.253no
thermophileno99.84no
glucose-fermentyes88.32no

External links

@ref: 2229

culture collection no.: DSM 5577, ATCC 49370, NCDO 1837, CCUG 30060, JCM 9698, CCM 4544, CECT 4025, CGMCC 1.2461, CIP 103315, KCTC 3526, LMG 9849, NCFB 1837, NCIMB 13121, NRIC 1776, VTT E-93504

straininfo link

  • @ref: 76293
  • straininfo: 3489

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny11034505Leuconostoc kimchii sp. nov., a new species from kimchi.Kim J, Chun J, Han HUInt J Syst Evol Microbiol10.1099/00207713-50-5-19152000Bacterial Typing Techniques, Base Composition, DNA, Bacterial/chemistry/genetics, DNA, Ribosomal/chemistry/genetics, Korea, Leuconostoc/chemistry/*classification/*genetics/physiology, Molecular Sequence Data, Nucleic Acid Hybridization, Phenotype, Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Vegetables/*microbiologyGenetics
Enzymology18167460Expression of alpha-galactosidase gene from Leuconostoc mesenteroides SY1 in Leuconostoc citreum.Park JY, Jeong SJ, Lee AR, Park JY, Jeong WJ, Kim JHJ Microbiol Biotechnol70902007Blotting, Western, DNA, Bacterial/chemistry/genetics, Electroporation, Gene Expression, Leuconostoc/*enzymology/genetics, Polymerase Chain Reaction, Transcription, Genetic/genetics/physiology, alpha-Galactosidase/*biosynthesis/geneticsGenetics
Phylogeny19406772Leuconostoc palmae sp. nov., a novel lactic acid bacterium isolated from palm wine.Ehrmann MA, Freiding S, Vogel RFInt J Syst Evol Microbiol10.1099/ijs.0.005983-02009*Arecaceae, Bacterial Proteins/genetics, Bacterial Typing Techniques, Base Composition, DNA, Bacterial/analysis, DNA, Ribosomal/analysis, Fermentation, Genes, rRNA, Lactic Acid/metabolism, Leuconostoc/*classification/genetics/isolation & purification/physiology, Molecular Sequence Data, Nucleic Acid Hybridization, Phylogeny, RNA, Ribosomal, 16S/genetics, Rec A Recombinases/genetics, Senegal, Sequence Analysis, DNA, Species Specificity, Wine/*microbiologyGenetics
Metabolism20820868Mannitol production by lactic acid bacteria grown in supplemented carob syrup.Carvalheiro F, Moniz P, Duarte LC, Esteves MP, Girio FMJ Ind Microbiol Biotechnol10.1007/s10295-010-0823-52010Culture Media/metabolism, Fabaceae/chemistry, *Fermentation, Fructose/metabolism, Glucose/metabolism, *Industrial Microbiology, Lactobacillus/*metabolism, Leuconostoc/*metabolism, Mannitol/*metabolismBiotechnology

Reference

@idauthorscataloguedoi/urltitlejournalpubmed
2229Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 5577)https://www.dsmz.de/collection/catalogue/details/culture/DSM-5577
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
34244Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/15099
49880Curators of the CCUGCulture Collection University of Gothenburg (CCUG) (CCUG 30060)https://www.ccug.se/strain?id=30060
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
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
76293Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID3489.1StrainInfo: A central database for resolving microbial strain identifiers
118298Curators of the CIPCollection of Institut Pasteur (CIP 103315)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20103315