Strain identifier

BacDive ID: 6822

Type strain: Yes

Species: Leuconostoc mesenteroides subsp. dextranicum

Strain history: CIP <- 1986, DSM <- NCDO <- NIRD <- S. Orla-Jensen, NRRL: strain B-3469, "Betacoccus bovis"

NCBI tax ID(s): 33966 (subspecies)

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General

@ref: 8730

BacDive-ID: 6822

DSM-Number: 20484

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

description: Leuconostoc mesenteroides subsp. dextranicum DSM 20484 is a facultative anaerobe, mesophilic human pathogen of the family Lactobacillaceae.

NCBI tax id

  • NCBI tax id: 33966
  • Matching level: subspecies

strain history

@refhistory
8730<- NCDO <- NIRD <- S. Orla-Jensen
67770NRIC 1539 <-- ATCC 19255 <-- NCDO 529 <-- NIRD <-- S. Orla-Jensen ("Betacoccus bovis").
120900CIP <- 1986, DSM <- NCDO <- NIRD <- S. Orla-Jensen, NRRL: strain B-3469, "Betacoccus bovis"

doi: 10.13145/bacdive6822.20230509.8.1

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 mesenteroides subsp. dextranicum
  • full scientific name: Leuconostoc mesenteroides subsp. dextranicum (Beijerinck 1912) Garvie 1983

  • synonyms

    @refsynonym
    20215Leuconostoc dextranicum
    20215Lactococcus dextranicus

@ref: 8730

domain: Bacteria

phylum: Firmicutes

class: Bacilli

order: Lactobacillales

family: Leuconostocaceae

genus: Leuconostoc

species: Leuconostoc mesenteroides subsp. dextranicum

full scientific name: Leuconostoc mesenteroides subsp. dextranicum (Beijerinck 1912) Garvie 1983

type strain: yes

Morphology

cell morphology

@refmotilityconfidencegram staincell shape
69480no97.62
69480100positive
120900nopositivecoccus-shaped

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
8730MRS 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
34909MEDIUM 40- for Lactobacillus and LeuconostocyesDistilled water make up to (1000.000 ml);Man Rogosa Sharp agar (68.000 g)
120900CIP Medium 40yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=40

culture temp

@refgrowthtypetemperaturerange
8730positivegrowth30mesophilic
34909positivegrowth30mesophilic
67770positivegrowth30mesophilic
120900positivegrowth10-37
120900nogrowth45thermophilic

Physiology and metabolism

oxygen tolerance

  • @ref: 120900
  • oxygen tolerance: facultative anaerobe

spore formation

@refspore formationconfidence
69481no100
69480no100

halophily

@refsaltgrowthtested relationconcentration
120900NaClpositivegrowth0-4 %
120900NaClnogrowth6 %
120900NaClnogrowth8 %
120900NaClnogrowth10 %

murein

  • @ref: 8730
  • murein short key: A11.20
  • type: A3alpha L-Lys-L-Ser-L-Ala2

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
68371sucrose+builds acid from17992
68371melibiose-builds acid from28053
68371lactose-builds acid from17716
68371maltose-builds acid from17306
68371cellobiose-builds acid from17057
68371salicin-builds acid from17814
68371esculin-builds acid from4853
68371arbutin-builds acid from18305
68371amygdalin-builds acid from27613
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
120900citrate-carbon source16947
120900nitrate-reduction17632
120900nitrite-reduction16301
120900nitrate+respiration17632

antibiotic resistance

  • @ref: 120900
  • metabolite: 0129 (2,4-Diamino-6,7-di-iso-propylpteridine phosphate)
  • is antibiotic: yes
  • is sensitive: no
  • is resistant: yes

metabolite production

  • @ref: 120900
  • metabolite: polysaccharides
  • production: yes

metabolite tests

  • @ref: 120900
  • 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
120900oxidase-
120900alcohol dehydrogenase-1.1.1.1
120900gelatinase-
120900caseinase-3.4.21.50
120900catalase-1.11.1.6
120900lysine decarboxylase-4.1.1.18
120900ornithine decarboxylase-4.1.1.17

API zym

@refControlAlkaline phosphataseEsteraseEsterase LipaseLipaseLeucine arylamidaseValine arylamidaseCystine arylamidaseTrypsinalpha- ChymotrypsinAcid phosphataseNaphthol-AS-BI-phosphohydrolasealpha- Galactosidasebeta- Galactosidasebeta- Glucuronidasealpha- Glucosidasebeta- GlucosidaseN-acetyl-beta- glucosaminidasealpha- Mannosidasealpha- Fucosidase
120900-+++-+--+-++--------

API 50CHac

@refQGLYERYDARALARARIBDXYLLXYLADOMDXGALGLUFRUMNESBERHADULINOMANSORMDMMDGNAGAMYARBESCSALCELMALLACMELSACTREINUMLZRAFAMDGLYGXLTGENTURLYXTAGDFUCLFUCDARLLARLGNT2KG5KG
8730-----------+++--------+--------++-----------------
8730-----------+++--------+--------++-----------------
8730-----------+++--------+--------++-----------------
120900----------+++--------+--------++/------------------

Isolation, sampling and environmental information

taxonmaps

  • @ref: 69479
  • File name: preview.99_41.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_22;96_35;97_36;98_39;99_41&stattab=map
  • Last taxonomy: Leuconostoc
  • 16S sequence: LC096223
  • Sequence Identity:
  • Total samples: 44756
  • soil counts: 3647
  • aquatic counts: 6333
  • animal counts: 32069
  • plant counts: 2707

Safety information

risk assessment

@refpathogenicity humanbiosafety levelbiosafety level comment
8730yes, in single cases1Risk group (German classification)
1209001Risk group (French classification)

Sequence information

16S sequences

@refdescriptionaccessionlengthdatabaseNCBI tax ID
20218Leuconostoc mesenteroides strain ATCC 19255 16S ribosomal RNA gene, partial sequenceKC510252804ena1245
20218Leuconostoc mesenteroides subsp. dextranicum strain CCUG 30065 16S-23S ribosomal RNA intergenic spacer, complete sequenceJQ012781371ena33966
20218Leuconostoc mesenteroides subsp. dextranicum gene for 16S rRNA, partial sequence, strain: JCM 9700AB5969401473ena33966
20218Leuconostoc mesenteroides strain LMG 6908 16S-23S ribosomal RNA intergenic spacer, partial sequenceHM443964374ena1245
20218Leuconostoc mesenteroides subsp. dextranicum gene for 16S rRNA, partial sequence, strain: NBRC 100495AB6811931476ena33966
20218Leuconostoc mesenteroides gene for 16S ribosomal RNA, partial sequenceD31671161ena33966
20218Leuconostoc mesenteroides DNA for 16S ribosomal RNA, strain NCFB 529AB0232441449ena33966
67770Leuconostoc mesenteroides subsp. dextranicum gene for 16S ribosomal RNA, partial sequence, strain: JCM 9700LC0962231493ena33966

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Leuconostoc mesenteroides subsp. dextranicum DSM 20484GCA_001047695completencbi33966
66792Leuconostoc mesenteroides subsp. dextranicum strain DSM 2048433966.9plasmidpatric33966
66792Leuconostoc mesenteroides subsp. dextranicum strain DSM 2048433966.4completepatric33966
66792Leuconostoc mesenteroides subsp. dextranicum strain NBRC 10049533966.10wgspatric33966
66792Leuconostoc mesenteroides dextranicum DSM 204842645727607completeimg33966
67770Leuconostoc mesenteroides subsp. dextranicum NBRC 100495GCA_007990145contigncbi33966

GC content

  • @ref: 8730
  • GC-content: 40.8

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno100no
motileno95.758no
flagellatedno97.432no
gram-positiveyes96.988no
anaerobicno89.666no
aerobicno96.941no
halophileyes94.113no
spore-formingno94.905no
thermophileno99.308yes
glucose-utilyes89.277no
glucose-fermentyes92.809no

External links

@ref: 8730

culture collection no.: DSM 20484, ATCC 19255, CCM 2086, NCDO 529, NRRL B-3469, JCM 9700, CCUG 21966, CCUG 30065, CECT 912, CGMCC 1.2141, CIP 102423, IMET 10694, KCTC 3530, LMG 6908, NBRC 100495, NCFB 529, NCIMB 12007, NRIC 1539, VKM B-1225, VTT E-93492, VKM 1225

straininfo link

  • @ref: 76288
  • straininfo: 359518

literature

  • topic: Phylogeny
  • Pubmed-ID: 32228772
  • title: Leuconostoc litchii sp. nov., a novel lactic acid bacterium isolated from lychee.
  • authors: Chen YS, Wang LT, Wu YC, Mori K, Tamura T, Chang CH, Chang YC, Wu HC, Yi HH, Wang PY
  • journal: Int J Syst Evol Microbiol
  • DOI: 10.1099/ijsem.0.003938
  • year: 2020
  • mesh: Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, Fatty Acids/chemistry, Fermentation, Fruit/*microbiology, Lactic Acid, Leuconostoc/*classification/isolation & purification, Leuconostoc mesenteroides, Litchi/*microbiology, Nucleic Acid Hybridization, *Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Taiwan
  • topic2: Transcriptome

Reference

@idauthorscataloguedoi/urltitlejournalpubmed
8730Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 20484)https://www.dsmz.de/collection/catalogue/details/culture/DSM-20484
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
34909Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/14108
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
76288Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID359518.1StrainInfo: A central database for resolving microbial strain identifiers
120900Curators of the CIPCollection of Institut Pasteur (CIP 102423)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20102423