Strain identifier

BacDive ID: 6830

Type strain: Yes

Species: Leuconostoc gelidum

Strain Designation: SML9

Strain history: CIP <- 1989, NCFB <- 1988, Shaw: strain SMl9, 1a21

NCBI tax ID(s): 927691 (strain), 1244 (species)

For citation purpose refer to the digital object identifier (doi) of the current version.
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General

@ref: 2230

BacDive-ID: 6830

DSM-Number: 5578

keywords: genome sequence, 16S sequence, Bacteria, anaerobe, mesophilic

description: Leuconostoc gelidum SML9 is an anaerobe, mesophilic bacterium that was isolated from vakuum-packaged beef.

NCBI tax id

NCBI tax idMatching level
927691strain
1244species

strain history

@refhistory
2230<- NCFB <- B.G. Shaw, SML9
67770NRIC 1778 <-- NCFB 2775.
119567CIP <- 1989, NCFB <- 1988, Shaw: strain SMl9, 1a21

doi: 10.13145/bacdive6830.20230509.8.1

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 gelidum
  • full scientific name: Leuconostoc gelidum Shaw and Harding 1989

@ref: 2230

domain: Bacteria

phylum: Firmicutes

class: Bacilli

order: Lactobacillales

family: Leuconostocaceae

genus: Leuconostoc

species: Leuconostoc gelidum subsp. gelidum

full scientific name: Leuconostoc gelidum subsp. gelidum (Shaw and Harding 1989) Rahkila et al. 2014

strain designation: SML9

type strain: yes

Morphology

cell morphology

@refmotilityconfidencegram staincell shape
69480no97.018
69480100positive
119567nopositiveoval-shaped

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
2230COLUMBIA BLOOD MEDIUM (DSMZ Medium 693)yeshttps://mediadive.dsmz.de/medium/693Name: COLUMBIA BLOOD MEDIUM (DSMZ Medium 693) Composition: Defibrinated sheep blood 50.0 g/l Columbia agar base
2230MRS 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
36378MEDIUM 40- for Lactobacillus and LeuconostocyesDistilled water make up to (1000.000 ml);Man Rogosa Sharp agar (68.000 g)
119567CIP Medium 40yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=40

culture temp

@refgrowthtypetemperaturerange
2230positivegrowth25mesophilic
36378positivegrowth25mesophilic
67770positivegrowth25mesophilic
119567positivegrowth10-25psychrophilic
119567nogrowth30mesophilic
119567nogrowth37mesophilic
119567nogrowth45thermophilic

Physiology and metabolism

oxygen tolerance

@refoxygen tolerance
2230anaerobe
119567facultative anaerobe

spore formation

@refspore formationconfidence
69481no100
69480no100

murein

  • @ref: 2230
  • 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
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
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
119567nitrate-reduction17632
119567nitrite-reduction16301
119567nitrate+respiration17632

metabolite tests

@refChebi-IDmetabolitevoges-proskauer-testmethylred-test
11956715688acetoin-
11956717234glucose-

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
119567oxidase-
119567alcohol dehydrogenase-1.1.1.1
119567catalase-1.11.1.6
119567lysine decarboxylase-4.1.1.18
119567ornithine 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
119567--+--+----++++-+----

API 50CHac

@refQGLYERYDARALARARIBDXYLLXYLADOMDXGALGLUFRUMNESBERHADULINOMANSORMDMMDGNAGAMYARBESCSALCELMALLACMELSACTREINUMLZRAFAMDGLYGXLTGENTURLYXTAGDFUCLFUCDARLLARLGNT2KG5KG
2230----+++----+++-----------+-+--+++--+----+---------

Isolation, sampling and environmental information

isolation

@refsample type
2230vakuum-packaged beef
67770Vacuum-packed meats
119567Food, Vacuum packed meat

isolation source categories

Cat1Cat2Cat3
#Engineered#Food production#Bottled, canned, packed food
#Engineered#Food production#Meat

taxonmaps

  • @ref: 69479
  • File name: preview.99_3716.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_22;96_35;97_36;98_457;99_3716&stattab=map
  • Last taxonomy: Leuconostoc gelidum
  • 16S sequence: LC096221
  • Sequence Identity:
  • Total samples: 22220
  • soil counts: 1578
  • aquatic counts: 2226
  • animal counts: 17034
  • plant counts: 1382

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
22301Risk group (German classification)
1195671Risk group (French classification)

Sequence information

16S sequences

@refdescriptionaccessionlengthdatabaseNCBI tax ID
20218Leuconostoc gelidum gene for 16S rRNA, strain:NRIC 1778AB0229211445ena927691
20218Leuconostoc gelidum DNA, 16S-23S rRNA intergenic spacer region, strain: NRIC 1778AB290439380ena927691
2230Leuconostoc gelidum 16S ribosomal RNA gene, partial sequenceAF1754021505ena927691
67770Leuconostoc gelidum subsp. gelidum gene for 16S ribosomal RNA, partial sequence, strain: JCM 9697LC0962211489ena1607839

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Leuconostoc gelidum subsp. gelidum KCTC 3527GCA_000166715contigncbi927691
66792Leuconostoc gelidum KCTC 3527927691.3wgspatric927691
66792Leuconostoc gelidum gelidum KCTC 3527651324068draftimg927691

GC content

@refGC-contentmethod
223037.0
6777037thermal denaturation, midpoint method (Tm)

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno100no
motileno96.118no
flagellatedno98.095no
gram-positiveyes96.513no
anaerobicno91.278no
halophileyes95.403no
spore-formingno96.001no
glucose-utilyes86.598no
aerobicno97.441yes
thermophileno99.848yes
glucose-fermentyes92.079no

External links

@ref: 2230

culture collection no.: DSM 5578, ATCC 49366, NCFB 2775, NCIMB 12897, JCM 9697, CCM 4189, CCUG 30198, CCUG 32249, CCUG 32696, CECT 4026, CIP 103318, KCTC 3527, LMG 18297, LMG 9850, NRIC 1778, VTT E-98972

straininfo link

  • @ref: 76295
  • straininfo: 3491

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
Enzymology17229480Characterization of a Leuconostoc gelidum bacteriophage from pork.Greer GG, Dilts BD, Ackermann HWInt J Food Microbiol10.1016/j.ijfoodmicro.2006.09.0212007Adipose Tissue/microbiology, Aerobiosis, Anaerobiosis, Animals, Bacteriophages/*isolation & purification, Colony Count, Microbial, Consumer Product Safety, Food Contamination/*analysis, Food Microbiology, Food Packaging/*methods, Food Preservation/*methods, Humans, Leuconostoc/*isolation & purification, Meat/*microbiology, Swine, Time Factors, VacuumPhylogeny
Pathogenicity17846581Effect of Leuconostoc spp. on the formation of Streptococcus mutans biofilm.Kang MS, Kang IC, Kim SM, Lee HC, Oh JSJ Microbiol25702007Biofilms/drug effects/*growth & development, Chromatography, Thin Layer, Dextrans/chemistry/metabolism/pharmacology, Leuconostoc/*metabolism, Streptococcus mutans/drug effects/*growth & developmentMetabolism
Genetics21131494Genome Sequence of Leuconostoc gelidum KCTC 3527, Isolated from Kimchi.Kim DS, Choi SH, Kim DW, Kim RN, Nam SH, Kang A, Kim A, Park HSJ Bacteriol10.1128/JB.01371-102010DNA, Bacterial/*chemistry/*genetics, Fermentation, *Genome, Bacterial, Korea, Leuconostoc/*genetics, Molecular Sequence Data, Sequence Analysis, DNA, Vegetables/*microbiologyTranscriptome
Phylogeny21705441Leuconostoc miyukkimchii sp. nov., isolated from brown algae (Undaria pinnatifida) kimchi.Lee SH, Park MS, Jung JY, Jeon COInt J Syst Evol Microbiol10.1099/ijs.0.032367-02011Anaerobiosis, Bacterial Typing Techniques, Base Composition, Cluster Analysis, DNA, Bacterial/chemistry/genetics, DNA, Ribosomal/chemistry/genetics, *Food Microbiology, Hydrogen-Ion Concentration, Korea, Leuconostoc/*classification/genetics/*isolation & purification, Molecular Sequence Data, Nucleic Acid Hybridization, Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Temperature, Undaria/*microbiologyBiotechnology
Phylogeny24431060Reclassification of Leuconostoc gasicomitatum as Leuconostoc gelidum subsp. gasicomitatum comb. nov., description of Leuconostoc gelidum subsp. aenigmaticum subsp. nov., designation of Leuconostoc gelidum subsp. gelidum subsp. nov. and emended description of Leuconostoc gelidum.Rahkila R, De Bruyne K, Johansson P, Vandamme P, Bjorkroth JInt J Syst Evol Microbiol10.1099/ijs.0.058263-02014Animals, Chickens, DNA, Bacterial/genetics, Genes, Bacterial, Leuconostoc/*classification/genetics/isolation & purification, Meat/*microbiology, Molecular Sequence Data, Multilocus Sequence Typing, Nucleic Acid Hybridization, *Phylogeny, RNA, Ribosomal, 16S/genetics, Ribotyping, Sequence Analysis, DNA, Swine, TurkeysGenetics

Reference

@idauthorscataloguedoi/urltitlejournalpubmed
2230Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 5578)https://www.dsmz.de/collection/catalogue/details/culture/DSM-5578
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
36378Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/15103
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
76295Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID3491.1StrainInfo: A central database for resolving microbial strain identifiers
119567Curators of the CIPCollection of Institut Pasteur (CIP 103318)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20103318