Strain identifier
BacDive ID: 6830
Type strain:
Species: Leuconostoc gelidum
Strain Designation: SML9
Strain history: CIP <- 1989, NCFB <- 1988, Shaw: strain SMl9, 1a21
NCBI tax ID(s): 927691 (strain), 1244 (species)
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 id | Matching level |
---|---|
927691 | strain |
1244 | species |
strain history
@ref | history |
---|---|
2230 | <- NCFB <- B.G. Shaw, SML9 |
67770 | NRIC 1778 <-- NCFB 2775. |
119567 | CIP <- 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
@ref | motility | confidence | gram stain | cell shape |
---|---|---|---|---|
69480 | no | 97.018 | ||
69480 | 100 | positive | ||
119567 | no | positive | oval-shaped |
Culture and growth conditions
culture medium
@ref | name | growth | link | composition |
---|---|---|---|---|
2230 | COLUMBIA BLOOD MEDIUM (DSMZ Medium 693) | yes | https://mediadive.dsmz.de/medium/693 | Name: COLUMBIA BLOOD MEDIUM (DSMZ Medium 693) Composition: Defibrinated sheep blood 50.0 g/l Columbia agar base |
2230 | MRS MEDIUM (DSMZ Medium 11) | yes | https://mediadive.dsmz.de/medium/11 | Name: 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 |
36378 | MEDIUM 40- for Lactobacillus and Leuconostoc | yes | Distilled water make up to (1000.000 ml);Man Rogosa Sharp agar (68.000 g) | |
119567 | CIP Medium 40 | yes | https://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=40 |
culture temp
@ref | growth | type | temperature | range |
---|---|---|---|---|
2230 | positive | growth | 25 | mesophilic |
36378 | positive | growth | 25 | mesophilic |
67770 | positive | growth | 25 | mesophilic |
119567 | positive | growth | 10-25 | psychrophilic |
119567 | no | growth | 30 | mesophilic |
119567 | no | growth | 37 | mesophilic |
119567 | no | growth | 45 | thermophilic |
Physiology and metabolism
oxygen tolerance
@ref | oxygen tolerance |
---|---|
2230 | anaerobe |
119567 | facultative anaerobe |
spore formation
@ref | spore formation | confidence |
---|---|---|
69481 | no | 100 |
69480 | no | 100 |
murein
- @ref: 2230
- murein short key: A11.05
- type: A3alpha L-Lys-L-Ala2
metabolite utilization
@ref | metabolite | utilization activity | kind of utilization tested | Chebi-ID |
---|---|---|---|---|
68371 | Potassium 5-ketogluconate | - | builds acid from | |
68371 | Potassium 2-ketogluconate | - | builds acid from | |
68371 | gluconate | - | builds acid from | 24265 |
68371 | L-arabitol | - | builds acid from | 18403 |
68371 | D-arabitol | - | builds acid from | 18333 |
68371 | L-fucose | - | builds acid from | 18287 |
68371 | D-fucose | - | builds acid from | 28847 |
68371 | D-tagatose | - | builds acid from | 16443 |
68371 | D-lyxose | - | builds acid from | 62318 |
68371 | turanose | + | builds acid from | 32528 |
68371 | gentiobiose | - | builds acid from | 28066 |
68371 | xylitol | - | builds acid from | 17151 |
68371 | glycogen | - | builds acid from | 28087 |
68371 | starch | - | builds acid from | 28017 |
68371 | raffinose | + | builds acid from | 16634 |
68371 | melezitose | - | builds acid from | 6731 |
68371 | inulin | - | builds acid from | 15443 |
68371 | trehalose | + | builds acid from | 27082 |
68371 | sucrose | + | builds acid from | 17992 |
68371 | melibiose | + | builds acid from | 28053 |
68371 | lactose | - | builds acid from | 17716 |
68371 | maltose | - | builds acid from | 17306 |
68371 | cellobiose | + | builds acid from | 17057 |
68371 | salicin | - | builds acid from | 17814 |
68371 | esculin | + | builds acid from | 4853 |
68371 | arbutin | - | builds acid from | 18305 |
68371 | amygdalin | - | builds acid from | 27613 |
68371 | N-acetylglucosamine | - | builds acid from | 59640 |
68371 | methyl alpha-D-glucopyranoside | - | builds acid from | 320061 |
68371 | methyl alpha-D-mannoside | - | builds acid from | 43943 |
68371 | D-sorbitol | - | builds acid from | 17924 |
68371 | D-mannitol | - | builds acid from | 16899 |
68371 | myo-inositol | - | builds acid from | 17268 |
68371 | galactitol | - | builds acid from | 16813 |
68371 | L-rhamnose | - | builds acid from | 62345 |
68371 | L-sorbose | - | builds acid from | 17266 |
68371 | D-mannose | + | builds acid from | 16024 |
68371 | D-fructose | + | builds acid from | 15824 |
68371 | D-glucose | + | builds acid from | 17634 |
68371 | D-galactose | - | builds acid from | 12936 |
68371 | methyl beta-D-xylopyranoside | - | builds acid from | 74863 |
68371 | ribitol | - | builds acid from | 15963 |
68371 | L-xylose | - | builds acid from | 65328 |
68371 | D-xylose | + | builds acid from | 65327 |
68371 | D-ribose | + | builds acid from | 16988 |
68371 | L-arabinose | + | builds acid from | 30849 |
68371 | D-arabinose | - | builds acid from | 17108 |
68371 | erythritol | - | builds acid from | 17113 |
68371 | glycerol | - | builds acid from | 17754 |
119567 | nitrate | - | reduction | 17632 |
119567 | nitrite | - | reduction | 16301 |
119567 | nitrate | + | respiration | 17632 |
metabolite tests
@ref | Chebi-ID | metabolite | voges-proskauer-test | methylred-test |
---|---|---|---|---|
119567 | 15688 | acetoin | - | |
119567 | 17234 | glucose | - |
enzymes
@ref | value | activity | ec |
---|---|---|---|
68382 | alpha-fucosidase | - | 3.2.1.51 |
68382 | alpha-mannosidase | - | 3.2.1.24 |
68382 | N-acetyl-beta-glucosaminidase | - | 3.2.1.52 |
68382 | beta-glucosidase | - | 3.2.1.21 |
68382 | alpha-glucosidase | + | 3.2.1.20 |
68382 | beta-glucuronidase | - | 3.2.1.31 |
68382 | beta-galactosidase | + | 3.2.1.23 |
68382 | alpha-galactosidase | + | 3.2.1.22 |
68382 | naphthol-AS-BI-phosphohydrolase | + | |
68382 | acid phosphatase | + | 3.1.3.2 |
68382 | alpha-chymotrypsin | - | 3.4.21.1 |
68382 | trypsin | - | 3.4.21.4 |
68382 | cystine arylamidase | - | 3.4.11.3 |
68382 | valine arylamidase | - | |
68382 | leucine arylamidase | + | 3.4.11.1 |
68382 | lipase (C 14) | - | |
68382 | esterase lipase (C 8) | - | |
68382 | esterase (C 4) | + | |
68382 | alkaline phosphatase | - | 3.1.3.1 |
119567 | oxidase | - | |
119567 | alcohol dehydrogenase | - | 1.1.1.1 |
119567 | catalase | - | 1.11.1.6 |
119567 | lysine decarboxylase | - | 4.1.1.18 |
119567 | ornithine decarboxylase | - | 4.1.1.17 |
API zym
@ref | Control | Alkaline phosphatase | Esterase | Esterase Lipase | Lipase | Leucine arylamidase | Valine arylamidase | Cystine arylamidase | Trypsin | alpha- Chymotrypsin | Acid phosphatase | Naphthol-AS-BI-phosphohydrolase | alpha- Galactosidase | beta- Galactosidase | beta- Glucuronidase | alpha- Glucosidase | beta- Glucosidase | N-acetyl-beta- glucosaminidase | alpha- Mannosidase | alpha- Fucosidase |
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
119567 | - | - | + | - | - | + | - | - | - | - | + | + | + | + | - | + | - | - | - | - |
API 50CHac
@ref | Q | GLY | ERY | DARA | LARA | RIB | DXYL | LXYL | ADO | MDX | GAL | GLU | FRU | MNE | SBE | RHA | DUL | INO | MAN | SOR | MDM | MDG | NAG | AMY | ARB | ESC | SAL | CEL | MAL | LAC | MEL | SAC | TRE | INU | MLZ | RAF | AMD | GLYG | XLT | GEN | TUR | LYX | TAG | DFUC | LFUC | DARL | LARL | GNT | 2KG | 5KG |
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
2230 | - | - | - | - | + | + | + | - | - | - | - | + | + | + | - | - | - | - | - | - | - | - | - | - | - | + | - | + | - | - | + | + | + | - | - | + | - | - | - | - | + | - | - | - | - | - | - | - | - | - |
Isolation, sampling and environmental information
isolation
@ref | sample type |
---|---|
2230 | vakuum-packaged beef |
67770 | Vacuum-packed meats |
119567 | Food, Vacuum packed meat |
isolation source categories
Cat1 | Cat2 | Cat3 |
---|---|---|
#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
@ref | biosafety level | biosafety level comment |
---|---|---|
2230 | 1 | Risk group (German classification) |
119567 | 1 | Risk group (French classification) |
Sequence information
16S sequences
@ref | description | accession | length | database | NCBI tax ID |
---|---|---|---|---|---|
20218 | Leuconostoc gelidum gene for 16S rRNA, strain:NRIC 1778 | AB022921 | 1445 | ena | 927691 |
20218 | Leuconostoc gelidum DNA, 16S-23S rRNA intergenic spacer region, strain: NRIC 1778 | AB290439 | 380 | ena | 927691 |
2230 | Leuconostoc gelidum 16S ribosomal RNA gene, partial sequence | AF175402 | 1505 | ena | 927691 |
67770 | Leuconostoc gelidum subsp. gelidum gene for 16S ribosomal RNA, partial sequence, strain: JCM 9697 | LC096221 | 1489 | ena | 1607839 |
Genome sequences
@ref | description | accession | assembly level | database | NCBI tax ID |
---|---|---|---|---|---|
66792 | Leuconostoc gelidum subsp. gelidum KCTC 3527 | GCA_000166715 | contig | ncbi | 927691 |
66792 | Leuconostoc gelidum KCTC 3527 | 927691.3 | wgs | patric | 927691 |
66792 | Leuconostoc gelidum gelidum KCTC 3527 | 651324068 | draft | img | 927691 |
GC content
@ref | GC-content | method |
---|---|---|
2230 | 37.0 | |
67770 | 37 | thermal denaturation, midpoint method (Tm) |
Genome-based predictions
predictions
trait | prediction | confidence | training_data |
---|---|---|---|
spore-forming | no | 100 | no |
motile | no | 96.118 | no |
flagellated | no | 98.095 | no |
gram-positive | yes | 96.513 | no |
anaerobic | no | 91.278 | no |
halophile | yes | 95.403 | no |
spore-forming | no | 96.001 | no |
glucose-util | yes | 86.598 | no |
aerobic | no | 97.441 | yes |
thermophile | no | 99.848 | yes |
glucose-ferment | yes | 92.079 | no |
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
topic | Pubmed-ID | title | authors | journal | DOI | year | mesh | topic2 |
---|---|---|---|---|---|---|---|---|
Phylogeny | 11034505 | Leuconostoc kimchii sp. nov., a new species from kimchi. | Kim J, Chun J, Han HU | Int J Syst Evol Microbiol | 10.1099/00207713-50-5-1915 | 2000 | Bacterial 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/*microbiology | Genetics |
Enzymology | 17229480 | Characterization of a Leuconostoc gelidum bacteriophage from pork. | Greer GG, Dilts BD, Ackermann HW | Int J Food Microbiol | 10.1016/j.ijfoodmicro.2006.09.021 | 2007 | Adipose 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, Vacuum | Phylogeny |
Pathogenicity | 17846581 | Effect of Leuconostoc spp. on the formation of Streptococcus mutans biofilm. | Kang MS, Kang IC, Kim SM, Lee HC, Oh JS | J Microbiol | 2570 | 2007 | Biofilms/drug effects/*growth & development, Chromatography, Thin Layer, Dextrans/chemistry/metabolism/pharmacology, Leuconostoc/*metabolism, Streptococcus mutans/drug effects/*growth & development | Metabolism |
Genetics | 21131494 | Genome Sequence of Leuconostoc gelidum KCTC 3527, Isolated from Kimchi. | Kim DS, Choi SH, Kim DW, Kim RN, Nam SH, Kang A, Kim A, Park HS | J Bacteriol | 10.1128/JB.01371-10 | 2010 | DNA, Bacterial/*chemistry/*genetics, Fermentation, *Genome, Bacterial, Korea, Leuconostoc/*genetics, Molecular Sequence Data, Sequence Analysis, DNA, Vegetables/*microbiology | Transcriptome |
Phylogeny | 21705441 | Leuconostoc miyukkimchii sp. nov., isolated from brown algae (Undaria pinnatifida) kimchi. | Lee SH, Park MS, Jung JY, Jeon CO | Int J Syst Evol Microbiol | 10.1099/ijs.0.032367-0 | 2011 | Anaerobiosis, 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/*microbiology | Biotechnology |
Phylogeny | 24431060 | Reclassification 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 J | Int J Syst Evol Microbiol | 10.1099/ijs.0.058263-0 | 2014 | Animals, 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, Turkeys | Genetics |
Reference
@id | authors | catalogue | doi/url | title | journal | pubmed |
---|---|---|---|---|---|---|
2230 | Curators of the DSMZ | Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 5578) | https://www.dsmz.de/collection/catalogue/details/culture/DSM-5578 | |||
20215 | Parte, A.C., Sardà Carbasse, J., Meier-Kolthoff, J.P., Reimer, L.C. and Göker, M. | 10.1099/ijsem.0.004332 | List of Prokaryotic names with Standing in Nomenclature (LPSN) moves to the DSMZ | |||
20218 | Verslyppe, B., De Smet, W., De Baets, B., De Vos, P., Dawyndt P. | 10.1016/j.syapm.2013.11.002 | StrainInfo introduces electronic passports for microorganisms. | Syst Appl Microbiol. 37: 42-50 2014 | 24321274 | |
36378 | Curators of the CIP | https://brclims.pasteur.fr/brcWeb/souche/detail/1/15103 | ||||
66792 | Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmann | https://diaspora-project.de/progress.html#genomes | Automatically annotated for the DiASPora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information) | |||
67770 | Curators of the JCM | https://jcm.brc.riken.jp/en/ | ||||
68371 | Automatically annotated from API 50CH acid | |||||
68382 | Automatically annotated from API zym | |||||
69479 | João 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 | |||
69480 | Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmann | https://diaspora-project.de/progress.html#genomes | Predictions based on genome sequence made in the Diaspora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information) | |||
69481 | Xiao-Yin To, René Mreches, Martin Binder, Alice C. McHardy, Philipp C. Münch | 10.21203/rs.3.rs-2527258/v1 | Predictions based on the model GenomeNet Sporulation v. 1 | |||
76295 | Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J. | 10.60712/SI-ID3491.1 | StrainInfo: A central database for resolving microbial strain identifiers | |||
119567 | Curators of the CIP | Collection of Institut Pasteur (CIP 103318) | https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20103318 |