Strain identifier

BacDive ID: 5117

Type strain: Yes

Species: Salmonella enterica

Strain Designation: LT2

Strain history: CIP <- 1960, M. Demerec, Genetics Dept., Carnegie Inst., New-York, USA: strain LT2, Salmonella typhimurium

NCBI tax ID(s): 28901 (species)

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General

@ref: 6727

BacDive-ID: 5117

DSM-Number: 17058

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

description: Salmonella enterica LT2 is an aerobe, mesophilic bacterium that was isolated from Unknown source.

NCBI tax id

  • NCBI tax id: 28901
  • Matching level: species

strain history

@refhistory
6727<- CIP; CIP 60.62 <- M. Demerec, Carnegie Institute, Cold Spring Harbor, NY; LT2
67770CIP 60.62 <-- M. Demerec; Carnigie Inst., USA; LT2.
119044CIP <- 1960, M. Demerec, Genetics Dept., Carnegie Inst., New-York, USA: strain LT2, Salmonella typhimurium

doi: 10.13145/bacdive5117.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/pseudomonadota
  • domain: Bacteria
  • phylum: Pseudomonadota
  • class: Gammaproteobacteria
  • order: Enterobacterales
  • family: Enterobacteriaceae
  • genus: Salmonella
  • species: Salmonella enterica
  • full scientific name: Salmonella enterica (ex Kauffmann and Edwards 1952) Le Minor and Popoff 1987

  • synonyms

    @refsynonym
    20215Bacillus typhi
    20215Bacillus typhimurium
    20215Bacillus enteritidis
    20215Bacillus choleraesuis
    20215Salmonella typhi
    20215Salmonella choleraesuis
    20215Salmonella paratyphi
    20215Salmonella typhimurium
    20215Salmonella enteritidis

@ref: 6727

domain: Bacteria

phylum: Proteobacteria

class: Gammaproteobacteria

order: Enterobacteriales, not validated

family: Enterobacteriaceae

genus: Salmonella

species: Salmonella enterica subsp. enterica

full scientific name: Salmonella enterica subsp. enterica (ex Kauffmann and Edwards 1952) Le Minor and Popoff 1987

strain designation: LT2

type strain: yes

Morphology

cell morphology

@refcell lengthcell widthmotilityconfidencegram staincell shape
229452 µm0.5-1.5 µm
69480yes95.083
6948099.993negative
119044yesnegativerod-shaped

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
6727COLUMBIA 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
6727TRYPTICASE SOY YEAST EXTRACT MEDIUM (DSMZ Medium 92)yeshttps://mediadive.dsmz.de/medium/92Name: TRYPTICASE SOY YEAST EXTRACT MEDIUM (DSMZ Medium 92) Composition: Trypticase soy broth 30.0 g/l Agar 15.0 g/l Yeast extract 3.0 g/l Distilled water
33584MEDIUM 72- for trypto casein soja agaryesDistilled water make up to (1000.000 ml);Trypto casein soy agar (40.000 g)
119044CIP Medium 72yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=72

culture temp

@refgrowthtypetemperaturerange
6727positivegrowth37mesophilic
33584positivegrowth30mesophilic
55324positivegrowth30mesophilic
67770positivegrowth37mesophilic
119044positivegrowth30-41
119044nogrowth5psychrophilic
119044nogrowth10psychrophilic

Physiology and metabolism

oxygen tolerance

@refoxygen tolerance
55324aerobe
119044facultative anaerobe

spore formation

@refspore formationconfidence
69481no100
69480no99.84

compound production

  • @ref: 22945
  • compound: Hydrogen sulfide

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
22945168082-dehydro-D-gluconate-growth
22945479273-coumarate-growth
22945739183-O-methyl-D-glucose-growth
22945510573-phenylpropionate-growth
22945863945-aminovalerate-growth
2294515963ribitol-builds acid from
2294515963ribitol-growth
2294522599arabinose+builds acid from
2294516150benzoate-growth
2294517750betaine-growth
2294527689decanoate-growth
2294525646octanoate-growth
2294517057cellobiose-builds acid from
2294516383cis-aconitate+growth
2294516947citrate+growth
2294515570D-alanine+growth
2294518333D-arabitol-growth
2294517057cellobiose-growth
2294515824D-fructose+growth
2294512936D-galactose+growth
2294518024D-galacturonic acid-growth
2294530612D-glucarate+growth
229458391D-gluconate+growth
2294517315D-glucosamine+growth
2294517634D-glucose+growth
2294515748D-glucuronate+growth
2294562318D-lyxose-growth
2294516899D-mannitol+growth
2294516024D-mannose+growth
2294528053melibiose+growth
2294516634raffinose-growth
2294516988D-ribose+growth
2294517924D-sorbitol+growth
2294516443D-tagatose+growth
2294516551D-trehalose+growth
2294565327D-xylose+growth
22945370543-hydroxybutyrate-growth
2294533871glycerate+growth
2294524996lactate+growth
2294517113erythritol-growth
229454853esculin-growth
2294516000ethanolamine+growth
2294529806fumarate+growth
2294516537galactarate+builds acid from
2294516537galactarate+growth
2294516813galactitol+builds acid from
2294516813galactitol+growth
2294524175galacturonate-builds acid from
229455291gelatin-hydrolysis
2294528066gentiobiose-growth
2294558044gentisate+growth
2294517234glucose+builds gas from
2294517859glutarate-growth
2294517754glycerol+growth
2294518295histamine-growth
2294517268myo-inositol+builds acid from
2294516977L-alanine+growth
2294530849L-arabinose+growth
2294518403L-arabitol-growth
2294529991L-aspartate+growth
2294518287L-fucose+growth
2294529985L-glutamate+growth
2294515589L-malate+growth
2294517203L-proline+growth
2294562345L-rhamnose+growth
2294517115L-serine+growth
2294517266L-sorbose-growth
2294530924L-tartrate+growth
2294517716lactose-builds acid from
2294517716lactose-growth
229456359lactulose-growth
2294515792malonate-growth
2294568428maltitol-growth
2294517306maltose+builds acid from
2294517306maltose+growth
2294561993maltotriose+growth
2294529864mannitol+builds acid from
2294537684mannose+builds acid from
229456731melezitose-growth
2294528053melibiose+builds acid from
2294530928meso-tartrate+growth
2294555507methyl alpha-D-galactoside+growth
22945320061methyl alpha-D-glucopyranoside+growth
2294517540methyl beta-D-galactoside-growth
2294517268myo-inositol+growth
22945506227N-acetyl-D-glucosamine+growth
22945309162-oxoglutarate-growth
2294518394palatinose-growth
2294518401phenylacetate-growth
2294517272propionate+growth
2294536241protocatechuate-growth
2294517148putrescine-growth
2294526490quinate-growth
2294516634raffinose-builds acid from
2294526546rhamnose+builds acid from
2294517814salicin-builds acid from
2294530911sorbitol+builds acid from
2294530031succinate+growth
2294517992sucrose-builds acid from
2294517992sucrose-growth
2294515708trans-aconitate-growth
2294527082trehalose+builds acid from
2294562517tricarballylate+growth
2294518123trigonelline-growth
2294516765tryptamine-growth
2294532528turanose-growth
2294516199urea-hydrolysis
2294517151xylitol+builds acid from
2294517151xylitol-growth
2294516865gamma-aminobutyric acid-growth
2294517632nitrate+reduction
6836830849L-arabinose+fermentation
6836827613amygdalin-fermentation
6836828053melibiose+fermentation
6836817992sucrose-fermentation
6836862345L-rhamnose+fermentation
6836830911sorbitol+fermentation
6836817268myo-inositol+fermentation
6836816899D-mannitol+fermentation
6836817634D-glucose+fermentation
683685291gelatin-hydrolysis
6836827897tryptophan-energy source
6836816199urea-hydrolysis
6836816947citrate+assimilation
6836818257ornithine+degradation
6836825094lysine+degradation
6836829016arginine+hydrolysis
11904429864mannitol+fermentation
11904416947citrate+carbon source
11904417716lactose-fermentation
11904417632nitrate+reduction
11904416301nitrite+reduction
11904415792malonate-assimilation
119044132112sodium thiosulfate+builds gas from
11904417234glucose+degradation
6837418257ornithine+degradation
6837429016arginine+hydrolysis
6837425094lysine+degradation
6837416199urea-hydrolysis
6837418403L-arabitol-builds acid from
6837418024D-galacturonic acid-builds acid from
68374Potassium 5-ketogluconate+builds acid from
6837416899D-mannitol+builds acid from
6837417306maltose+builds acid from
6837415963ribitol-builds acid from
6837418394palatinose-builds acid from
6837415792malonate-assimilation
6837427897tryptophan-energy source
6837417634D-glucose+builds acid from
6837417992sucrose-builds acid from
6837430849L-arabinose+builds acid from
6837418333D-arabitol-builds acid from
6837427082trehalose-builds acid from
6837462345L-rhamnose+builds acid from
6837417268myo-inositol+builds acid from
6837417057cellobiose-builds acid from
6837430911sorbitol+builds acid from

antibiotic resistance

  • @ref: 119044
  • metabolite: 0129 (2,4-Diamino-6,7-di-iso-propylpteridine phosphate)
  • is antibiotic: yes
  • is sensitive: no
  • is resistant: yes

metabolite production

@refChebi-IDmetaboliteproduction
2294535581indoleno
2294516136hydrogen sulfideyes
6837435581indoleno
6836835581indoleno
6836816136hydrogen sulfideyes
11904435581indoleno

metabolite tests

@refChebi-IDmetaboliteindole testvoges-proskauer-testmethylred-test
6837435581indole-
6836835581indole-
11904415688acetoin-
11904417234glucose+

enzymes

@refvalueactivityec
22945beta-galactosidase-3.2.1.23
22945beta-glucuronidase-3.2.1.31
22945catalase+1.11.1.6
22945gelatinase-
22945lysine decarboxylase+4.1.1.18
22945ornithine decarboxylase+4.1.1.17
22945cytochrome oxidase-1.9.3.1
22945urease-3.5.1.5
68374L-aspartate arylamidase-3.4.11.21
68374alpha-maltosidase-
68374alpha-galactosidase+3.2.1.22
68374alpha-glucosidase-3.2.1.20
68374beta-galactosidase-3.2.1.23
68374N-acetyl-beta-glucosaminidase-3.2.1.52
68374beta-glucuronidase-3.2.1.31
68374beta-glucosidase-3.2.1.21
68374lipase+
68374urease-3.5.1.5
68374lysine decarboxylase+4.1.1.18
68374arginine dihydrolase+3.5.3.6
68374ornithine decarboxylase+4.1.1.17
68368cytochrome oxidase-1.9.3.1
68368gelatinase-
68368tryptophan deaminase-4.1.99.1
68368urease-3.5.1.5
68368ornithine decarboxylase+4.1.1.17
68368lysine decarboxylase+4.1.1.18
68368arginine dihydrolase+3.5.3.6
68368beta-galactosidase-3.2.1.23
119044oxidase-
119044beta-galactosidase-3.2.1.23
119044alcohol dehydrogenase-1.1.1.1
119044gelatinase-
119044catalase+1.11.1.6
119044lysine decarboxylase+4.1.1.18
119044ornithine decarboxylase+4.1.1.17
119044phenylalanine ammonia-lyase-4.3.1.24
119044tryptophan deaminase-
119044urease-3.5.1.5

API 20E

@refONPGADH ArgLDC LysODCCITH2SURETDA TrpINDVPGELGLUMANINOSorRHASACMELAMYARAOX
6727-+++++-----+++++-+-+-
6727-+++++---+-+++++-+-+-
6727-+++++---+-+++++-+-+-
6727-+++++---+/--+++++-+-+-

API ID32E

@refODCADH ArgLDC LysURELARLGAT5KGLIPRPbeta GLUMANMALADOPLEbeta GURMNTINDbeta NAGbeta GALGLUSACLARADARLalpha GLUalpha GALTRERHAINOCELSORalphaMALAspA
55324+++---+++-++-------+-+--+-++-+--

Isolation, sampling and environmental information

isolation

  • @ref: 119044
  • sample type: Unknown source

taxonmaps

  • @ref: 69479
  • File name: preview.99_9.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_6;96_7;97_7;98_8;99_9&stattab=map
  • Last taxonomy: Salmonella enterica
  • 16S sequence: AE006468
  • Sequence Identity:
  • Total samples: 28103
  • soil counts: 1084
  • aquatic counts: 2005
  • animal counts: 23018
  • plant counts: 1996

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
67272Risk group (German classification)
1190442Risk group (French classification)

Sequence information

16S sequences

@refdescriptionaccessionlengthdatabaseNCBI tax ID
20218Salmonella enterica subsp. enterica strain DSM 17058 16S ribosomal RNA gene, partial sequenceHQ012017936ena59201
20218Salmonella enterica strain LT2 operon rrn, 16S-23S intergenic spacer region and tRNA-Glu gene, complete sequenceAF046813393ena28901
20218Salmonella enterica strain LT2 operon rrn, 16S-23S intergenic spacer region, tRNA-Ile and tRNA-Ala genes, complete sequencesAF046814516ena28901
20218Salmonella enterica subsp. enterica serovar Typhimurium gene for 16S rRNA, partial sequenceD12814326ena90371
20218Salmonella enterica subsp. enterica gene for 16S rRNA, partial sequence, strain: NBRC 13245AB6803801467ena59201
6727Salmonella enterica subsp. enterica serovar Typhimurium str. LT2, complete genomeAE0064684857450ena99287

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Salmonella enterica subsp. enterica serovar Typhimurium str. LT2GCA_000006945completencbi99287
66792Salmonella enterica FDAARGOS_94GCA_001558355completencbi28901
66792Salmonella enterica subsp. enterica serovar Typhimurium LT2GCA_014334155completencbi90371
66792Salmonella enterica subsp. enterica serovar Typhimurium LT2GCA_002289225scaffoldncbi90371
66792Salmonella enterica subsp. enterica NCTC12416GCA_900456445contigncbi59201
66792Salmonella enterica strain FDAARGOS_87828901.13769completepatric28901
66792Salmonella enterica subsp. enterica serovar Typhimurium str. LT299287.12completepatric99287
66792Salmonella enterica subsp. enterica strain NCTC1241659201.937wgspatric59201
66792Salmonella enterica subsp. enterica serovar Typhimurium LT2GCA_010191885contigncbi90371
66792Salmonella enterica subsp. enterica serovar Typhimurium LT2GCA_010649825contigncbi90371

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno100no
motileyes90.098no
motileyes90.098no
flagellatedno50no
flagellatedno50no
gram-positiveno98.71no
gram-positiveno98.71no
anaerobicno89.892yes
anaerobicno89.892yes
halophileno93.786no
halophileno93.786no
spore-formingno93.964no
spore-formingno93.964no
thermophileno98.767yes
thermophileno98.767yes
glucose-utilyes92.886no
glucose-utilyes92.886no
aerobicyes70.242yes
aerobicyes70.242yes
glucose-fermentyes93.073no
glucose-fermentyes93.073no

External links

@ref: 6727

culture collection no.: DSM 17058, ATCC 43971, CIP 60.62, NCIMB 11450, NCTC 12416, CCUG 42060, JCM 32817, NBRC 13245

straininfo link

  • @ref: 74610
  • straininfo: 46974

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Pathogenicity25381884Characterization of Salmonella Typhimurium DNA gyrase as a target of quinolones.Kongsoi S, Yokoyama K, Suprasert A, Utrarachkij F, Nakajima C, Suthienkul O, Suzuki YDrug Test Anal10.1002/dta.17442014Anti-Bacterial Agents/chemistry/*pharmacology, DNA Gyrase/*metabolism, Humans, Molecular Targeted Therapy, Quinolones/chemistry/*pharmacology, Recombinant Proteins/metabolism, Salmonella Infections/drug therapy/*microbiology, Salmonella typhimurium/drug effects/*enzymology, Topoisomerase II Inhibitors/chemistry/*pharmacologyMetabolism
25924957Identification and antimicrobial activity detection of lactic Acid bacteria isolated from corn stover silage.Li D, Ni K, Pang H, Wang Y, Cai Y, Jin QAsian-Australas J Anim Sci10.5713/ajas.14.04392015
Phylogeny26954218Screening of Probiotic Activities of Lactobacilli Strains Isolated from Traditional Tibetan Qula, A Raw Yak Milk Cheese.Zhang B, Wang Y, Tan Z, Li Z, Jiao Z, Huang QAsian-Australas J Anim Sci10.5713/ajas.15.08492016
32047250Power of Scanning Electron Microscopy and Energy Dispersive X-Ray Analysis in Rapid Microbial Detection and Identification at the Single Cell Level.Khan MSI, Oh SW, Kim YJSci Rep10.1038/s41598-020-59448-82020Bacteria/*ultrastructure, Electron Probe Microanalysis/*methods, Microscopy, Electron, Scanning/*methods, Single-Cell Analysis/*methods

Reference

@idauthorscataloguedoi/urltitlejournalpubmed
6727Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 17058)https://www.dsmz.de/collection/catalogue/details/culture/DSM-17058
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
22945Leon Le Minor, Michel Y. Popoff10.1099/00207713-37-4-465Designation of Salmonella enterica sp. nov., nom. rev., as the Type and Only Species of the Genus Salmonella: Request for an OpinionIJSEM 37: 465-468 198710319519
33584Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/9880
55324Curators of the CCUGCulture Collection University of Gothenburg (CCUG) (CCUG 42060)https://www.ccug.se/strain?id=42060
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/
68368Automatically annotated from API 20E
68374Automatically annotated from API ID32E
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
74610Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID46974.1StrainInfo: A central database for resolving microbial strain identifiers
119044Curators of the CIPCollection of Institut Pasteur (CIP 60.62)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%2060.62