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BacDive ID 157848
Type strain
Strain Designation strain 6
Culture col. no. DSM 107291 strain 6
NCBI tax ID(s) 59201
Links
For citation purpose refer to the digital object identifier (doi) of the current version.

Archive

version 9.3 (current version):
version 9.3 (current version)

General

@ref: 64421

BacDive-ID: 157848

DSM-Number: 107291

keywords: genome sequence, Bacteria, mesophilic, Gram-negative

description: Salmonella enterica subsp. enterica strain 6 is a mesophilic, Gram-negative bacterium that was isolated from male patient with diarrhea.

NCBI tax id

  • NCBI tax id: 59201
  • Matching level: subspecies

strain history

  • @ref: 64421
  • history: <- N. Chanishvili, The Eliava Institute of Bacteriophage, MIcrobiology & Virology; strain 6 <- unknown

doi: 10.13145/bacdive157848.20250331.9.3

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

  • synonyms

    • @ref: 20215
    • synonym: Salmonella choleraesuis subsp. choleraesuis

@ref: 64421

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: strain 6

type strain: no

Morphology

cell morphology

@refgram stainconfidence
125438negative100
125439negative92.6

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
64421COLUMBIA 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
64421NUTRIENT AGAR (DSMZ Medium 1)yeshttps://mediadive.dsmz.de/medium/1Name: NUTRIENT AGAR (DSMZ Medium 1) Composition: Agar 15.0 g/l Peptone 5.0 g/l Meat extract 3.0 g/l Distilled water

culture temp

  • @ref: 64421
  • growth: positive
  • type: growth
  • temperature: 37

Physiology and metabolism

spore formation

  • @ref: 125439
  • spore formation: no
  • confidence: 94.6

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
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

metabolite production

@refChebi-IDmetaboliteproduction
6836815688acetoinyes
6836835581indoleno
6836816136hydrogen sulfideyes

metabolite tests

@refChebi-IDmetabolitevoges-proskauer-testindole test
6836815688acetoin+
6836835581indole-

enzymes

@refvalueactivityec
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

API 20E

@refONPGADH ArgLDC LysODCCITH2SURETDA TrpINDVPGELGLUMANINOSorRHASACMELAMYARAOX
64421-+++++---+-+++++-+-+-

Isolation, sampling and environmental information

isolation

  • @ref: 64421
  • sample type: male patient with diarrhea
  • geographic location: Tbilisi
  • country: Georgia
  • origin.country: GEO
  • continent: Asia

isolation source categories

Cat1Cat2Cat3
#Infection#Patient
#Infection#Disease
#Host Body-Site#Gastrointestinal tract
#Host#Human#Male

Safety information

risk assessment

  • @ref: 64421
  • biosafety level: 2
  • biosafety level comment: Risk group (German classification)

Sequence information

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Salmonella enterica subsp. enterica serovar Newport strain 6108619.166wgspatric108619
66792Salmonella enterica subsp. enterica serovar Typhi strain 690370.2310wgspatric90370
66792Salmonella enterica subsp. enterica serovar Typhimurium strain 690371.4773wgspatric90371

Genome-based predictions

predictions

@refmodeltraitdescriptionpredictionconfidencetraining_data
125439BacteriaNetoxygen_toleranceOxygenic conditions needed for growthaerobe84.9
125439BacteriaNetgram_stainReaction to gram-stainingnegative92.6
125439BacteriaNetmotilityAbility to perform movementyes69.2
125439BacteriaNetspore_formationAbility to form endo- or exosporesno94.6
125438gram-positivegram-positivePositive reaction to Gram-stainingno100no
125438anaerobicanaerobicAbility to grow under anoxygenic conditions (including facultative anaerobes)no94.499no
125438spore-formingspore-formingAbility to form endo- or exosporesno89.032no
125438aerobicaerobicAbility to grow under oxygenic conditions (including facultative aerobes)no75.918no
125438thermophilethermophilicAbility to grow at temperatures above or equal to 45°Cno98no
125438motile2+flagellatedAbility to perform flagellated movementyes76.978no

External links

@ref: 64421

culture collection no.: DSM 107291

straininfo link

  • @ref: 110703
  • straininfo: 397018

literature

  • topic: Metabolism
  • Pubmed-ID: 2672681
  • title: Mutagenicity of antiviral substances of nucleobase analogue type in Salmonella typhimurium employing metabolic activation by mouse liver homogenate or cell-free plant extracts.
  • authors: el-Tarras A, Braun R, Stenz E, Schuster G
  • journal: Zentralbl Mikrobiol
  • year: 1989
  • mesh: Animals, Antiviral Agents/metabolism/*toxicity, Biotransformation, Liver Extracts/metabolism, Male, Mice, *Mutagenicity Tests, *Mutation, Plant Extracts/metabolism, Salmonella typhimurium/drug effects, Uracil/*analogs & derivatives/toxicity, Zea mays/metabolism
  • topic2: Pathogenicity

Reference

@idauthorstitledoi/urlcatalogue
20215Parte, A.C., Sardà Carbasse, J., Meier-Kolthoff, J.P., Reimer, L.C. and Göker, M.List of Prokaryotic names with Standing in Nomenclature (LPSN) moves to the DSMZ10.1099/ijsem.0.004332
64421Curators of the DSMZhttps://www.dsmz.de/collection/catalogue/details/culture/DSM-107291Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 107291)
66792Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg OvermannAutomatically annotated for the DiASPora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information)https://diaspora-project.de/progress.html#genomes
68368Automatically annotated from API 20E
110703Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.StrainInfo: A central database for resolving microbial strain identifiers10.60712/SI-ID397018.1
125438Julia Koblitz, Lorenz Christian Reimer, Rüdiger Pukall, Jörg OvermannPredicting bacterial phenotypic traits through improved machine learning using high-quality, curated datasets10.1101/2024.08.12.607695
125439Philipp Münch, René Mreches, Martin Binder, Hüseyin Anil Gündüz, Xiao-Yin To, Alice McHardydeepG: Deep Learning for Genome Sequence Data. R package version 0.3.1https://github.com/GenomeNet/deepG

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