Strain identifier

BacDive ID: 136283

Type strain: No

Species: Shigella sonnei

Strain Designation: 1120-66

Strain history: CIP <- 1994, ATCC <- NCDC: strain 1120-66 <- Gorgas Memorial Hosp., Panama

NCBI tax ID(s): 624 (species)

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

@ref: 35641

BacDive-ID: 136283

keywords: genome sequence, Bacteria, facultative anaerobe, mesophilic, motile

description: Shigella sonnei 1120-66 is a facultative anaerobe, mesophilic, motile bacterium that was isolated from Human feces.

NCBI tax id

  • NCBI tax id: 624
  • Matching level: species

strain history

  • @ref: 35641
  • history: CIP <- 1994, ATCC <- NCDC: strain 1120-66 <- Gorgas Memorial Hosp., Panama

doi: 10.13145/bacdive136283.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/pseudomonadota
  • domain: Bacteria
  • phylum: Pseudomonadota
  • class: Gammaproteobacteria
  • order: Enterobacterales
  • family: Enterobacteriaceae
  • genus: Shigella
  • species: Shigella sonnei
  • full scientific name: Shigella sonnei (Levine 1920) Weldin 1927 (Approved Lists 1980)
  • synonyms

    • @ref: 20215
    • synonym: Bacterium sonnei

@ref: 35641

domain: Bacteria

phylum: Proteobacteria

class: Gammaproteobacteria

order: Enterobacterales

family: Enterobacteriaceae

genus: Shigella

species: Shigella sonnei

strain designation: 1120-66

type strain: no

Morphology

cell morphology

@refmotilityconfidencegram staincell shape
69480yes95.955
6948099.985negative
35641nonegativerod-shaped

Culture and growth conditions

culture medium

@refnamegrowthcompositionlink
35641MEDIUM 3 - Columbia agaryesColumbia agar (39.000 g);distilled water (1000.000 ml)
35641CIP Medium 3yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=3
35641CIP Medium 72yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=72

culture temp

@refgrowthtypetemperaturerange
35641positivegrowth30mesophilic
35641positivegrowth10-41
35641nogrowth5psychrophilic

Physiology and metabolism

oxygen tolerance

  • @ref: 35641
  • oxygen tolerance: facultative anaerobe

spore formation

@refspore formationconfidence
69481no100
69480no99.741

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
6836828053melibiose-fermentation
6836817992sucrose-fermentation
6836862345L-rhamnose-fermentation
6836830911sorbitol-fermentation
6836817268myo-inositol-fermentation
6836817634D-glucose-fermentation
683685291gelatin-hydrolysis
6836827897tryptophan-energy source
6836816199urea-hydrolysis
6836816947citrate-assimilation
6836818257ornithine-degradation
6836825094lysine-degradation
6836829016arginine-hydrolysis
3564129864mannitol-fermentation
3564116947citrate-carbon source
3564117234glucose+fermentation
3564117716lactose-fermentation
3564117632nitrate+reduction
3564116301nitrite+reduction
3564115792malonate-assimilation
35641132112sodium thiosulfate-builds gas from
3564117234glucose+degradation

antibiotic resistance

  • @ref: 35641
  • metabolite: 0129 (2,4-Diamino-6,7-di-iso-propylpteridine phosphate)
  • is antibiotic: yes
  • is sensitive: no
  • is resistant: yes

metabolite production

@refChebi-IDmetaboliteproduction
6836817997dinitrogenno
6836815688acetoinno
6836835581indoleno
6836816136hydrogen sulfideno
3564135581indoleno

metabolite tests

@refChebi-IDmetabolitevoges-proskauer-testindole testmethylred-test
6836815688acetoin-
6836835581indole-
3564115688acetoin-
3564117234glucose+

enzymes

@refvalueactivityec
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
35641oxidase-
35641beta-galactosidase+3.2.1.23
35641alcohol dehydrogenase+1.1.1.1
35641gelatinase-
35641catalase+1.11.1.6
35641lysine decarboxylase-4.1.1.18
35641ornithine decarboxylase+4.1.1.17
35641phenylalanine ammonia-lyase-4.3.1.24
35641tryptophan deaminase-
35641urease-3.5.1.5
68382alkaline phosphatase+3.1.3.1
68382esterase (C 4)+
68382esterase lipase (C 8)-
68382lipase (C 14)-
68382leucine arylamidase+3.4.11.1
68382valine arylamidase+
68382cystine arylamidase-3.4.11.3
68382trypsin-3.4.21.4
68382alpha-chymotrypsin-3.4.21.1
68382acid phosphatase+3.1.3.2
68382naphthol-AS-BI-phosphohydrolase+
68382alpha-galactosidase-3.2.1.22
68382beta-galactosidase+3.2.1.23
68382beta-glucuronidase+3.2.1.31
68382alpha-glucosidase+3.2.1.20
68382beta-glucosidase-3.2.1.21
68382N-acetyl-beta-glucosaminidase-3.2.1.52
68382alpha-mannosidase-3.2.1.24
68382alpha-fucosidase-3.2.1.51

fatty acid profile

  • fatty acids

    @reffatty acidpercentageECL
    50969C12:03.412
    50969C13:01.813
    50969C14:06.214
    50969C15:010.415
    50969C16:020.416
    50969C17:02.117
    50969C12:0 ALDE ?1.210.915
    50969C13:0 3OH/C15:1 i I/H1.514.469
    50969C14:0 3OH/C16:1 ISO I5.515.485
    50969C15:1 ω8c0.814.792
    50969C16:1 ω7c23.115.819
    50969C17:0 CYCLO4.216.888
    50969C17:1 ω8c116.792
    50969C18:1 ω7c /12t/9t17.717.824
    50969C18:2 ω6,9c/C18:0 ANTE0.817.724
  • type of FA analysis: whole cell analysis
  • method/protocol: CCUG

API zym

@refControlAlkaline phosphataseEsteraseEsterase LipaseLipaseLeucine arylamidaseValine arylamidaseCystine arylamidaseTrypsinalpha- ChymotrypsinAcid phosphataseNaphthol-AS-BI-phosphohydrolasealpha- Galactosidasebeta- Galactosidasebeta- Glucuronidasealpha- Glucosidasebeta- GlucosidaseN-acetyl-beta- glucosaminidasealpha- Mannosidasealpha- Fucosidase
35641-++--++---++-+++----

API 20E

@refONPGADH ArgLDC LysODCCITH2SURETDA TrpINDVPGELGLUINOSorRHASACMELN2
35641------------------

API biotype100

@refGLUFRUGALTREMNESBEMELSACRAFMTEMALLACLTEMbGaMaGaCELGENMbGuESCRIBARAXYLPLERHAFUCMLZDARLLARLXLTDULTAGGLYINOMANMTLTURSORADOHBGLYXERYMDG3MDGSATMUCLTATDTATMTATDMLTLMLTCATETATETTECITGRTGAT2KG5KGTRYNAGGNTPACPATpOBEQATGTEmOBEBATPPATCMTTGEBETPCEABTHINLATCAPCYTHISSUCFUMGREGYTAVTETNTTNGLNITA3OBUAPTGTTPRODALALALASERMNTPROPTYR2KT
35641+++++-+++++--++----++--++------+-+--------------++-----+---++--------------+---++--------++++-+----

Isolation, sampling and environmental information

isolation

@refsample typesampling dateisolation date
50969Human feces1966
35641Human, Feces1966

isolation source categories

Cat1Cat2Cat3
#Host#Human
#Host Body Product#Gastrointestinal tract#Feces (Stool)

Safety information

risk assessment

  • @ref: 35641
  • biosafety level: 2
  • biosafety level comment: Risk group (French classification)

Sequence information

Genome sequences

  • @ref: 66792
  • description: Shigella sonnei strain FDAARGOS_776
  • accession: 624.1857
  • assembly level: wgs
  • database: patric
  • NCBI tax ID: 624

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno100no
gram-positiveno98.248no
anaerobicno94.984no
halophileno87.558no
spore-formingno93.705no
glucose-utilyes94.058no
thermophileno98.73yes
flagellatedno59.43no
aerobicyes84.684no
motileyes89.289no
glucose-fermentyes92.953no

External links

@ref: 35641

culture collection no.: CIP 104223, ATCC 25931, CCUG 32351, NCDC 1120-66

straininfo link

  • @ref: 93478
  • straininfo: 305279

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Pathogenicity23528983Study of probiotic potential of four wild Lactobacillus rhamnosus strains.Tuo Y, Zhang W, Zhang L, Ai L, Zhang Y, Han X, Yi HAnaerobe10.1016/j.anaerobe.2013.03.0072013*Antibiosis, Bacterial Adhesion, Cell Wall, China, Cytokines/metabolism, DNA, Bacterial/genetics, Escherichia coli/physiology, Feces/microbiology, Food Microbiology, Gastrointestinal Tract/*microbiology, HT29 Cells, Host-Pathogen Interactions, Humans, Immunomodulation, Infant, Intestinal Mucosa/microbiology, Lactobacillus rhamnosus/immunology/*isolation & purification/*physiology, Leukocytes, Mononuclear/immunology/metabolism, *Probiotics, Salmonella typhimurium/physiology, Shigella sonnei/physiologyMetabolism
Pathogenicity26805974Evaluation of probiotic properties of Lactobacillus plantarum WLPL04 isolated from human breast milk.Jiang M, Zhang F, Wan C, Xiong Y, Shah NP, Wei H, Tao XJ Dairy Sci10.3168/jds.2015-104342016Animals, Caco-2 Cells, Cytokines/*immunology, Female, Gram-Negative Bacteria/*growth & development, Gram-Positive Bacteria/*growth & development, Humans, Lactobacillus plantarum/isolation & purification/*physiology, Milk, Human/*microbiology, *ProbioticsEnzymology
Pathogenicity30395485Anti-adhesion of probiotic Enterococcus faecium WEFA23 against five pathogens and the beneficial effect of its S-layer proteins against Listeria monocytogenes.He Y, Xu X, Zhang F, Xu D, Liu Z, Tao X, Wei HCan J Microbiol10.1139/cjm-2018-00312018*Antibiosis, Apoptosis, Bacterial Adhesion, Caco-2 Cells, Enterococcus faecium/*physiology, Escherichia coli O157/pathogenicity, Humans, Listeria monocytogenes/pathogenicity, Membrane Glycoproteins/*metabolism, Probiotics/*pharmacology, Salmonella typhimurium/pathogenicity, Shigella sonnei/pathogenicity, Staphylococcus aureus/pathogenicityMetabolism
Pathogenicity32694956Screening of the Dichloromethane: Methanolic Extract of Centella asiatica for Antibacterial Activities against Salmonella typhi, Escherichia coli, Shigella sonnei, Bacillus subtilis, and Staphylococcus aureus.Sieberi BM, Omwenga GI, Wambua RK, Samoei JC, Ngugi MPScientificWorldJournal10.1155/2020/63787122020Anti-Bacterial Agents/isolation & purification/*pharmacology, Bacillus subtilis/drug effects/physiology, Bacteria/classification/*drug effects, Bacterial Infections/*drug therapy/microbiology, Centella/*chemistry, Escherichia coli/drug effects/physiology, Host-Pathogen Interactions/drug effects, Humans, Kenya, Methanol/chemistry, Methylene Chloride/isolation & purification/*pharmacology, Microbial Sensitivity Tests/methods, Phytochemicals/isolation & purification/pharmacology, Phytotherapy/methods, Plant Extracts/pharmacology, Salmonella typhi/drug effects/physiology, Shigella sonnei/drug effects/physiology, Staphylococcus aureus/drug effects/physiology, Triterpenes/*pharmacologyPhylogeny
Phylogeny34381426Selective Thermotolerant Lactic Acid Bacteria Isolated From Fermented Juice of Epiphytic Lactic Acid Bacteria and Their Effects on Fermentation Quality of Stylo Silages.Pitiwittayakul N, Bureenok S, Schonewille JTFront Microbiol10.3389/fmicb.2021.6739462021
35206082Probiotic Effects and Metabolic Products of Enterococcus faecalis LD33 with Respiration Capacity.Jiao Y, Yang H, Shigwedha N, Zhang S, Liu F, Zhang LFoods10.3390/foods110406062022
36367551Antibacterial Mechanism of Eugenol Against Shigella sonnei and Its Antibacterial Application in Lettuce Juice.Su R, Bai X, Liu X, Song L, Liu X, Zhan X, Guo D, Wang Y, Chang Y, Shi CFoodborne Pathog Dis10.1089/fpd.2022.00462022*Shigella sonnei, Eugenol/pharmacology, Lettuce/microbiology, Microbial Sensitivity Tests, Anti-Bacterial Agents/pharmacology, *Dysentery, Bacillary

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
35641Curators of the CIPhttps://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20104223Collection of Institut Pasteur (CIP 104223)
50969Curators of the CCUGhttps://www.ccug.se/strain?id=32351Culture Collection University of Gothenburg (CCUG) (CCUG 32351)
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
68382Automatically annotated from API zym
69480Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg OvermannPredictions based on genome sequence made in the Diaspora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information)https://diaspora-project.de/progress.html#genomes
69481Xiao-Yin To, René Mreches, Martin Binder, Alice C. McHardy, Philipp C. MünchPredictions based on the model GenomeNet Sporulation v. 110.21203/rs.3.rs-2527258/v1
93478Reimer, 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-ID305279.1