Strain identifier
BacDive ID: 136283
Type strain:
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)
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
@ref | motility | confidence | gram stain | cell shape |
---|---|---|---|---|
69480 | yes | 95.955 | ||
69480 | 99.985 | negative | ||
35641 | no | negative | rod-shaped |
Culture and growth conditions
culture medium
@ref | name | growth | composition | link |
---|---|---|---|---|
35641 | MEDIUM 3 - Columbia agar | yes | Columbia agar (39.000 g);distilled water (1000.000 ml) | |
35641 | CIP Medium 3 | yes | https://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=3 | |
35641 | CIP Medium 72 | yes | https://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=72 |
culture temp
@ref | growth | type | temperature | range |
---|---|---|---|---|
35641 | positive | growth | 30 | mesophilic |
35641 | positive | growth | 10-41 | |
35641 | no | growth | 5 | psychrophilic |
Physiology and metabolism
oxygen tolerance
- @ref: 35641
- oxygen tolerance: facultative anaerobe
spore formation
@ref | spore formation | confidence |
---|---|---|
69481 | no | 100 |
69480 | no | 99.741 |
metabolite utilization
@ref | Chebi-ID | metabolite | utilization activity | kind of utilization tested |
---|---|---|---|---|
68368 | 28053 | melibiose | - | fermentation |
68368 | 17992 | sucrose | - | fermentation |
68368 | 62345 | L-rhamnose | - | fermentation |
68368 | 30911 | sorbitol | - | fermentation |
68368 | 17268 | myo-inositol | - | fermentation |
68368 | 17634 | D-glucose | - | fermentation |
68368 | 5291 | gelatin | - | hydrolysis |
68368 | 27897 | tryptophan | - | energy source |
68368 | 16199 | urea | - | hydrolysis |
68368 | 16947 | citrate | - | assimilation |
68368 | 18257 | ornithine | - | degradation |
68368 | 25094 | lysine | - | degradation |
68368 | 29016 | arginine | - | hydrolysis |
35641 | 29864 | mannitol | - | fermentation |
35641 | 16947 | citrate | - | carbon source |
35641 | 17234 | glucose | + | fermentation |
35641 | 17716 | lactose | - | fermentation |
35641 | 17632 | nitrate | + | reduction |
35641 | 16301 | nitrite | + | reduction |
35641 | 15792 | malonate | - | assimilation |
35641 | 132112 | sodium thiosulfate | - | builds gas from |
35641 | 17234 | glucose | + | 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
@ref | Chebi-ID | metabolite | production |
---|---|---|---|
68368 | 17997 | dinitrogen | no |
68368 | 15688 | acetoin | no |
68368 | 35581 | indole | no |
68368 | 16136 | hydrogen sulfide | no |
35641 | 35581 | indole | no |
metabolite tests
@ref | Chebi-ID | metabolite | voges-proskauer-test | indole test | methylred-test |
---|---|---|---|---|---|
68368 | 15688 | acetoin | - | ||
68368 | 35581 | indole | - | ||
35641 | 15688 | acetoin | - | ||
35641 | 17234 | glucose | + |
enzymes
@ref | value | activity | ec |
---|---|---|---|
68368 | gelatinase | - | |
68368 | tryptophan deaminase | - | 4.1.99.1 |
68368 | urease | - | 3.5.1.5 |
68368 | ornithine decarboxylase | - | 4.1.1.17 |
68368 | lysine decarboxylase | - | 4.1.1.18 |
68368 | arginine dihydrolase | - | 3.5.3.6 |
68368 | beta-galactosidase | - | 3.2.1.23 |
35641 | oxidase | - | |
35641 | beta-galactosidase | + | 3.2.1.23 |
35641 | alcohol dehydrogenase | + | 1.1.1.1 |
35641 | gelatinase | - | |
35641 | catalase | + | 1.11.1.6 |
35641 | lysine decarboxylase | - | 4.1.1.18 |
35641 | ornithine decarboxylase | + | 4.1.1.17 |
35641 | phenylalanine ammonia-lyase | - | 4.3.1.24 |
35641 | tryptophan deaminase | - | |
35641 | urease | - | 3.5.1.5 |
68382 | alkaline phosphatase | + | 3.1.3.1 |
68382 | esterase (C 4) | + | |
68382 | esterase lipase (C 8) | - | |
68382 | lipase (C 14) | - | |
68382 | leucine arylamidase | + | 3.4.11.1 |
68382 | valine arylamidase | + | |
68382 | cystine arylamidase | - | 3.4.11.3 |
68382 | trypsin | - | 3.4.21.4 |
68382 | alpha-chymotrypsin | - | 3.4.21.1 |
68382 | acid phosphatase | + | 3.1.3.2 |
68382 | naphthol-AS-BI-phosphohydrolase | + | |
68382 | alpha-galactosidase | - | 3.2.1.22 |
68382 | beta-galactosidase | + | 3.2.1.23 |
68382 | beta-glucuronidase | + | 3.2.1.31 |
68382 | alpha-glucosidase | + | 3.2.1.20 |
68382 | beta-glucosidase | - | 3.2.1.21 |
68382 | N-acetyl-beta-glucosaminidase | - | 3.2.1.52 |
68382 | alpha-mannosidase | - | 3.2.1.24 |
68382 | alpha-fucosidase | - | 3.2.1.51 |
fatty acid profile
fatty acids
@ref fatty acid percentage ECL 50969 C12:0 3.4 12 50969 C13:0 1.8 13 50969 C14:0 6.2 14 50969 C15:0 10.4 15 50969 C16:0 20.4 16 50969 C17:0 2.1 17 50969 C12:0 ALDE ? 1.2 10.915 50969 C13:0 3OH/C15:1 i I/H 1.5 14.469 50969 C14:0 3OH/C16:1 ISO I 5.5 15.485 50969 C15:1 ω8c 0.8 14.792 50969 C16:1 ω7c 23.1 15.819 50969 C17:0 CYCLO 4.2 16.888 50969 C17:1 ω8c 1 16.792 50969 C18:1 ω7c /12t/9t 17.7 17.824 50969 C18:2 ω6,9c/C18:0 ANTE 0.8 17.724 - type of FA analysis: whole cell analysis
- method/protocol: CCUG
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 |
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
35641 | - | + | + | - | - | + | + | - | - | - | + | + | - | + | + | + | - | - | - | - |
API 20E
@ref | ONPG | ADH Arg | LDC Lys | ODC | CIT | H2S | URE | TDA Trp | IND | VP | GEL | GLU | INO | Sor | RHA | SAC | MEL | N2 |
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
35641 | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - |
API biotype100
@ref | GLU | FRU | GAL | TRE | MNE | SBE | MEL | SAC | RAF | MTE | MAL | LAC | LTE | MbGa | MaGa | CEL | GEN | MbGu | ESC | RIB | ARA | XYL | PLE | RHA | FUC | MLZ | DARL | LARL | XLT | DUL | TAG | GLY | INO | MAN | MTL | TUR | SOR | ADO | HBG | LYX | ERY | MDG | 3MDG | SAT | MUC | LTAT | DTAT | MTAT | DMLT | LMLT | CATE | TATE | TTE | CIT | GRT | GAT | 2KG | 5KG | TRY | NAG | GNT | PAC | PAT | pOBE | QAT | GTE | mOBE | BAT | PPAT | CMT | TGE | BET | PCE | ABT | HIN | LAT | CAP | CYT | HIS | SUC | FUM | GRE | GYT | AVT | ETN | TTN | GLN | ITA | 3OBU | APT | GTT | PRO | DALA | LALA | SER | MNT | PROP | TYR | 2KT |
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
35641 | + | + | + | + | + | - | + | + | + | + | + | - | - | + | + | - | - | - | - | + | + | - | - | + | + | - | - | - | - | - | - | + | - | + | - | - | - | - | - | - | - | - | - | - | - | - | - | - | + | + | - | - | - | - | - | + | - | - | - | + | + | - | - | - | - | - | - | - | - | - | - | - | - | - | - | + | - | - | - | + | + | - | - | - | - | - | - | - | - | + | + | + | + | - | + | - | - | - | - |
Isolation, sampling and environmental information
isolation
@ref | sample type | sampling date | isolation date |
---|---|---|---|
50969 | Human feces | 1966 | |
35641 | Human, Feces | 1966 |
isolation source categories
Cat1 | Cat2 | Cat3 |
---|---|---|
#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
trait | prediction | confidence | training_data |
---|---|---|---|
spore-forming | no | 100 | no |
gram-positive | no | 98.248 | no |
anaerobic | no | 94.984 | no |
halophile | no | 87.558 | no |
spore-forming | no | 93.705 | no |
glucose-util | yes | 94.058 | no |
thermophile | no | 98.73 | yes |
flagellated | no | 59.43 | no |
aerobic | yes | 84.684 | no |
motile | yes | 89.289 | no |
glucose-ferment | yes | 92.953 | no |
External links
@ref: 35641
culture collection no.: CIP 104223, ATCC 25931, CCUG 32351, NCDC 1120-66
straininfo link
- @ref: 93478
- straininfo: 305279
literature
topic | Pubmed-ID | title | authors | journal | DOI | year | mesh | topic2 |
---|---|---|---|---|---|---|---|---|
Pathogenicity | 23528983 | Study of probiotic potential of four wild Lactobacillus rhamnosus strains. | Tuo Y, Zhang W, Zhang L, Ai L, Zhang Y, Han X, Yi H | Anaerobe | 10.1016/j.anaerobe.2013.03.007 | 2013 | *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/physiology | Metabolism |
Pathogenicity | 26805974 | Evaluation 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 X | J Dairy Sci | 10.3168/jds.2015-10434 | 2016 | Animals, 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, *Probiotics | Enzymology |
Pathogenicity | 30395485 | Anti-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 H | Can J Microbiol | 10.1139/cjm-2018-0031 | 2018 | *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/pathogenicity | Metabolism |
Pathogenicity | 32694956 | Screening 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 MP | ScientificWorldJournal | 10.1155/2020/6378712 | 2020 | Anti-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/*pharmacology | Phylogeny |
Phylogeny | 34381426 | Selective 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 JT | Front Microbiol | 10.3389/fmicb.2021.673946 | 2021 | ||
35206082 | Probiotic Effects and Metabolic Products of Enterococcus faecalis LD33 with Respiration Capacity. | Jiao Y, Yang H, Shigwedha N, Zhang S, Liu F, Zhang L | Foods | 10.3390/foods11040606 | 2022 | |||
36367551 | Antibacterial 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 C | Foodborne Pathog Dis | 10.1089/fpd.2022.0046 | 2022 | *Shigella sonnei, Eugenol/pharmacology, Lettuce/microbiology, Microbial Sensitivity Tests, Anti-Bacterial Agents/pharmacology, *Dysentery, Bacillary |
Reference
@id | authors | title | doi/url | catalogue |
---|---|---|---|---|
20215 | Parte, 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 DSMZ | 10.1099/ijsem.0.004332 | |
35641 | Curators of the CIP | https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20104223 | Collection of Institut Pasteur (CIP 104223) | |
50969 | Curators of the CCUG | https://www.ccug.se/strain?id=32351 | Culture Collection University of Gothenburg (CCUG) (CCUG 32351) | |
66792 | Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmann | Automatically annotated for the DiASPora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information) | https://diaspora-project.de/progress.html#genomes | |
68368 | Automatically annotated from API 20E | |||
68382 | Automatically annotated from API zym | |||
69480 | Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmann | Predictions 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 | |
69481 | Xiao-Yin To, René Mreches, Martin Binder, Alice C. McHardy, Philipp C. Münch | Predictions based on the model GenomeNet Sporulation v. 1 | 10.21203/rs.3.rs-2527258/v1 | |
93478 | Reimer, 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 identifiers | 10.60712/SI-ID305279.1 |