Shigella boydii P288 is an aerobe, Gram-negative, rod-shaped bacterium of the family Enterobacteriaceae.
Gram-negative rod-shaped aerobe genome sequence 16S sequence Bacteria| @ref 20215 |
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|
| Domain Bacteria |
| Phylum Pseudomonadota |
| Class Gammaproteobacteria |
| Order Enterobacterales |
| Family Enterobacteriaceae |
| Genus Shigella |
| Species Shigella boydii |
| Full scientific name Shigella boydii Ewing 1949 (Approved Lists 1980) |
| @ref | Name | Growth | Medium link | Composition | |
|---|---|---|---|---|---|
| 40739 | MEDIUM 72- for trypto casein soja agar | Distilled water make up to (1000.000 ml);Trypto casein soy agar (40.000 g) | |||
| 116980 | CIP Medium 72 | Medium recipe at CIP | |||
| 3205 | TRYPTICASE SOY YEAST EXTRACT MEDIUM (DSMZ Medium 92) | Medium recipe at MediaDive | Name: 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 | ||
| 3205 | COLUMBIA BLOOD MEDIUM (DSMZ Medium 693) | Medium recipe at MediaDive | Name: COLUMBIA BLOOD MEDIUM (DSMZ Medium 693) Composition: Defibrinated sheep blood 50.0 g/l Columbia agar base |
| @ref | Spore formation | Confidence | |
|---|---|---|---|
| 125439 | 95.2 |
| @ref | Chebi-ID | Metabolite | Utilization activity | Kind of utilization tested | |
|---|---|---|---|---|---|
| 68368 | 27613 ChEBI | amygdalin | - | fermentation | from API 20E |
| 68368 | 29016 ChEBI | arginine | - | hydrolysis | from API 20E |
| 68368 | 16947 ChEBI | citrate | - | assimilation | from API 20E |
| 68368 | 17634 ChEBI | D-glucose | + | fermentation | from API 20E |
| 68368 | 16899 ChEBI | D-mannitol | + | fermentation | from API 20E |
| 68368 | 5291 ChEBI | gelatin | - | hydrolysis | from API 20E |
| 68368 | 62345 ChEBI | L-rhamnose | - | fermentation | from API 20E |
| 68368 | 25094 ChEBI | lysine | - | degradation | from API 20E |
| 68368 | 28053 ChEBI | melibiose | - | fermentation | from API 20E |
| 68368 | 17268 ChEBI | myo-inositol | - | fermentation | from API 20E |
| 116980 | 17632 ChEBI | nitrate | + | reduction | |
| 116980 | 16301 ChEBI | nitrite | - | reduction | |
| 68368 | 18257 ChEBI | ornithine | - | degradation | from API 20E |
| 68368 | 30911 ChEBI | sorbitol | - | fermentation | from API 20E |
| 68368 | 17992 ChEBI | sucrose | - | fermentation | from API 20E |
| 68368 | 27897 ChEBI | tryptophan | - | energy source | from API 20E |
| 68368 | 16199 ChEBI | urea | - | hydrolysis | from API 20E |
| @ref | Value | Activity | Ec | |
|---|---|---|---|---|
| 68382 | acid phosphatase | + | 3.1.3.2 | from API zym |
| 116980 | alcohol dehydrogenase | - | 1.1.1.1 | |
| 68382 | alkaline phosphatase | + | 3.1.3.1 | from API zym |
| 68382 | alpha-chymotrypsin | - | 3.4.21.1 | from API zym |
| 68382 | alpha-fucosidase | - | 3.2.1.51 | from API zym |
| 68382 | alpha-galactosidase | - | 3.2.1.22 | from API zym |
| 68382 | alpha-glucosidase | + | 3.2.1.20 | from API zym |
| 68382 | alpha-mannosidase | - | 3.2.1.24 | from API zym |
| 68368 | arginine dihydrolase | - | 3.5.3.6 | from API 20E |
| 68382 | beta-galactosidase | - | 3.2.1.23 | from API zym |
| 68368 | beta-galactosidase | - | 3.2.1.23 | from API 20E |
| 68382 | beta-glucosidase | - | 3.2.1.21 | from API zym |
| 68382 | beta-glucuronidase | - | 3.2.1.31 | from API zym |
| 116980 | catalase | + | 1.11.1.6 | |
| 68382 | cystine arylamidase | - | 3.4.11.3 | from API zym |
| 68368 | cytochrome oxidase | - | 1.9.3.1 | from API 20E |
| 68382 | esterase (C 4) | + | from API zym | |
| 68382 | esterase lipase (C 8) | - | from API zym | |
| 68368 | gelatinase | - | from API 20E | |
| 68382 | leucine arylamidase | + | 3.4.11.1 | from API zym |
| 68382 | lipase (C 14) | - | from API zym | |
| 116980 | lysine decarboxylase | - | 4.1.1.18 | |
| 68368 | lysine decarboxylase | - | 4.1.1.18 | from API 20E |
| 68382 | N-acetyl-beta-glucosaminidase | - | 3.2.1.52 | from API zym |
| 68382 | naphthol-AS-BI-phosphohydrolase | - | from API zym | |
| 116980 | ornithine decarboxylase | - | 4.1.1.17 | |
| 68368 | ornithine decarboxylase | - | 4.1.1.17 | from API 20E |
| 116980 | oxidase | - | ||
| 68382 | trypsin | - | 3.4.21.4 | from API zym |
| 68368 | tryptophan deaminase | - | 4.1.99.1 | from API 20E |
| 116980 | urease | - | 3.5.1.5 | |
| 68368 | urease | - | 3.5.1.5 | from API 20E |
| 68382 | valine arylamidase | + | from API zym |
| @ref | ONPG | ADH (Arg) | LDC (Lys) | ODC | CIT | H2S productionH2S | URE | TDA (Trp) | IND | Acetoin production (Voges Proskauer test)VP | GEL | GLU | MAN | INO | Sor | RHA | SAC | MEL | AMY | ARA | OX | Nitrite productionNO2 | Reduction to N2N2 | MotilityMOB | Growth on MacConkey mediumMAC | OF-O | OF-F | |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| 3205 | - | - | - | - | - | - | - | - | - | + | - | + | + | - | - | - | - | - | - | + | - | not determinedn.d. | not determinedn.d. | not determinedn.d. | not determinedn.d. | not determinedn.d. | not determinedn.d. | |
| 3205 | - | - | - | - | - | - | - | - | - | - | - | + | + | - | - | - | - | - | - | +/- | - | not determinedn.d. | not determinedn.d. | not determinedn.d. | not determinedn.d. | not determinedn.d. | not determinedn.d. |
| @ref | Country | Country ISO 3 Code | Continent | |
|---|---|---|---|---|
| 3205 | India | IND | Asia |
Global distribution of 16S sequence HF558388 (>99% sequence identity) for Enterobacteriaceae from Microbeatlas ![]()
| @ref | Description | Assembly level | INSDC accession | BV-BRC accession | IMG accession | NCBI tax ID | Score | |
|---|---|---|---|---|---|---|---|---|
| 124043 | ASM1672628v1 assembly for Shigella boydii FDAARGOS_1139 | complete | 621 | 95.12 | ||||
| 66792 | ASM294673v1 assembly for Shigella boydii ATCC 8700 | complete | 621 | 67.43 | ||||
| 66792 | 57940_F01 assembly for Shigella boydii NCTC12985 | contig | 621 | 57.71 | ||||
| 66792 | ASM357253v1 assembly for Shigella boydii DMB SH130 | contig | 621 |
| @ref | Trait | Model | Prediction | Confidence in % | In training data |
|---|---|---|---|---|---|
| 125439 | spore_formation | BacteriaNetⓘ | no | 95.20 | no |
| 125439 | motility | BacteriaNetⓘ | yes | 64.90 | no |
| 125439 | gram_stain | BacteriaNetⓘ | negative | 92.30 | no |
| 125439 | oxygen_tolerance | BacteriaNetⓘ | aerobe | 93.50 | no |
| @ref | Trait | Model | Prediction | Confidence in % | In training data |
|---|---|---|---|---|---|
| 125438 | gram-positive | gram-positiveⓘ | no | 99.69 | no |
| 125438 | anaerobic | anaerobicⓘ | no | 93.43 | yes |
| 125438 | aerobic | aerobicⓘ | no | 64.50 | yes |
| 125438 | spore-forming | spore-formingⓘ | no | 87.90 | no |
| 125438 | thermophilic | thermophileⓘ | no | 97.00 | yes |
| 125438 | flagellated | motile2+ⓘ | yes | 69.02 | no |
| Topic | Title | Authors | Journal | DOI | Year | |
|---|---|---|---|---|---|---|
| Development of a Droplet Digital Polymerase Chain Reaction for Rapid and Simultaneous Identification of Common Foodborne Pathogens in Soft Cheese. | Cremonesi P, Cortimiglia C, Picozzi C, Minozzi G, Malvisi M, Luini M, Castiglioni B. | Front Microbiol | 10.3389/fmicb.2016.01725 | 2016 | ||
| Occurrence of CRISPR-Cas genes and lack of association with antibiotic resistance in Shigella isolates collected from patients with diarrhea in Ahvaz, southwest Iran. | Ekrami A, Taheri B, Daneshfar S, Moradi M, Ghorbani A, Akhash N, Jafarzadeh Z, Farshadzadeh Z, Saki M. | BMC Infect Dis | 10.1186/s12879-025-12100-0 | 2025 | ||
| Green Solid-State Synthesis of Antibacterial Binary Organic Material: Crystal Growth, Physicochemical Properties, Thermal Study, Antibacterial Activity, and Hirshfeld Surface Analysis. | Rai A, Chaudhary S, Dube SP, Bajda S, Raghuwanshi R, Mishra SK, Palumbo G, Rai RN. | Int J Mol Sci | 10.3390/ijms26125509 | 2025 | ||
| Complete Genome Sequences of Five SO-1-Like Siphoviridae Bacteriophages That Infect Enterobacteriales. | Purnell MG, Andersen K, Bell A, Briscoe JT, Brown HMF, Carr EL, Doney J, Folsom PF, Green C, Harris EH, Huhem E, Jensen RM, Johnson L, Jones C, Lambert AS, Loertscher E, Newey CR, Porter M, Rallison J, Sharma R, Sork C, Soule S, Stewart JB, Stoker T, Tayler S, Thompson DW, Thurgood TL, Walker J, Breakwell DP, Casjens SR, Grose JH. | Microbiol Resour Announc | 10.1128/mra.01224-21 | 2022 | ||
| Phylogeny | Characterization of Shigella flexneri Serotype 6 Strains Isolated from Bangladesh and Identification of a New Phylogenetic Cluster. | Shahnaij M, Amin MB, Hoque MM, Mondol AS, Rana KJ, Azmi IJ, Talukder KA. | J Bacteriol | 10.1128/jb.00406-22 | 2023 | |
| Berberine and its nanoformulations and extracts: potential strategies and future perspectives against multi-drug resistant bacterial infections. | Yang X, Wang Y, Li L, Tang D, Yan Z, Li M, Jiang J, Bi D. | Front Microbiol | 10.3389/fmicb.2025.1643409 | 2025 | ||
| Immunogenicity and preclinical efficacy characterization of ShecVax, a combined vaccine against Shigella and enterotoxigenic Escherichia coli. | Li S, Upadhyay I, Seo H, Vakamalla SSR, Madhwal A, Sack DA, Zhang W. | Infect Immun | 10.1128/iai.00004-25 | 2025 | ||
| Prevalence of Shigella boydii in Bangladesh: Isolation and Characterization of a Rare Phage MK-13 That Can Robustly Identify Shigellosis Caused by Shigella boydii Type 1. | Akter M, Brown N, Clokie M, Yeasmin M, Tareq TM, Baddam R, Azad MAK, Ghosh AN, Ahmed N, Talukder KA. | Front Microbiol | 10.3389/fmicb.2019.02461 | 2019 | ||
| Genetics | Multiple Mechanisms Confer Resistance to Azithromycin in Shigella in Bangladesh: a Comprehensive Whole Genome-Based Approach. | Nusrin S, Asad A, Hayat S, Islam B, Begum R, Nabila FH, Islam Z. | Microbiol Spectr | 10.1128/spectrum.00741-22 | 2022 | |
| Pullulan or chitosan based active coating by incorporating polyphenols from lemon peel in raw poultry meat. | Maru VR, Gupta S, Ranade V, Variyar PS. | J Food Sci Technol | 10.1007/s13197-020-04841-4 | 2021 | ||
| In silico analysis and a comparative genomics approach to predict pathogenic trehalase genes in the complete genome of Antarctica Shigella sp. PAMC28760. | Shrestha P, Karmacharya J, Han SR, Park H, Oh TJ. | Virulence | 10.1080/21505594.2022.2117679 | 2022 | ||
| Efficiency of Biosynthesized Silver and Zinc Nanoparticles Against Multi-Drug Resistant Pathogens. | Punjabi K, Mehta S, Chavan R, Chitalia V, Deogharkar D, Deshpande S. | Front Microbiol | 10.3389/fmicb.2018.02207 | 2018 | ||
| Biotechnology | Multiplex 16S rRNA-derived geno-biochip for detection of 16 bacterial pathogens from contaminated foods. | Shin HH, Hwang BH, Cha HJ. | Biotechnol J | 10.1002/biot.201600043 | 2016 | |
| Bacteriophages Isolated From Turkeys Infecting Diverse Salmonella Serovars. | Lu Z, Marchant J, Thompson S, Melgarejo H, Ignatova D, Kopic S, Damaj R, Trejo H, Paramo R, Reed A, Breidt F, Kathariou S. | Front Microbiol | 10.3389/fmicb.2022.933751 | 2022 | ||
| Phylogeny | Specific discrimination of three pathogenic Salmonella enterica subsp. enterica serotypes by carB-based oligonucleotide microarray. | Shin HH, Hwang BH, Seo JH, Cha HJ. | Appl Environ Microbiol | 10.1128/aem.02978-13 | 2014 | |
| In Silico Analysis of the cadF Gene and Development of a Duplex Polymerase Chain Reaction for Species-Specific Identification of Campylobacter jejuni and Campylobacter coli. | Shams S, Bakhshi B, Tohidi Moghadam T. | Jundishapur J Microbiol | 10.5812/jjm.29645 | 2016 | ||
| Enzymology | Development of a Flow Cytometry-Based Method for Rapid Detection of Escherichia coli and Shigella Spp. Using an Oligonucleotide Probe. | Xue Y, Wilkes JG, Moskal TJ, Williams AJ, Cooper WM, Nayak R, Rafii F, Buzatu DA. | PLoS One | 10.1371/journal.pone.0150038 | 2016 | |
| Rapid single cell detection of Staphylococcus aureus by aptamer-conjugated gold nanoparticles. | Chang YC, Yang CY, Sun RL, Cheng YF, Kao WC, Yang PC. | Sci Rep | 10.1038/srep01863 | 2013 | ||
| Enzymology | Rapid concentration and molecular enrichment approach for sensitive detection of Escherichia coli and Shigella species in potable water samples. | Maheux AF, Bissonnette L, Boissinot M, Bernier JL, Huppe V, Picard FJ, Berube E, Bergeron MG. | Appl Environ Microbiol | 10.1128/aem.02337-10 | 2011 | |
| Development and evaluation of oligonucleotide chip based on the 16S-23S rRNA gene spacer region for detection of pathogenic microorganisms associated with sepsis. | Kim CM, Song ES, Jang HJ, Kim HJ, Lee S, Shin JH, Kim SJ, Jeong SH, Jeong J, Koh K, Choi GE, Lee EY, Chang CL. | J Clin Microbiol | 10.1128/jcm.01130-09 | 2010 | ||
| Phylogeny | Direct identification of Vibrio vulnificus in clinical specimens by nested PCR. | Lee SE, Kim SY, Kim SJ, Kim HS, Shin JH, Choi SH, Chung SS, Rhee JH. | J Clin Microbiol | 10.1128/jcm.36.10.2887-2892.1998 | 1998 | |
| Analysis of the type 1 pilin gene cluster fim in Salmonella: its distinct evolutionary histories in the 5' and 3' regions. | Boyd EF, Hartl DL. | J Bacteriol | 10.1128/jb.181.4.1301-1308.1999 | 1999 | ||
| A broadly immunogenic polyvalent Shigella multiepitope fusion antigen protein protects against Shigella sonnei and Shigella flexneri lethal pulmonary challenges in mice. | Li S, Anvari S, Ptacek G, Upadhyay I, Kaminski RW, Sack DA, Zhang W. | Infect Immun | 10.1128/iai.00316-23 | 2023 | ||
| Phylogeny | Selection and validation of a multilocus variable-number tandem-repeat analysis panel for typing Shigella spp. | Gorge O, Lopez S, Hilaire V, Lisanti O, Ramisse V, Vergnaud G. | J Clin Microbiol | 10.1128/jcm.02027-07 | 2008 | |
| Enzymology | Evaluation of antibacterial activity, phenol and flavonoid contents of Thespesia populnea flower extracts. | Saravanakumar A, Venkateshwaran K, Vanitha J, Ganesh M, Vasudevan M, Sivakumar T | Pak J Pharm Sci | 2009 | ||
| Determination of the profile of fatty acids of 4 species of Shigella spp by chromatography of gases. | Robles Valderrama E, Hurtado Bocanegra MD, Gonzalez Arreaga ME, Ramirez Garcia P, Duran Diaz A, Ayala Patino R, Martinez Perez ME | Rev Latinoam Microbiol | 2002 |
| #3205 | Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 7532 |
| #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. IJSEM ( DOI 10.1099/ijsem.0.004332 ) |
| #20218 | Verslyppe, B., De Smet, W., De Baets, B., De Vos, P., Dawyndt P.: StrainInfo introduces electronic passports for microorganisms.. Syst Appl Microbiol. 37: 42 - 50 2014 ( DOI 10.1016/j.syapm.2013.11.002 , PubMed 24321274 ) |
| #40739 | ; Curators of the CIP; |
| #58445 | Culture Collection University of Gothenburg (CCUG) ; Curators of the CCUG; CCUG 49022 |
| #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) . |
| #68368 | Automatically annotated from API 20E . |
| #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.: MicrobeAtlas 1.0 beta . |
| #116980 | Collection of Institut Pasteur ; Curators of the CIP; CIP 82.50 |
| #124043 | Isabel Schober, Julia Koblitz: Data extracted from sequence databases, automatically matched based on designation and taxonomy . |
| #125438 | Julia Koblitz, Lorenz Christian Reimer, Rüdiger Pukall, Jörg Overmann: Predicting bacterial phenotypic traits through improved machine learning using high-quality, curated datasets. 2024 ( DOI 10.1101/2024.08.12.607695 ) |
| #125439 | Philipp Münch, René Mreches, Martin Binder, Hüseyin Anil Gündüz, Xiao-Yin To, Alice McHardy: deepG: Deep Learning for Genome Sequence Data. R package version 0.3.1 . |
| #126262 | A. Lissin, I. Schober, J. F. Witte, H. Lüken, A. Podstawka, J. Koblitz, B. Bunk, P. Dawyndt, P. Vandamme, P. de Vos, J. Overmann, L. C. Reimer: StrainInfo—the central database for linked microbial strain identifiers. ( DOI 10.1093/database/baaf059 ) |
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