Name: Shigella boydii P288
Creator: BacDive
License: http://creativecommons.org/licenses/by-nc/4.0/

Strain identifier

BacDive ID: 5174

Type strain:

Species: Shigella boydii

Strain Designation: P288

Culture col. no.: DSM 7532, ATCC 8700, CCUG 49022, CIP 82.50, NCTC 12985

Strain history: CIP <- 1982, ATCC <- NCTC, Shigella paradysenteriae <- J. Boyd: strain P288

NCBI tax ID(s): 621 (species)

SI-ID 34992

ATCC 8700, NCTC 12985, DSM 7532, CIP 82.50, BCRC 15959, CCRC 15959, CCUG 49022

Other strains from Shigella boydii

S. boydii 54264, CIP 54.75
S. boydii 75-25-3, CIP 54.108
S. boydii 901, CIP 57.47, NCTC 9356
S. boydii CIP 56.36
S. boydii 4350-54, CIP 58.18, NCTC 9765
S. boydii 258, CIP 73.2
S. boydii 7001, CIP 54.73
S. boydii 2045-54, 425, CIP 58.22, NCTC 9362, ...
S. boydii 541106, CIP 56.18
S. boydii 2770/51, CIP 58.17, ATCC 12035, ...
S. boydii 703, CIP 58.19, ATCC 12034, NCTC ...
S. boydii 140/56, 5518/56, CIP 67.11
S. boydii D 27, CIP 53.42
S. boydii Nil-2-c, CIP 52.50, NCTC 9329
S. boydii H 21582, CIP 51.6
S. boydii A12, CIP 53.44, NCTC 6721
S. boydii 54125, CIP 54.76
S. boydii 55, CIP 56.35
S. boydii CIP 58.20, NCTC 10024, DRL 120/55
S. boydii 425, CIP 58.21, ATCC 12032, NCTC ...
S. boydii type, CIP 52.48
S. boydii 426/FA, CIP 52.52, NCTC 9331
S. boydii 6917, CIP 52.54, NCTC 9333
S. boydii 1296/7, CIP 51.4, NCTC 9355
S. boydii Congo, CIP 51.3
S. boydii PSH-125, CIP 52.51, NCTC 9330
S. boydii M 279, CIP 52.53, NCTC 9332
S. boydii 592, CIP 58.4
S. boydii 123, CIP 58.23, ATCC 12033, NCTC ...
S. boydii 1693, CIP 58.24
S. boydii CCUG 9564, NCTC 9357
S. boydii CCUG 21249
S. boydii CCUG 21261
S. boydii CCUG 37891
S. boydii CCUG 37892
S. boydii CCUG 37893
S. boydii CCUG 45096
S. boydii CIP 111949

Section

Shigella boydii P288 is an aerobe, mesophilic, Gram-negative bacterium of the family Enterobacteriaceae.

Gram-negative
rod-shaped
aerobe
mesophilic
16S sequence
Bacteria
genome sequence

Information on the name and the taxonomic classification. Name and taxonomic classification

	Last LPSN update	14-12-2023 (DD-MM-YYYY)
	Domain	"Bacteria"
	Phylum	*Pseudomonadota*
	Class	*Gammaproteobacteria*
	Order	*Enterobacterales*
	Family	*Enterobacteriaceae*
	Genus	*Shigella*
	Species	**Shigella boydii**
	Full Scientific Name (LPSN)	Shigella boydii Ewing 1949 (Approved Lists 1980)

Information on morphological and physiological properties Morphology

[Ref.: #116980]	Gram stain	negative

[Ref.: #116980]	Cell shape	rod-shaped

[Ref.: #116980]	Motility	no

Information on culture and growth conditions Culture and growth conditions

[Ref.: #3205]

Culture medium

CASO AGAR (MERCK 105458) (DSMZ Medium 220)

[Ref.: #3205]

Culture medium growth

[Ref.: #3205]

Culture medium link

Medium recipe at MediaDive

[Ref.: #3205]

Culture medium composition

expand / minimize

[Ref.: #40739]

Culture medium

MEDIUM 72- for trypto casein soja agar

[Ref.: #40739]

Culture medium growth

[Ref.: #40739]

Culture medium composition

expand / minimize

[Ref.: #116980]

Culture medium

CIP Medium 72

[Ref.: #116980]

Culture medium growth

[Ref.: #116980]

Culture medium link

Medium recipe provided by DSMZ

		Temperature
[Ref.: #3205]	growth	37 °C
[Ref.: #40739]	growth	30 °C
[Ref.: #58445]	growth	37 °C

[Ref.: #3205]	Temperature range	mesophilic
[Ref.: #40739]	Temperature range	mesophilic
[Ref.: #58445]	Temperature range	mesophilic

Information on physiology and metabolism Physiology and metabolism

[Ref.: #58445]	Oxygen tolerance	aerobe
[Ref.: #116980]	Oxygen tolerance	obligate aerobe

	Metabolite	Utilization activity	Kind of utilization tested
[Ref.: #68368]	amygdalin ChEBI	-	fermentation	* from API 20E
[Ref.: #68368]	arginine ChEBI	-	hydrolysis	* from API 20E
[Ref.: #68368]	citrate ChEBI	-	assimilation	* from API 20E
[Ref.: #68368]	D-glucose ChEBI	+	fermentation	* from API 20E
[Ref.: #68368]	D-mannitol ChEBI	+	fermentation	* from API 20E
[Ref.: #68368]	gelatin ChEBI	-	hydrolysis	* from API 20E
[Ref.: #68368]	L-rhamnose ChEBI	-	fermentation	* from API 20E
[Ref.: #68368]	lysine ChEBI	-	degradation	* from API 20E
[Ref.: #68368]	melibiose ChEBI	-	fermentation	* from API 20E
[Ref.: #68368]	myo-inositol ChEBI	-	fermentation	* from API 20E
[Ref.: #116980]	nitrate ChEBI	+	reduction
[Ref.: #116980]	nitrite ChEBI	-	reduction
[Ref.: #68368]	ornithine ChEBI	-	degradation	* from API 20E
[Ref.: #68368]	sorbitol ChEBI	-	fermentation	* from API 20E
[Ref.: #68368]	sucrose ChEBI	-	fermentation	* from API 20E
[Ref.: #68368]	tryptophan ChEBI	-	energy source	* from API 20E
[Ref.: #68368]	urea ChEBI	-	hydrolysis	* from API 20E
	Only first 10 entries are displayed. Click here to see all.

	Metabolite	Production
[Ref.: #116980]	indole ChEBI	no
[Ref.: #68368]	hydrogen sulfide ChEBI	no	* from API 20E
[Ref.: #68368]	indole ChEBI	no	* from API 20E

	Physiological tests	Metabolite	Indole test
[Ref.: #68368]		indole ChEBI	-	* from API 20E

	Enzyme	Enzyme activity	EC number
[Ref.: #68382]	acid phosphatase	+	3.1.3.2	* from API zym
[Ref.: #116980]	alcohol dehydrogenase	-	1.1.1.1
[Ref.: #68382]	alkaline phosphatase	+	3.1.3.1	* from API zym
[Ref.: #68382]	alpha-chymotrypsin	-	3.4.21.1	* from API zym
[Ref.: #68382]	alpha-fucosidase	-	3.2.1.51	* from API zym
[Ref.: #68382]	alpha-galactosidase	-	3.2.1.22	* from API zym
[Ref.: #68382]	alpha-glucosidase	+	3.2.1.20	* from API zym
[Ref.: #68382]	alpha-mannosidase	-	3.2.1.24	* from API zym
[Ref.: #68368]	arginine dihydrolase	-	3.5.3.6	* from API 20E
[Ref.: #68382]	beta-galactosidase	-	3.2.1.23	* from API zym, API 20E
[Ref.: #68382]	beta-glucosidase	-	3.2.1.21	* from API zym
[Ref.: #68382]	beta-glucuronidase	-	3.2.1.31	* from API zym
[Ref.: #116980]	catalase	+	1.11.1.6
[Ref.: #68382]	cystine arylamidase	-	3.4.11.3	* from API zym
[Ref.: #68368]	cytochrome oxidase	-	1.9.3.1	* from API 20E
[Ref.: #68382]	esterase (C 4)	+		* from API zym
[Ref.: #68382]	esterase lipase (C 8)	-		* from API zym
[Ref.: #68368]	gelatinase	-		* from API 20E
[Ref.: #68382]	leucine arylamidase	+	3.4.11.1	* from API zym
[Ref.: #68382]	lipase (C 14)	-		* from API zym
[Ref.: #116980]	lysine decarboxylase	-	4.1.1.18
[Ref.: #68368]	lysine decarboxylase	-	4.1.1.18	* from API 20E
[Ref.: #68382]	N-acetyl-beta-glucosaminidase	-	3.2.1.52	* from API zym
[Ref.: #68382]	naphthol-AS-BI-phosphohydrolase	-		* from API zym
[Ref.: #116980]	ornithine decarboxylase	-	4.1.1.17
[Ref.: #68368]	ornithine decarboxylase	-	4.1.1.17	* from API 20E
[Ref.: #116980]	oxidase	-
[Ref.: #68382]	trypsin	-	3.4.21.4	* from API zym
[Ref.: #68368]	tryptophan deaminase	-	4.1.99.1	* from API 20E
[Ref.: #116980]	urease	-	3.5.1.5
[Ref.: #68368]	urease	-	3.5.1.5	* from API 20E
[Ref.: #68382]	valine arylamidase	+		* from API zym
	Only first 10 entries are displayed. Click here to see all.

API® 20E:

Note that the displayed test results represent raw data and therefore may deviate!

	API ID	beta-GalactosidaseONPG	Arginine dihydrolaseADH (Arg)	Lysine decarboxylaseLDC (Lys)	Ornithine decarboxylaseODC	Citrate utilizationCIT	H2S productionH2S	Urease/urea hydrolysisURE	Tryptophan deaminaseTDA (Trp)	Indole productionIND	Acetoin production (Voges Proskauer test)VP	Gelatinase/gelatin hydrolysisGEL	Fermentation/oxidation of D-glucoseGLU	Fermentation/oxidation of D-mannitolMAN	Fermentation/oxidation of inositolINO	Fermentation/oxidation of sorbitolSor	Fermentation/oxidation of L-rhamnoseRHA	Fermentation/oxidation of sucroseSAC	Fermentation/oxidation of melibioseMEL	Fermentation/oxidation of amygdalinAMY	Fermentation/oxidation of L-arabinoseARA	Cytochrome oxidaseOX	Nitrite productionNO2	Reduction to N2N2	MotilityMOB	Growth on MacConkey mediumMAC	Oxidative catabolisation of D-glucoseOF-O	Fermentation of D-glucoseOF-F
[Ref.: #3205]	16633	-	-	-	-	-	-	-	-	-	+	-	+	+	-	-	-	-	-	-	+	-	not determinedn.d.	not determinedn.d.	not determinedn.d.	not determinedn.d.	not determinedn.d.	not determinedn.d.
[Ref.: #3205]	18228	-	-	-	-	-	-	-	-	-	-	-	+	+	-	-	-	-	-	-	+/-	-	not determinedn.d.	not determinedn.d.	not determinedn.d.	not determinedn.d.	not determinedn.d.	not determinedn.d.

API® zym:

Note that the displayed test results represent raw data and therefore may deviate!

	API ID	Control	2-naphthyl phosphateAlkaline phosphatase	2-naphthyl butyrateEsterase (C 4)	2-naphtyl caprylateEsterase Lipase (C 8)	2-naphthyl myristateLipase (C 14)	L-leucyl-2-naphthylamideLeucine arylamidase	L-valyl-2-naphthylamideValine arylamidase	L-cystyl-2-naphthylamideCystine arylamidase	N-benzoyl-DL-arginine-2-naphthylamideTrypsin	N-glutaryl-phenylalanine-2-naphthylamidealpha- Chymotrypsin	2-naphthyl phosphateAcid phosphatase	Naphthol-AS-BI-phosphateNaphthol-AS-BI-phosphohydrolase	6-Br-2-naphthyl-alphaD-galactpyranosidealpha- Galactosidase	2-naphthyl-betaD-galactpyranosidebeta- Galactosidase	Naphthol-AS-BI-betaD-glucuronidebeta- Glucuronidase	2-naphthyl-alphaD-glucopyranosidealpha- Glucosidase	6-Br-2-naphthyl-betaD-glucopyranosidebeta- Glucosidase	1-naphthyl-N-acetyl-betaD-glucosaminideN-acetyl-beta- glucosaminidase	6-Br-2-naphthyl-alphaD-mannopyranosidealpha- Mannosidase	2-naphthyl-alphaL-fucopyranosidealpha- Fucosidase
[Ref.: #116980]	13543	-	+	+	-	-	+	+	-	-	-	+	-	-	-	-	+	-	-	-	-

Information on isolation source, the sampling and environmental conditions Isolation, sampling and environmental information

[Ref.: #3205]	Country	India
[Ref.: #3205]	Country ISO 3 Code	IND
[Ref.: #3205]	Continent	Asia
* marker position based on {}

[Ref.: #69479]

Global distribution of 16S sequence HF558388 (>99% sequence identity) for Enterobacteriaceae from Microbeatlas

Aquatic Samples	5613
Soil Samples	2111
Animal Samples	88071
Plant Samples	1835
Total Samples	97630

Information on possible application of the strain and its possible interaction with e.g. potential hosts Safety information

[Ref.: #3205]	Biosafety level	2	Risk group (German classification) According to TRBA 466
[Ref.: #116980]	Biosafety level	2	Risk group (French classification)

Information on genomic background e.g. entries in nucleic sequence databass Sequence information

16S Sequence information:

	Sequence accession description	Seq. accession number	Sequence length (bp)	Sequence database	Associated NCBI tax ID
[Ref.: #20218]	Shigella boydii partial 16S rRNA gene, strain P288	HF558388	1515	ENA	621 tax ID	*

Genome sequence information:

Only first 5 entries are displayed. Click here to see all.

	Sequence accession description	Seq. accession number	Assembly level	Sequence database	Associated NCBI tax ID
[Ref.: #66792]	Shigella boydii ATCC 8700	GCA_003572535	contig	GenBank	621 tax ID	*
[Ref.: #66792]	Shigella boydii ATCC 8700	GCA_002946735	complete	GenBank	621 tax ID	*
[Ref.: #66792]	Shigella boydii strain ATCC 8700	621.213	complete	PATRIC	621 tax ID	*
[Ref.: #66792]	Shigella boydii strain DMB SH130	621.253	wgs	PATRIC	621 tax ID	*
[Ref.: #66792]	Shigella boydii strain FDAARGOS_1139	621.337	complete	PATRIC	621 tax ID	*
[Ref.: #66792]	Shigella boydii strain NCTC12985	621.296	wgs	PATRIC	621 tax ID	*

Data predicted using genome information as a basis Genome-based predictions

	Trait	Prediction	Confidence in %	In training data
	Predictions from Diaspora project based on: Shigella boydii ATCC 8700 NCBI: GCA_002946735.1
[Ref.: #69480]	flagellated	no	58.115	no
[Ref.: #69480]	gram-positive	no	98.599	no
[Ref.: #69480]	anaerobic	no	95.575	yes
[Ref.: #69480]	aerobic	yes	77.823	no
[Ref.: #69480]	halophile	no	91.67	no
[Ref.: #69480]	spore-forming	no	94.548	no
[Ref.: #69480]	glucose-util	yes	92.847	no
[Ref.: #69480]	thermophile	no	98.526	yes
[Ref.: #69480]	motile	yes	87.301	no
[Ref.: #69480]	glucose-ferment	yes	91.674	yes

Availability in culture collections External links

[Ref.: #3205]

Culture collection no.

DSM 7532, ATCC 8700, CCUG 49022, CIP 82.50, NCTC 12985

[Ref.: #74666]

SI-ID 34992

Literature:

Topic	Title	Authors	Journal	DOI	Year
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	*

References

#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 .

#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) .

#74666

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 . ( DOI 10.60712/SI-ID34992.1 )

#116980 Collection of Institut Pasteur ; Curators of the CIP; CIP 82.50
* These data were automatically processed and therefore are not curated

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Shigella boydii ATCC 8700

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