Name: Shigella flexneri 24570
Creator: BacDive
License: https://creativecommons.org/licenses/by/4.0/

Strain identifier

BacDive ID: 5171

Type strain:

Species: Shigella flexneri

Strain Designation: 24570

Culture col. no.: DSM 4782, ATCC 29903, KCTC 22192, WDCM 00125, CCUG 56439, CIP 82.48, BCRC 13984, KCTC 22529, CECT 8175, NCTC 13631

Strain history: CIP <- 1982, ATCC <- D.J. Brenner, CDC: strain 24570

NCBI tax ID(s): 623 (species)

SI-ID 44862

ATCC 29903, DSM 4782, BCRC 13984, CCRC 13984, VTT E-082767, CCUG 56439, CECT 8175, CIP 82.48

Special Collections

Other strains from Shigella flexneri

Section

When using BacDive for research please cite our paper

Shigella flexneri 24570 is an aerobe, mesophilic, Gram-negative human pathogen that has multiple antibiotic resistances.

antibiotic resistance
Gram-negative
aerobe
human pathogen
mesophilic
16S sequence
Bacteria
genome sequence

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

	Last LPSN update	09-12-2024 (DD-MM-YYYY)
	Domain	*Bacteria*
	Phylum	*Pseudomonadota*
	Class	*Gammaproteobacteria*
	Order	*Enterobacterales*
	Family	*Enterobacteriaceae*
	Genus	*Shigella*
	Species	**Shigella flexneri**
	Full Scientific Name (LPSN)	Shigella flexneri Castellani and Chalmers 1919 (Approved Lists 1980)

Information on morphological and physiological properties Morphology

[Ref.: #67771]	Gram stain	negative
[Ref.: #119397]	Gram stain	negative
[Ref.: #125438]	Gram stain	negative Confidence in %99.694

[Ref.: #119397]	Cell shape	rod-shaped

[Ref.: #119397]	Motility	no

Information on culture and growth conditions Culture and growth conditions

[Ref.: #36625]

Culture medium

MEDIUM 72- for trypto casein soja agar

[Ref.: #36625]

Culture medium growth

[Ref.: #36625]

Culture medium composition

expand / minimize

[Ref.: #1822]

Culture medium

TRYPTICASE SOY YEAST EXTRACT MEDIUM (DSMZ Medium 92)

[Ref.: #1822]

Culture medium growth

[Ref.: #1822]

Culture medium link

Medium recipe provided by DSMZ

[Ref.: #1822]

Culture medium

COLUMBIA BLOOD MEDIUM (DSMZ Medium 693)

[Ref.: #1822]

Culture medium growth

[Ref.: #1822]

Culture medium link

Medium recipe provided by DSMZ

[Ref.: #119397]

Culture medium

CIP Medium 72

[Ref.: #119397]

Culture medium growth

[Ref.: #119397]

Culture medium link

Medium recipe provided by DSMZ

	Kind of temperature		Temperature
[Ref.: #1822]		growth	37 °C
[Ref.: #36625]		growth	30 °C
[Ref.: #60957]		growth	30 °C
[Ref.: #67771]		growth	37 °C
[Ref.: #119397]		growth	30-41 °C
[Ref.: #119397]	no	growth	5 °C
[Ref.: #119397]	no	growth	10 °C

Information on physiology and metabolism Physiology and metabolism

[Ref.: #60957]	Oxygen tolerance	aerobe
[Ref.: #67771]	Oxygen tolerance	aerobe
[Ref.: #119397]	Oxygen tolerance	facultative anaerobe
[Ref.: #125439]	Oxygen tolerance	obligate aerobe Confidence in %95.1

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

Antibiotic susceptibility testing

Test 1

Test 2

Reference

[Ref.: #1822]
Mueller-Hinton Agar



yes
Inhibition zone diameter in mm
8-10
resistant0
24
32
30
24
30-32
40
38-40
34-36
30
34
22
22
resistant0
12-14
resistant0
34
34
16
30
28
resistant0
16
32
18-20
26-28
40
resistant0
34
32-34
resistant0
resistant0
resistant0
resistant0
30

[Ref.: #1822]
Mueller Hinton
30

aerob
yes
Inhibition zone diameter in mm
6-8
resistant0
24-26
30
28-30
24
28-30
40
38
36-38
30
34-36
22
20-22
resistant0
16
resistant0
38
40
16
30-32
24-26
resistant0
18
22
18-20
28
36
resistant0
30
36-38
10
resistant0
6
resistant0
30

Only first 15 entries are displayed. Click here to see all.

	Metabolite	Utilization activity	Kind of utilization tested
[Ref.: #68368]	amygdalin ChEBI	-	fermentation	* from API 20E
[Ref.: #68374]	arginine ChEBI	-	hydrolysis	* from API ID32E, API 20E
[Ref.: #68374]	cellobiose ChEBI	-	builds acid from	* from API ID32E
[Ref.: #119397]	citrate ChEBI	-	carbon source
[Ref.: #68368]	citrate ChEBI	-	assimilation	* from API 20E
[Ref.: #68374]	D-arabitol ChEBI	-	builds acid from	* from API ID32E
[Ref.: #68374]	D-galacturonic acid ChEBI	+	builds acid from	* from API ID32E
[Ref.: #68368]	D-glucose ChEBI	+	fermentation	* from API 20E
[Ref.: #68374]	D-glucose ChEBI	-	builds acid from	* from API ID32E
[Ref.: #68368]	D-mannitol ChEBI	+	fermentation	* from API 20E
[Ref.: #68374]	D-mannitol ChEBI	-	builds acid from	* from API ID32E
[Ref.: #68368]	gelatin ChEBI	-	hydrolysis	* from API 20E
[Ref.: #119397]	glucose ChEBI	+	fermentation
[Ref.: #119397]	glucose ChEBI	+	degradation
[Ref.: #68368]	L-arabinose ChEBI	+	fermentation	* from API 20E
[Ref.: #68374]	L-arabinose ChEBI	-	builds acid from	* from API ID32E
[Ref.: #68374]	L-arabitol ChEBI	-	builds acid from	* from API ID32E
[Ref.: #68374]	L-rhamnose ChEBI	-	builds acid from	* from API ID32E
[Ref.: #68368]	L-rhamnose ChEBI	-	fermentation	* from API 20E
[Ref.: #119397]	lactose ChEBI	-	fermentation
[Ref.: #68374]	lysine ChEBI	-	degradation	* from API ID32E, API 20E
[Ref.: #119397]	malonate ChEBI	-	assimilation
[Ref.: #68374]	malonate ChEBI	-	assimilation	* from API ID32E
[Ref.: #68374]	maltose ChEBI	-	builds acid from	* from API ID32E
[Ref.: #119397]	mannitol ChEBI	+	fermentation
[Ref.: #68368]	melibiose ChEBI	+	fermentation	* from API 20E
[Ref.: #68374]	myo-inositol ChEBI	-	builds acid from	* from API ID32E
[Ref.: #68368]	myo-inositol ChEBI	-	fermentation	* from API 20E
[Ref.: #119397]	nitrate ChEBI	+	reduction
[Ref.: #119397]	nitrite ChEBI	+	reduction
[Ref.: #68374]	ornithine ChEBI	-	degradation	* from API ID32E, API 20E
[Ref.: #68374]	palatinose ChEBI	-	builds acid from	* from API ID32E
[Ref.: #68374]	Potassium 5-ketogluconate ChEBI	-	builds acid from	* from API ID32E
[Ref.: #68374]	ribitol ChEBI	-	builds acid from	* from API ID32E
[Ref.: #119397]	sodium thiosulfate ChEBI	-	builds gas from
[Ref.: #68374]	sorbitol ChEBI	-	builds acid from	* from API ID32E
[Ref.: #68368]	sorbitol ChEBI	-	fermentation	* from API 20E
[Ref.: #68374]	sucrose ChEBI	-	builds acid from	* from API ID32E
[Ref.: #68374]	trehalose ChEBI	-	builds acid from	* from API ID32E
[Ref.: #68374]	tryptophan ChEBI	+	energy source	* from API ID32E, API 20E
[Ref.: #68374]	urea ChEBI	-	hydrolysis	* from API ID32E, API 20E
	Only first 10 entries are displayed. Click here to see all.

	Antibiotica	Metabolite	Antibiotic sensitivity	Antibiotic resistance
[Ref.: #119397]		0129 (2,4-Diamino-6,7-di-iso-propylpteridine phosphate)	no	yes

	Metabolite	Production
[Ref.: #119397]	indole ChEBI	yes
[Ref.: #68368]	hydrogen sulfide ChEBI	no	* from API 20E
[Ref.: #68374]	indole ChEBI	yes	* from API ID32E, API 20E

	Metabolite	Voges-Proskauer-test	Methylred-test	Indole test
[Ref.: #119397]	acetoin ChEBI	-
[Ref.: #119397]	glucose ChEBI		+
[Ref.: #68374]	indole ChEBI			+	* from API ID32E, API 20E

	Enzyme	Enzyme activity	EC number
[Ref.: #68382]	acid phosphatase	+	3.1.3.2	* from API zym
[Ref.: #119397]	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.: #68374]	alpha-galactosidase	+	3.2.1.22	* from API ID32E
[Ref.: #68382]	alpha-galactosidase	-	3.2.1.22	* from API zym
[Ref.: #68382]	alpha-glucosidase	+	3.2.1.20	* from API zym, API ID32E
[Ref.: #68374]	alpha-maltosidase	-		* from API ID32E
[Ref.: #68382]	alpha-mannosidase	-	3.2.1.24	* from API zym
[Ref.: #68374]	arginine dihydrolase	-	3.5.3.6	* from API ID32E, API 20E
[Ref.: #119397]	beta-galactosidase	-	3.2.1.23
[Ref.: #68382]	beta-galactosidase	-	3.2.1.23	* from API zym, API ID32E, API 20E
[Ref.: #68382]	beta-glucosidase	-	3.2.1.21	* from API zym, API ID32E
[Ref.: #68382]	beta-glucuronidase	-	3.2.1.31	* from API zym, API ID32E
[Ref.: #119397]	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.: #119397]	gelatinase	-
[Ref.: #68368]	gelatinase	-		* from API 20E
[Ref.: #68374]	L-aspartate arylamidase	-	3.4.11.21	* from API ID32E
[Ref.: #68382]	leucine arylamidase	+	3.4.11.1	* from API zym
[Ref.: #68374]	lipase	-		* from API ID32E
[Ref.: #68382]	lipase (C 14)	-		* from API zym
[Ref.: #119397]	lysine decarboxylase	-	4.1.1.18
[Ref.: #68374]	lysine decarboxylase	-	4.1.1.18	* from API ID32E, API 20E
[Ref.: #68382]	N-acetyl-beta-glucosaminidase	-	3.2.1.52	* from API zym, API ID32E
[Ref.: #68382]	naphthol-AS-BI-phosphohydrolase	+		* from API zym
[Ref.: #119397]	ornithine decarboxylase	-	4.1.1.17
[Ref.: #68374]	ornithine decarboxylase	-	4.1.1.17	* from API ID32E, API 20E
[Ref.: #119397]	oxidase	-
[Ref.: #119397]	phenylalanine ammonia-lyase	-	4.3.1.24
[Ref.: #68382]	trypsin	+	3.4.21.4	* from API zym
[Ref.: #119397]	tryptophan deaminase	-
[Ref.: #68368]	tryptophan deaminase	-	4.1.99.1	* from API 20E
[Ref.: #119397]	urease	-	3.5.1.5
[Ref.: #68374]	urease	-	3.5.1.5	* from API ID32E, 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.: #1822]	19862	-	-	-	-	-	-	-	-	+	-	-	+	+	-	-	-	-	+	-	+	-	not determinedn.d.	not determinedn.d.	not determinedn.d.	not determinedn.d.	not determinedn.d.	not determinedn.d.
[Ref.: #1822]	19680	-	-	-	-	-	-	-	-	+	-	-	+	+	-	-	-	+	+	-	+	-	not determinedn.d.	not determinedn.d.	not determinedn.d.	not determinedn.d.	not determinedn.d.	not determinedn.d.
[Ref.: #1822]	19398	-	-	-	-	-	-	-	-	+	+	-	+	+	-	-	-	-	+	-	+	-	not determinedn.d.	not determinedn.d.	not determinedn.d.	not determinedn.d.	not determinedn.d.	not determinedn.d.

API® Biotype100:

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

	API ID	ControlQ	D-glucose as carbon sourceGLU	D-fructose as carbon sourceFRU	D-galactose as carbon sourceGAL	D-trehalose as carbon sourceTRE	D-mannose as carbon sourceMNE	L-sorbose as carbon sourceSBE	D-melibiose as carbon sourceMEL	sucrose as carbon sourceSAC	D-raffinose as carbon sourceRAF	maltotriose as carbon sourceMTE	maltose as carbon sourceMAL	lactose as carbon sourceLAC	lactulose as carbon sourceLTE	1-O-methyl-beta-galactopyranoside as carbon sourceMbGa	1-O-methyl-alpha-galactopyranoside as carbon sourceMaGa	D-cellobiose as carbon sourceCEL	gentiobiose as carbon sourceGEN	1-O-methyl-beta-D-glucopyranoside as carbon sourceMbGu	esculin as carbon sourceESC	D-ribose as carbon sourceRIB	L-arabinose as carbon sourceARA	D-xylose as carbon sourceXYL	palatinose as carbon sourcePLE	L-rhamnose as carbon sourceRHA	L-fucose as carbon sourceFUC	D-melezitose as carbon sourceMLZ	D-arabitol as carbon sourceDARL	L-arabitol as carbon sourceLARL	xylitol as carbon sourceXLT	dulcitol as carbon sourceDUL	D-tagatose as carbon sourceTAG	glycerol as carbon sourceGLY	myo-inositol as carbon sourceINO	D-mannitol as carbon sourceMAN	maltitol as carbon sourceMTL	D-turanose as carbon sourceTUR	D-sorbitol as carbon sourceSOR	adonitol as carbon sourceADO	hydroxyquinoline-beta-glucuronide as carbon sourceHBG	D-lyxose as carbon sourceLYX	i-erythritol as carbon sourceERY	1-O-methyl-alpha-D-glucoside as carbon sourceMDG	3-O-methyl-D-glucose as carbon source3MDG	D-saccharate as carbon sourceSAT	mucate as carbon sourceMUC	L-tartrate as carbon sourceLTAT	D-tartrate as carbon sourceDTAT	meso-tartrate as carbon sourceMTAT	D-malate as carbon sourceDMLT	L-malate as carbon sourceLMLT	cis-aconitate as carbon sourceCATE	trans-aconitate as carbon sourceTATE	tricarballylate as carbon sourceTTE	citrate as carbon sourceCIT	D-glucuronate as carbon sourceGRT	D-galacturonate as carbon sourceGAT	2-ketogluconate as carbon source2KG	5-ketogluconate as carbon source5KG	tryptophan as carbon sourceTRY	N-acetyl-D-glucosamine as carbon sourceNAG	D-gluconate as carbon sourceGNT	phenylacetate as carbon sourcePAC	protocatechuate as carbon sourcePAT	4-hydroxybenzoate as carbon sourcepOBE	quinate as carbon sourceQAT	gentisate as carbon sourceGTE	3-hydroxybenzoate as carbon sourcemOBE	benzoate as carbon sourceBAT	3-phenylpropionate as carbon sourcePPAT	m-coumarate as carbon sourceCMT	trigonelline as carbon sourceTGE	betaine as carbon sourceBET	putrescine as carbon sourcePCE	4-aminobutyrate as carbon sourceABT	histamine as carbon sourceHIN	DL-lactate as carbon sourceLAT	caprate as carbon sourceCAP	caprylate as carbon sourceCYT	L-histidine as carbon sourceHIS	succinate as carbon sourceSUC	fumarate as carbon sourceFUM	glutarate as carbon sourceGRE	DL-glycerate as carbon sourceGYT	5-aminovalerate as carbon sourceAVT	ethanolamine as carbon sourceETN	tryptamine as carbon sourceTTN	D-glucosamine as carbon sourceGLN	itaconate as carbon sourceITA	3-hydroxybutyrate as carbon source3OBU	L-aspartate as carbon sourceAPT	L-glutamate as carbon sourceGTT	L-proline as carbon sourcePRO	D-alanine as carbon sourceDALA	L-alanine as carbon sourceLALA	L-serine as carbon sourceSER	malonate as carbon sourceMNT	propionate as carbon sourcePROP	L-tyrosine as carbon sourceTYR	2-ketoglutarate as carbon source2KT
[Ref.: #119397]	3458	not determinedn.d.	+	+	+	+	+	-	+	-	+	+	+	-	-	-	+	-	-	-	-	-	+	-	-	-	+	-	-	-	-	-	-	+	-	+	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	+	-	-	-	-	+	+	-	-	-	+	+	-	-	-	-	-	-	-	-	-	-	-	-	-	-	+	-	-	-	+	+	-	-	-	-	-	+	-	-	-	-	-	-	+	-	-	-	-	-

API® ID32E:

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

	API ID	Ornithine decarboxylaseODC	Arginine dihydrolaseADH (Arg)	Lysine decarboxylaseLDC (Lys)	Urease/urea hydrolysisURE	Acid from L-arabitolLARL	Acid from D-galacturonic acidGAT	Acid from 5-Ketogluconate5KG	LipaseLIP	Phenol red (Acidification)RP	beta-Glucosidasebeta GLU	Acid from D-mannitolMAN	Acid from maltoseMAL	Acid from D-adonitolADO	Acid from palatinosePLE	beta-Glucuronidasebeta GUR	MalonateMNT	Indole productionIND	N-Acetyl-beta-Glucosaminidasebeta NAG	beta-Galactosidasebeta GAL	Acid from D-glucoseGLU	Acid from sucroseSAC	Acid from L-arabinoseLARA	Acid from D-arabitolDARL	alpha-Glucosidasealpha GLU	alpha-Galactosidasealpha GAL	Acid from trehaloseTRE	Acid from L-rhamnoseRHA	Acid from inositolINO	Acid from cellobioseCEL	Acid from sorbitolSOR	alpha-MaltosidasealphaMAL	L-aspartic acid arylamidaseAspA
[Ref.: #60957]	1854	-	-	-	-	-	+	-	-	+	-	-	-	-	-	-	-	+	-	-	-	-	-	-	+	+	-	-	-	-	-	-	-

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.: #119397]	13539	-	+	-	-	-	+	+	-	+	-	+	+	-	-	-	+	-	-	-	-

	Pathway	Enzyme coverage	Annotated reactions
	Pathway annotation	Computationally determined by
[Ref.: #66794]	L-lactaldehyde degradation	100	3 of 3
[Ref.: #66794]	coenzyme A metabolism	100	4 of 4
[Ref.: #66794]	anapleurotic synthesis of oxalacetate	100	1 of 1
[Ref.: #66794]	aerobactin biosynthesis	100	1 of 1
[Ref.: #66794]	4-hydroxyphenylacetate degradation	100	10 of 10
[Ref.: #66794]	ppGpp biosynthesis	100	4 of 4
[Ref.: #66794]	methylglyoxal degradation	100	5 of 5
[Ref.: #66794]	taurine degradation	100	1 of 1
[Ref.: #66794]	adipate degradation	100	2 of 2
[Ref.: #66794]	suberin monomers biosynthesis	100	2 of 2
[Ref.: #66794]	CDP-diacylglycerol biosynthesis	100	2 of 2
[Ref.: #66794]	UDP-GlcNAc biosynthesis	100	3 of 3
[Ref.: #66794]	starch degradation	100	10 of 10
[Ref.: #66794]	biotin biosynthesis	100	4 of 4
[Ref.: #66794]	sulfopterin metabolism	100	4 of 4
[Ref.: #66794]	formaldehyde oxidation	100	3 of 3
[Ref.: #66794]	acetate fermentation	100	4 of 4
[Ref.: #66794]	enterobactin biosynthesis	100	3 of 3
[Ref.: #66794]	tetrahydrofolate metabolism	100	14 of 14
[Ref.: #66794]	folate polyglutamylation	100	1 of 1
[Ref.: #66794]	ubiquinone biosynthesis	100	7 of 7
[Ref.: #66794]	sulfoquinovose degradation	100	3 of 3
[Ref.: #66794]	gluconeogenesis	100	8 of 8
[Ref.: #66794]	vitamin K metabolism	100	5 of 5
[Ref.: #66794]	palmitate biosynthesis	95.45	21 of 22
[Ref.: #66794]	NAD metabolism	94.44	17 of 18
[Ref.: #66794]	heme metabolism	92.86	13 of 14
[Ref.: #66794]	glutathione metabolism	92.86	13 of 14
[Ref.: #66794]	photosynthesis	92.86	13 of 14
[Ref.: #66794]	vitamin B6 metabolism	90.91	10 of 11
[Ref.: #66794]	pentose phosphate pathway	90.91	10 of 11
[Ref.: #66794]	Entner Doudoroff pathway	90	9 of 10
[Ref.: #66794]	threonine metabolism	90	9 of 10
[Ref.: #66794]	valine metabolism	88.89	8 of 9
[Ref.: #66794]	serine metabolism	88.89	8 of 9
[Ref.: #66794]	lipid A biosynthesis	88.89	8 of 9
[Ref.: #66794]	chorismate metabolism	88.89	8 of 9
[Ref.: #66794]	molybdenum cofactor biosynthesis	88.89	8 of 9
[Ref.: #66794]	C4 and CAM-carbon fixation	87.5	7 of 8
[Ref.: #66794]	degradation of sugar alcohols	87.5	14 of 16
[Ref.: #66794]	isoleucine metabolism	87.5	7 of 8
[Ref.: #66794]	reductive acetyl coenzyme A pathway	85.71	6 of 7
[Ref.: #66794]	vitamin B1 metabolism	84.62	11 of 13
[Ref.: #66794]	glycolate and glyoxylate degradation	83.33	5 of 6
[Ref.: #66794]	purine metabolism	82.98	78 of 94
[Ref.: #66794]	gallate degradation	80	4 of 5
[Ref.: #66794]	peptidoglycan biosynthesis	80	12 of 15
[Ref.: #66794]	glycogen metabolism	80	4 of 5
[Ref.: #66794]	metabolism of amino sugars and derivatives	80	4 of 5
[Ref.: #66794]	pyrimidine metabolism	80	36 of 45
[Ref.: #66794]	alanine metabolism	79.31	23 of 29
[Ref.: #66794]	glutamate and glutamine metabolism	78.57	22 of 28
[Ref.: #66794]	citric acid cycle	78.57	11 of 14
[Ref.: #66794]	aspartate and asparagine metabolism	77.78	7 of 9
[Ref.: #66794]	d-mannose degradation	77.78	7 of 9
[Ref.: #66794]	phenylalanine metabolism	76.92	10 of 13
[Ref.: #66794]	urea cycle	76.92	10 of 13
[Ref.: #66794]	glycogen biosynthesis	75	3 of 4
[Ref.: #66794]	lactate fermentation	75	3 of 4
[Ref.: #66794]	dTDPLrhamnose biosynthesis	75	6 of 8
[Ref.: #66794]	CMP-KDO biosynthesis	75	3 of 4
[Ref.: #66794]	6-hydroxymethyl-dihydropterin diphosphate biosynthesis	75	6 of 8
[Ref.: #66794]	flavin biosynthesis	73.33	11 of 15
[Ref.: #66794]	oxidative phosphorylation	72.53	66 of 91
[Ref.: #66794]	degradation of sugar acids	72	18 of 25
[Ref.: #66794]	cardiolipin biosynthesis	71.43	5 of 7
[Ref.: #66794]	lipid metabolism	70.97	22 of 31
[Ref.: #66794]	glycolysis	70.59	12 of 17
[Ref.: #66794]	leucine metabolism	69.23	9 of 13
[Ref.: #66794]	non-pathway related	68.42	26 of 38
[Ref.: #66794]	degradation of pentoses	67.86	19 of 28
[Ref.: #66794]	allantoin degradation	66.67	6 of 9
[Ref.: #66794]	CO2 fixation in Crenarchaeota	66.67	6 of 9
[Ref.: #66794]	cyanate degradation	66.67	2 of 3
[Ref.: #66794]	octane oxidation	66.67	2 of 3
[Ref.: #66794]	selenocysteine biosynthesis	66.67	4 of 6
[Ref.: #66794]	methane metabolism	66.67	2 of 3
[Ref.: #66794]	acetoin degradation	66.67	2 of 3
[Ref.: #66794]	tryptophan metabolism	65.79	25 of 38
[Ref.: #66794]	isoprenoid biosynthesis	65.38	17 of 26
[Ref.: #66794]	proline metabolism	63.64	7 of 11
[Ref.: #66794]	ketogluconate metabolism	62.5	5 of 8
[Ref.: #66794]	methionine metabolism	61.54	16 of 26
[Ref.: #66794]	degradation of hexoses	61.11	11 of 18
[Ref.: #66794]	hydrogen production	60	3 of 5
[Ref.: #66794]	lipoate biosynthesis	60	3 of 5
[Ref.: #66794]	propanol degradation	57.14	4 of 7
[Ref.: #66794]	cysteine metabolism	55.56	10 of 18
[Ref.: #66794]	nitrate assimilation	55.56	5 of 9
[Ref.: #66794]	phenol degradation	55	11 of 20
[Ref.: #66794]	arginine metabolism	54.17	13 of 24
[Ref.: #66794]	sulfate reduction	53.85	7 of 13
[Ref.: #66794]	3-phenylpropionate degradation	53.33	8 of 15
[Ref.: #66794]	lysine metabolism	52.38	22 of 42
[Ref.: #66794]	histidine metabolism	51.72	15 of 29
[Ref.: #66794]	carnitine metabolism	50	4 of 8
[Ref.: #66794]	myo-inositol biosynthesis	50	5 of 10
[Ref.: #66794]	toluene degradation	50	2 of 4
[Ref.: #66794]	pantothenate biosynthesis	50	3 of 6
[Ref.: #66794]	ribulose monophosphate pathway	50	1 of 2
[Ref.: #66794]	propionate fermentation	50	5 of 10
[Ref.: #66794]	quinate degradation	50	1 of 2
[Ref.: #66794]	butanoate fermentation	50	2 of 4
[Ref.: #66794]	ethanol fermentation	50	1 of 2
[Ref.: #66794]	cis-vaccenate biosynthesis	50	1 of 2
[Ref.: #66794]	tyrosine metabolism	50	7 of 14
[Ref.: #66794]	polyamine pathway	47.83	11 of 23
[Ref.: #66794]	ascorbate metabolism	45.45	10 of 22
[Ref.: #66794]	d-xylose degradation	45.45	5 of 11
[Ref.: #66794]	metabolism of disaccharids	45.45	5 of 11
[Ref.: #66794]	degradation of aromatic, nitrogen containing compounds	41.67	5 of 12
[Ref.: #66794]	ethylmalonyl-CoA pathway	40	2 of 5
[Ref.: #66794]	coenzyme M biosynthesis	40	4 of 10
[Ref.: #66794]	glycine metabolism	40	4 of 10
[Ref.: #66794]	3-chlorocatechol degradation	40	2 of 5
[Ref.: #66794]	phosphatidylethanolamine bioynthesis	38.46	5 of 13
[Ref.: #66794]	phenylpropanoid biosynthesis	38.46	5 of 13
[Ref.: #66794]	acetyl CoA biosynthesis	33.33	1 of 3
[Ref.: #66794]	IAA biosynthesis	33.33	1 of 3
[Ref.: #66794]	methanogenesis from CO2	33.33	4 of 12
[Ref.: #66794]	sphingosine metabolism	33.33	2 of 6
[Ref.: #66794]	vitamin B12 metabolism	32.35	11 of 34
[Ref.: #66794]	androgen and estrogen metabolism	31.25	5 of 16
[Ref.: #66794]	arachidonic acid metabolism	27.78	5 of 18
[Ref.: #66794]	cyclohexanol degradation	25	1 of 4
		Only first 10 entries are displayed. Click here to see all.

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

[Ref.: #69479]

Global distribution of 16S sequence X96963 (>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.: #1822]	Pathogenicity (human)	yes
[Ref.: #1822]	Pathogenicity (animal)	yes
[Ref.: #1822]	Biosafety level	2	Risk group (German classification) According to TRBA 466
[Ref.: #119397]	Biosafety level	2	Risk group (French classification)

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

16S Sequence information:

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

	Sequence accession description	Seq. accession number	Sequence length (bp)	Sequence database	Associated NCBI tax ID
[Ref.: #124043]	Shigella flexneri strain ATCC 29903 16S ribosomal RNA gene, partial sequence.	MN527009	491	GenBank ENA	623 tax ID	*
[Ref.: #124043]	Shigella flexneri strain ATCC 29903 16S ribosomal RNA gene, partial sequence.	OR660251	1094	GenBank ENA	623 tax ID	*
[Ref.: #124043]	Shigella flexneri strain ATCC 29903 16S ribosomal RNA gene, partial sequence.	MN527276	491	GenBank ENA	623 tax ID	*
[Ref.: #124043]	Shigella flexneri strain ATCC 29903 16S ribosomal RNA gene, partial sequence.	MN535393	491	GenBank ENA	623 tax ID	*
[Ref.: #124043]	Shigella flexneri strain ATCC 29903 16S ribosomal RNA gene, partial sequence.	OQ618959	1361	GenBank ENA	623 tax ID	*
[Ref.: #124043]	Shigella flexneri strain ATCC 29903 16S ribosomal RNA gene, partial sequence.	OQ619001	1354	GenBank ENA	623 tax ID	*
[Ref.: #124043]	Shigella flexneri strain ATCC 29903 16S ribosomal RNA gene, partial sequence.	OQ619024	1329	GenBank ENA	623 tax ID	*
[Ref.: #124043]	Shigella flexneri strain ATCC 29903 16S ribosomal RNA gene, partial sequence.	OQ619031	1356	GenBank ENA	623 tax ID	*
[Ref.: #124043]	Shigella flexneri strain ATCC 29903 16S ribosomal RNA gene, partial sequence.	OQ619032	1232	GenBank ENA	623 tax ID	*
[Ref.: #124043]	Shigella flexneri strain ATCC 29903 16S ribosomal RNA gene, partial sequence.	OQ619096	1364	GenBank ENA	623 tax ID	*
[Ref.: #20218]	S.flexneri 16S rRNA gene	X96963	1488	GenBank ENA	623 tax ID	*
[Ref.: #124043]	Shigella flexneri strain ATCC 29903 16S ribosomal RNA gene, partial sequence.	OQ619115	1305	GenBank ENA	623 tax ID	*

Genome sequence information:

	Sequence accession description	Seq. accession number	Assembly level	Sequence database	Associated NCBI tax ID
[Ref.: #66792]	Shigella flexneri 2a ATCC 29903	GCA_002950215	complete	GenBank ENA	42897 tax ID	*
[Ref.: #66792]	Shigella flexneri 2a strain ATCC 29903	42897.55	complete	PATRIC	42897 tax ID	*
[Ref.: #66792]	Shigella flexneri ATCC 29903	2859793810	complete	JGI IMG/M	623 tax ID	*

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

	Model	Trait	Prediction	Confidence in %	In training data
	Predictions from bacterial phenotypic traits through improved machine learning using high-quality, curated datasets based on: Shigella flexneri 2a ATCC 29903 NCBI: GCA_002950215.1
[Ref.: #125438]	gram-positive	gram-positiveⓘ	no	99.694	yes
[Ref.: #125438]	anaerobic	anaerobicⓘ	no	94.664	no
[Ref.: #125438]	aerobic	aerobicⓘ	no	73.515	no
[Ref.: #125438]	spore-forming	spore-formingⓘ	no	88.948	no
[Ref.: #125438]	thermophile	thermophilicⓘ	no	98	yes
[Ref.: #125438]	motile2+	flagellatedⓘ	yes	75.792	no

	Model	Trait	Prediction	Confidence in %
	Predictions from Deep Learning for Genome Sequence Data. R package version 0.3.1 based on: Shigella flexneri 2a strain ATCC 29903 PATRIC: 42897.55
[Ref.: #125439]	BacteriaNet	spore_formationⓘ	no	76.2
[Ref.: #125439]	BacteriaNet	motilityⓘ	yes	59.1
[Ref.: #125439]	BacteriaNet	gram_stainⓘ	negative	70.3
[Ref.: #125439]	BacteriaNet	oxygen_toleranceⓘ	obligate aerobe	95.1

Availability in culture collections External links

[Ref.: #1822]

Culture collection no.

DSM 4782, ATCC 29903, KCTC 22192, WDCM 00125, CCUG 56439, CIP 82.48, BCRC 13984, KCTC 22529, CECT 8175, NCTC 13631

[Ref.: #74663]

SI-ID 44862

Literature:

	Title	Authors	Journal	DOI	Year
Genetics	Draft Genome Sequence of 24570, the Type Strain of Shigella flexneri.	Baker KS, Parkhill J, Thomson NR	Genome Announc	10.1128/genomeA.00393-15	2015	*
Pathogenicity	[Mechanism of resistance of Shigella flexneri 2a resistant to new quinolone antibiotics].	Oonaka K, Fukuyama M, Tanaka M, Sato K, Ohnishi K, Ajima I, Murata M	Kansenshogaku Zasshi	10.11150/kansenshogakuzasshi1970.72.365	1998	*
Genetics	Virulence phenotypes of Shigella flexneri 2a avirulent mutant 24570 can be complemented by the plasmid-coded positive regulator virF gene.	Qi MS, Yoshikura H, Watanabe H	FEMS Microbiol Lett	10.1111/j.1574-6968.1992.tb05264.x	1992	*
Pathogenicity	[Membrane component of Shigella flexneri and their relationship to bacteria antigenicity and virulence].	Jin L, Su X	Wei Sheng Wu Xue Bao		1990	*
	Probiotic characteristics of Lactobacillus strains isolated from cheese and their antibacterial properties against gastrointestinal tract pathogens.	Zhang X, Ali Esmail G, Fahad Alzeer A, Valan Arasu M, Vijayaraghavan P, Choon Choi K, Abdullah Al-Dhabi N	Saudi J Biol Sci	10.1016/j.sjbs.2020.10.022	2020	*

References

#1822

Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 4782

#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 )

#36625 ; Curators of the CIP;
#60957 Culture Collection University of Gothenburg (CCUG) ; Curators of the CCUG; CCUG 56439

#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) .

#66794

Antje Chang, Lisa Jeske, Sandra Ulbrich, Julia Hofmann, Julia Koblitz, Ida Schomburg, Meina Neumann-Schaal, Dieter Jahn, Dietmar Schomburg: BRENDA, the ELIXIR core data resource in 2021: new developments and updates. Nucleic Acids Res. 49: D498 - D508 2020 ( DOI 10.1093/nar/gkaa1025 , PubMed 33211880 )

#67771 Korean Collection for Type Cultures (KCTC) ; Curators of the KCTC;

#68368

Automatically annotated from API 20E .

#68374

Automatically annotated from API ID32E .

#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 .

#74663

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-ID44862.1 )

#119397 Collection of Institut Pasteur ; Curators of the CIP; CIP 82.48

#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 .

* These data were automatically processed and therefore are not curated

Change proposal

You found an error in BacDive? Please tell us about it!

Note that changes will be reviewed and judged. If your changes are legitimate, changes will occur within the next BacDive update. Only proposed changes supported by the according reference will be reviewed. The BacDive team reserves the right to reject proposed changes.

Search for species Shigella flexneri in external resources:
SILVA
BRENDA
PANGAEA
GBIF

Shigella flexneri 2a ATCC 29903

Shigella flexneri 2a strain ATCC 29903

Change proposal

Change proposal