Citrobacter pasteurii Na 1a | Type strain | DSM 28879, CIP 55.13

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Information on culture and growth conditions Culture and growth conditions

[Ref.: #42054]

Culture medium

MEDIUM 3 - Columbia agar

[Ref.: #42054]

Culture medium growth

[Ref.: #42054]

Culture medium composition

Culture medium

CASO AGAR (MERCK 105458) (DSMZ Medium 220)

Culture medium growth

Medium recipe at MediaDive

Culture medium link

Culture medium composition

Culture medium

TRYPTICASE SOY YEAST EXTRACT MEDIUM (DSMZ Medium 92)

Culture medium growth

Medium recipe at MediaDive

Culture medium link

Culture medium composition

Culture medium

COLUMBIA BLOOD MEDIUM (DSMZ Medium 693)

Culture medium growth

Medium recipe at MediaDive

Culture medium link

Culture medium composition

Culture medium

CIP Medium 72

Culture medium growth

Medium recipe provided by DSMZ

Culture medium link

Culture medium

CIP Medium 3

Culture medium growth

Medium recipe provided by DSMZ

Culture medium link

		Temperature
[Ref.: #21549]	growth	28 °C
[Ref.: #21549]	growth	30 °C
[Ref.: #42054]	growth	30 °C

Information on physiology and metabolism Physiology and metabolism

[Ref.: #121621]	Oxygen tolerance	facultative anaerobe
[Ref.: #125439]	Oxygen tolerance	aerobe Confidence in %90.8

	Metabolite	Utilization activity	Kind of utilization tested
[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-arabinose ChEBI	+	fermentation	* 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.: #121621]	nitrate ChEBI	+	reduction
[Ref.: #121621]	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.: #121621]	indole ChEBI	no
[Ref.: #68368]	acetoin ChEBI	no	* from API 20E
[Ref.: #68368]	hydrogen sulfide ChEBI	yes	* from API 20E
[Ref.: #68368]	indole ChEBI	no	* from API 20E

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

	Enzyme	Enzyme activity	EC number
[Ref.: #68382]	acid phosphatase	+	3.1.3.2	* from API zym
[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.: #121621]	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.: #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.: #68368]	ornithine decarboxylase	-	4.1.1.17	* from API 20E
[Ref.: #121621]	oxidase	-
[Ref.: #68382]	trypsin	-	3.4.21.4	* from API zym
[Ref.: #68368]	tryptophan deaminase	-	4.1.99.1	* from API 20E
[Ref.: #121621]	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.: #21549]	19719	+	+	-	-	+	+	-	-	-	-	-	+	+	-	+	+	+	-	+/-	+	not determinedn.d.	not determinedn.d.	not determinedn.d.	not determinedn.d.	not determinedn.d.	not determinedn.d.	not determinedn.d.
[Ref.: #21549]	18446	+	+	-	-	+	+	-	-	-	-	-	+	+	-	+	+	+	-	+	+	-	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.: #121621]	12823	-	+	-	-	-	+	-	-	-	-	+	+	-	+	-	-	+	-	-	-

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

[Ref.: #21549]	Sample type/isolated from	human diarrhoeal stool
[Ref.: #21549]	Geographic location (country and/or sea, region)	Kentucky
[Ref.: #21549]	Country	USA
[Ref.: #21549]	Country ISO 3 Code	USA
[Ref.: #21549]	Continent	North America

[Ref.: #121621]	Sample type/isolated from	Human, Stool, diarrhea, outbreak
[Ref.: #121621]	Geographic location (country and/or sea, region)	Kentucky
[Ref.: #121621]	Country	United States of America
[Ref.: #121621]	Country ISO 3 Code	USA
[Ref.: #121621]	Continent	North America
[Ref.: #121621]	Isolation date	1955
* marker position based on {}

Isolation sources categories

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

What are isolation sources categories?

[Ref.: #69479]

Global distribution of 16S sequence KP057683 (>99% sequence identity) for Citrobacter from Microbeatlas

Aquatic Samples	1036
Soil Samples	374
Animal Samples	8174
Plant Samples	497
Total Samples	10081

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

[Ref.: #21549]	Pathogenicity (human)	yes, in single cases
[Ref.: #21549]	Biosafety level	1	Risk group (German classification) According to TRBA 466
[Ref.: #121621]	Biosafety level	1	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.: #21549]	Citrobacter pasteurii strain CIP 55.13 16S ribosomal RNA gene, partial sequence	KP057683	1492	GenBank ENA	1563222 tax ID
[Ref.: #124043]	Citrobacter pasteurii strain CIP55.13 16S ribosomal RNA gene, partial sequence.	OR660260	1135	GenBank ENA	1563222 tax ID	*

Genome sequence information:

	Sequence accession description	Seq. accession number	Assembly level	Sequence database	Associated NCBI tax ID
[Ref.: #66792]	Citrobacter pasteurii CIP 55.13	GCA_000826205	contig	GenBank ENA	1563222 tax ID	*
[Ref.: #66792]	Citrobacter pasteurii strain FDAARGOS 1424	1563222.16	complete	PATRIC	1563222 tax ID	*
[Ref.: #66792]	Citrobacter sp. CIP 55.13	1563222.3	wgs	PATRIC	1563222 tax ID	*
[Ref.: #66792]	Citrobacter pasteurii CIP 55.13	2648501483	draft	JGI IMG/M	1563222 tax ID	*

GC-content

51.80 mol%

sequence analysis

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: Citrobacter pasteurii strain FDAARGOS 1424 strain Not applicable PATRIC: 1563222.16
[Ref.: #125438]	gram-positive	gram-positiveⓘ	no	100	no
[Ref.: #125438]	anaerobic	anaerobicⓘ	no	94.637	yes
[Ref.: #125438]	spore-forming	spore-formingⓘ	no	88.627	no
[Ref.: #125438]	aerobic	aerobicⓘ	no	76.895	yes
[Ref.: #125438]	thermophile	thermophilicⓘ	no	98	no
[Ref.: #125438]	motile2+	flagellatedⓘ	yes	78.664	no

	Model	Trait	Prediction	Confidence in %
	Predictions from Deep Learning for Genome Sequence Data. R package version 0.3.1 based on: Citrobacter pasteurii strain FDAARGOS 1424 PATRIC: 1563222.16
[Ref.: #125439]	BacteriaNet	spore_formationⓘ	no	80.1
[Ref.: #125439]	BacteriaNet	motilityⓘ	yes	69.9
[Ref.: #125439]	BacteriaNet	gram_stainⓘ	negative	79.8
[Ref.: #125439]	BacteriaNet	oxygen_toleranceⓘ	aerobe	90.8

Availability in culture collections External links