Name: Citrobacter portucalensis A60
Creator: BacDive
License: http://creativecommons.org/licenses/by-nc/4.0/

Strain identifier

BacDive ID: 140426

Type strain:

Species: Citrobacter portucalensis

Strain Designation: A60

Culture col. no.: DSM 104542, CECT 9236, CIP 111602

Strain history: CIP <- 2017, L. Peixe, Porto Univ., Porto, Portugal: strain A60

NCBI tax ID(s): 1639133 (species)

SI-ID 408082

DSM 104542

Other strains from Citrobacter portucalensis

C. portucalensis DM2.TOL, CIP 106652
C. portucalensis DM2.SSS, CIP 106650
C. portucalensis DM2.CC, CIP 106653
C. portucalensis DM2.TOO, CIP 106651

Section

Citrobacter portucalensis A60 is a facultative anaerobe, Gram-negative, motile human pathogen that was isolated from water well.

Gram-negative
motile
rod-shaped
facultative anaerobe
human pathogen
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	*Citrobacter*
	Species	**Citrobacter portucalensis**
	Full Scientific Name (LPSN)	Citrobacter portucalensis Ribeiro et al. 2017

Information on morphological and physiological properties Morphology

[Ref.: #43514]	Gram stain	negative
[Ref.: #121947]	Gram stain	negative

[Ref.: #43514]	Cell length	4-5 µm

[Ref.: #43514]	Cell width	1-2 µm

[Ref.: #43514]	Cell shape	rod-shaped
[Ref.: #121947]	Cell shape	rod-shaped

[Ref.: #43514]	Motility	yes
[Ref.: #121947]	Motility	yes

[Ref.: #43514]	Colony color	bright, translucent
[Ref.: #43514]	Cultivation medium used	TSB

Multimedia content

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Intellectual property rights:

Information on culture and growth conditions Culture and growth conditions

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Culture medium

TSB

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Culture medium growth

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Culture medium

COLUMBIA BLOOD MEDIUM (DSMZ Medium 693)

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Culture medium growth

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Culture medium link

Medium recipe at MediaDive

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Culture medium composition

expand / minimize

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Culture medium

TRYPTICASE SOY BROTH AGAR (DSMZ Medium 535)

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Culture medium growth

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Culture medium link

Medium recipe at MediaDive

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Culture medium composition

expand / minimize

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Culture medium

CIP Medium 72

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Culture medium growth

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Culture medium link

Medium recipe provided by DSMZ

		Temperature
[Ref.: #43033]	growth	37 °C
[Ref.: #43514]	growth	20-37 °C
[Ref.: #43514]	growth	50 °C

[Ref.: #43033]	Temperature range	mesophilic
[Ref.: #43514]	Temperature range	thermophilic

	pH	Kind of pH		pH
[Ref.: #43514]			growth	5-10

Information on physiology and metabolism Physiology and metabolism

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Oxygen tolerance

facultative anaerobe

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Ability of spore formation

	Halophily	Salt	Tested relation		Salt conc.
[Ref.: #43514]		NaCl		growth	0-15	%(w/v)

	Metabolite	Utilization activity	Kind of utilization tested
[Ref.: #43514]	2-dehydro-D-gluconate ChEBI	+	builds acid from
[Ref.: #43514]	5-dehydro-D-gluconate ChEBI	+	builds acid from
[Ref.: #43514]	amygdalin ChEBI	-	builds acid from
[Ref.: #68368]	amygdalin ChEBI	+	fermentation	* from API 20E
[Ref.: #43514]	arbutin ChEBI	+	builds acid from
[Ref.: #68368]	arginine ChEBI	-	hydrolysis	* from API 20E
[Ref.: #43514]	cellobiose ChEBI	+	builds acid from
[Ref.: #43514]	citrate ChEBI	+	carbon source
[Ref.: #68368]	citrate ChEBI	+	assimilation	* from API 20E
[Ref.: #43514]	D-arabinose ChEBI	-	builds acid from
[Ref.: #43514]	D-arabitol ChEBI	-	builds acid from
[Ref.: #43514]	D-fructose ChEBI	+	builds acid from
[Ref.: #43514]	D-fucose ChEBI	-	builds acid from
[Ref.: #43514]	D-galactose ChEBI	+	builds acid from
[Ref.: #43514]	D-glucose ChEBI	+	builds acid from
[Ref.: #68368]	D-glucose ChEBI	+	fermentation	* from API 20E
[Ref.: #43514]	D-lyxose ChEBI	-	builds acid from
[Ref.: #43514]	D-mannitol ChEBI	+	builds acid from
[Ref.: #68368]	D-mannitol ChEBI	+	fermentation	* from API 20E
[Ref.: #43514]	D-mannose ChEBI	+	builds acid from
[Ref.: #43514]	D-ribose ChEBI	+	builds acid from
[Ref.: #43514]	D-sorbitol ChEBI	+	builds acid from
[Ref.: #43514]	D-tagatose ChEBI	-	builds acid from
[Ref.: #43514]	D-xylose ChEBI	+	builds acid from
[Ref.: #43514]	erythritol ChEBI	-	builds acid from
[Ref.: #43514]	esculin ferric citrate	-	builds acid from
[Ref.: #43514]	galactitol ChEBI	-	builds acid from
[Ref.: #43514]	gelatin ChEBI	-	degradation
[Ref.: #68368]	gelatin ChEBI	-	hydrolysis	* from API 20E
[Ref.: #43514]	gentiobiose ChEBI	+	builds acid from
[Ref.: #43514]	glucose ChEBI	+	fermentation
[Ref.: #43514]	glycerol ChEBI	+	builds acid from
[Ref.: #43514]	glycogen ChEBI	-	builds acid from
[Ref.: #43514]	inulin ChEBI	-	builds acid from
[Ref.: #43514]	L-arabinose ChEBI	+	builds acid from
[Ref.: #68368]	L-arabinose ChEBI	+	fermentation	* from API 20E
[Ref.: #43514]	L-arabitol ChEBI	-	builds acid from
[Ref.: #43514]	L-arginine ChEBI	-	assimilation
[Ref.: #43514]	L-fucose ChEBI	+	builds acid from
[Ref.: #43514]	L-lysine ChEBI	-	assimilation
[Ref.: #43514]	L-ornithine ChEBI	-	assimilation
[Ref.: #43514]	L-rhamnose ChEBI	+	builds acid from
[Ref.: #68368]	L-rhamnose ChEBI	+	fermentation	* from API 20E
[Ref.: #43514]	L-sorbose ChEBI	+	builds acid from
[Ref.: #43514]	L-tryptophan ChEBI	-	assimilation
[Ref.: #43514]	L-xylose ChEBI	-	builds acid from
[Ref.: #43514]	lactose ChEBI	+	builds acid from
[Ref.: #68368]	lysine ChEBI	-	degradation	* from API 20E
[Ref.: #43514]	maltose ChEBI	+	builds acid from
[Ref.: #43514]	melezitose ChEBI	-	builds acid from
[Ref.: #43514]	melibiose ChEBI	+	builds acid from
[Ref.: #68368]	melibiose ChEBI	+	fermentation	* from API 20E
[Ref.: #43514]	methyl alpha-D-glucopyranoside ChEBI	-	builds acid from
[Ref.: #43514]	methyl alpha-D-mannoside ChEBI	-	builds acid from
[Ref.: #43514]	methyl beta-D-xylopyranoside ChEBI	-	builds acid from
[Ref.: #43514]	myo-inositol ChEBI	+	builds acid from
[Ref.: #43514]	N-acetylglucosamine ChEBI	+	builds acid from
[Ref.: #43514]	nitrate ChEBI	+	reduction
[Ref.: #68368]	ornithine ChEBI	-	degradation	* from API 20E
[Ref.: #43514]	potassium gluconate ChEBI	+	builds acid from
[Ref.: #43514]	raffinose ChEBI	+	builds acid from
[Ref.: #43514]	ribitol ChEBI	-	builds acid from
[Ref.: #43514]	salicin ChEBI	+	builds acid from
[Ref.: #68368]	sorbitol ChEBI	+	fermentation	* from API 20E
[Ref.: #43514]	starch ChEBI	-	builds acid from
[Ref.: #43514]	sucrose ChEBI	+	builds acid from
[Ref.: #68368]	sucrose ChEBI	+	fermentation	* from API 20E
[Ref.: #43514]	trehalose ChEBI	+	builds acid from
[Ref.: #43514]	tryptophan ChEBI	-	energy source
[Ref.: #68368]	tryptophan ChEBI	-	energy source	* from API 20E
[Ref.: #43514]	turanose ChEBI	-	builds acid from
[Ref.: #68368]	urea ChEBI	-	hydrolysis	* from API 20E
[Ref.: #43514]	xylitol ChEBI	-	builds acid from
	Only first 10 entries are displayed. Click here to see all.

	Metabolite	Production
[Ref.: #43514]	acetoin ChEBI	no
[Ref.: #43514]	dinitrogen ChEBI	no
[Ref.: #43514]	hydrogen sulfide ChEBI	yes
[Ref.: #43514]	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

	Metabolite	Voges-Proskauer-test	Methylred-test	Indole test
[Ref.: #43514]	acetoin ChEBI	-
[Ref.: #43514]	glucose ChEBI		+
[Ref.: #43514]	indole ChEBI			-
[Ref.: #68368]	acetoin ChEBI	-			* from API 20E
[Ref.: #68368]	indole ChEBI			-	* from API 20E

	Enzyme	Enzyme activity	EC number
[Ref.: #68368]	arginine dihydrolase	-	3.5.3.6	* from API 20E
[Ref.: #68368]	beta-galactosidase	+	3.2.1.23	* from API 20E
[Ref.: #43514]	catalase	-	1.11.1.6
[Ref.: #43514]	cytochrome oxidase	-	1.9.3.1
[Ref.: #68368]	cytochrome oxidase	-	1.9.3.1	* from API 20E
[Ref.: #68368]	gelatinase	-		* from API 20E
[Ref.: #68368]	lysine decarboxylase	-	4.1.1.18	* from API 20E
[Ref.: #68368]	ornithine decarboxylase	-	4.1.1.17	* from API 20E
[Ref.: #43514]	tryptophan deaminase	-	4.1.99.1
[Ref.: #68368]	tryptophan deaminase	-	4.1.99.1	* from API 20E
[Ref.: #43514]	urease	+	3.5.1.5
[Ref.: #68368]	urease	-	3.5.1.5	* from API 20E
	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.: #43033]	17939	+	-	-	-	+	+	-	-	-	-	-	+	+	-	+	+	+	+	+	+	-	not determinedn.d.	not determinedn.d.	not determinedn.d.	not determinedn.d.	not determinedn.d.	not determinedn.d.
[Ref.: #43033]	17705	+	-	-	-	+	+	-	-	-	-	-	+	+	+	+	+	+	+	+	+	-	not determinedn.d.	not determinedn.d.	not determinedn.d.	not determinedn.d.	not determinedn.d.	not determinedn.d.

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

[Ref.: #43033]	Sample type/isolated from	water well
[Ref.: #43033]	Geographic location (country and/or sea, region)	Taboeira, Cadima, Cantanhede
[Ref.: #43033]	Country	Portugal
[Ref.: #43033]	Country ISO 3 Code	PRT
[Ref.: #43033]	Continent	Europe

[Ref.: #43514]	Sample type/isolated from	water well sample collected in Cantanhede City
[Ref.: #43514]	Geographic location (country and/or sea, region)	Cantanhede City
[Ref.: #43514]	Country	Portugal
[Ref.: #43514]	Country ISO 3 Code	PRT
[Ref.: #43514]	Continent	Europe
[Ref.: #43514]	Isolation date	2008

[Ref.: #121947]	Sample type/isolated from	Environment, Water well
[Ref.: #121947]	Country	Portugal
[Ref.: #121947]	Country ISO 3 Code	PRT
[Ref.: #121947]	Continent	Europe
[Ref.: #121947]	Isolation date	2006
* marker position based on {}

Isolation sources categories

#Environmental

#Aquatic

What are isolation sources categories?

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

[Ref.: #43033]	Pathogenicity (human)	yes, in single cases
[Ref.: #43033]	Biosafety level	1	Risk group (German classification) According to TRBA 466
[Ref.: #121947]	Biosafety level	1	Risk group (French classification)

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

Genome sequence information:

	Sequence accession description	Seq. accession number	Assembly level	Sequence database	Associated NCBI tax ID
[Ref.: #66792]	Citrobacter portucalensis A60	GCA_002042885	contig	GenBank	1639133 tax ID	*
[Ref.: #66792]	Citrobacter portucalensis A60	2874289006	draft	JGI IMG/M	1639133 tax ID	*

[Ref.: #43514]	GC-content	52 mol%
[Ref.: #43033]	GC-content	52.0 mol%

Availability in culture collections External links

[Ref.: #43033]

Culture collection no.

DSM 104542, CECT 9236, CIP 111602

[Ref.: #96699]

SI-ID 408082

Literature:

Topic	Title	Authors	Journal	DOI	Year
Phylogeny	Citrobacter portucalensis sp. nov., isolated from an aquatic sample.	Ribeiro TG, Goncalves BR, da Silva MS, Novais A, Machado E, Carrico JA, Peixe L	Int J Syst Evol Microbiol	10.1099/ijsem.0.002154	2017	*

References

#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 )

#43033

Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 104542

#43514

Teresa Gonçalves Ribeiro, Bruno Ribeiro Gonçalves, Mickael Santos da Silva, Ângela Novais, Elisabete Machado, Joao Andre Carriço, Luísa Peixe: Citrobacter portucalensis sp. nov., isolated from an aquatic sample. IJSEM 67: 3513 - 3517 2017 ( DOI 10.1099/ijsem.0.002154 , PubMed 28857032 )

#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 .

#96699

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-ID408082.1 )

#121947 Collection of Institut Pasteur ; Curators of the CIP; CIP 111602
* These data were automatically processed and therefore are not curated

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