Citrobacter pasteurii (DSM 28879, CIP 55.13, Na 1a)

Name: Citrobacter pasteurii (DSM 28879, CIP 55.13, Na 1a)
Creator: BacDive
License: http://creativecommons.org/licenses/by/4.0/

BacDive ID 130292

Type strain

Strain Designation Na 1a

Culture col. no. DSM 28879 CIP 55.13 Na 1a

NCBI tax ID(s) 1563222

Special Collections DSMZ CIP

History 1955, P.R. Edwards, Kentucky, USA: strain Na 1a, Citrobacter freundii <- D. Clermont, CIP; Na 1a <- P. R. Edwards, Kentucky, USA CIP <- 1955, P.R. Edwards, Kentucky, USA: strain Na 1a, Citrobacter freundii

Links

Citrobacter pasteurii Na 1a is a facultative anaerobe, Gram-negative, motile bacterium that was isolated from human diarrhoeal stool.

Gram-negative motile rod-shaped facultative anaerobe genome sequence 16S sequence Bacteria

Name and taxonomic classification

SI-ID 67873

DSM 28879,CIP 55.13

@ref 20215

Last LPSN update 2026-02-09 11:31:11

Domain Bacteria

Phylum Pseudomonadota

Class Gammaproteobacteria

Order Enterobacterales

Family Enterobacteriaceae

Genus Citrobacter

Species Citrobacter pasteurii

Full scientific name Citrobacter pasteurii Clermont et al. 2015

Morphology

Cell morphology

@ref	Gram stain	Cell shape	Motility	Confidence
125438	negative			100
121621	negative	rod-shaped

Multimedia

@ref:	21549
multimedia content:	DSM_28879.jpg
multimedia.multimedia content:	https://www.dsmz.de/microorganisms/photos/DSM_28879.jpg
intellectual property rights:	© Leibniz-Institut DSMZ
manual_annotation:	1

Culture and growth conditions

Culture medium

@ref	Name	Medium link	Composition
42054	MEDIUM 3 - Columbia agar		Columbia agar (39.000 g);distilled water (1000.000 ml)
21549	CASO AGAR (MERCK 105458) (DSMZ Medium 220)	Medium recipe at MediaDive	Name: CASO AGAR (Merck 105458) (DSMZ Medium 220) Composition: Agar 15.0 g/l Casein peptone 15.0 g/l NaCl 5.0 g/l Soy peptone 5.0 g/l Distilled water
21549	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
21549	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
121621	CIP Medium 72	Medium recipe at CIP
121621	CIP Medium 3	Medium recipe at CIP

Culture temp

@ref	Growth	Type	Temperature (°C)
21549	positive	growth	28
21549	positive	growth	30
42054	positive	growth	30

Physiology and metabolism

Oxygen tolerance

@ref	Oxygen tolerance	Confidence
121621	facultative anaerobe
125439	aerobe	90.8

Metabolite utilization

@ref	Chebi-ID	Metabolite	Utilization activity	Kind of utilization tested
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	30849 ChEBI	L-arabinose	+	fermentation	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
121621	17632 ChEBI	nitrate	+	reduction
121621	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

Metabolite production

@ref	Chebi-ID	Metabolite
68368	15688 ChEBI	acetoin	from API 20E
68368	16136 ChEBI	hydrogen sulfide	from API 20E
121621	35581 ChEBI	indole
68368	35581 ChEBI	indole	from API 20E

Metabolite tests

@ref	Chebi-ID	Metabolite	Voges-proskauer-test	Indole test
68368	15688 ChEBI	acetoin	-		from API 20E
68368	35581 ChEBI	indole		-	from API 20E

Enzymes

@ref	Value	Activity	Ec
68382	acid phosphatase	+	3.1.3.2	from API zym
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
121621	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
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
68368	ornithine decarboxylase	-	4.1.1.17	from API 20E
121621	oxidase	-
68382	trypsin	-	3.4.21.4	from API zym
68368	tryptophan deaminase	-	4.1.99.1	from API 20E
121621	urease	+	3.5.1.5
68368	urease	-	3.5.1.5	from API 20E
68382	valine arylamidase	-		from API zym

API 20E

@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
21549	+	+	-	-	+	+	-	-	-	-	-	+	+	-	+	+	+	-	+/-	+	not determinedn.d.	not determinedn.d.	not determinedn.d.	not determinedn.d.	not determinedn.d.	not determinedn.d.	not determinedn.d.
21549	+	+	-	-	+	+	-	-	-	-	-	+	+	-	+	+	+	-	+	+	-	not determinedn.d.	not determinedn.d.	not determinedn.d.	not determinedn.d.	not determinedn.d.	not determinedn.d.

API zym

@ref	Control	Alkaline phosphatase	Esterase (C 4)	2-naphtyl caprylateEsterase Lipase (C 8)	Lipase (C 14)	L-leucyl-2-naphthylamideLeucine arylamidase	L-valyl-2-naphthylamideValine arylamidase	L-cystyl-2-naphthylamideCystine arylamidase	Trypsin	alpha- Chymotrypsin	Acid phosphatase	Naphthol-AS-BI-phosphateNaphthol-AS-BI-phosphohydrolase	alpha- Galactosidase	beta- Galactosidase	beta- Glucuronidase	alpha- Glucosidase	beta- Glucosidase	N-acetyl-beta- glucosaminidase	alpha- Mannosidase	alpha- Fucosidase
121621	-	+	-	-	-	+	-	-	-	-	+	+	-	+	-	-	+	-	-	-

Isolation, sampling and environmental information

Isolation source categories

Cat1	Cat2	Cat3
#Host	#Human	-
#Host Body Product	#Gastrointestinal tract	#Feces (Stool)

Isolation

@ref	Sample type	Geographic location	Country	Country ISO 3 Code	Continent	Isolation date
21549	human diarrhoeal stool	Kentucky	USA	USA	North America
121621	Human, Stool, diarrhea, outbreak	Kentucky	United States of America	USA	North America	1955

Taxonmaps

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

Interaction and safety

Risk assessment

@ref	Pathogenicity human	Biosafety level	Biosafety level comment
21549	yes, in single cases	1	Risk group (German classification)
121621		1	Risk group (French classification)

Sequence information

Genome sequences

@ref	Description	Assembly level	INSDC accession	BV-BRC accession	IMG accession	NCBI tax ID	Score
124043	ASM1904776v1 assembly for Citrobacter pasteurii FDAARGOS 1424	complete	GCA_019047765	1563222.16	8120208920	1563222	98.1
66792	Citrobacter_pasteurii_55-13 assembly for Citrobacter pasteurii CIP 55.13	contig	GCA_000826205	1563222.3	2648501483	1563222	67.71

16S sequences

@ref	Description	Accession	Length	NCBI tax ID
21549	Citrobacter pasteurii strain CIP 55.13 16S ribosomal RNA gene, partial sequence	KP057683	1492	1563222
124043	Citrobacter pasteurii strain CIP55.13 16S ribosomal RNA gene, partial sequence.	OR660260	1135	1563222
124043	Citrobacter pasteurii strain CIP 55.13 16S ribosomal RNA gene, partial sequence.	PP858377	755	1563222

GC content

@ref	GC-content (mol%)	Method
21549	51.80	sequence analysis

Genome-based predictions

Predictions

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	Trait	Model	Prediction	Confidence in %	In training data
125439	spore_formation	BacteriaNetⓘ	no	80.10	no
125439	motility	BacteriaNetⓘ	yes	69.90	no
125439	gram_stain	BacteriaNetⓘ	negative	79.80	no
125439	oxygen_tolerance	BacteriaNetⓘ	aerobe	90.80	no

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	Trait	Model	Prediction	Confidence in %	In training data
125438	gram-positive	gram-positiveⓘ	no	100.00	no
125438	anaerobic	anaerobicⓘ	no	94.64	yes
125438	spore-forming	spore-formingⓘ	no	88.63	no
125438	aerobic	aerobicⓘ	no	76.90	yes
125438	thermophilic	thermophileⓘ	no	98.00	no
125438	flagellated	motile2+ⓘ	yes	78.66	no

Literature

Topic	Title	Authors	Journal	DOI	Year
	Discovery and structure of the antimicrobial lasso peptide citrocin.	Cheung-Lee WL, Parry ME, Jaramillo Cartagena A, Darst SA, Link AJ.	J Biol Chem	10.1074/jbc.ra118.006494	2019
	qnrE1, a Member of a New Family of Plasmid-Located Quinolone Resistance Genes, Originated from the Chromosome of Enterobacter Species.	Albornoz E, Tijet N, De Belder D, Gomez S, Martino F, Corso A, Melano RG, Petroni A.	Antimicrob Agents Chemother	10.1128/aac.02555-16	2017
	Identification and Genome Analysis of an Arsenic-Metabolizing Strain of Citrobacter youngae IITK SM2 in Middle Indo-Gangetic Plain Groundwater.	Verma A, Murugan PA, Chinnasamy HV, Singh A, Matheshwaran S.	Biomed Res Int	10.1155/2022/6384742	2022
Metabolism	Citrobacter freundii fitness during bloodstream infection.	Anderson MT, Mitchell LA, Zhao L, Mobley HLT.	Sci Rep	10.1038/s41598-018-30196-0	2018
	Mechanism of Action of Ribosomally Synthesized and Post-Translationally Modified Peptides.	Ongpipattanakul C, Desormeaux EK, DiCaprio A, van der Donk WA, Mitchell DA, Nair SK.	Chem Rev	10.1021/acs.chemrev.2c00210	2022
Phylogeny	Multilocus sequence analysis of the genus Citrobacter and description of Citrobacter pasteurii sp. nov.	Clermont D, Motreff L, Passet V, Fernandez JC, Bizet C, Brisse S	Int J Syst Evol Microbiol	10.1099/ijs.0.000122	2015

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 )
#21549	Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 28879
#42054	; Curators of the CIP;
#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 .
#121621	Collection of Institut Pasteur ; Curators of the CIP; CIP 55.13
#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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Citrobacter pasteurii (DSM 28879, CIP 55.13, Na 1a)

Name and taxonomic classification

Morphology

Cell morphology

Multimedia

Culture and growth conditions

Culture medium

Culture temp

Physiology and metabolism

Oxygen tolerance

Metabolite utilization

Metabolite production

Metabolite tests

Enzymes

API 20E

API zym

Isolation, sampling and environmental information

Isolation source categories

Isolation

Taxonmaps

Interaction and safety

Risk assessment

Sequence information

Genome sequences

Genome browser: GCA_019047765

16S sequences

GC content

Genome-based predictions

Predictions

Literature

Literature

References

BacDive

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