Name: Cedecea davisae 005
Creator: BacDive
License: http://creativecommons.org/licenses/by-nc/4.0/

Strain identifier

BacDive ID: 4320

Type strain:

Species: Cedecea davisae

Strain Designation: 005

Culture col. no.: DSM 4568, ATCC 33431, CDC 3278-77, CIP 80.34, CCUG 12370, JCM 1685, BCRC 14815, CECT 842, LMG 7862, NBRC 105702, NCIMB 11889, NCTC 13724

Strain history: Y. Kosako 82080 <-- R. Sakazaki 282 <-- CDC 3278-77 <-- P. A. D. Grimont 005.

NCBI tax ID(s): 566551 (strain), 158484 (species)

Other strains from Cedecea davisae

C. davisae ST027313(HKI), F147, Nü38,
C. davisae CIP 104922
C. davisae CIP 104936
C. davisae CCUG 21141
C. davisae CCUG 21142
C. davisae CCUG 21143
C. davisae CCUG 21187
C. davisae CCUG 21188
C. davisae CCUG 23276
C. davisae CCUG 23277

Section

Cedecea davisae 005 is an aerobe, mesophilic bacterium that was isolated from stool.

aerobe
mesophilic
16S sequence
Bacteria
genome sequence

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

	Last LPSN update	07-12-2022 (DD-MM-YYYY)
	Domain	"Bacteria"
	Phylum	*Pseudomonadota*
	Class	*Gammaproteobacteria*
	Order	*Enterobacterales*
	Family	*Enterobacteriaceae*
	Genus	*Cedecea*
	Species	**Cedecea davisae**
	Full Scientific Name (PNU)	Cedecea davisae Grimont et al. 1981

Information on morphological and physiological properties Morphology

[Ref.: #69480]	Gram stain	negative Confidence in %99.917

[Ref.: #69480]	Motility	yes Confidence in %97.383

Information on culture and growth conditions Culture and growth conditions

[Ref.: #1774]

Culture medium

NUTRIENT AGAR (DSMZ Medium 1)

[Ref.: #1774]

Culture medium growth

[Ref.: #1774]

Culture medium link

Medium recipe provided by DSMZ

[Ref.: #1774]

Culture medium composition

expand / minimize

[Ref.: #38419]

Culture medium

MEDIUM 3 - Columbia agar

[Ref.: #38419]

Culture medium growth

[Ref.: #38419]

Culture medium composition

expand / minimize

		Temperature
[Ref.: #1774]	growth	30 °C
[Ref.: #38419]	growth	30 °C
[Ref.: #45680]	growth	37 °C
[Ref.: #67770]	growth	37 °C

[Ref.: #1774]	Temperature range	mesophilic
[Ref.: #38419]	Temperature range	mesophilic
[Ref.: #45680]	Temperature range	mesophilic
[Ref.: #67770]	Temperature range	mesophilic

Information on physiology and metabolism Physiology and metabolism

[Ref.: #45680]

Oxygen tolerance

aerobe

[Ref.: #69481]	Ability of spore formation	no Confidence in %100
[Ref.: #69480]	Ability of spore formation	no Confidence in %99.474

	Pathway	Enzyme coverage	Annotated reactions
	Pathway annotation	Computationally determined by
[Ref.: #66794]	cellulose degradation	100	5 of 5
[Ref.: #66794]	vitamin K metabolism	100	5 of 5
[Ref.: #66794]	methylglyoxal degradation	100	5 of 5
[Ref.: #66794]	acetoin degradation	100	3 of 3
[Ref.: #66794]	aerobactin biosynthesis	100	1 of 1
[Ref.: #66794]	formaldehyde oxidation	100	3 of 3
[Ref.: #66794]	lipoate biosynthesis	100	5 of 5
[Ref.: #66794]	coenzyme A metabolism	100	4 of 4
[Ref.: #66794]	starch degradation	100	10 of 10
[Ref.: #66794]	suberin monomers biosynthesis	100	2 of 2
[Ref.: #66794]	biotin biosynthesis	100	4 of 4
[Ref.: #66794]	adipate degradation	100	2 of 2
[Ref.: #66794]	L-lactaldehyde degradation	100	3 of 3
[Ref.: #66794]	UDP-GlcNAc biosynthesis	100	3 of 3
[Ref.: #66794]	sulfopterin metabolism	100	4 of 4
[Ref.: #66794]	teichoic acid biosynthesis	100	1 of 1
[Ref.: #66794]	ppGpp biosynthesis	100	4 of 4
[Ref.: #66794]	palmitate biosynthesis	100	22 of 22
[Ref.: #66794]	pentose phosphate pathway	100	11 of 11
[Ref.: #66794]	Entner Doudoroff pathway	100	10 of 10
[Ref.: #66794]	tetrahydrofolate metabolism	100	14 of 14
[Ref.: #66794]	folate polyglutamylation	100	1 of 1
[Ref.: #66794]	cis-vaccenate biosynthesis	100	2 of 2
[Ref.: #66794]	threonine metabolism	100	10 of 10
[Ref.: #66794]	ethanol fermentation	100	2 of 2
[Ref.: #66794]	phenylacetate degradation (aerobic)	100	5 of 5
[Ref.: #66794]	CDP-diacylglycerol biosynthesis	100	2 of 2
[Ref.: #66794]	anapleurotic synthesis of oxalacetate	100	1 of 1
[Ref.: #66794]	ribulose monophosphate pathway	100	2 of 2
[Ref.: #66794]	gluconeogenesis	100	8 of 8
[Ref.: #66794]	taurine degradation	100	1 of 1
[Ref.: #66794]	acetate fermentation	100	4 of 4
[Ref.: #66794]	ubiquinone biosynthesis	100	7 of 7
[Ref.: #66794]	enterobactin biosynthesis	100	3 of 3
[Ref.: #66794]	NAD metabolism	94.44	17 of 18
[Ref.: #66794]	photosynthesis	92.86	13 of 14
[Ref.: #66794]	vitamin B6 metabolism	90.91	10 of 11
[Ref.: #66794]	molybdenum cofactor biosynthesis	88.89	8 of 9
[Ref.: #66794]	serine metabolism	88.89	8 of 9
[Ref.: #66794]	aspartate and asparagine metabolism	88.89	8 of 9
[Ref.: #66794]	d-mannose degradation	88.89	8 of 9
[Ref.: #66794]	chorismate metabolism	88.89	8 of 9
[Ref.: #66794]	C4 and CAM-carbon fixation	87.5	7 of 8
[Ref.: #66794]	isoleucine metabolism	87.5	7 of 8
[Ref.: #66794]	glutamate and glutamine metabolism	85.71	24 of 28
[Ref.: #66794]	glutathione metabolism	85.71	12 of 14
[Ref.: #66794]	heme metabolism	85.71	12 of 14
[Ref.: #66794]	reductive acetyl coenzyme A pathway	85.71	6 of 7
[Ref.: #66794]	methionine metabolism	84.62	22 of 26
[Ref.: #66794]	vitamin B1 metabolism	84.62	11 of 13
[Ref.: #66794]	pyrimidine metabolism	82.22	37 of 45
[Ref.: #66794]	glycogen metabolism	80	4 of 5
[Ref.: #66794]	peptidoglycan biosynthesis	80	12 of 15
[Ref.: #66794]	citric acid cycle	78.57	11 of 14
[Ref.: #66794]	lipid A biosynthesis	77.78	7 of 9
[Ref.: #66794]	valine metabolism	77.78	7 of 9
[Ref.: #66794]	phenylalanine metabolism	76.92	10 of 13
[Ref.: #66794]	leucine metabolism	76.92	10 of 13
[Ref.: #66794]	urea cycle	76.92	10 of 13
[Ref.: #66794]	purine metabolism	76.6	72 of 94
[Ref.: #66794]	CMP-KDO biosynthesis	75	3 of 4
[Ref.: #66794]	6-hydroxymethyl-dihydropterin diphosphate biosynthesis	75	6 of 8
[Ref.: #66794]	glycogen biosynthesis	75	3 of 4
[Ref.: #66794]	ketogluconate metabolism	75	6 of 8
[Ref.: #66794]	flavin biosynthesis	73.33	11 of 15
[Ref.: #66794]	proline metabolism	72.73	8 of 11
[Ref.: #66794]	metabolism of disaccharids	72.73	8 of 11
[Ref.: #66794]	alanine metabolism	72.41	21 of 29
[Ref.: #66794]	histidine metabolism	72.41	21 of 29
[Ref.: #66794]	oxidative phosphorylation	71.43	65 of 91
[Ref.: #66794]	cardiolipin biosynthesis	71.43	5 of 7
[Ref.: #66794]	non-pathway related	71.05	27 of 38
[Ref.: #66794]	lipid metabolism	70.97	22 of 31
[Ref.: #66794]	arginine metabolism	66.67	16 of 24
[Ref.: #66794]	lysine metabolism	66.67	28 of 42
[Ref.: #66794]	selenocysteine biosynthesis	66.67	4 of 6
[Ref.: #66794]	CO2 fixation in Crenarchaeota	66.67	6 of 9
[Ref.: #66794]	glycolate and glyoxylate degradation	66.67	4 of 6
[Ref.: #66794]	cyanate degradation	66.67	2 of 3
[Ref.: #66794]	octane oxidation	66.67	2 of 3
[Ref.: #66794]	isoprenoid biosynthesis	65.38	17 of 26
[Ref.: #66794]	glycolysis	64.71	11 of 17
[Ref.: #66794]	d-xylose degradation	63.64	7 of 11
[Ref.: #66794]	dTDPLrhamnose biosynthesis	62.5	5 of 8
[Ref.: #66794]	cysteine metabolism	61.11	11 of 18
[Ref.: #66794]	degradation of pentoses	60.71	17 of 28
[Ref.: #66794]	myo-inositol biosynthesis	60	6 of 10
[Ref.: #66794]	metabolism of amino sugars and derivatives	60	3 of 5
[Ref.: #66794]	tryptophan metabolism	57.89	22 of 38
[Ref.: #66794]	propanol degradation	57.14	4 of 7
[Ref.: #66794]	degradation of sugar acids	56	14 of 25
[Ref.: #66794]	ascorbate metabolism	54.55	12 of 22
[Ref.: #66794]	phenylpropanoid biosynthesis	53.85	7 of 13
[Ref.: #66794]	degradation of sugar alcohols	50	8 of 16
[Ref.: #66794]	quinate degradation	50	1 of 2
[Ref.: #66794]	pantothenate biosynthesis	50	3 of 6
[Ref.: #66794]	propionate fermentation	50	5 of 10
[Ref.: #66794]	butanoate fermentation	50	2 of 4
[Ref.: #66794]	degradation of aromatic, nitrogen containing compounds	50	6 of 12
[Ref.: #66794]	tyrosine metabolism	50	7 of 14
[Ref.: #66794]	toluene degradation	50	2 of 4
[Ref.: #66794]	glycine metabolism	50	5 of 10
[Ref.: #66794]	carnitine metabolism	50	4 of 8
[Ref.: #66794]	3-phenylpropionate degradation	46.67	7 of 15
[Ref.: #66794]	phenol degradation	45	9 of 20
[Ref.: #66794]	nitrate assimilation	44.44	4 of 9
[Ref.: #66794]	coenzyme M biosynthesis	40	4 of 10
[Ref.: #66794]	gallate degradation	40	2 of 5
[Ref.: #66794]	3-chlorocatechol degradation	40	2 of 5
[Ref.: #66794]	ethylmalonyl-CoA pathway	40	2 of 5
[Ref.: #66794]	hydrogen production	40	2 of 5
[Ref.: #66794]	arachidonate biosynthesis	40	2 of 5
[Ref.: #66794]	glycine betaine biosynthesis	40	2 of 5
[Ref.: #66794]	sulfate reduction	38.46	5 of 13
[Ref.: #66794]	androgen and estrogen metabolism	37.5	6 of 16
[Ref.: #66794]	sphingosine metabolism	33.33	2 of 6
[Ref.: #66794]	methane metabolism	33.33	1 of 3
[Ref.: #66794]	(5R)-carbapenem carboxylate biosynthesis	33.33	1 of 3
[Ref.: #66794]	acetyl CoA biosynthesis	33.33	1 of 3
[Ref.: #66794]	arachidonic acid metabolism	33.33	6 of 18
[Ref.: #66794]	degradation of hexoses	33.33	6 of 18
[Ref.: #66794]	IAA biosynthesis	33.33	1 of 3
[Ref.: #66794]	4-hydroxymandelate degradation	33.33	3 of 9
[Ref.: #66794]	polyamine pathway	30.43	7 of 23
[Ref.: #66794]	4-hydroxyphenylacetate degradation	30	3 of 10
[Ref.: #66794]	chlorophyll metabolism	27.78	5 of 18
[Ref.: #66794]	cyclohexanol degradation	25	1 of 4
[Ref.: #66794]	lactate fermentation	25	1 of 4
[Ref.: #66794]	phosphatidylethanolamine bioynthesis	23.08	3 of 13
[Ref.: #66794]	allantoin degradation	22.22	2 of 9
		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.: #1774]	Sample type/isolated from	stool
[Ref.: #1774]	Geographic location (country and/or sea, region)	New Jersey
[Ref.: #1774]	Country	USA
[Ref.: #1774]	Country ISO 3 Code	USA
[Ref.: #1774]	Continent	North America

[Ref.: #45680]	Sample type/isolated from	Human stool
[Ref.: #45680]	Geographic location (country and/or sea, region)	New Jersey
[Ref.: #45680]	Country	USA
[Ref.: #45680]	Country ISO 3 Code	USA
[Ref.: #45680]	Continent	North America

[Ref.: #67770]	Sample type/isolated from	Stool
[Ref.: #67770]	Geographic location (country and/or sea, region)	NJ
[Ref.: #67770]	Country	USA
[Ref.: #67770]	Country ISO 3 Code	USA
[Ref.: #67770]	Continent	North America
* marker position based on {}

Isolation sources categories

#Host Body Product

#Gastrointestinal tract

#Feces (Stool)

What are isolation sources categories?

[Ref.: #69479]

Global distribution of 16S sequence AF493976 (>99% sequence identity) for Enterobacteriaceae from Microbeatlas

Aquatic Samples	2
Soil Samples
Animal Samples	9
Plant Samples
Total Samples	11

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

[Ref.: #1774]

Biosafety level

Risk group (German classification)
According to TRBA 466

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]	Cedecea davisae DSM 4568 16S ribosomal RNA gene, partial sequence	AF493976	1403	ENA	566551 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.: #67770]	Cedecea davisae DSM 4568 DSM 4568	GCA_000412335	scaffold	GenBank	566551 tax ID
[Ref.: #67770]	Cedecea davisae NCTC13724	GCA_900446735	contig	GenBank	158484 tax ID
[Ref.: #66792]	Cedecea davisae DSM 4568	566551.4	wgs	PATRIC	566551 tax ID	*
[Ref.: #66792]	Cedecea davisae strain NCTC13724	158484.3	wgs	PATRIC	158484 tax ID	*
[Ref.: #66792]	Cedecea davisae 005, DSM 4568	2541046972	draft	JGI IMG/M	566551 tax ID	*
[Ref.: #66792]	Cedecea davisae NCTC 13724	2808606631	draft	JGI IMG/M	158484 tax ID	*

[Ref.: #67770]

GC-content

48-49.6 mol%

thermal denaturation, midpoint method (Tm)

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

	Trait	Prediction	Confidence in %	In training data
	Predictions from Diaspora project based on: Cedecea davisae DSM 4568 DSM 4568 NCBI: GCA_000412335.2
[Ref.: #69480]	spore-forming	no	99.474	no
[Ref.: #69480]	anaerobic	no	96.661	yes
[Ref.: #69480]	gram-positive	no	99.917	yes
[Ref.: #69480]	thermophile	no	99.869	yes
[Ref.: #69480]	motile	yes	97.383	no

	Trait	Prediction	Confidence in %	In training data
	Predictions from GenomeNet Sporulation v. 1 based on: Cedecea davisae DSM 4568 DSM 4568 NCBI: GCA_000412335.2
[Ref.: #69481]	spore-forming	no	100	no

Availability in culture collections External links

[Ref.: #1774]

Culture collection no.

DSM 4568, ATCC 33431, CDC 3278-77, CIP 80.34, CCUG 12370, JCM 1685, BCRC 14815, CECT 842, LMG 7862, NBRC 105702, NCIMB 11889, NCTC 13724

[Ref.: #20218]

Associated Passport(s) in StrainInfo

149708, 6924, 6926, 229527

Literature:

Topic	Title	Authors	Journal	DOI	Year
Phylogeny	[Screening and identification of steroidal saponins-producing endophytes from Paris polyphylla var. chinensis Franch].	Zhao M, He SR, Chen XJ, Huang CP, Wang YD, Zhang XJ, Feng DS	Wei Sheng Wu Xue Bao		2005	*
Phylogeny	Cedecea sulfonylureivorans sp. nov., a novel chlorimuron-ethyldegrading bacterium isolated from an herbicides-degrading consortium.	Li Q, Wang J, Ma Q, Han X, Zhang W, Ruan Z	Arch Microbiol	10.1007/s00203-022-03362-2	2022	*

References

#1774

Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 4568

#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 )

#38419 ; Curators of the CIP;
#45680 Culture Collection University of Gothenburg (CCUG) ; Curators of the CCUG; CCUG 12370

#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 )

#67770 Japan Collection of Microorganism (JCM) ; Curators of the JCM;

#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) .

#69481

Xiao-Yin To, René Mreches, Martin Binder, Alice C. McHardy, Philipp C. Münch: Predictions based on the model GenomeNet Sporulation v. 1 . ( DOI 10.21203/rs.3.rs-2527258/v1 )

* These data were automatically processed and therefore are not curated

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Cedecea davisae DSM 4568 DSM 4568

Cedecea davisae DSM 4568 DSM 4568

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