Caulobacter vibrioides (DSM 25117, CB2A)

Name: Caulobacter vibrioides (DSM 25117, CB2A)
Creator: BacDive
License: http://creativecommons.org/licenses/by/4.0/

BacDive ID 2335

Type strain

Strain Designation CB2A

Culture col. no. DSM 25117 CB2A

NCBI tax ID(s) 155892

Special Collections DSMZ

Links

Caulobacter vibrioides CB2A is a mesophilic prokaryote that was isolated from tap water, spontaneous S-layer negative variant of C. vibrioides CB 2 .

mesophilic genome sequence 16S sequence

Name and taxonomic classification

SI-ID 408095

DSM 25117

@ref 20215

Last LPSN update 2025-12-16 09:47:17

Domain Pseudomonadati

Phylum Pseudomonadota

Class Alphaproteobacteria

Order Caulobacterales

Family Caulobacteraceae

Genus Caulobacter

Species Caulobacter vibrioides

Full scientific name Caulobacter vibrioides Henrici and Johnson 1935 (Approved Lists 1980)

Synonyms (1)

Caulobacter crescentus

BacDive ID	Other strains from **Caulobacter vibrioides** (8)	Type strain
2334	C. vibrioides CB 51, DSM 9893, KCTC 23677, CIP 106452, ... (type strain)
2332	C. vibrioides CB 2, DSM 4727, ATCC 15252, CIP 101123, NCIMB ...
2333	C. vibrioides CB-G, DSM 4738, ATCC 11764, CIP 70.55, NCIMB ...
135842	C. vibrioides 719.85, CIP 101900
136129	C. vibrioides 717.86, CIP 102705
138065	C. vibrioides 646.86, CIP 102644
139101	C. vibrioides CB 15, CIP 103742, ATCC 19089
144142	C. vibrioides CCUG 23150, LMG 11145

Morphology

Cell morphology

@ref	Gram stain	Confidence
125439	negative	98.2
125438	negative	95.963

Culture and growth conditions

Culture medium

@ref	Name	Growth	Medium link	Composition
17910	CAULOBACTER PYE MEDIUM (DSMZ Medium 1462)		Medium recipe at MediaDive	Name: CAULOBACTER PYE MEDIUM (DSMZ Medium 1462) Composition: Agar 12.0 g/l (optional) Peptone 2.0 g/l Yeast extract 1.0 g/l CaCl2 x 2 H2O 0.07 g/l Distilled water

Culture temp

@ref	Growth	Type	Temperature (°C)	Range
17910	positive	growth	30	mesophilic

Physiology and metabolism

Oxygen tolerance

@ref	Oxygen tolerance	Confidence
125439	obligate aerobe	99.1

Spore formation

@ref	Spore formation	Confidence
125439		98.3

Pathway annotation

Computationally determined by

@ref	pathway	enzyme coverage	annotated reactions
66794	cellulose degradation	100	5 of 5
66794	valine metabolism	100	9 of 9
66794	CDP-diacylglycerol biosynthesis	100	2 of 2
66794	ppGpp biosynthesis	100	4 of 4
66794	coenzyme A metabolism	100	4 of 4
66794	biotin biosynthesis	100	4 of 4
66794	formaldehyde oxidation	100	3 of 3
66794	palmitate biosynthesis	100	22 of 22
66794	adipate degradation	100	2 of 2
66794	methylglyoxal degradation	100	5 of 5
66794	cis-vaccenate biosynthesis	100	2 of 2
66794	propanol degradation	100	7 of 7
66794	UDP-GlcNAc biosynthesis	100	3 of 3
66794	quinate degradation	100	2 of 2
66794	Entner Doudoroff pathway	100	10 of 10
66794	ethanol fermentation	100	2 of 2
66794	folate polyglutamylation	100	1 of 1
66794	anapleurotic synthesis of oxalacetate	100	1 of 1
66794	taurine degradation	100	1 of 1
66794	suberin monomers biosynthesis	100	2 of 2
66794	tetrahydrofolate metabolism	92.86	13 of 14
66794	leucine metabolism	92.31	12 of 13
66794	threonine metabolism	90	9 of 10
66794	molybdenum cofactor biosynthesis	88.89	8 of 9
66794	chorismate metabolism	88.89	8 of 9
66794	lipid A biosynthesis	88.89	8 of 9
66794	serine metabolism	88.89	8 of 9
66794	CO2 fixation in Crenarchaeota	88.89	8 of 9
66794	C4 and CAM-carbon fixation	87.5	7 of 8
66794	isoleucine metabolism	87.5	7 of 8
66794	photosynthesis	85.71	12 of 14
66794	glutathione metabolism	85.71	12 of 14
66794	ubiquinone biosynthesis	85.71	6 of 7
66794	reductive acetyl coenzyme A pathway	85.71	6 of 7
66794	citric acid cycle	85.71	12 of 14
66794	phenylalanine metabolism	84.62	11 of 13
66794	NAD metabolism	83.33	15 of 18
66794	alanine metabolism	82.76	24 of 29
66794	glutamate and glutamine metabolism	82.14	23 of 28
66794	ethylmalonyl-CoA pathway	80	4 of 5
66794	phenylacetate degradation (aerobic)	80	4 of 5
66794	propionate fermentation	80	8 of 10
66794	pyrimidine metabolism	80	36 of 45
66794	glycogen metabolism	80	4 of 5
66794	cysteine metabolism	77.78	14 of 18
66794	vitamin B1 metabolism	76.92	10 of 13
66794	purine metabolism	75.53	71 of 94
66794	acetate fermentation	75	3 of 4
66794	gluconeogenesis	75	6 of 8
66794	sulfopterin metabolism	75	3 of 4
66794	glycogen biosynthesis	75	3 of 4
66794	6-hydroxymethyl-dihydropterin diphosphate biosynthesis	75	6 of 8
66794	CMP-KDO biosynthesis	75	3 of 4
66794	butanoate fermentation	75	3 of 4
66794	flavin biosynthesis	73.33	11 of 15
66794	methionine metabolism	73.08	19 of 26
66794	vitamin B6 metabolism	72.73	8 of 11
66794	proline metabolism	72.73	8 of 11
66794	histidine metabolism	72.41	21 of 29
66794	cardiolipin biosynthesis	71.43	5 of 7
66794	heme metabolism	71.43	10 of 14
66794	non-pathway related	68.42	26 of 38
66794	degradation of sugar acids	68	17 of 25
66794	IAA biosynthesis	66.67	2 of 3
66794	d-mannose degradation	66.67	6 of 9
66794	L-lactaldehyde degradation	66.67	2 of 3
66794	glycolate and glyoxylate degradation	66.67	4 of 6
66794	octane oxidation	66.67	2 of 3
66794	3-phenylpropionate degradation	66.67	10 of 15
66794	cyanate degradation	66.67	2 of 3
66794	acetoin degradation	66.67	2 of 3
66794	peptidoglycan biosynthesis	66.67	10 of 15
66794	lipid metabolism	64.52	20 of 31
66794	tyrosine metabolism	64.29	9 of 14
66794	pentose phosphate pathway	63.64	7 of 11
66794	d-xylose degradation	63.64	7 of 11
66794	ketogluconate metabolism	62.5	5 of 8
66794	arginine metabolism	62.5	15 of 24
66794	urea cycle	61.54	8 of 13
66794	isoprenoid biosynthesis	61.54	16 of 26
66794	degradation of hexoses	61.11	11 of 18
66794	creatinine degradation	60	3 of 5
66794	lipoate biosynthesis	60	3 of 5
66794	starch degradation	60	6 of 10
66794	tryptophan metabolism	57.89	22 of 38
66794	degradation of sugar alcohols	56.25	9 of 16
66794	allantoin degradation	55.56	5 of 9
66794	lysine metabolism	54.76	23 of 42
66794	glycolysis	52.94	9 of 17
66794	kanosamine biosynthesis II	50	1 of 2
66794	myo-inositol biosynthesis	50	5 of 10
66794	arachidonic acid metabolism	50	9 of 18
66794	aminopropanol phosphate biosynthesis	50	1 of 2
66794	phenylmercury acetate degradation	50	1 of 2
66794	degradation of aromatic, nitrogen containing compounds	50	6 of 12
66794	androgen and estrogen metabolism	50	8 of 16
66794	glycine metabolism	50	5 of 10
66794	cyclohexanol degradation	50	2 of 4
66794	dTDPLrhamnose biosynthesis	50	4 of 8
66794	ascorbate metabolism	50	11 of 22
66794	mannosylglycerate biosynthesis	50	1 of 2
66794	degradation of pentoses	50	14 of 28
66794	carotenoid biosynthesis	50	11 of 22
66794	metabolism of disaccharids	45.45	5 of 11
66794	oxidative phosphorylation	45.05	41 of 91
66794	4-hydroxymandelate degradation	44.44	4 of 9
66794	vitamin B12 metabolism	44.12	15 of 34
66794	vitamin K metabolism	40	2 of 5
66794	glycine betaine biosynthesis	40	2 of 5
66794	gallate degradation	40	2 of 5
66794	D-cycloserine biosynthesis	40	2 of 5
66794	phenol degradation	40	8 of 20
66794	metabolism of amino sugars and derivatives	40	2 of 5
66794	arachidonate biosynthesis	40	2 of 5
66794	3-chlorocatechol degradation	40	2 of 5
66794	dolichyl-diphosphooligosaccharide biosynthesis	36.36	4 of 11
66794	(5R)-carbapenem carboxylate biosynthesis	33.33	1 of 3
66794	acetyl CoA biosynthesis	33.33	1 of 3
66794	selenocysteine biosynthesis	33.33	2 of 6
66794	pantothenate biosynthesis	33.33	2 of 6
66794	sphingosine metabolism	33.33	2 of 6
66794	enterobactin biosynthesis	33.33	1 of 3
66794	nitrate assimilation	33.33	3 of 9
66794	phenylpropanoid biosynthesis	30.77	4 of 13
66794	phosphatidylethanolamine bioynthesis	30.77	4 of 13
66794	sulfate reduction	30.77	4 of 13
66794	polyamine pathway	30.43	7 of 23
66794	bile acid biosynthesis, neutral pathway	29.41	5 of 17
66794	aclacinomycin biosynthesis	28.57	2 of 7
66794	alginate biosynthesis	25	1 of 4
66794	carnitine metabolism	25	2 of 8
66794	catecholamine biosynthesis	25	1 of 4
66794	lactate fermentation	25	1 of 4
66794	toluene degradation	25	1 of 4
66794	aspartate and asparagine metabolism	22.22	2 of 9
66794	chlorophyll metabolism	22.22	4 of 18

Isolation, sampling and environmental information

Isolation source categories

Cat1	Cat2	Cat3
#Environmental	#Aquatic	-
#Host	#Microbial	#Bacteria

Isolation

@ref	Sample type	Host species	Country	Country ISO 3 Code	Continent
17910	tap water, spontaneous S-layer negative variant of C. vibrioides CB 2 (DSM 4727)	Caulobacter vibrioides	USA	USA	North America

Interaction and safety

Risk assessment

@ref	Biosafety level	Biosafety level comment
17910	1	Risk group (German classification) According to TRBA 466

Sequence information

Genome sequences

@ref	Description	Assembly level	INSDC accession	BV-BRC accession	IMG accession	NCBI tax ID	Score
66792	ASM385643v1 assembly for Caulobacter vibrioides CB2A	complete	GCA_003856435	155892.23	2840726624	155892	95.96

16S sequences

@ref	Description	Accession	Length	Database	NCBI tax ID
17910	Caulobacter crescentus 16S ribosomal RNA gene, complete sequence	M83799	1426		155892

Genome-based predictions

Predictions

Predictions from Deep Learning for Genome Sequence Data. R package version 0.3.1 based on: Caulobacter vibrioides CB2A
IMG: 2840726624

@ref	Trait	Model	Prediction	Confidence in %	In training data
125439	spore_formation	BacteriaNetⓘ	no	98.30	no
125439	motility	BacteriaNetⓘ	yes	72.40	no
125439	gram_stain	BacteriaNetⓘ	negative	98.20	no
125439	oxygen_tolerance	BacteriaNetⓘ	obligate aerobe	99.10	no

Predictions from bacterial phenotypic traits through improved machine learning using high-quality, curated datasets based on: Caulobacter vibrioides CB2A
NCBI: GCA_003856435.1

@ref	Trait	Model	Prediction	Confidence in %	In training data
125438	gram-positive	gram-positiveⓘ	no	95.96	no
125438	anaerobic	anaerobicⓘ	no	95.27	no
125438	aerobic	aerobicⓘ	yes	88.50	no
125438	spore-forming	spore-formingⓘ	no	89.45	no
125438	thermophilic	thermophileⓘ	no	97.96	no
125438	flagellated	motile2+ⓘ	yes	73.23	no

Literature

References

#17910	Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 25117
#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 )
#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 )
#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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