Siphonobacter aquaeclarae (DSM 21668, NCAIM B 02328, P2)

Name: Siphonobacter aquaeclarae (DSM 21668, NCAIM B 02328, P2)
Creator: BacDive
License: http://creativecommons.org/licenses/by/4.0/

BacDive ID 5747

Type strain

Strain Designation P2

Culture col. no. DSM 21668 NCAIM B 02328 P2

NCBI tax ID(s) 563176

Special Collections DSMZ Literature strains

Links

Siphonobacter aquaeclarae P2 is a facultative anaerobe, mesophilic, Gram-negative prokaryote that was isolated from inner surface of an ultra pure cooling water system in a power plant.

Gram-negative rod-shaped facultative anaerobe mesophilic genome sequence 16S sequence

Name and taxonomic classification

SI-ID 371121

NCAIM B 02328,DSM 21668

@ref 20215

Last LPSN update 2025-12-16 09:48:08

Domain Pseudomonadati

Phylum Bacteroidota

Class Cytophagia

Order Cytophagales

Family Spirosomataceae

Genus Siphonobacter

Species Siphonobacter aquaeclarae

Full scientific name Siphonobacter aquaeclarae Táncsics et al. 2010

Morphology

Cell morphology

@ref	Gram stain	Cell length	Cell width	Cell shape	Confidence
29717	negative	1.3-2.7 µm	0.3-0.4 µm	rod-shaped
125439	negative				99.5
125438	negative				97.294

Pigmentation

29717

Productionyes

Culture and growth conditions

Culture medium

@ref	Name	Growth	Medium link	Composition
15875	R2A MEDIUM (DSMZ Medium 830)		Medium recipe at MediaDive	Name: R2A MEDIUM (DSMZ Medium 830) Composition: Agar 15.0 g/l Casamino acids 0.5 g/l Starch 0.5 g/l Glucose 0.5 g/l Proteose peptone 0.5 g/l Yeast extract 0.5 g/l K2HPO4 0.3 g/l Na-pyruvate 0.3 g/l MgSO4 x 7 H2O 0.05 g/l Distilled water

Culture temp

@ref	Growth	Type	Temperature (°C)	Range
15875	positive	growth	28	mesophilic
29717	positive	growth	04-37
29717	positive	optimum	30-37	mesophilic

Culture pH

@ref	Ability	Type	PH	PH range
29717	positive	optimum	7
29717	positive	growth	05-09	alkaliphile

Physiology and metabolism

Oxygen tolerance

@ref	Oxygen tolerance	Confidence
29717	facultative anaerobe
125438	aerobe	90.479
125439	obligate aerobe	94

Spore formation

@ref	Spore formation	Confidence
125439		98.6
125438		90.75

Observation

29717

Observationaggregates in chains

Metabolite utilization

@ref	Chebi-ID	Metabolite	Utilization activity	Kind of utilization tested
29717	17057 ChEBI	cellobiose	+	carbon source
29717	28757 ChEBI	fructose	+	carbon source
29717	33984 ChEBI	fucose	+	carbon source
29717	28260 ChEBI	galactose	+	carbon source
29717	17234 ChEBI	glucose	+	carbon source
29717	17716 ChEBI	lactose	+	carbon source
29717	17306 ChEBI	maltose	+	carbon source
29717	37684 ChEBI	mannose	+	carbon source
29717	28053 ChEBI	melibiose	+	carbon source
29717	506227 ChEBI	N-acetylglucosamine	+	carbon source
29717	16634 ChEBI	raffinose	+	carbon source
29717	26546 ChEBI	rhamnose	+	carbon source
29717	17992 ChEBI	sucrose	+	carbon source
29717	27082 ChEBI	trehalose	+	carbon source

Enzymes

@ref	Value	Activity	Ec
29717	acid phosphatase	+	3.1.3.2
29717	alkaline phosphatase	+	3.1.3.1
29717	catalase	+	1.11.1.6

Pathway annotation

Computationally determined by

@ref	pathway	enzyme coverage	annotated reactions
66794	suberin monomers biosynthesis	100	2 of 2
66794	vitamin K metabolism	100	5 of 5
66794	L-lactaldehyde degradation	100	3 of 3
66794	gluconeogenesis	100	8 of 8
66794	quinate degradation	100	2 of 2
66794	palmitate biosynthesis	100	22 of 22
66794	kanosamine biosynthesis II	100	2 of 2
66794	cis-vaccenate biosynthesis	100	2 of 2
66794	molybdenum cofactor biosynthesis	100	9 of 9
66794	adipate degradation	100	2 of 2
66794	coenzyme A metabolism	100	4 of 4
66794	sulfopterin metabolism	100	4 of 4
66794	CDP-diacylglycerol biosynthesis	100	2 of 2
66794	methylglyoxal degradation	100	5 of 5
66794	anapleurotic synthesis of oxalacetate	100	1 of 1
66794	folate polyglutamylation	100	1 of 1
66794	CMP-KDO biosynthesis	100	4 of 4
66794	ceramide biosynthesis	100	1 of 1
66794	UDP-GlcNAc biosynthesis	100	3 of 3
66794	ppGpp biosynthesis	100	4 of 4
66794	tetrahydrofolate metabolism	92.86	13 of 14
66794	pentose phosphate pathway	90.91	10 of 11
66794	starch degradation	90	9 of 10
66794	Entner Doudoroff pathway	90	9 of 10
66794	chorismate metabolism	88.89	8 of 9
66794	serine metabolism	88.89	8 of 9
66794	C4 and CAM-carbon fixation	87.5	7 of 8
66794	alanine metabolism	86.21	25 of 29
66794	propanol degradation	85.71	6 of 7
66794	heme metabolism	85.71	12 of 14
66794	reductive acetyl coenzyme A pathway	85.71	6 of 7
66794	vitamin B1 metabolism	84.62	11 of 13
66794	phenylalanine metabolism	84.62	11 of 13
66794	NAD metabolism	83.33	15 of 18
66794	peptidoglycan biosynthesis	80	12 of 15
66794	threonine metabolism	80	8 of 10
66794	cellulose degradation	80	4 of 5
66794	glycogen metabolism	80	4 of 5
66794	gallate degradation	80	4 of 5
66794	photosynthesis	78.57	11 of 14
66794	glutathione metabolism	78.57	11 of 14
66794	valine metabolism	77.78	7 of 9
66794	d-mannose degradation	77.78	7 of 9
66794	CO2 fixation in Crenarchaeota	77.78	7 of 9
66794	lipid A biosynthesis	77.78	7 of 9
66794	lipid metabolism	77.42	24 of 31
66794	purine metabolism	76.6	72 of 94
66794	glycolysis	76.47	13 of 17
66794	pyrimidine metabolism	75.56	34 of 45
66794	isoleucine metabolism	75	6 of 8
66794	biotin biosynthesis	75	3 of 4
66794	acetate fermentation	75	3 of 4
66794	6-hydroxymethyl-dihydropterin diphosphate biosynthesis	75	6 of 8
66794	glycogen biosynthesis	75	3 of 4
66794	dTDPLrhamnose biosynthesis	75	6 of 8
66794	flavin biosynthesis	73.33	11 of 15
66794	proline metabolism	72.73	8 of 11
66794	metabolism of disaccharids	72.73	8 of 11
66794	degradation of sugar acids	72	18 of 25
66794	cardiolipin biosynthesis	71.43	5 of 7
66794	citric acid cycle	71.43	10 of 14
66794	glutamate and glutamine metabolism	71.43	20 of 28
66794	4-hydroxyphenylacetate degradation	70	7 of 10
66794	propionate fermentation	70	7 of 10
66794	leucine metabolism	69.23	9 of 13
66794	isoprenoid biosynthesis	69.23	18 of 26
66794	carotenoid biosynthesis	68.18	15 of 22
66794	degradation of pentoses	67.86	19 of 28
66794	octane oxidation	66.67	2 of 3
66794	enterobactin biosynthesis	66.67	2 of 3
66794	cyanate degradation	66.67	2 of 3
66794	formaldehyde oxidation	66.67	2 of 3
66794	acetoin degradation	66.67	2 of 3
66794	lysine metabolism	66.67	28 of 42
66794	methionine metabolism	65.38	17 of 26
66794	tyrosine metabolism	64.29	9 of 14
66794	d-xylose degradation	63.64	7 of 11
66794	vitamin B6 metabolism	63.64	7 of 11
66794	degradation of sugar alcohols	62.5	10 of 16
66794	ketogluconate metabolism	62.5	5 of 8
66794	cysteine metabolism	61.11	11 of 18
66794	tryptophan metabolism	60.53	23 of 38
66794	metabolism of amino sugars and derivatives	60	3 of 5
66794	myo-inositol biosynthesis	60	6 of 10
66794	degradation of aromatic, nitrogen containing compounds	58.33	7 of 12
66794	aclacinomycin biosynthesis	57.14	4 of 7
66794	ubiquinone biosynthesis	57.14	4 of 7
66794	aspartate and asparagine metabolism	55.56	5 of 9
66794	degradation of hexoses	55.56	10 of 18
66794	non-pathway related	55.26	21 of 38
66794	histidine metabolism	55.17	16 of 29
66794	glycolate and glyoxylate degradation	50	3 of 6
66794	coenzyme M biosynthesis	50	5 of 10
66794	ribulose monophosphate pathway	50	1 of 2
66794	sphingosine metabolism	50	3 of 6
66794	arginine metabolism	50	12 of 24
66794	cyclohexanol degradation	50	2 of 4
66794	aminopropanol phosphate biosynthesis	50	1 of 2
66794	butanoate fermentation	50	2 of 4
66794	ethanol fermentation	50	1 of 2
66794	3-phenylpropionate degradation	46.67	7 of 15
66794	sulfate reduction	46.15	6 of 13
66794	phosphatidylethanolamine bioynthesis	46.15	6 of 13
66794	urea cycle	46.15	6 of 13
66794	phenol degradation	45	9 of 20
66794	arachidonic acid metabolism	44.44	8 of 18
66794	oxidative phosphorylation	43.96	40 of 91
66794	androgen and estrogen metabolism	43.75	7 of 16
66794	polyamine pathway	43.48	10 of 23
66794	vitamin B12 metabolism	41.18	14 of 34
66794	arachidonate biosynthesis	40	2 of 5
66794	glycine betaine biosynthesis	40	2 of 5
66794	3-chlorocatechol degradation	40	2 of 5
66794	glycine metabolism	40	4 of 10
66794	O-antigen biosynthesis	40	2 of 5
66794	phenylacetate degradation (aerobic)	40	2 of 5
66794	lipoate biosynthesis	40	2 of 5
66794	carnitine metabolism	37.5	3 of 8
66794	ascorbate metabolism	36.36	8 of 22
66794	selenocysteine biosynthesis	33.33	2 of 6
66794	IAA biosynthesis	33.33	1 of 3
66794	sulfoquinovose degradation	33.33	1 of 3
66794	acetyl CoA biosynthesis	33.33	1 of 3
66794	nitrate assimilation	33.33	3 of 9
66794	4-hydroxymandelate degradation	33.33	3 of 9
66794	(5R)-carbapenem carboxylate biosynthesis	33.33	1 of 3
66794	pantothenate biosynthesis	33.33	2 of 6
66794	phenylpropanoid biosynthesis	30.77	4 of 13
66794	dolichyl-diphosphooligosaccharide biosynthesis	27.27	3 of 11
66794	cholesterol biosynthesis	27.27	3 of 11
66794	lactate fermentation	25	1 of 4
66794	alginate biosynthesis	25	1 of 4
66794	toluene degradation	25	1 of 4
66794	allantoin degradation	22.22	2 of 9

Isolation, sampling and environmental information

Isolation source categories

Cat1	Cat2	Cat3
#Engineered	#Industrial	#Plant (Factory)

Isolation

@ref	Sample type	Geographic location	Country	Country ISO 3 Code	Continent
15875	inner surface of an ultra pure cooling water system in a power plant	Budapest	Hungary	HUN	Europe

Taxonmaps

69479

Global distribution of 16S sequence FJ177421 (>99% sequence identity) for Siphonobacter aquaeclarae subclade from Microbeatlas

Aquatic Samples	821
Soil Samples	464
Animal Samples	812
Plant Samples	313
Total Samples	2410

Interaction and safety

Risk assessment

@ref	Biosafety level	Biosafety level comment
15875	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	IMG-taxon 2622736636 annotated assembly for Siphonobacter aquaeclarae DSM 21668	scaffold	GCA_900103285	563176.3	2622736636	563176	73.92

16S sequences

@ref	Description	Accession	Length	Database	NCBI tax ID
15875	Siphonobacter aquaeclarae strain P2 16S ribosomal RNA gene, partial sequence	FJ177421	1351		563176

GC content

@ref	GC-content (mol%)	Method
15875	54.5	high performance liquid chromatography (HPLC)
29717	54.5

Genome-based predictions

Predictions

Predictions from Deep Learning for Genome Sequence Data. R package version 0.3.1 based on: Siphonobacter aquaeclarae DSM 21668
NCBI: GCA_900103285

@ref	Trait	Model	Prediction	Confidence in %	In training data
125439	spore_formation	BacteriaNetⓘ	no	98.60	no
125439	motility	BacteriaNetⓘ	no	66.00	no
125439	gram_stain	BacteriaNetⓘ	negative	99.50	no
125439	oxygen_tolerance	BacteriaNetⓘ	obligate aerobe	94.00	no

Predictions from bacterial phenotypic traits through improved machine learning using high-quality, curated datasets based on: Siphonobacter aquaeclarae DSM 21668
NCBI: GCA_900103285.1

@ref	Trait	Model	Prediction	Confidence in %	In training data
125438	gram-positive	gram-positiveⓘ	no	97.29	yes
125438	anaerobic	anaerobicⓘ	no	97.75	yes
125438	aerobic	aerobicⓘ	yes	90.48	no
125438	spore-forming	spore-formingⓘ	no	90.75	no
125438	thermophilic	thermophileⓘ	no	97.45	yes
125438	flagellated	motile2+ⓘ	no	89.00	no

Literature

Topic	Title	Authors	Journal	DOI	Year
Genetics	Draft genome sequence of Dyadobacter tibetensis type strain (Y620-1) isolated from glacial ice.	Liu Y, Hu A, Shen L, Yao T, Jiao N, Wang N, Xu B.	Stand Genomic Sci	10.4056/sigs.5649756	2014
Phylogeny	Siphonobacter curvatus sp. nov., isolated from a freshwater river.	Lee Y, Jeon CO	Int J Syst Evol Microbiol	10.1099/ijsem.0.002769	2018
Phylogeny	Siphonobacter aquaeclarae gen. nov., sp. nov., a novel member of the family 'Flexibacteraceae', phylum Bacteroidetes.	Tancsics A, Keki Z, Marialigeti K, Schumann P, Toth EM	Int J Syst Evol Microbiol	10.1099/ijs.0.019398-0	2009

References

#15875	Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 21668
#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 )
#26100	IJSEM 2567 2010 ( DOI 10.1099/ijs.0.019398-0 , PubMed 20008110 )
#29717	Barberan A, Caceres Velazquez H, Jones S, Fierer N.: Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information. mSphere 2: 2017 ( DOI 10.1128/mSphere.00237-17 , PubMed 28776041 ) - originally annotated from #26100
#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 )
#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 .
#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 )

Rate our new design

Content

About us

Siphonobacter aquaeclarae (DSM 21668, NCAIM B 02328, P2)

Name and taxonomic classification

Morphology

Cell morphology

Pigmentation

Culture and growth conditions

Culture medium

Culture temp

Culture pH

Physiology and metabolism

Oxygen tolerance

Spore formation

Observation

Metabolite utilization

Enzymes

Pathway annotation

Isolation, sampling and environmental information

Isolation source categories

Isolation

Taxonmaps

Interaction and safety

Risk assessment

Sequence information

Genome sequences

Genome browser: GCA_900103285

16S sequences

GC content

Genome-based predictions

Predictions

Literature

Literature

References

BacDive

Help

Social Media