Azonexus hydrophilus (DSM 23864, BCRC 17657, LMG 24005)

Name: Azonexus hydrophilus (DSM 23864, BCRC 17657, LMG 24005)
Creator: BacDive
License: http://creativecommons.org/licenses/by/4.0/

BacDive ID 13889

Type strain

Strain Designation d8-1

Culture col. no. DSM 23864 BCRC 17657 LMG 24005 d8-1

NCBI tax ID(s) 1121032 418702

Special Collections DSMZ Literature strains

History <- LMG <- W.-M. Chen, National Kaohsiung Marine University, Dept. of Seafood Science, Taiwan

Links

Azonexus hydrophilus d8-1 is a facultative aerobe, Gram-negative, motile bacterium that was isolated from freshwater .

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

Name and taxonomic classification

SI-ID 307421

BCRC 17657,CCRC 17657,LMG 24005,DSM 23864

@ref 20215

Last LPSN update 2026-02-09 11:21:16

Domain Bacteria

Phylum Pseudomonadota

Class Betaproteobacteria

Order Rhodocyclales

Family Azonexaceae

Genus Azonexus

Species Azonexus hydrophilus

Full scientific name Azonexus hydrophilus Chou et al. 2008

Morphology

Cell morphology

@ref	Gram stain	Cell length	Cell width	Cell shape	Confidence
32398	negative	1.65 µm	0.4 µm	rod-shaped
125439	negative				98.8
125439					90.6
125438	negative				98

Culture and growth conditions

Culture medium

@ref	Name	Growth	Medium link	Composition
17413	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)
17413	positive	growth	28
32398	positive	growth	35-40
32398	positive	optimum	37.5

Culture pH

@ref	Ability	Type	PH
32398	positive	optimum	7.5

Physiology and metabolism

Oxygen tolerance

32398

Oxygen tolerancefacultative aerobe

Spore formation

@ref	Spore formation	Confidence
32398
125439		99.4
125438		92.668

Halophily

@ref	Salt	Growth	Tested relation	Concentration
32398	NaCl	positive	growth	0-1 %
32398	NaCl	positive	optimum	0.5 %

Metabolite utilization

@ref	Chebi-ID	Metabolite	Utilization activity	Kind of utilization tested
32398	17240 ChEBI	itaconate	+	carbon source
32398	51850 ChEBI	methyl pyruvate	+	carbon source
32398	17632 ChEBI	nitrate	+	reduction

Enzymes

@ref	Value	Activity	Ec
32398	alkaline phosphatase	+	3.1.3.1
32398	catalase	+	1.11.1.6
32398	cytochrome oxidase	+	1.9.3.1
32398	urease	+	3.5.1.5

Pathway annotation

Computationally determined by

@ref	pathway	enzyme coverage	annotated reactions
66794	adipate degradation	100	2 of 2
66794	ubiquinone biosynthesis	100	7 of 7
66794	ppGpp biosynthesis	100	4 of 4
66794	reductive acetyl coenzyme A pathway	100	7 of 7
66794	methylglyoxal degradation	100	5 of 5
66794	hydrogen production	100	5 of 5
66794	cis-vaccenate biosynthesis	100	2 of 2
66794	palmitate biosynthesis	100	22 of 22
66794	butanoate fermentation	100	4 of 4
66794	coenzyme A metabolism	100	4 of 4
66794	isoleucine metabolism	100	8 of 8
66794	photosynthesis	100	14 of 14
66794	anapleurotic synthesis of oxalacetate	100	1 of 1
66794	folate polyglutamylation	100	1 of 1
66794	suberin monomers biosynthesis	100	2 of 2
66794	UDP-GlcNAc biosynthesis	100	3 of 3
66794	CDP-diacylglycerol biosynthesis	100	2 of 2
66794	denitrification	100	2 of 2
66794	biotin biosynthesis	100	4 of 4
66794	tetrahydrofolate metabolism	92.86	13 of 14
66794	propionate fermentation	90	9 of 10
66794	molybdenum cofactor biosynthesis	88.89	8 of 9
66794	valine metabolism	88.89	8 of 9
66794	lipid A biosynthesis	88.89	8 of 9
66794	chorismate metabolism	88.89	8 of 9
66794	C4 and CAM-carbon fixation	87.5	7 of 8
66794	propanol degradation	85.71	6 of 7
66794	glutamate and glutamine metabolism	85.71	24 of 28
66794	NAD metabolism	83.33	15 of 18
66794	vitamin B6 metabolism	81.82	9 of 11
66794	threonine metabolism	80	8 of 10
66794	phenylacetate degradation (aerobic)	80	4 of 5
66794	peptidoglycan biosynthesis	80	12 of 15
66794	heme metabolism	78.57	11 of 14
66794	citric acid cycle	78.57	11 of 14
66794	d-mannose degradation	77.78	7 of 9
66794	aspartate and asparagine metabolism	77.78	7 of 9
66794	serine metabolism	77.78	7 of 9
66794	purine metabolism	77.66	73 of 94
66794	phenylalanine metabolism	76.92	10 of 13
66794	leucine metabolism	76.92	10 of 13
66794	6-hydroxymethyl-dihydropterin diphosphate biosynthesis	75	6 of 8
66794	gluconeogenesis	75	6 of 8
66794	CMP-KDO biosynthesis	75	3 of 4
66794	acetate fermentation	75	3 of 4
66794	cardiolipin biosynthesis	71.43	5 of 7
66794	vitamin B1 metabolism	69.23	9 of 13
66794	sulfate reduction	69.23	9 of 13
66794	lipid metabolism	67.74	21 of 31
66794	octane oxidation	66.67	2 of 3
66794	IAA biosynthesis	66.67	2 of 3
66794	acetyl CoA biosynthesis	66.67	2 of 3
66794	glycolate and glyoxylate degradation	66.67	4 of 6
66794	formaldehyde oxidation	66.67	2 of 3
66794	selenocysteine biosynthesis	66.67	4 of 6
66794	CO2 fixation in Crenarchaeota	66.67	6 of 9
66794	L-lactaldehyde degradation	66.67	2 of 3
66794	acetoin degradation	66.67	2 of 3
66794	alanine metabolism	65.52	19 of 29
66794	glycolysis	64.71	11 of 17
66794	proline metabolism	63.64	7 of 11
66794	dTDPLrhamnose biosynthesis	62.5	5 of 8
66794	pyrimidine metabolism	62.22	28 of 45
66794	urea cycle	61.54	8 of 13
66794	isoprenoid biosynthesis	61.54	16 of 26
66794	flavin biosynthesis	60	9 of 15
66794	cellulose degradation	60	3 of 5
66794	Entner Doudoroff pathway	60	6 of 10
66794	gallate degradation	60	3 of 5
66794	lipoate biosynthesis	60	3 of 5
66794	degradation of aromatic, nitrogen containing compounds	58.33	7 of 12
66794	non-pathway related	57.89	22 of 38
66794	methionine metabolism	57.69	15 of 26
66794	nitrate assimilation	55.56	5 of 9
66794	cysteine metabolism	55.56	10 of 18
66794	tryptophan metabolism	55.26	21 of 38
66794	oxidative phosphorylation	54.95	50 of 91
66794	pentose phosphate pathway	54.55	6 of 11
66794	lysine metabolism	52.38	22 of 42
66794	histidine metabolism	51.72	15 of 29
66794	arginine metabolism	50	12 of 24
66794	ethanol fermentation	50	1 of 2
66794	aminopropanol phosphate biosynthesis	50	1 of 2
66794	sulfopterin metabolism	50	2 of 4
66794	tyrosine metabolism	50	7 of 14
66794	glycine metabolism	50	5 of 10
66794	coenzyme M biosynthesis	50	5 of 10
66794	3-phenylpropionate degradation	46.67	7 of 15
66794	phosphatidylethanolamine bioynthesis	46.15	6 of 13
66794	metabolism of disaccharids	45.45	5 of 11
66794	allantoin degradation	44.44	4 of 9
66794	polyamine pathway	43.48	10 of 23
66794	glutathione metabolism	42.86	6 of 14
66794	arachidonate biosynthesis	40	2 of 5
66794	ethylmalonyl-CoA pathway	40	2 of 5
66794	factor 420 biosynthesis	40	2 of 5
66794	3-chlorocatechol degradation	40	2 of 5
66794	degradation of hexoses	38.89	7 of 18
66794	vitamin B12 metabolism	38.24	13 of 34
66794	ketogluconate metabolism	37.5	3 of 8
66794	carnitine metabolism	37.5	3 of 8
66794	cholesterol biosynthesis	36.36	4 of 11
66794	degradation of pentoses	35.71	10 of 28
66794	phenol degradation	35	7 of 20
66794	cyanate degradation	33.33	1 of 3
66794	enterobactin biosynthesis	33.33	1 of 3
66794	pantothenate biosynthesis	33.33	2 of 6
66794	methanogenesis from CO2	33.33	4 of 12
66794	sphingosine metabolism	33.33	2 of 6
66794	androgen and estrogen metabolism	31.25	5 of 16
66794	bile acid biosynthesis, neutral pathway	29.41	5 of 17
66794	ascorbate metabolism	27.27	6 of 22
66794	dolichyl-diphosphooligosaccharide biosynthesis	27.27	3 of 11
66794	d-xylose degradation	27.27	3 of 11
66794	carotenoid biosynthesis	27.27	6 of 22
66794	alginate biosynthesis	25	1 of 4
66794	toluene degradation	25	1 of 4
66794	cyclohexanol degradation	25	1 of 4
66794	lactate fermentation	25	1 of 4
66794	glycogen biosynthesis	25	1 of 4
66794	degradation of sugar alcohols	25	4 of 16
66794	phenylpropanoid biosynthesis	23.08	3 of 13
66794	arachidonic acid metabolism	22.22	4 of 18

Isolation, sampling and environmental information

Isolation source categories

Cat1	Cat2	Cat3
#Environmental	#Aquatic	#Freshwater
#Environmental	#Aquatic	#Spring

Isolation

@ref	Sample type	Geographic location	Country	Country ISO 3 Code	Continent
17413	freshwater (spring)	Hsinchu County, Nature Valley	Taiwan, Province of China	TWN	Asia

Taxonmaps

69479

Global distribution of 16S sequence EF158390 (>99% sequence identity) for Azonexus hydrophilus subclade from Microbeatlas

Aquatic Samples	3015
Soil Samples	603
Animal Samples	498
Plant Samples	207
Total Samples	4323

Interaction and safety

Risk assessment

@ref	Biosafety level	Biosafety level comment
17413	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	ASM42960v1 assembly for Azonexus hydrophilus DSM 23864	scaffold	GCA_000429605	1121032.3	2524023152	1121032	75.45

16S sequences

@ref	Description	Accession	Length	Database	NCBI tax ID
17413	Azonexus hydrophilus strain d8-1 16S ribosomal RNA gene, partial sequence	EF158390	1454		1121032

GC content

17413

GC-content (mol%)64-66

Genome-based predictions

Predictions

Predictions from Deep Learning for Genome Sequence Data. R package version 0.3.1 based on: Azonexus hydrophilus DSM 23864
NCBI: GCA_000429605

@ref	Trait	Model	Prediction	Confidence in %	In training data
125439	spore_formation	BacteriaNetⓘ	no	99.40	no
125439	motility	BacteriaNetⓘ	yes	90.60	no
125439	gram_stain	BacteriaNetⓘ	negative	98.80	no
125439	oxygen_tolerance	BacteriaNetⓘ	anaerobe	73.20	no

Predictions from bacterial phenotypic traits through improved machine learning using high-quality, curated datasets based on: Azonexus hydrophilus DSM 23864 DSM 23864
NCBI: GCA_000429605.1

@ref	Trait	Model	Prediction	Confidence in %	In training data
125438	gram-positive	gram-positiveⓘ	no	98.00	no
125438	anaerobic	anaerobicⓘ	no	86.18	yes
125438	aerobic	aerobicⓘ	yes	57.87	no
125438	spore-forming	spore-formingⓘ	no	92.67	yes
125438	thermophilic	thermophileⓘ	no	93.95	yes
125438	flagellated	motile2+ⓘ	yes	83.71	no

Literature

Topic	Title	Authors	Journal	DOI	Year
	Genomic Insights Into A Novel, Alkalitolerant Nitrogen Fixing Bacteria, Azonexus sp. Strain ZS02.	Salah ZB, Charles CJ, Humphreys PN, Laws AP, Rout SP	J Genomics	10.7150/jgen.28153	2019
Phylogeny	Azonexus hydrophilus sp. nov., a nifH gene-harbouring bacterium isolated from freshwater.	Chou JH, Jiang SR, Cho JC, Song J, Lin MC, Chen WM	Int J Syst Evol Microbiol	10.1099/ijs.0.65434-0	2008

References

#17413	Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 23864
#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 )
#28622	IJSEM 946 2008 ( DOI 10.1099/ijs.0.65434-0 , PubMed 18398200 )
#32398	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 #28622
#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

Azonexus hydrophilus (DSM 23864, BCRC 17657, LMG 24005)

Name and taxonomic classification

Morphology

Cell morphology

Culture and growth conditions

Culture medium

Culture temp

Culture pH

Physiology and metabolism

Oxygen tolerance

Spore formation

Halophily

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_000429605

16S sequences

GC content

Genome-based predictions

Predictions

Literature

Literature

References

BacDive

Help

Social Media