Hyphomicrobium sulfonivorans (DSM 13863, ATCC BAA-113, S1)

Name: Hyphomicrobium sulfonivorans (DSM 13863, ATCC BAA-113, S1)
Creator: BacDive
License: http://creativecommons.org/licenses/by/4.0/

BacDive ID 6185

Type strain

Strain Designation S1

Culture col. no. DSM 13863 ATCC BAA-113 S1

NCBI tax ID(s) 121290

Special Collections DSMZ

Links

Hyphomicrobium sulfonivorans S1 is a mesophilic prokaryote that was isolated from garden soil.

mesophilic genome sequence 16S sequence

Name and taxonomic classification

SI-ID 87706

ATCC BAA-113,DSM 13863

@ref 20215

Last LPSN update 2025-12-16 09:48:15

Domain Pseudomonadati

Phylum Pseudomonadota

Class Alphaproteobacteria

Order Hyphomicrobiales

Family Hyphomicrobiaceae

Genus Hyphomicrobium

Species Hyphomicrobium sulfonivorans

Full scientific name Hyphomicrobium sulfonivorans Borodina et al. 2002

Morphology

Cell morphology

@ref	Gram stain	Confidence
125439	negative	99.8

Culture and growth conditions

Culture medium

@ref	Name	Growth	Medium link	Composition
5178	CORYNEBACTERIUM AGAR (DSMZ Medium 53)		Medium recipe at MediaDive	Name: CORYNEBACTERIUM AGAR (DSMZ Medium 53) Composition: Agar 15.0 g/l Casein peptone 10.0 g/l NaCl 5.0 g/l Glucose 5.0 g/l Yeast extract 5.0 g/l Distilled water
5178	METHYLOTROPHIC ARTHROBACTER AND HYPHOMICROBIUM MEDIUM (DSMZ Medium 939)		Medium recipe at MediaDive	Name: METHYLOTROPHIC ARTHROBACTER AND HYPHOMICROBIUM MEDIUM (DSMZ Medium 939) Composition: Methanol 7.92 g/l Na2HPO4 x 2 H2O 7.9 g/l KH2PO4 1.5 g/l NH4Cl 0.8 g/l EDTA 0.5 g/l MgSO4 x 7 H2O 0.1 g/l CaCl2 x 2 H2O 0.0734 g/l FeSO4 x 7 H2O 0.05 g/l MnCl2 x 4 H2O 0.025 g/l ZnSO4 x 7 H2O 0.01 g/l CoCl2 x 6 H2O 0.005 g/l (NH4)6Mo7O24 0.005 g/l CuSO4 x 5 H2O 0.002 g/l Distilled water

Culture temp

@ref	Growth	Type	Temperature (°C)	Range
5178	positive	growth	30	mesophilic

Physiology and metabolism

Oxygen tolerance

@ref	Oxygen tolerance	Confidence
125439	obligate aerobe	99.8

Spore formation

@ref	Spore formation	Confidence
125439		98.9

Pathway annotation

Computationally determined by

@ref	pathway	enzyme coverage	annotated reactions
66794	adipate degradation	100	2 of 2
66794	palmitate biosynthesis	100	22 of 22
66794	cis-vaccenate biosynthesis	100	2 of 2
66794	ppGpp biosynthesis	100	4 of 4
66794	CMP-KDO biosynthesis	100	4 of 4
66794	methylglyoxal degradation	100	5 of 5
66794	cardiolipin biosynthesis	100	7 of 7
66794	valine metabolism	100	9 of 9
66794	formaldehyde oxidation	100	3 of 3
66794	coenzyme A metabolism	100	4 of 4
66794	biotin biosynthesis	100	4 of 4
66794	sulfopterin metabolism	100	4 of 4
66794	CDP-diacylglycerol biosynthesis	100	2 of 2
66794	folate polyglutamylation	100	1 of 1
66794	UDP-GlcNAc biosynthesis	100	3 of 3
66794	suberin monomers biosynthesis	100	2 of 2
66794	anapleurotic synthesis of oxalacetate	100	1 of 1
66794	photosynthesis	92.86	13 of 14
66794	threonine metabolism	90	9 of 10
66794	propionate fermentation	90	9 of 10
66794	glutamate and glutamine metabolism	89.29	25 of 28
66794	aspartate and asparagine metabolism	88.89	8 of 9
66794	lipid A biosynthesis	88.89	8 of 9
66794	chorismate metabolism	88.89	8 of 9
66794	molybdenum cofactor biosynthesis	88.89	8 of 9
66794	serine metabolism	88.89	8 of 9
66794	vitamin B12 metabolism	88.24	30 of 34
66794	C4 and CAM-carbon fixation	87.5	7 of 8
66794	reductive acetyl coenzyme A pathway	85.71	6 of 7
66794	citric acid cycle	85.71	12 of 14
66794	tetrahydrofolate metabolism	85.71	12 of 14
66794	proline metabolism	81.82	9 of 11
66794	methanofuran biosynthesis	80	4 of 5
66794	glycogen metabolism	80	4 of 5
66794	ethylmalonyl-CoA pathway	80	4 of 5
66794	peptidoglycan biosynthesis	80	12 of 15
66794	d-mannose degradation	77.78	7 of 9
66794	CO2 fixation in Crenarchaeota	77.78	7 of 9
66794	NAD metabolism	77.78	14 of 18
66794	phenylalanine metabolism	76.92	10 of 13
66794	lactate fermentation	75	3 of 4
66794	butanoate fermentation	75	3 of 4
66794	isoleucine metabolism	75	6 of 8
66794	6-hydroxymethyl-dihydropterin diphosphate biosynthesis	75	6 of 8
66794	gluconeogenesis	75	6 of 8
66794	vitamin B6 metabolism	72.73	8 of 11
66794	heme metabolism	71.43	10 of 14
66794	glutathione metabolism	71.43	10 of 14
66794	propanol degradation	71.43	5 of 7
66794	ubiquinone biosynthesis	71.43	5 of 7
66794	leucine metabolism	69.23	9 of 13
66794	vitamin B1 metabolism	69.23	9 of 13
66794	alanine metabolism	68.97	20 of 29
66794	lipid metabolism	67.74	21 of 31
66794	purine metabolism	67.02	63 of 94
66794	cyanate degradation	66.67	2 of 3
66794	methane metabolism	66.67	2 of 3
66794	acetyl CoA biosynthesis	66.67	2 of 3
66794	L-lactaldehyde degradation	66.67	2 of 3
66794	acetoin degradation	66.67	2 of 3
66794	flavin biosynthesis	66.67	10 of 15
66794	glycolysis	64.71	11 of 17
66794	pentose phosphate pathway	63.64	7 of 11
66794	methionine metabolism	61.54	16 of 26
66794	cysteine metabolism	61.11	11 of 18
66794	non-pathway related	60.53	23 of 38
66794	lipoate biosynthesis	60	3 of 5
66794	metabolism of amino sugars and derivatives	60	3 of 5
66794	Entner Doudoroff pathway	60	6 of 10
66794	cellulose degradation	60	3 of 5
66794	phenylacetate degradation (aerobic)	60	3 of 5
66794	lysine metabolism	59.52	25 of 42
66794	histidine metabolism	58.62	17 of 29
66794	methanogenesis from CO2	58.33	7 of 12
66794	arginine metabolism	58.33	14 of 24
66794	pyrimidine metabolism	57.78	26 of 45
66794	tryptophan metabolism	55.26	21 of 38
66794	sulfate reduction	53.85	7 of 13
66794	isoprenoid biosynthesis	53.85	14 of 26
66794	polyamine pathway	52.17	12 of 23
66794	glycogen biosynthesis	50	2 of 4
66794	sphingosine metabolism	50	3 of 6
66794	glycine metabolism	50	5 of 10
66794	ribulose monophosphate pathway	50	1 of 2
66794	ethanol fermentation	50	1 of 2
66794	aminopropanol phosphate biosynthesis	50	1 of 2
66794	phenylmercury acetate degradation	50	1 of 2
66794	glycolate and glyoxylate degradation	50	3 of 6
66794	acetate fermentation	50	2 of 4
66794	ketogluconate metabolism	50	4 of 8
66794	tyrosine metabolism	50	7 of 14
66794	3-phenylpropionate degradation	46.67	7 of 15
66794	phosphatidylethanolamine bioynthesis	46.15	6 of 13
66794	urea cycle	46.15	6 of 13
66794	metabolism of disaccharids	45.45	5 of 11
66794	nitrate assimilation	44.44	4 of 9
66794	oxidative phosphorylation	41.76	38 of 91
66794	ascorbate metabolism	40.91	9 of 22
66794	factor 420 biosynthesis	40	2 of 5
66794	hydrogen production	40	2 of 5
66794	arachidonate biosynthesis	40	2 of 5
66794	4-hydroxyphenylacetate degradation	40	4 of 10
66794	gallate degradation	40	2 of 5
66794	degradation of hexoses	38.89	7 of 18
66794	arachidonic acid metabolism	38.89	7 of 18
66794	dTDPLrhamnose biosynthesis	37.5	3 of 8
66794	enterobactin biosynthesis	33.33	1 of 3
66794	selenocysteine biosynthesis	33.33	2 of 6
66794	IAA biosynthesis	33.33	1 of 3
66794	(5R)-carbapenem carboxylate biosynthesis	33.33	1 of 3
66794	octane oxidation	33.33	1 of 3
66794	pantothenate biosynthesis	33.33	2 of 6
66794	degradation of aromatic, nitrogen containing compounds	33.33	4 of 12
66794	degradation of pentoses	32.14	9 of 28
66794	androgen and estrogen metabolism	31.25	5 of 16
66794	phenylpropanoid biosynthesis	30.77	4 of 13
66794	coenzyme M biosynthesis	30	3 of 10
66794	phenol degradation	30	6 of 20
66794	benzoyl-CoA degradation	28.57	2 of 7
66794	toluene degradation	25	1 of 4
66794	cyclohexanol degradation	25	1 of 4
66794	degradation of sugar alcohols	25	4 of 16
66794	carnitine metabolism	25	2 of 8
66794	bile acid biosynthesis, neutral pathway	23.53	4 of 17

Isolation, sampling and environmental information

Isolation source categories

Cat1	Cat2	Cat3
#Environmental	#Terrestrial	#Soil
#Engineered	#Agriculture	#Garden

Isolation

@ref	Sample type	Geographic location	Continent
5178	garden soil	Warwickshire	Europe

Taxonmaps

69479

Global distribution of 16S sequence AF235089 (>99% sequence identity) for Hyphomicrobium sulfonivorans subclade from Microbeatlas

Aquatic Samples	1191
Soil Samples	407
Animal Samples	98
Plant Samples	54
Total Samples	1750

Interaction and safety

Risk assessment

@ref	Biosafety level	Biosafety level comment
5178	1	Risk group (German classification) According to TRBA 466

Sequence information

Genome sequences

@ref	Description	Assembly level	INSDC accession	BV-BRC accession	NCBI tax ID	Score	IMG accession
66792	Hyphomicrobium sulfonivorans S1	complete			121290	84.12	2503692000
66792	ASM1330656v1 assembly for Hyphomicrobium sulfonivorans S1	contig	GCA_013306565	121290.7	121290	70.97

16S sequences

@ref	Description	Accession	Length	Database	NCBI tax ID
5178	Hyphomicrobium sulfonivorans 16S ribosomal RNA gene, partial sequence	AF235089	1411		121290

Genome-based predictions

Predictions

Predictions from Deep Learning for Genome Sequence Data. R package version 0.3.1 based on: Hyphomicrobium sulfonivorans S1
NCBI: GCA_013306565

@ref	Trait	Model	Prediction	Confidence in %	In training data
125439	spore_formation	BacteriaNetⓘ	no	98.90	no
125439	motility	BacteriaNetⓘ	yes	82.80	no
125439	gram_stain	BacteriaNetⓘ	negative	99.80	no
125439	oxygen_tolerance	BacteriaNetⓘ	obligate aerobe	99.80	no

Literature

Topic	Title	Authors	Journal	DOI	Year
Metabolism	Purification and characterization of dimethylsulfide monooxygenase from Hyphomicrobium sulfonivorans.	Boden R, Borodina E, Wood AP, Kelly DP, Murrell JC, Schafer H.	J Bacteriol	10.1128/jb.00977-10	2011

References

#5178	Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 13863
#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 )
#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 .
#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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Hyphomicrobium sulfonivorans (DSM 13863, ATCC BAA-113, S1)

Name and taxonomic classification

Morphology

Cell morphology

Culture and growth conditions

Culture medium

Culture temp

Physiology and metabolism

Oxygen tolerance

Spore formation

Pathway annotation

Isolation, sampling and environmental information

Isolation source categories

Isolation

Taxonmaps

Interaction and safety

Risk assessment

Sequence information

Genome sequences

Genome browser: GCA_013306565

16S sequences

Genome-based predictions

Predictions

Literature

Literature

References

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