Varunaivibrio sulfuroxidans (DSM 101688, JCM 31027, TC 8)

Name: Varunaivibrio sulfuroxidans (DSM 101688, JCM 31027, TC 8)
Creator: BacDive
License: http://creativecommons.org/licenses/by/4.0/

BacDive ID 132624

Type strain

Culture col. no. DSM 101688 JCM 31027 TC 8

NCBI tax ID(s) 1773489

Special Collections DSMZ JCM Literature strains

History DSMZ <- C. Vetriani, Rutgers, State Univ. New Jersey, New Brunswick, USA; TC8 <- S. Patwardhan {2014} JCM <-- C. Vetriani; Rutgers Univ., USA; TC8.

Links

Varunaivibrio sulfuroxidans DSM 101688 is a facultative anaerobe, chemoautotroph, Gram-negative bacterium that was isolated from sediment from a submarine coastal gas vent.

Gram-negative motile vibrio-shaped facultative anaerobe chemoautotroph genome sequence 16S sequence Bacteria

Name and taxonomic classification

SI-ID 405343

JCM 31027,DSM 101688

@ref 20215

Last LPSN update 2026-05-29 08:37:54

Domain Bacteria

Phylum Pseudomonadota

Class Alphaproteobacteria

Order Rhodospirillales

Family Thalassospiraceae

Genus Varunaivibrio

Species Varunaivibrio sulfuroxidans

Full scientific name Varunaivibrio sulfuroxidans Patwardhan and Vetriani 2016

Morphology

Cell morphology

@ref	Gram stain	Cell length	Cell width	Cell shape	Confidence
43161	negative	1-1.5 µm	0.6 µm	vibrio-shaped
125438	negative				96.5
125439	negative				96.555

Culture and growth conditions

Culture medium

@ref	Name	Growth	Medium link	Composition
24413	SULFURIMONAS MJ MEDIUM (DSMZ Medium 1011)		Medium recipe at MediaDive	Name: SULFURIMONAS MJ MEDIUM (DSMZ Medium 1011; with strain-specific modifications) Composition: MgCl2 x 6 H2O 4.13452 g/l KNO3 1.97824 g/l NaHCO3 1.48368 g/l Na2S2O3 x 5 H2O 1.48368 g/l KCl 0.326409 g/l NH4Cl 0.24728 g/l K2HPO4 0.138477 g/l MgSO4 x 7 H2O 0.0296736 g/l Nitrilotriacetic acid 0.0148368 g/l Fe(NH4)2(SO4)2 x 6 H2O 0.0098912 g/l NaCl 0.0098912 g/l MnSO4 x H2O 0.0049456 g/l CoSO4 x 7 H2O 0.00178042 g/l ZnSO4 x 7 H2O 0.00178042 g/l CaCl2 x 2 H2O 0.00098912 g/l FeSO4 x 7 H2O 0.00098912 g/l NiCl2 x 6 H2O 0.000296736 g/l AlK(SO4)2 x 12 H2O 0.000197824 g/l CuSO4 x 5 H2O 9.8912e-05 g/l Pyridoxine hydrochloride 9.8912e-05 g/l Na2MoO4 x 2 H2O 9.8912e-05 g/l H3BO3 9.8912e-05 g/l p-Aminobenzoic acid 4.9456e-05 g/l (DL)-alpha-Lipoic acid 4.9456e-05 g/l Calcium D-(+)-pantothenate 4.9456e-05 g/l Nicotinic acid 4.9456e-05 g/l Riboflavin 4.9456e-05 g/l Thiamine HCl 4.9456e-05 g/l Folic acid 1.97824e-05 g/l Biotin 1.97824e-05 g/l Na2WO4 x 2 H2O 3.95648e-06 g/l Na2SeO3 x 5 H2O 2.96736e-06 g/l Vitamin B12 9.8912e-07 g/l Distilled water

Culture temp

@ref	Growth	Type	Temperature (°C)
24413	positive	growth	30
43161	positive	optimum	30
43161	positive	growth	20-35
67770	positive	growth	30

Culture pH

@ref	Ability	Type	PH	PH range
43161	positive	optimum	6.0-7.0
43161	positive	growth	4.5-8.5	alkaliphile

Physiology and metabolism

Oxygen tolerance

@ref	Oxygen tolerance	Confidence
43161	facultative anaerobe
43161	microaerophile
125439	obligate aerobe	90.486

Nutrition type

@ref	Type
43161	chemoautotroph
43161	chemoheterotroph
43161	chemoorganoheterotroph
43161	chemolithoheterotroph

Spore formation

@ref	Type of spore	Confidence
43161	spore
125438		90.557
125439		98.995

Halophily

@ref	Salt	Growth	Tested relation	Concentration
43161	NaCl	positive	growth	5-45 g/L
43161	NaCl	positive	optimum	15-20 g/L

Observation

67770

Observationquinones: Q-9, Q-8

Metabolite utilization

@ref	Chebi-ID	Metabolite	Utilization activity	Kind of utilization tested
43161	16526 ChEBI	carbon dioxide	+	carbon source
43161		casamino acids	+	carbon source
43161	16947 ChEBI	citrate	+	carbon source
43161	15379 ChEBI	dioxygen	+	electron acceptor
43161	33403 ChEBI	elemental sulfur	+	electron donor
43161	29034 ChEBI	ferric iron	+	electron acceptor
43161	18050 ChEBI	L-glutamine	+	carbon source
43161	24996 ChEBI	lactate	+	carbon source
43161	17632 ChEBI	nitrate	+	electron acceptor
43161		peptone	+	carbon source
43161	15361 ChEBI	pyruvate	+	carbon source
43161	16094 ChEBI	thiosulfate	+	electron donor
43161		tryptone	+	carbon source
43161		yeast extract	+	carbon source

Antibiotic resistance

@ref	ChEBI	Metabolite	Sensitivity conc.
43161	28971	ampicillin	100000 µg/mL
43161	17698	chloramphenicol	100000 µg/mL
43161	6104	kanamycin	100000 µg/mL
43161	17076	streptomycin	100000 µg/mL

Enzymes

@ref	Value	Activity	Ec
43161	catalase	-	1.11.1.6

Pathway annotation

Computationally determined by

@ref	pathway	enzyme coverage	annotated reactions
66794	teichoic acid biosynthesis	100	1 of 1
66794	valine metabolism	100	9 of 9
66794	L-lactaldehyde degradation	100	3 of 3
66794	CMP-KDO biosynthesis	100	4 of 4
66794	cis-vaccenate biosynthesis	100	2 of 2
66794	adipate degradation	100	2 of 2
66794	coenzyme A metabolism	100	4 of 4
66794	formaldehyde oxidation	100	3 of 3
66794	reductive acetyl coenzyme A pathway	100	7 of 7
66794	denitrification	100	2 of 2
66794	photosynthesis	100	14 of 14
66794	CDP-diacylglycerol biosynthesis	100	2 of 2
66794	folate polyglutamylation	100	1 of 1
66794	ppGpp biosynthesis	100	4 of 4
66794	anapleurotic synthesis of oxalacetate	100	1 of 1
66794	ceramide biosynthesis	100	1 of 1
66794	suberin monomers biosynthesis	100	2 of 2
66794	UDP-GlcNAc biosynthesis	100	3 of 3
66794	palmitate biosynthesis	100	22 of 22
66794	threonine metabolism	90	9 of 10
66794	chorismate metabolism	88.89	8 of 9
66794	molybdenum cofactor biosynthesis	88.89	8 of 9
66794	lipid A biosynthesis	88.89	8 of 9
66794	aspartate and asparagine metabolism	88.89	8 of 9
66794	C4 and CAM-carbon fixation	87.5	7 of 8
66794	gluconeogenesis	87.5	7 of 8
66794	ubiquinone biosynthesis	85.71	6 of 7
66794	vitamin B12 metabolism	82.35	28 of 34
66794	ethylmalonyl-CoA pathway	80	4 of 5
66794	Entner Doudoroff pathway	80	8 of 10
66794	methylglyoxal degradation	80	4 of 5
66794	glycine betaine biosynthesis	80	4 of 5
66794	peptidoglycan biosynthesis	80	12 of 15
66794	heme metabolism	78.57	11 of 14
66794	glutamate and glutamine metabolism	78.57	22 of 28
66794	tetrahydrofolate metabolism	78.57	11 of 14
66794	CO2 fixation in Crenarchaeota	77.78	7 of 9
66794	serine metabolism	77.78	7 of 9
66794	phenylalanine metabolism	76.92	10 of 13
66794	acetate fermentation	75	3 of 4
66794	6-hydroxymethyl-dihydropterin diphosphate biosynthesis	75	6 of 8
66794	sulfopterin metabolism	75	3 of 4
66794	glutathione metabolism	71.43	10 of 14
66794	cardiolipin biosynthesis	71.43	5 of 7
66794	glycolysis	70.59	12 of 17
66794	purine metabolism	70.21	66 of 94
66794	leucine metabolism	69.23	9 of 13
66794	glycolate and glyoxylate degradation	66.67	4 of 6
66794	enterobactin biosynthesis	66.67	2 of 3
66794	acetyl CoA biosynthesis	66.67	2 of 3
66794	octane oxidation	66.67	2 of 3
66794	NAD metabolism	66.67	12 of 18
66794	d-mannose degradation	66.67	6 of 9
66794	acetoin degradation	66.67	2 of 3
66794	methionine metabolism	65.38	17 of 26
66794	pyrimidine metabolism	64.44	29 of 45
66794	citric acid cycle	64.29	9 of 14
66794	oxidative phosphorylation	63.74	58 of 91
66794	proline metabolism	63.64	7 of 11
66794	isoleucine metabolism	62.5	5 of 8
66794	alanine metabolism	62.07	18 of 29
66794	isoprenoid biosynthesis	61.54	16 of 26
66794	vitamin B1 metabolism	61.54	8 of 13
66794	lipid metabolism	61.29	19 of 31
66794	non-pathway related	60.53	23 of 38
66794	phenylacetate degradation (aerobic)	60	3 of 5
66794	propionate fermentation	60	6 of 10
66794	glycogen metabolism	60	3 of 5
66794	flavin biosynthesis	60	9 of 15
66794	histidine metabolism	58.62	17 of 29
66794	tryptophan metabolism	57.89	22 of 38
66794	cysteine metabolism	55.56	10 of 18
66794	pentose phosphate pathway	54.55	6 of 11
66794	arginine metabolism	54.17	13 of 24
66794	butanoate fermentation	50	2 of 4
66794	ethanol fermentation	50	1 of 2
66794	cyclohexanol degradation	50	2 of 4
66794	ketogluconate metabolism	50	4 of 8
66794	tyrosine metabolism	50	7 of 14
66794	biotin biosynthesis	50	2 of 4
66794	phenylmercury acetate degradation	50	1 of 2
66794	glycine metabolism	50	5 of 10
66794	carnitine metabolism	50	4 of 8
66794	aminopropanol phosphate biosynthesis	50	1 of 2
66794	degradation of aromatic, nitrogen containing compounds	50	6 of 12
66794	lysine metabolism	47.62	20 of 42
66794	degradation of hexoses	44.44	8 of 18
66794	nitrate assimilation	44.44	4 of 9
66794	propanol degradation	42.86	3 of 7
66794	coenzyme M biosynthesis	40	4 of 10
66794	lipoate biosynthesis	40	2 of 5
66794	myo-inositol biosynthesis	40	4 of 10
66794	arachidonate biosynthesis	40	2 of 5
66794	factor 420 biosynthesis	40	2 of 5
66794	polyamine pathway	39.13	9 of 23
66794	arachidonic acid metabolism	38.89	7 of 18
66794	phosphatidylethanolamine bioynthesis	38.46	5 of 13
66794	degradation of sugar alcohols	37.5	6 of 16
66794	dTDPLrhamnose biosynthesis	37.5	3 of 8
66794	vitamin B6 metabolism	36.36	4 of 11
66794	degradation of sugar acids	36	9 of 25
66794	degradation of pentoses	35.71	10 of 28
66794	IAA biosynthesis	33.33	1 of 3
66794	pantothenate biosynthesis	33.33	2 of 6
66794	sphingosine metabolism	33.33	2 of 6
66794	4-hydroxymandelate degradation	33.33	3 of 9
66794	(5R)-carbapenem carboxylate biosynthesis	33.33	1 of 3
66794	cyanate degradation	33.33	1 of 3
66794	selenocysteine biosynthesis	33.33	2 of 6
66794	androgen and estrogen metabolism	31.25	5 of 16
66794	urea cycle	30.77	4 of 13
66794	phenol degradation	30	6 of 20
66794	starch degradation	30	3 of 10
66794	benzoyl-CoA degradation	28.57	2 of 7
66794	carotenoid biosynthesis	27.27	6 of 22
66794	dolichyl-diphosphooligosaccharide biosynthesis	27.27	3 of 11
66794	metabolism of disaccharids	27.27	3 of 11
66794	d-xylose degradation	27.27	3 of 11
66794	cholesterol biosynthesis	27.27	3 of 11
66794	lactate fermentation	25	1 of 4
66794	toluene degradation	25	1 of 4
66794	glycogen biosynthesis	25	1 of 4
66794	vitamin E metabolism	25	1 of 4
66794	alginate biosynthesis	25	1 of 4
66794	sulfate reduction	23.08	3 of 13

Isolation, sampling and environmental information

Isolation source categories

Cat1	Cat2	Cat3
#Environmental	#Aquatic	#Marine
#Environmental	#Aquatic	#Sediment
#Environmental	#Terrestrial	#Coast

Isolation

@ref	Sample type	Sampling date	Geographic location	Country	Country ISO 3 Code	Continent	Latitude	Longitude
24413	sediment from a submarine coastal gas vent		Tyrrhenian Sea, Tor Caldara	Italy	ITA	Europe	41.4858	12.5897 41.4858/12.5897
43161	surface sediment of an active shallow-water gas vent	2013-08	Tor Caldara in the Tyrrhenian Sea, Italy	Italy	ITA	Europe	41	12 41/12
67770	Sulfidic shallow-water marine gas vent located at Tor Caldara in the Tyrrhenian Sea			Italy	ITA	Europe

Taxonmaps

69479

Global distribution of 16S sequence KU294728 (>99% sequence identity) for Varunaivibrio sulfuroxidans subclade from Microbeatlas

Aquatic Samples	108
Soil Samples	11
Animal Samples	10
Plant Samples	4
Total Samples	133

Interaction and safety

Risk assessment

@ref	Biosafety level	Biosafety level comment
24413	1	Risk group (German classification)

Sequence information

Genome sequences

@ref	Description	Assembly level	INSDC accession	BV-BRC accession	IMG accession	NCBI tax ID	Score
124043	ASM2931863v1 assembly for Varunaivibrio sulfuroxidans TC8	complete	GCA_029318635	1773489.24		1773489	99.08
67770	ASM434172v1 assembly for Varunaivibrio sulfuroxidans DSM 101688	contig	GCA_004341725	1773489.15	2784746782	1773489	73.89

16S sequences

@ref	Description	Accession	Length	Database	NCBI tax ID
24413	Varunaivibrio sulfuroxidans strain TC8 16S ribosomal RNA gene, partial sequence	KU294728	1360		1773489

GC content

@ref	GC-content (mol%)	Method
24413	59.9	high performance liquid chromatography (HPLC)

Genome-based predictions

Predictions

Predictions from Deep Learning for Genome Sequence Data. R package version 0.3.1 based on: ASM2931863v1 assembly for Varunaivibrio sulfuroxidans TC8
NCBI: GCA_029318635

@ref	Trait	Model	Prediction	Confidence in %	In training data
125439	oxygen_tolerance	BacteriaNetⓘ	obligate aerobe	90.49	no
125439	motility	BacteriaNetⓘ	yes	65.13	no
125439	gram_stain	BacteriaNetⓘ	negative	96.56	no
125439	spore_formation	BacteriaNetⓘ	no	99.00	no

Predictions from bacterial phenotypic traits through improved machine learning using high-quality, curated datasets based on: Varunaivibrio sulfuroxidans strain DSM 101688
PATRIC: 1773489.15

@ref	Trait	Model	Prediction	Confidence in %	In training data
125438	gram-positive	gram-positiveⓘ	no	96.50	yes
125438	anaerobic	anaerobicⓘ	no	79.09	yes
125438	spore-forming	spore-formingⓘ	no	90.56	yes
125438	aerobic	aerobicⓘ	no	54.77	yes
125438	thermophilic	thermophileⓘ	no	89.12	no
125438	flagellated	motile2+ⓘ	yes	79.88	no

Literature

Topic	Title	Authors	Journal	DOI	Year
Phylogeny	Varunaivibrio sulfuroxidans gen. nov., sp. nov., a facultatively chemolithoautotrophic, mesophilic alphaproteobacterium from a shallow-water gas vent at Tor Caldara, Tyrrhenian Sea.	Patwardhan S, Vetriani C	Int J Syst Evol Microbiol	10.1099/ijsem.0.001235	2016

References

#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 )
#24413	Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 101688
#43161	Sushmita Patwardhan and Costantino Vetriani: Varunaivibrio sulfuroxidans gen. nov., sp. nov., a facultatively chemolithoautotrophic, mesophilic alphaproteobacterium from a shallow-water gas vent at Tor Caldara, Tyrrhenian Sea. IJSEM 66: 3579 - 3584 2016 ( DOI 10.1099/ijsem.0.001235 , PubMed 27298285 )
#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 .
#124043	Isabel Schober, Julia Koblitz: Data extracted from sequence databases, automatically matched based on designation and taxonomy .
#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 )

Content

About us

Varunaivibrio sulfuroxidans (DSM 101688, JCM 31027, TC 8)

Name and taxonomic classification

Morphology

Cell morphology

Culture and growth conditions

Culture medium

Culture temp

Culture pH

Physiology and metabolism

Oxygen tolerance

Nutrition type

Spore formation

Halophily

Observation

Metabolite utilization

Antibiotic resistance

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_029318635

16S sequences

GC content

Genome-based predictions

Predictions

Literature

Literature

References

BacDive

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