Hydrogenivirga caldilitoris (DSM 16510, ATCC BAA-821, JCM 12173)

Name: Hydrogenivirga caldilitoris (DSM 16510, ATCC BAA-821, JCM 12173)
Creator: BacDive
License: http://creativecommons.org/licenses/by/4.0/

BacDive ID 509

Type strain

Strain Designation ISBSK3

Culture col. no. DSM 16510 ATCC BAA-821 JCM 12173 ISBSK3

NCBI tax ID(s) 246264

Special Collections DSMZ JCM Literature strains

History <- S. Nakagawa; ISBSK3 S. Nakagawa IBSK3.

Links

Hydrogenivirga caldilitoris ISBSK3 is an anaerobe, Gram-negative, motile bacterium that was isolated from coastal hot spring.

Gram-negative motile rod-shaped anaerobe genome sequence 16S sequence Bacteria

Name and taxonomic classification

SI-ID 134430

ATCC BAA-821,JCM 12173,DSM 16510

@ref 20215

Last LPSN update 2026-02-09 11:17:53

Domain Bacteria

Phylum Aquificota

Class Aquificia

Order Aquificales

Family Aquificaceae

Genus Hydrogenivirga

Species Hydrogenivirga caldilitoris

Full scientific name Hydrogenivirga caldilitoris Nakagawa et al. 2004

Morphology

Cell morphology

@ref	Gram stain	Cell length	Cell width	Cell shape	Motility	Confidence
30178	negative	2 µm	0.3 µm	rod-shaped
125438	negative					97.983

Multimedia

@ref:	66793
multimedia content:	EM_DSM_16510_1.jpg
multimedia.multimedia content:	EM_DSM_16510_1.jpg
caption:	electron microscopic image
intellectual property rights:	© HZI/Manfred Rohde
manual_annotation:	1

@ref:	66793
multimedia content:	EM_DSM_16510_2.jpg
multimedia.multimedia content:	EM_DSM_16510_2.jpg
caption:	electron microscopic image
intellectual property rights:	© HZI/Manfred Rohde
manual_annotation:	1

@ref:	66793
multimedia content:	EM_DSM_16510_3.jpg
multimedia.multimedia content:	EM_DSM_16510_3.jpg
caption:	electron microscopic image
intellectual property rights:	© HZI/Manfred Rohde
manual_annotation:	1

@ref:	66793
multimedia content:	EM_DSM_16510_4.jpg
multimedia.multimedia content:	EM_DSM_16510_4.jpg
caption:	electron microscopic image
intellectual property rights:	© HZI/Manfred Rohde
manual_annotation:	1

@ref:	66793
multimedia content:	EM_DSM_16510_5.jpg
multimedia.multimedia content:	EM_DSM_16510_5.jpg
caption:	electron microscopic image
intellectual property rights:	© HZI/Manfred Rohde
manual_annotation:	1

Culture and growth conditions

Culture medium

@ref	Name	Growth	Medium link	Composition
6383	HNW MEDIUM (DSMZ Medium 997)		Medium recipe at MediaDive	Name: HNW MEDIUM (DSMZ Medium 997) Composition: MgCl2 x 6 H2O 418.0 g/l Na2S 100.0 g/l NaHCO3 100.0 g/l NaNO3 100.0 g/l KCl 33.0 g/l NH4Cl 25.0 g/l K2HPO4 14.0 g/l MgSO4 x 7 H2O 3.0 g/l C6H9NO6 1.5 g/l NaCl 1.0 g/l Fe(NH4)2(SO4)2 x 6 H2O 1.0 g/l MnSO4 x 2 H2O 0.5 g/l CoSO4 x 7 H2O 0.18 g/l ZnSO4 x 7 H2O 0.18 g/l FeSO4 x 7 H2O 0.1 g/l CaCl2 x 2 H2O 0.1 g/l NiCl2 x 6 H2O 0.025 g/l AlK(SO4)2 x 12 H2O 0.02 g/l CuSO4 x 5 H2O 0.01 g/l H3BO3 0.01 g/l Na2MoO4 x 2 H2O 0.01 g/l Na2SeO3 x 5 H2O 0.0003 g/l Na2WO4 x 2 H2O 0.0001 g/l Pyridoxine hydrochloride 0.0001 g/l Thiamine HCl 5e-05 g/l Riboflavin 5e-05 g/l Nicotinic acid 5e-05 g/l Calcium D-(+)-pantothenate 5e-05 g/l p-Aminobenzoic acid 5e-05 g/l (DL)-alpha-Lipoic acid 5e-05 g/l Folic acid 2e-05 g/l Biotin 2e-05 g/l Vitamin B12 1e-06 g/l Distilled water

Culture temp

@ref	Growth	Type	Temperature (°C)
6383	positive	growth	75
30178	positive	growth	55-77
30178	positive	optimum	75
67770	positive	growth	75

Culture pH

@ref	Ability	Type	PH
30178	positive	optimum	6.75
30178	positive	growth	5.5-8.3

Physiology and metabolism

Oxygen tolerance

@ref	Oxygen tolerance	Confidence
30178	anaerobe
125439	anaerobe	99.8

Spore formation

@ref	Spore formation	Confidence
125438		91.27

Halophily

@ref	Salt	Growth	Tested relation	Concentration
30178	NaCl	positive	growth	0.5-4 %
30178	NaCl	positive	optimum	2 %

Observation

30178

Observationaggregates in clumps

Metabolite utilization

@ref	Chebi-ID	Metabolite	Utilization activity	Kind of utilization tested
30178	17632 ChEBI	nitrate	+	reduction

Pathway annotation

Computationally determined by

@ref	pathway	enzyme coverage	annotated reactions
66794	reductive acetyl coenzyme A pathway	100	7 of 7
66794	denitrification	100	2 of 2
66794	hydrogen production	100	5 of 5
66794	CDP-diacylglycerol biosynthesis	100	2 of 2
66794	UDP-GlcNAc biosynthesis	100	3 of 3
66794	coenzyme A metabolism	100	4 of 4
66794	suberin monomers biosynthesis	100	2 of 2
66794	anapleurotic synthesis of oxalacetate	100	1 of 1
66794	L-lactaldehyde degradation	100	3 of 3
66794	biotin biosynthesis	100	4 of 4
66794	methylglyoxal degradation	100	5 of 5
66794	ppGpp biosynthesis	100	4 of 4
66794	folate polyglutamylation	100	1 of 1
66794	chorismate metabolism	100	9 of 9
66794	palmitate biosynthesis	95.45	21 of 22
66794	tetrahydrofolate metabolism	92.86	13 of 14
66794	lipid A biosynthesis	88.89	8 of 9
66794	molybdenum cofactor biosynthesis	88.89	8 of 9
66794	NAD metabolism	88.89	16 of 18
66794	ubiquinone biosynthesis	85.71	6 of 7
66794	pentose phosphate pathway	81.82	9 of 11
66794	peptidoglycan biosynthesis	80	12 of 15
66794	threonine metabolism	80	8 of 10
66794	lipoate biosynthesis	80	4 of 5
66794	heme metabolism	78.57	11 of 14
66794	photosynthesis	78.57	11 of 14
66794	valine metabolism	77.78	7 of 9
66794	6-hydroxymethyl-dihydropterin diphosphate biosynthesis	75	6 of 8
66794	CMP-KDO biosynthesis	75	3 of 4
66794	sulfopterin metabolism	75	3 of 4
66794	acetate fermentation	75	3 of 4
66794	propanol degradation	71.43	5 of 7
66794	cardiolipin biosynthesis	71.43	5 of 7
66794	phenylalanine metabolism	69.23	9 of 13
66794	vitamin B1 metabolism	69.23	9 of 13
66794	purine metabolism	68.09	64 of 94
66794	glutamate and glutamine metabolism	67.86	19 of 28
66794	flavin biosynthesis	66.67	10 of 15
66794	aspartate and asparagine metabolism	66.67	6 of 9
66794	d-mannose degradation	66.67	6 of 9
66794	octane oxidation	66.67	2 of 3
66794	serine metabolism	66.67	6 of 9
66794	nitrate assimilation	66.67	6 of 9
66794	formaldehyde oxidation	66.67	2 of 3
66794	selenocysteine biosynthesis	66.67	4 of 6
66794	acetoin degradation	66.67	2 of 3
66794	vitamin B6 metabolism	63.64	7 of 11
66794	isoleucine metabolism	62.5	5 of 8
66794	pyrimidine metabolism	62.22	28 of 45
66794	isoprenoid biosynthesis	57.69	15 of 26
66794	glutathione metabolism	57.14	8 of 14
66794	citric acid cycle	57.14	8 of 14
66794	CO2 fixation in Crenarchaeota	55.56	5 of 9
66794	alanine metabolism	55.17	16 of 29
66794	glycolysis	52.94	9 of 17
66794	non-pathway related	52.63	20 of 38
66794	histidine metabolism	51.72	15 of 29
66794	glycolate and glyoxylate degradation	50	3 of 6
66794	pantothenate biosynthesis	50	3 of 6
66794	1,4-dihydroxy-6-naphthoate biosynthesis	50	3 of 6
66794	dolichol and dolichyl phosphate biosynthesis	50	1 of 2
66794	cis-vaccenate biosynthesis	50	1 of 2
66794	ethanol fermentation	50	1 of 2
66794	adipate degradation	50	1 of 2
66794	glycine metabolism	50	5 of 10
66794	methionine metabolism	50	13 of 26
66794	ketogluconate metabolism	50	4 of 8
66794	C4 and CAM-carbon fixation	50	4 of 8
66794	gluconeogenesis	50	4 of 8
66794	phenylmercury acetate degradation	50	1 of 2
66794	leucine metabolism	46.15	6 of 13
66794	urea cycle	46.15	6 of 13
66794	arginine metabolism	45.83	11 of 24
66794	metabolism of disaccharids	45.45	5 of 11
66794	proline metabolism	45.45	5 of 11
66794	tryptophan metabolism	44.74	17 of 38
66794	degradation of hexoses	44.44	8 of 18
66794	tyrosine metabolism	42.86	6 of 14
66794	lysine metabolism	42.86	18 of 42
66794	degradation of aromatic, nitrogen containing compounds	41.67	5 of 12
66794	myo-inositol biosynthesis	40	4 of 10
66794	propionate fermentation	40	4 of 10
66794	glycogen metabolism	40	2 of 5
66794	Entner Doudoroff pathway	40	4 of 10
66794	oxidative phosphorylation	39.56	36 of 91
66794	cysteine metabolism	38.89	7 of 18
66794	lipid metabolism	38.71	12 of 31
66794	IAA biosynthesis	33.33	1 of 3
66794	acetyl CoA biosynthesis	33.33	1 of 3
66794	sulfate reduction	30.77	4 of 13
66794	phosphatidylethanolamine bioynthesis	30.77	4 of 13
66794	polyamine pathway	30.43	7 of 23
66794	coenzyme M biosynthesis	30	3 of 10
66794	benzoyl-CoA degradation	28.57	2 of 7
66794	chlorophyll metabolism	27.78	5 of 18
66794	ascorbate metabolism	27.27	6 of 22
66794	degradation of pentoses	25	7 of 28
66794	lactate fermentation	25	1 of 4
66794	cyclohexanol degradation	25	1 of 4
66794	glycogen biosynthesis	25	1 of 4
66794	butanoate fermentation	25	1 of 4
66794	androgen and estrogen metabolism	25	4 of 16
66794	phenol degradation	25	5 of 20
66794	methanogenesis from CO2	25	3 of 12
66794	toluene degradation	25	1 of 4

Isolation, sampling and environmental information

Isolation source categories

Cat1	Cat2	Cat3
#Environmental	#Aquatic	#Thermal spring
#Condition	#Thermophilic (>45°C)	-
#Environmental	#Terrestrial	#Coast

Isolation

@ref	Sample type	Geographic location	Country	Country ISO 3 Code	Continent
6383	coastal hot spring	Kagoshima Prefecture, Ibusuki	Japan	JPN	Asia
67770	Coastal hot spring in Ibusuki	Kagoshima	Japan	JPN	Asia

Taxonmaps

69479

Global distribution of 16S sequence AB120294 (>99% sequence identity) for Hydrogenivirga caldilitoris subclade from Microbeatlas

Aquatic Samples	15
Soil Samples	1
Animal Samples
Plant Samples
Total Samples	16

Interaction and safety

Risk assessment

@ref	Biosafety level	Biosafety level comment
6383	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
67770	ASM366400v1 assembly for Hydrogenivirga caldilitoris DSM 16510	contig	GCA_003664005	246264.3	2681812961	246264	77.48

16S sequences

@ref	Description	Accession	Length	Database	NCBI tax ID
6383	Hydrogenivirga caldilitoris gene for 16S rRNA, partial sequence	AB120294	1492		246264

GC content

@ref	GC-content (mol%)	Method
30178	49.2
67770	49.2	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: Hydrogenivirga caldilitoris DSM 16510
NCBI: GCA_003664005

@ref	Trait	Model	Prediction	Confidence in %	In training data
125439	spore_formation	BacteriaNetⓘ	yes	52.40	no
125439	motility	BacteriaNetⓘ	no	54.60	no
125439	gram_stain	BacteriaNetⓘ	variable	66.40	no
125439	oxygen_tolerance	BacteriaNetⓘ	anaerobe	99.80	no

Predictions from bacterial phenotypic traits through improved machine learning using high-quality, curated datasets based on: Hydrogenivirga caldilitoris strain DSM 16510
PATRIC: 246264.3

@ref	Trait	Model	Prediction	Confidence in %	In training data
125438	gram-positive	gram-positiveⓘ	no	97.98	no
125438	anaerobic	anaerobicⓘ	yes	57.35	yes
125438	spore-forming	spore-formingⓘ	no	91.27	no
125438	thermophilic	thermophileⓘ	yes	73.25	yes
125438	aerobic	aerobicⓘ	no	78.23	no
125438	flagellated	motile2+ⓘ	yes	53.70	no

Literature

Topic	Title	Authors	Journal	DOI	Year
Phylogeny	Hydrogenivirga caldilitoris gen. nov., sp. nov., a novel extremely thermophilic, hydrogen- and sulfur-oxidizing bacterium from a coastal hydrothermal field.	Nakagawa S, Nakamura S, Inagaki F, Takai K, Shirai N, Sako Y	Int J Syst Evol Microbiol	10.1099/ijs.0.03031-0	2004

References

#6383	Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 16510
#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 )
#26527	IJSEM 2079 2004 ( DOI 10.1099/ijs.0.03031-0 , PubMed 15545438 )
#30178	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 #26527
#66793	Mukherjee et al.: GEBA: 1,003 reference genomes of bacterial and archaeal isolates expand coverage of the tree of life. 35: 676 - 683 2017 ( DOI 10.1038/nbt.3886 , PubMed 28604660 )
#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 .
#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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Hydrogenivirga caldilitoris (DSM 16510, ATCC BAA-821, JCM 12173)

Name and taxonomic classification

Morphology

Cell morphology

Multimedia

Culture and growth conditions

Culture medium

Culture temp

Culture pH

Physiology and metabolism

Oxygen tolerance

Spore formation

Halophily

Observation

Metabolite utilization

Pathway annotation

Isolation, sampling and environmental information

Isolation source categories

Isolation

Taxonmaps

Interaction and safety

Risk assessment

Sequence information

Genome sequences

Genome browser: GCA_003664005

16S sequences

GC content

Genome-based predictions

Predictions

Literature

Literature

References

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