Thermovibrio ammonificans (DSM 15698, JCM 12110, HB-1)

Name: Thermovibrio ammonificans (DSM 15698, JCM 12110, HB-1)
Creator: BacDive
License: http://creativecommons.org/licenses/by/4.0/

BacDive ID 17646

Type strain

Strain Designation HB-1

Culture col. no. DSM 15698 JCM 12110 HB-1

NCBI tax ID(s) 648996 228745

Special Collections DSMZ JCM Literature strains

History <- C. Vetriani, Rutgers Univ.; HB-1 <- C. Vetriani {2001} C. Vetriani HB-1.

Links

Thermovibrio ammonificans HB-1 is an anaerobe, Gram-negative, motile bacterium that was isolated from wall of black smoker chimney.

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

Name and taxonomic classification

SI-ID 130854

DSM 15698,JCM 12110

@ref 20215

Last LPSN update 2026-02-09 11:22:16

Domain Bacteria

Phylum Aquificota

Class Aquificia

Order Desulfurobacteriales

Family Desulfurobacteriaceae

Genus Thermovibrio

Species Thermovibrio ammonificans

Full scientific name Thermovibrio ammonificans Vetriani et al. 2004

Morphology

Cell morphology

@ref	Gram stain	Cell length	Cell width	Cell shape	Confidence
29981	negative	1 µm	0.6 µm	rod-shaped
125438	negative				97.212
125439	negative				95.5

Pigmentation

29981

Productionyes

Culture and growth conditions

Culture medium

@ref	Name	Growth	Medium link	Composition
6064	THERMOVIBRIO AMMONIFICANS MEDIUM (DSMZ Medium 792a)		Medium recipe at MediaDive	Name: THERMOVIBRIO AMMONIFICANS MEDIUM (DSMZ Medium 792a) Composition: MgCl2 x 6 H2O 2.72547 g/l KNO3 0.99108 g/l KH2PO4 0.49554 g/l KCl 0.327056 g/l Na2S x 9 H2O 0.148662 g/l NaBr 0.049554 g/l MgSO4 x 7 H2O 0.0297324 g/l NaCl 0.0099108 g/l SrCl2 x 6 H2O 0.00693757 g/l MnSO4 x H2O 0.0049554 g/l (NH4)2Ni(SO4)2 x 6 H2O 0.00277502 g/l CoCl2 x 6 H2O 0.00178394 g/l ZnSO4 x 7 H2O 0.00178394 g/l FeSO4 x 7 H2O 0.00099108 g/l CaCl2 x 2 H2O 0.00099108 g/l Sodium resazurin 0.00049554 g/l AlK(SO4)2 x 12 H2O 0.000178394 g/l Na2SeO4 9.9108e-05 g/l Na2WO4 x 2 H2O 9.9108e-05 g/l H3BO3 9.9108e-05 g/l CuSO4 x 5 H2O 9.9108e-05 g/l Na2MoO4 x 2 H2O 9.9108e-05 g/l KI 4.9554e-05 g/l Distilled water

Culture temp

@ref	Growth	Type	Temperature (°C)
6064	positive	growth	75
29981	positive	growth	60-80
29981	positive	optimum	75
67770	positive	growth	75

Culture pH

@ref	Ability	Type	PH
29981	positive	optimum	5.5
29981	positive	growth	05-07

Physiology and metabolism

Oxygen tolerance

@ref	Oxygen tolerance	Confidence
6064	anaerobe
29981	anaerobe
125438	anaerobe	91.19
125439	anaerobe	100

Spore formation

@ref	Spore formation	Confidence
29981
125438		90.371
125439		98.9

Halophily

@ref	Salt	Growth	Tested relation	Concentration
29981	NaCl	positive	growth	0.5-4.5 %
29981	NaCl	positive	optimum	2 %

Enzymes

@ref	Value	Activity	Ec
29981	catalase	+	1.11.1.6

Isolation, sampling and environmental information

Isolation source categories

Cat1	Cat2	Cat3
#Environmental	#Aquatic	#Hydrothermal vent

Isolation

@ref	Sample type	Geographic location	Latitude	Longitude
6064	wall of black smoker chimney	Deep-Sea hydrothermal vent	9.8333	-104.3 9.8333/-104.3
67770	Walls of an active deep-sea hydrothermal vent chimney on the East Pacific Rise

Interaction and safety

Risk assessment

@ref	Biosafety level	Biosafety level comment
6064	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	ASM18580v1 assembly for Thermovibrio ammonificans HB-1	complete	GCA_000185805	648996.5	649633104	648996	97.8

16S sequences

@ref	Description	Accession	Length	Database	NCBI tax ID
6064	Thermovibrio ammoniificans strain HB-1 16S ribosomal RNA gene, partial sequence	AY263403	1472		648996

GC content

@ref	GC-content (mol%)	Method
6064	54.6
67770	54.6	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: Thermovibrio ammonificans HB-1
PATRIC: 648996.5

@ref	Trait	Model	Prediction	Confidence in %	In training data
125439	spore_formation	BacteriaNetⓘ	no	98.90	no
125439	motility	BacteriaNetⓘ	no	68.20	no
125439	gram_stain	BacteriaNetⓘ	negative	95.50	no
125439	oxygen_tolerance	BacteriaNetⓘ	anaerobe	100.00	no

Predictions from bacterial phenotypic traits through improved machine learning using high-quality, curated datasets based on: Thermovibrio ammonificans HB-1 HB-1
NCBI: GCA_000185805.1

@ref	Trait	Model	Prediction	Confidence in %	In training data
125438	gram-positive	gram-positiveⓘ	no	97.21	no
125438	anaerobic	anaerobicⓘ	yes	91.19	yes
125438	aerobic	aerobicⓘ	no	93.58	yes
125438	spore-forming	spore-formingⓘ	no	90.37	no
125438	thermophilic	thermophileⓘ	yes	79.66	no
125438	flagellated	motile2+ⓘ	yes	55.14	no

Literature

Topic	Title	Authors	Journal	DOI	Year
	Genomic analyses of bacterial porin-cytochrome gene clusters.	Shi L, Fredrickson JK, Zachara JM	Front Microbiol	10.3389/fmicb.2014.00657	2014
Genetics	Complete genome sequence of Thermovibrio ammonificans HB-1(T), a thermophilic, chemolithoautotrophic bacterium isolated from a deep-sea hydrothermal vent.	Giovannelli D, Ricci J, Perez-Rodriguez I, Hugler M, O'Brien C, Keddis R, Grosche A, Goodwin L, Bruce D, Davenport KW, Detter C, Han J, Han S, Ivanova N, Land ML, Mikhailova N, Nolan M, Pitluck S, Tapia R, Woyke T, Vetriani C	Stand Genomic Sci	10.4056/sigs.2856770	2012
Phylogeny	Thermovibrio ammonificans sp. nov., a thermophilic, chemolithotrophic, nitrate-ammonifying bacterium from deep-sea hydrothermal vents.	Vetriani C, Speck MD, Ellor SV, Lutz RA, Starovoytov V	Int J Syst Evol Microbiol	10.1099/ijs.0.02781-0	2004

References

#6064	Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 15698
#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 )
#26349	IJSEM 175 2004 ( DOI 10.1099/ijs.0.02781-0 , PubMed 14742477 )
#29981	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 #26349
#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) .
#67770	Japan Collection of Microorganism (JCM) ; Curators of the JCM;
#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

Thermovibrio ammonificans (DSM 15698, JCM 12110, HB-1)

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

Halophily

Enzymes

Isolation, sampling and environmental information

Isolation source categories

Isolation

Interaction and safety

Risk assessment

Sequence information

Genome sequences

Genome browser: GCA_000185805

16S sequences

GC content

Genome-based predictions

Predictions

Literature

Literature

References

BacDive

Help

Social Media