Archive BacDiveID:10.13145/bacdive18096.20250331.9.3

Strain identifier

BacDive ID: 18096

Type strain:

Species: Archaeoglobus fulgidus

Strain Designation: VC-16

Strain history: DSM 4304 <-- K. O. Stetter VC-16.

NCBI tax ID(s): 224325 (strain), 2234 (species)

For citation purpose refer to the digital object identifier (doi) of the current version.

General

@ref: 1648

BacDive-ID: 18096

DSM-Number: 4304

keywords: genome sequence, 16S sequence, Archaea, anaerobe, hyperthermophilic

description: Archaeoglobus fulgidus VC-16 is an anaerobe, hyperthermophilic archaeon that was isolated from submarine hot spring.

NCBI tax id

NCBI tax id	Matching level
2234	species
224325	strain

strain history

@ref	history
1648	<- K.O. Stetter, VC-16
67770	DSM 4304 <-- K. O. Stetter VC-16.

doi: 10.13145/bacdive18096.20250331.9.3

Name and taxonomic classification

LPSN

@ref: 20215
description: domain/archaea
keyword: phylum/methanobacteriota
domain: Archaea
phylum: Methanobacteriota
class: Archaeoglobi
order: Archaeoglobales
family: Archaeoglobaceae
genus: Archaeoglobus
species: Archaeoglobus fulgidus
full scientific name: Archaeoglobus fulgidus Stetter 1988

@ref: 1648

domain: Archaea

phylum: Euryarchaeota

class: Archaeoglobi

order: Archaeoglobales

family: Archaeoglobaceae

genus: Archaeoglobus

species: Archaeoglobus fulgidus

full scientific name: Archaeoglobus fulgidus Stetter 1988

strain designation: VC-16

type strain: yes

Morphology

cell morphology

@ref: 125439
motility: yes
confidence: 91.4

Culture and growth conditions

culture medium

@ref: 1648
name: ARCHAEOGLOBUS MEDIUM (DSMZ Medium 399)
growth: yes
link: https://mediadive.dsmz.de/medium/399
composition: Name: ARCHAEOGLOBUS MEDIUM (DSMZ Medium 399) Composition: MgCl2 x 6 H2O 3.95257 g/l NaHCO3 2.96443 g/l Na-L-lactate 1.48221 g/l Na2S x 9 H2O 0.494071 g/l Yeast extract 0.494071 g/l KCl 0.335968 g/l NH4Cl 0.247036 g/l K2HPO4 0.13834 g/l MgSO4 x 7 H2O 0.0296443 g/l Nitrilotriacetic acid 0.0148221 g/l NaCl 0.00988142 g/l MnSO4 x H2O 0.00494071 g/l Fe(NH4)2(SO4)2 x 7 H2O 0.00197628 g/l CoSO4 x 7 H2O 0.00177866 g/l ZnSO4 x 7 H2O 0.00177866 g/l FeSO4 x 7 H2O 0.000988142 g/l CaCl2 x 2 H2O 0.000988142 g/l Sodium resazurin 0.000494071 g/l NiCl2 x 6 H2O 0.000296443 g/l AlK(SO4)2 x 12 H2O 0.000197628 g/l CuSO4 x 5 H2O 9.88142e-05 g/l Na2MoO4 x 2 H2O 9.88142e-05 g/l H3BO3 9.88142e-05 g/l Na2WO4 x 2 H2O 3.95257e-06 g/l Na2SeO3 x 5 H2O 2.96443e-06 g/l Distilled water

culture temp

@ref	growth	type	temperature
1648	positive	growth	85
67770	positive	growth	80

Physiology and metabolism

oxygen tolerance

@ref	oxygen tolerance	confidence
1648	anaerobe
125439	facultative anaerobe	90.1

spore formation

@ref: 125439
spore formation: yes
confidence: 95.8

compound production

@ref: 1648
compound: isocitrate dehydrogenase

observation

@ref: 67770
observation: quinones: MK-7(H₁₄)

Isolation, sampling and environmental information

isolation

@ref	sample type	geographic location	country	origin.country	continent
1648	submarine hot spring	Vulcano island	Italy	ITA	Europe
67770	Hot sediments of marine hydrothermal system	Vulcano	Italy	ITA	Europe

isolation source categories

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

taxonmaps

@ref: 69479
File name: preview.99_187140.png
url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_17856;96_68819;97_89461;98_121737;99_187140&stattab=map
Last taxonomy: Archaeoglobus fulgidus subclade
16S sequence: Y00275
Sequence Identity:
Total samples: 95
soil counts: 3
aquatic counts: 91
animal counts: 1

Safety information

risk assessment

@ref: 1648
biosafety level: 1
biosafety level comment: Risk group (German classification)

Sequence information

16S sequences

@ref	description	accession	length	database	NCBI tax ID
67770	Archaeoglobus fulgidus strain VC-16 16S ribosomal RNA gene	X05567	1492	nuccore	224325
67770	Archaeoglobus fulgidus (VC-16) DNA for 16S ribosomal RNA	Y00275	1492	nuccore	224325

Genome sequences

@ref	description	accession	assembly level	database	NCBI tax ID
66792	Archaeoglobus fulgidus DSM 4304	GCA_000008665	complete	ncbi	224325
66792	Archaeoglobus fulgidus VC-16, DSM 4304	638154502	complete	img	224325
66792	Archaeoglobus fulgidus DSM 4304	224325.10	complete	patric	224325

GC content

@ref	GC-content	method
1648	46.0
67770	46	thermal denaturation, midpoint method (Tm)

Genome-based predictions

predictions

@ref	model	trait	description	prediction	confidence	training_data
125438	gram-positive	gram-positive	Positive reaction to Gram-staining	no	65.943	no
125438	anaerobic	anaerobic	Ability to grow under anoxygenic conditions (including facultative anaerobes)	yes	85.87	yes
125438	aerobic	aerobic	Ability to grow under oxygenic conditions (including facultative aerobes)	no	81.901	no
125438	spore-forming	spore-forming	Ability to form endo- or exospores	no	85.081	no
125438	thermophile	thermophilic	Ability to grow at temperatures above or equal to 45°C	yes	70.237	yes
125438	motile2+	flagellated	Ability to perform flagellated movement	no	86.708	no
125439	BacteriaNet	spore_formation	Ability to form endo- or exospores	yes	95.8
125439	BacteriaNet	motility	Ability to perform movement	yes	91.4
125439	BacteriaNet	gram_stain	Reaction to gram-staining	variable	88.9
125439	BacteriaNet	oxygen_tolerance	Oxygenic conditions needed for growth	facultative anaerobe	90.1

External links

@ref: 1648

culture collection no.: DSM 4304, ATCC 49558, JCM 9628, NBRC 100126

straininfo link

@ref: 87084
straininfo: 46110

literature

topic	Pubmed-ID	title	authors	journal	DOI	year	mesh	topic2
Enzymology	1659811	Spectroscopic studies on APS reductase isolated from the hyperthermophilic sulfate-reducing archaebacterium Archaeglobus fulgidus.	Lampreia J, Fauque G, Speich N, Dahl C, Moura I, Truper HG, Moura JJ	Biochem Biophys Res Commun	10.1016/s0006-291x(05)81424-x	1991	Archaea/enzymology, Binding Sites, Electron Spin Resonance Spectroscopy, Hot Temperature, Oxidation-Reduction, Oxidoreductases/chemistry/isolation & purification/metabolism, *Oxidoreductases Acting on Sulfur Group Donors, Spectrophotometry, Sulfates/metabolism	Stress
Enzymology	3137215	Vitamin contents of archaebacteria.	Noll KM, Barber TS	J Bacteriol	10.1128/jb.170.9.4315-4321.1988	1988	Archaea, Bacteria, Biological Assay, Biotin/analysis, Coenzymes/analysis, Escherichia coli, Lactobacillus casei/growth & development, Niacin/analysis, Pantothenic Acid/analysis, Pyridoxine/analysis, Riboflavin/analysis, Thioctic Acid/analysis, Vitamins/*analysis
Metabolism	3416881	5'-Methylbenzimidazolyl-cobamides are the corrinoids from some sulfate-reducing and sulfur-metabolizing bacteria.	Krautler B, Kohler HP, Stupperich E	Eur J Biochem	10.1111/j.1432-1033.1988.tb14303.x	1988	Bacteria/analysis/metabolism, Chemical Phenomena, Chemistry, Chromatography, High Pressure Liquid, Corrinoids, Magnetic Resonance Spectroscopy, Sulfur/metabolism, Vitamin B 12/analysis/isolation & purification	Enzymology
Enzymology	9627961	Dissimilatory ATP sulfurylase from the hyperthermophilic sulfate reducer Archaeoglobus fulgidus belongs to the group of homo-oligomeric ATP sulfurylases.	Sperling D, Kappler U, Wynen A, Dahl C, Truper HG	FEMS Microbiol Lett	10.1111/j.1574-6968.1998.tb13007.x	1998	Amino Acid Sequence, Archaeoglobus fulgidus/enzymology/genetics, Electrophoresis, Polyacrylamide Gel, Genes, Archaeal/genetics, Molecular Sequence Data, Phylogeny, Sequence Alignment, Sulfate Adenylyltransferase/analysis/classification/genetics	Phylogeny
Enzymology	9862122	The serine, threonine, and/or tyrosine-specific protein kinases and protein phosphatases of prokaryotic organisms: a family portrait.	Shi L, Potts M, Kennelly PJ	FEMS Microbiol Rev	10.1111/j.1574-6976.1998.tb00369.x	1998	Amino Acid Sequence, Archaeal Proteins/genetics, Archaeoglobus fulgidus/enzymology/genetics, Bacillus subtilis/enzymology/genetics, Bacterial Proteins/genetics, Borrelia burgdorferi Group/enzymology/genetics, Cyanobacteria/enzymology/genetics, Escherichia coli/enzymology/genetics, Haemophilus influenzae/enzymology/genetics, Helicobacter pylori/enzymology/genetics, Methanobacterium/enzymology/genetics, Methanococcus/enzymology/genetics, Molecular Sequence Data, Mycoplasma/enzymology/genetics, Open Reading Frames/genetics, Phosphoprotein Phosphatases/genetics, Protein Serine-Threonine Kinases/genetics, Protein-Tyrosine Kinases/genetics, Sequence Alignment	Genetics
Phylogeny	11540893	A possible biochemical missing link among archaebacteria.	Achenbach-Richter L, Stetter KO, Woese CR	Nature	10.1038/327348a0	1987	Archaea/classification/genetics/metabolism, Archaeoglobus/classification/genetics/metabolism, Base Sequence, Biological Evolution, Methane/metabolism, Methanococcus, Molecular Sequence Data, Phenotype, Phylogeny, RNA, Archaeal, RNA, Ribosomal, 16S/analysis, Sequence Analysis, RNA, Sequence Homology, Nucleic Acid, Sulfolobus, Sulfur/metabolism, Thermococcus	Metabolism
Cultivation	12586398	A variant of the hyperthermophile Archaeoglobus fulgidus adapted to grow at high salinity.	Goncalves LG, Huber R, da Costa MS, Santos H	FEMS Microbiol Lett	10.1111/j.1574-6968.2003.tb11523.x	2003	Acetates, Adaptation, Physiological, Archaeoglobus fulgidus/drug effects/growth & development/isolation & purification/metabolism, Culture Media, Glutamates/biosynthesis, Glycerophosphates/biosynthesis, Hot Temperature, Inositol Phosphates/biosynthesis, Osmotic Pressure, Sodium Chloride/*pharmacology	Stress
Enzymology	16086253	The putative lipase, AF1763, from Archaeoglobus fulgidusis is a carboxylesterase with a very high pH optimum.	Rusnak M, Nieveler J, Schmid RD, Petri R	Biotechnol Lett	10.1007/s10529-005-5621-1	2005	Archaeal Proteins/genetics/metabolism, Archaeoglobus/enzymology, Carboxylesterase/genetics/metabolism, Cloning, Molecular, Electrophoresis, Polyacrylamide Gel, Escherichia coli/genetics, Hydrogen-Ion Concentration, Kinetics, Lipase/genetics/metabolism, Plasmids/genetics, Recombinant Proteins/isolation & purification/metabolism, Sequence Analysis, DNA, Substrate Specificity, Temperature	Metabolism
Enzymology	16109946	Heat shock response of Archaeoglobus fulgidus.	Rohlin L, Trent JD, Salmon K, Kim U, Gunsalus RP, Liao JC	J Bacteriol	10.1128/JB.187.17.6046-6057.2005	2005	Amino Acid Sequence, Archaeal Proteins/genetics, Archaeoglobales/genetics, Conserved Sequence, Gene Expression Regulation, Archaeal, Heat-Shock Proteins/*genetics, Kinetics, Molecular Sequence Data, Oligonucleotide Array Sequence Analysis, Open Reading Frames, Polymerase Chain Reaction, Sequence Alignment, Sequence Homology, Amino Acid, Sequence Homology, Nucleic Acid	Genetics
Enzymology	18337701	Cloning and characterization of thermostable esterase from Archaeoglobus fulgidus.	Kim SB, Lee W, Ryu YW	J Microbiol	10.1007/s12275-007-0185-5	2008	Amino Acid Sequence, Archaeal Proteins/antagonists & inhibitors/chemistry/genetics/isolation & purification, Archaeoglobus fulgidus/enzymology/genetics, Carboxylesterase/antagonists & inhibitors/chemistry/genetics/isolation & purification, *Cloning, Molecular, Enzyme Stability, Kinetics, Molecular Sequence Data, Nitrophenols/pharmacology, Organic Chemicals/pharmacology, Sequence Alignment, Sequence Analysis, Protein, Surface-Active Agents/pharmacology, Temperature	Phylogeny
Phylogeny	18808198	Nucleotide triplet based molecular phylogeny of class I and class II aminoacyl t-RNA synthetase in three domain of life process: bacteria, archaea, and eukarya.	Mondal UK, Das B, Ghosh TC, Sen A, Bothra AK	J Biomol Struct Dyn	10.1080/07391102.2008.10507247	2008	Amino Acyl-tRNA Synthetases/genetics, Archaea/genetics, Bacteria/genetics, Base Sequence, Eukaryotic Cells, Evolution, Molecular, Molecular Sequence Data, Nucleotides/genetics, Phylogeny, RNA, Transfer/genetics, Sequence Alignment	Genetics
Metabolism	19624709	Temperature effect on the sulfur isotope fractionation during sulfate reduction by two strains of the hyperthermophilic Archaeoglobus fulgidus.	Mitchell K, Heyer A, Canfield DE, Hoek J, Habicht KS	Environ Microbiol	10.1111/j.1462-2920.2009.02002.x	2009	Archaeoglobus fulgidus/growth & development/metabolism, Chemical Fractionation, Extreme Heat, Sulfates/metabolism, Sulfur Isotopes, Temperature
Proteome	19768810	The crystal structure of the AF2331 protein from Archaeoglobus fulgidus DSM 4304 forms an unusual interdigitated dimer with a new type of alpha + beta fold.	Wang S, Kirillova O, Chruszcz M, Gront D, Zimmerman MD, Cymborowski MT, Shumilin IA, Skarina T, Gorodichtchenskaia E, Savchenko A, Edwards AM, Minor W	Protein Sci	10.1002/pro.251	2009	Archaeal Proteins/chemistry/genetics/metabolism, Archaeoglobus fulgidus/genetics, Computational Biology, Crystallography, X-Ray, Models, Molecular, Protein Conformation, Protein Folding, Protein Multimerization/genetics, Protein Structure, Tertiary/*genetics	Metabolism
Metabolism	24096454	Phenylalanine catabolism in Archaeoglobus fulgidus VC-16.	Parthasarathy A, Kahnt J, Chowdhury NP, Buckel W	Arch Microbiol	10.1007/s00203-013-0925-3	2013	Archaeoglobus fulgidus/classification/enzymology/growth & development/metabolism, Enzymes/isolation & purification/metabolism, Fermentation, Oxidation-Reduction, Phenylalanine/metabolism, Phylogeny, Sulfates/metabolism	Phylogeny
Metabolism	24763368	Anaerobic oxidation of long-chain n-alkanes by the hyperthermophilic sulfate-reducing archaeon, Archaeoglobus fulgidus.	Khelifi N, Amin Ali O, Roche P, Grossi V, Brochier-Armanet C, Valette O, Ollivier B, Dolla A, Hirschler-Rea A	ISME J	10.1038/ismej.2014.58	2014	Alkanes/metabolism, Anaerobiosis, Archaeal Proteins/chemistry/classification/genetics/metabolism, Archaeoglobus fulgidus/enzymology/genetics/growth & development/metabolism, Fatty Acids/metabolism, Hot Temperature, Oxidation-Reduction, Phylogeny, Sulfates/metabolism	Phylogeny
Metabolism	25661815	Improved enantioselectivity of thermostable esterase from Archaeoglobus fulgidus toward (S)-ketoprofen ethyl ester by directed evolution and characterization of mutant esterases.	Kim J, Kim S, Yoon S, Hong E, Ryu Y	Appl Microbiol Biotechnol	10.1007/s00253-015-6422-7	2015	Archaeoglobus fulgidus/enzymology/genetics, Directed Molecular Evolution, Enzyme Stability, Esterases/chemistry/genetics/metabolism, Esters/metabolism, Hot Temperature, Ketoprofen/*metabolism, Models, Molecular, Mutant Proteins/chemistry/genetics/metabolism, Polymerase Chain Reaction, Protein Conformation, Substrate Specificity	Enzymology
Metabolism	26345487	Assessment of the Carbon Monoxide Metabolism of the Hyperthermophilic Sulfate-Reducing Archaeon Archaeoglobus fulgidus VC-16 by Comparative Transcriptome Analyses.	Hocking WP, Roalkvam I, Magnussen C, Stokke R, Steen IH	Archaea	10.1155/2015/235384	2015	Archaeoglobus fulgidus/genetics/growth & development/metabolism, Carbon Monoxide/metabolism, Energy Metabolism, Gene Expression Profiling, Metabolic Networks and Pathways/genetics, Oxidation-Reduction, Sulfates/*metabolism	Transcriptome
	32595611	Rate and Extent of Growth of a Model Extremophile, Archaeoglobus fulgidus, Under High Hydrostatic Pressures.	Oliver GC, Cario A, Rogers KL	Front Microbiol	10.3389/fmicb.2020.01023	2020
Enzymology	33776585	Structural and Kinetic Characterization of Hyperthermophilic NADH-Dependent Persulfide Reductase from Archaeoglobus fulgidus.	Shabdar S, Anaclet B, Castineiras AG, Desir N, Choe N, Crane EJ 3rd, Sazinsky MH	Archaea	10.1155/2021/8817136	2021	Archaeoglobus fulgidus, NAD, Oxidoreductases, Shewanella, Sulfides

Reference

@id	authors	catalogue	doi/url	title	journal	pubmed
1648	Curators of the DSMZ	Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 4304)	https://www.dsmz.de/collection/catalogue/details/culture/DSM-4304
20215	Parte, A.C., Sardà Carbasse, J., Meier-Kolthoff, J.P., Reimer, L.C. and Göker, M.		10.1099/ijsem.0.004332	List of Prokaryotic names with Standing in Nomenclature (LPSN) moves to the DSMZ
66792	Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmann		https://diaspora-project.de/progress.html#genomes	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		10.1093/nar/gkaa1025	BRENDA, the ELIXIR core data resource in 2021: new developments and updates	Nucleic Acids Res. 49: D498-D508 2020	33211880
67770	Curators of the JCM		https://jcm.brc.riken.jp/en/
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.		https://microbeatlas.org/	MicrobeAtlas 1.0 beta
87084	Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.		10.60712/SI-ID46110.1	StrainInfo: A central database for resolving microbial strain identifiers
125438	Julia Koblitz, Lorenz Christian Reimer, Rüdiger Pukall, Jörg Overmann		10.1101/2024.08.12.607695	Predicting bacterial phenotypic traits through improved machine learning using high-quality, curated datasets
125439	Philipp Münch, René Mreches, Martin Binder, Hüseyin Anil Gündüz, Xiao-Yin To, Alice McHardy		https://github.com/GenomeNet/deepG	deepG: Deep Learning for Genome Sequence Data. R package version 0.3.1