Geovibrio thiophilus (DSM 11263, ATCC BAA-311, AAFu3)

Name: Geovibrio thiophilus (DSM 11263, ATCC BAA-311, AAFu3)
Creator: BacDive
License: http://creativecommons.org/licenses/by/4.0/

BacDive ID 3840

Type strain

Strain Designation AAFu3

Culture col. no. DSM 11263 ATCC BAA-311 AAFu3

NCBI tax ID(s) 139438

Special Collections DSMZ

History <- P. H. Janssen, University of Melbourne, Parkville, Australia; AAFu3 <- H. Platen {1989}

Links

Geovibrio thiophilus AAFu3 is an anaerobe bacterium that was isolated from methanogenic mixed culture growing with acetone.

anaerobe genome sequence 16S sequence Bacteria

Name and taxonomic classification

SI-ID 87758

ATCC BAA-311,DSM 11263

@ref 20215

Last LPSN update 2026-02-09 11:18:35

Domain Bacteria

Phylum Deferribacterota

Class Deferribacteres

Order Deferribacterales

Family Geovibrionaceae

Genus Geovibrio

Species Geovibrio thiophilus

Full scientific name Geovibrio thiophilus Janssen et al. 2002

Morphology

Cell morphology

@ref	Gram stain	Confidence
125438	negative	96.233
125439	negative	99.7

Culture and growth conditions

Culture medium

@ref	Name	Growth	Medium link	Composition
4270	ANAEROBIC FRESHWATER (FWM) MEDIUM (DSMZ Medium 503)		Medium recipe at MediaDive	Name: ANAEROBIC FRESHWATER (FWM) MEDIUM (DSMZ Medium 503; with strain-specific modifications) Composition: Sodium fumarate 3.19043 g/l Na2CO3 1.49551 g/l NaCl 0.997008 g/l Na acetate 0.817547 g/l KCl 0.498505 g/l MgCl2 x 6 H2O 0.398803 g/l Na2S x 9 H2O 0.299103 g/l NH4Cl 0.249252 g/l KH2PO4 0.199402 g/l CaCl2 x 2 H2O 0.149552 g/l HCl 0.00249252 g/l FeCl2 x 4 H2O 0.00149551 g/l Sodium resazurin 0.000498505 g/l NaOH 0.000498504 g/l Pyridoxine hydrochloride 0.000299103 g/l Nicotinic acid 0.000199402 g/l Thiamine-HCl x 2 H2O 0.000199402 g/l CoCl2 x 6 H2O 0.000189432 g/l Calcium pantothenate 9.97009e-05 g/l MnCl2 x 4 H2O 9.97009e-05 g/l Vitamin B12 9.97009e-05 g/l p-Aminobenzoic acid 7.97607e-05 g/l ZnCl2 6.97906e-05 g/l Na2MoO4 x 2 H2O 3.58923e-05 g/l NiCl2 x 6 H2O 2.39282e-05 g/l D-(+)-biotin 1.99402e-05 g/l H3BO3 5.98205e-06 g/l Na2WO4 x 2 H2O 3.98804e-06 g/l Na2SeO3 x 5 H2O 2.99103e-06 g/l CuCl2 x 2 H2O 1.99402e-06 g/l Distilled water

Culture temp

@ref	Growth	Type	Temperature (°C)
4270	positive	growth	30

Physiology and metabolism

Oxygen tolerance

4270

Oxygen toleranceanaerobe

Spore formation

@ref	Spore formation	Confidence
125439		99.6

Pathway annotation

Computationally determined by

@ref	pathway	enzyme coverage	annotated reactions
66794	palmitate biosynthesis	100	22 of 22
66794	adipate degradation	100	2 of 2
66794	UDP-GlcNAc biosynthesis	100	3 of 3
66794	glycine betaine biosynthesis	100	5 of 5
66794	CDP-diacylglycerol biosynthesis	100	2 of 2
66794	biotin biosynthesis	100	4 of 4
66794	denitrification	100	2 of 2
66794	sulfopterin metabolism	100	4 of 4
66794	coenzyme A metabolism	100	4 of 4
66794	ppGpp biosynthesis	100	4 of 4
66794	formaldehyde oxidation	100	3 of 3
66794	methylglyoxal degradation	100	5 of 5
66794	reductive acetyl coenzyme A pathway	100	7 of 7
66794	suberin monomers biosynthesis	100	2 of 2
66794	cis-vaccenate biosynthesis	100	2 of 2
66794	C4 and CAM-carbon fixation	100	8 of 8
66794	anapleurotic synthesis of oxalacetate	100	1 of 1
66794	folate polyglutamylation	100	1 of 1
66794	nitrate assimilation	88.89	8 of 9
66794	lipid A biosynthesis	88.89	8 of 9
66794	chorismate metabolism	88.89	8 of 9
66794	valine metabolism	88.89	8 of 9
66794	gluconeogenesis	87.5	7 of 8
66794	isoleucine metabolism	87.5	7 of 8
66794	ubiquinone biosynthesis	85.71	6 of 7
66794	heme metabolism	85.71	12 of 14
66794	1,4-dihydroxy-6-naphthoate biosynthesis	83.33	5 of 6
66794	vitamin B12 metabolism	82.35	28 of 34
66794	peptidoglycan biosynthesis	80	12 of 15
66794	hydrogen production	80	4 of 5
66794	threonine metabolism	80	8 of 10
66794	photosynthesis	78.57	11 of 14
66794	glutamate and glutamine metabolism	78.57	22 of 28
66794	tetrahydrofolate metabolism	78.57	11 of 14
66794	d-mannose degradation	77.78	7 of 9
66794	NAD metabolism	77.78	14 of 18
66794	aspartate and asparagine metabolism	77.78	7 of 9
66794	molybdenum cofactor biosynthesis	77.78	7 of 9
66794	phenylalanine metabolism	76.92	10 of 13
66794	vitamin B1 metabolism	76.92	10 of 13
66794	CMP-KDO biosynthesis	75	3 of 4
66794	acetate fermentation	75	3 of 4
66794	glycogen biosynthesis	75	3 of 4
66794	flavin biosynthesis	73.33	11 of 15
66794	cardiolipin biosynthesis	71.43	5 of 7
66794	citric acid cycle	71.43	10 of 14
66794	alanine metabolism	68.97	20 of 29
66794	purine metabolism	67.02	63 of 94
66794	acetoin degradation	66.67	2 of 3
66794	serine metabolism	66.67	6 of 9
66794	L-lactaldehyde degradation	66.67	2 of 3
66794	CO2 fixation in Crenarchaeota	66.67	6 of 9
66794	octane oxidation	66.67	2 of 3
66794	methionine metabolism	65.38	17 of 26
66794	glycolysis	64.71	11 of 17
66794	pyrimidine metabolism	64.44	29 of 45
66794	lysine metabolism	64.29	27 of 42
66794	proline metabolism	63.64	7 of 11
66794	6-hydroxymethyl-dihydropterin diphosphate biosynthesis	62.5	5 of 8
66794	sulfate reduction	61.54	8 of 13
66794	oxidative phosphorylation	61.54	56 of 91
66794	cysteine metabolism	61.11	11 of 18
66794	starch degradation	60	6 of 10
66794	propionate fermentation	60	6 of 10
66794	glycogen metabolism	60	3 of 5
66794	isoprenoid biosynthesis	57.69	15 of 26
66794	propanol degradation	57.14	4 of 7
66794	degradation of sugar alcohols	56.25	9 of 16
66794	pentose phosphate pathway	54.55	6 of 11
66794	vitamin B6 metabolism	54.55	6 of 11
66794	arginine metabolism	54.17	13 of 24
66794	leucine metabolism	53.85	7 of 13
66794	non-pathway related	52.63	20 of 38
66794	tryptophan metabolism	52.63	20 of 38
66794	lactate fermentation	50	2 of 4
66794	aminopropanol phosphate biosynthesis	50	1 of 2
66794	kanosamine biosynthesis II	50	1 of 2
66794	toluene degradation	50	2 of 4
66794	tyrosine metabolism	50	7 of 14
66794	butanoate fermentation	50	2 of 4
66794	ketogluconate metabolism	50	4 of 8
66794	glycine metabolism	50	5 of 10
66794	pantothenate biosynthesis	50	3 of 6
66794	ethanol fermentation	50	1 of 2
66794	lipid metabolism	48.39	15 of 31
66794	histidine metabolism	48.28	14 of 29
66794	urea cycle	46.15	6 of 13
66794	degradation of hexoses	44.44	8 of 18
66794	glutathione metabolism	42.86	6 of 14
66794	arachidonate biosynthesis	40	2 of 5
66794	3-chlorocatechol degradation	40	2 of 5
66794	factor 420 biosynthesis	40	2 of 5
66794	coenzyme M biosynthesis	40	4 of 10
66794	ethylmalonyl-CoA pathway	40	2 of 5
66794	Entner Doudoroff pathway	40	4 of 10
66794	polyamine pathway	39.13	9 of 23
66794	ascorbate metabolism	36.36	8 of 22
66794	degradation of pentoses	35.71	10 of 28
66794	selenocysteine biosynthesis	33.33	2 of 6
66794	acetyl CoA biosynthesis	33.33	1 of 3
66794	degradation of aromatic, nitrogen containing compounds	33.33	4 of 12
66794	IAA biosynthesis	33.33	1 of 3
66794	cyanate degradation	33.33	1 of 3
66794	(5R)-carbapenem carboxylate biosynthesis	33.33	1 of 3
66794	enterobactin biosynthesis	33.33	1 of 3
66794	glycolate and glyoxylate degradation	33.33	2 of 6
66794	phosphatidylethanolamine bioynthesis	30.77	4 of 13
66794	phenylpropanoid biosynthesis	30.77	4 of 13
66794	benzoyl-CoA degradation	28.57	2 of 7
66794	aclacinomycin biosynthesis	28.57	2 of 7
66794	metabolism of disaccharids	27.27	3 of 11
66794	d-xylose degradation	27.27	3 of 11
66794	3-phenylpropionate degradation	26.67	4 of 15
66794	phenol degradation	25	5 of 20
66794	cyclohexanol degradation	25	1 of 4
66794	dTDPLrhamnose biosynthesis	25	2 of 8

Isolation, sampling and environmental information

Isolation source categories

Cat1	Cat2	Cat3
#Engineered	#Laboratory	#Lab enrichment
#Condition	#Anoxic (anaerobic)	-

Isolation

@ref	Sample type	Geographic location	Country	Country ISO 3 Code	Continent
4270	methanogenic mixed culture growing with acetone	Konstanz, drainage ditch	Germany	DEU	Europe

Taxonmaps

69479

Global distribution of 16S sequence AJ299402 (>99% sequence identity) for Geovibrio thiophilus subclade from Microbeatlas

Aquatic Samples	14
Soil Samples	6
Animal Samples	2
Plant Samples
Total Samples	22

Interaction and safety

Risk assessment

@ref	Biosafety level	Biosafety level comment
4270	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	ASM408791v1 assembly for Geovibrio thiophilus DSM 11263	complete	GCA_004087915	139438.5	2836696539	139438	96.86

16S sequences

@ref	Description	Accession	Length	Database	NCBI tax ID
4270	Geovibrio thiophilus 16S rRNA gene	AJ299402	1474		139438

GC content

@ref	GC-content (mol%)	Method
4270	50.2	high performance liquid chromatography (HPLC)
4270	48.2	sequence analysis

Genome-based predictions

Predictions

Predictions from Deep Learning for Genome Sequence Data. R package version 0.3.1 based on: Geovibrio thiophilus strain DSM 11263
PATRIC: 139438.5

@ref	Trait	Model	Prediction	Confidence in %	In training data
125439	spore_formation	BacteriaNetⓘ	no	99.60	no
125439	motility	BacteriaNetⓘ	no	72.90	no
125439	gram_stain	BacteriaNetⓘ	negative	99.70	no
125439	oxygen_tolerance	BacteriaNetⓘ	obligate anaerobe	82.00	no

Predictions from bacterial phenotypic traits through improved machine learning using high-quality, curated datasets based on: Geovibrio thiophilus DSM 11263
NCBI: GCA_004087915.1

@ref	Trait	Model	Prediction	Confidence in %	In training data
125438	gram-positive	gram-positiveⓘ	no	96.23	no
125438	anaerobic	anaerobicⓘ	yes	78.53	yes
125438	aerobic	aerobicⓘ	no	79.79	yes
125438	spore-forming	spore-formingⓘ	no	82.74	no
125438	thermophilic	thermophileⓘ	no	86.84	yes
125438	flagellated	motile2+ⓘ	yes	73.22	no

Literature

Topic	Title	Authors	Journal	DOI	Year
Phylogeny	Geovibrio thiophilus sp. nov., a novel sulfur-reducing bacterium belonging to the phylum Deferribacteres.	Janssen PH, Liesack W, Schink B	Int J Syst Evol Microbiol	10.1099/00207713-52-4-1341	2002

References

#4270	Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 11263
#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 .
#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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Geovibrio thiophilus (DSM 11263, ATCC BAA-311, AAFu3)

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_004087915

16S sequences

GC content

Genome-based predictions

Predictions

Literature

Literature

References

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