Denitrovibrio acetiphilus (DSM 12809, NBRC 114555, N2460)

Name: Denitrovibrio acetiphilus (DSM 12809, NBRC 114555, N2460)
Creator: BacDive
License: http://creativecommons.org/licenses/by/4.0/

BacDive ID 3838

Type strain

Strain Designation N2460

Culture col. no. DSM 12809 NBRC 114555 N2460

NCBI tax ID(s) 522772 118000

Special Collections DSMZ

History <- S. Myhr, University of Bergen, Department of Microbiology, Bergen, Norway; N2460 <- S. Myhr {1995}

Links

Denitrovibrio acetiphilus N2460 is an anaerobe bacterium that was isolated from oil reservoir model column.

anaerobe genome sequence 16S sequence Bacteria

Name and taxonomic classification

SI-ID 49366

NBRC 114555,DSM 12809

@ref 20215

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

Domain Bacteria

Phylum Deferribacterota

Class Deferribacteres

Order Deferribacterales

Family Geovibrionaceae

Genus Denitrovibrio

Species Denitrovibrio acetiphilus

Full scientific name Denitrovibrio acetiphilus Myhr and Torsvik 2000

Morphology

Cell morphology

@ref	Gram stain	Confidence
125438	negative	96.546
125439	negative	99.8

Multimedia

@ref:	66793
multimedia content:	EM_DSM_12809_1.jpg
multimedia.multimedia content:	EM_DSM_12809_1.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
4832	DENITROVIBRIO MEDIUM (DSMZ Medium 881)		Medium recipe at MediaDive	Name: DENITROVIBRIO MEDIUM (DSMZ Medium 881) Composition: NaCl 19.9402 g/l Na2-fumarate 6.38086 g/l MgCl2 x 6 H2O 2.99103 g/l Na-acetate 1.63509 g/l Na2CO3 0.997009 g/l KH2PO4 0.997009 g/l Na2S x 9 H2O 0.498504 g/l KCl 0.498504 g/l NH4Cl 0.249252 g/l CaCl2 x 2 H2O 0.149551 g/l Na2SO4 0.0199402 g/l HCl 0.00249252 g/l FeCl2 x 4 H2O 0.00149551 g/l Sodium resazurin 0.000498504 g/l NaOH 0.000498504 g/l Pyridoxine hydrochloride 0.000299103 g/l Thiamine-HCl x 2 H2O 0.000199402 g/l Nicotinic acid 0.000199402 g/l CoCl2 x 6 H2O 0.000189432 g/l Vitamin B12 9.97009e-05 g/l Calcium pantothenate 9.97009e-05 g/l MnCl2 x 4 H2O 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)
4832	positive	growth	35

Physiology and metabolism

Oxygen tolerance

4832

Oxygen toleranceanaerobe

Spore formation

@ref	Spore formation	Confidence
125439		99.7

Pathway annotation

Computationally determined by

@ref	pathway	enzyme coverage	annotated reactions
66794	UDP-GlcNAc biosynthesis	100	3 of 3
66794	formaldehyde oxidation	100	3 of 3
66794	C4 and CAM-carbon fixation	100	8 of 8
66794	biotin biosynthesis	100	4 of 4
66794	coenzyme A metabolism	100	4 of 4
66794	sulfopterin metabolism	100	4 of 4
66794	palmitate biosynthesis	100	22 of 22
66794	CDP-diacylglycerol biosynthesis	100	2 of 2
66794	cis-vaccenate biosynthesis	100	2 of 2
66794	ppGpp biosynthesis	100	4 of 4
66794	suberin monomers biosynthesis	100	2 of 2
66794	folate polyglutamylation	100	1 of 1
66794	methylglyoxal degradation	100	5 of 5
66794	anapleurotic synthesis of oxalacetate	100	1 of 1
66794	chorismate metabolism	88.89	8 of 9
66794	lipid A biosynthesis	88.89	8 of 9
66794	molybdenum cofactor biosynthesis	88.89	8 of 9
66794	6-hydroxymethyl-dihydropterin diphosphate biosynthesis	87.5	7 of 8
66794	gluconeogenesis	87.5	7 of 8
66794	isoleucine metabolism	87.5	7 of 8
66794	heme metabolism	85.71	12 of 14
66794	reductive acetyl coenzyme A pathway	85.71	6 of 7
66794	ubiquinone biosynthesis	85.71	6 of 7
66794	1,4-dihydroxy-6-naphthoate biosynthesis	83.33	5 of 6
66794	vitamin B12 metabolism	82.35	28 of 34
66794	threonine metabolism	80	8 of 10
66794	hydrogen production	80	4 of 5
66794	peptidoglycan biosynthesis	80	12 of 15
66794	flavin biosynthesis	80	12 of 15
66794	photosynthesis	78.57	11 of 14
66794	tetrahydrofolate metabolism	78.57	11 of 14
66794	valine metabolism	77.78	7 of 9
66794	d-mannose degradation	77.78	7 of 9
66794	nitrate assimilation	77.78	7 of 9
66794	aspartate and asparagine metabolism	77.78	7 of 9
66794	vitamin B1 metabolism	76.92	10 of 13
66794	phenylalanine metabolism	76.92	10 of 13
66794	acetate fermentation	75	3 of 4
66794	glycogen biosynthesis	75	3 of 4
66794	glutamate and glutamine metabolism	75	21 of 28
66794	CMP-KDO biosynthesis	75	3 of 4
66794	proline metabolism	72.73	8 of 11
66794	NAD metabolism	72.22	13 of 18
66794	citric acid cycle	71.43	10 of 14
66794	cardiolipin biosynthesis	71.43	5 of 7
66794	leucine metabolism	69.23	9 of 13
66794	purine metabolism	68.09	64 of 94
66794	cyanate degradation	66.67	2 of 3
66794	serine metabolism	66.67	6 of 9
66794	octane oxidation	66.67	2 of 3
66794	selenocysteine biosynthesis	66.67	4 of 6
66794	L-lactaldehyde degradation	66.67	2 of 3
66794	acetoin degradation	66.67	2 of 3
66794	alanine metabolism	65.52	19 of 29
66794	vitamin B6 metabolism	63.64	7 of 11
66794	pyrimidine metabolism	62.22	28 of 45
66794	lysine metabolism	61.9	26 of 42
66794	isoprenoid biosynthesis	61.54	16 of 26
66794	oxidative phosphorylation	61.54	56 of 91
66794	methionine metabolism	61.54	16 of 26
66794	non-pathway related	60.53	23 of 38
66794	glycogen metabolism	60	3 of 5
66794	propionate fermentation	60	6 of 10
66794	starch degradation	60	6 of 10
66794	glycolysis	58.82	10 of 17
66794	tryptophan metabolism	57.89	22 of 38
66794	propanol degradation	57.14	4 of 7
66794	cysteine metabolism	55.56	10 of 18
66794	CO2 fixation in Crenarchaeota	55.56	5 of 9
66794	sulfate reduction	53.85	7 of 13
66794	urea cycle	53.85	7 of 13
66794	lipid metabolism	51.61	16 of 31
66794	glycolate and glyoxylate degradation	50	3 of 6
66794	aminopropanol phosphate biosynthesis	50	1 of 2
66794	adipate degradation	50	1 of 2
66794	pantothenate biosynthesis	50	3 of 6
66794	kanosamine biosynthesis II	50	1 of 2
66794	tyrosine metabolism	50	7 of 14
66794	butanoate fermentation	50	2 of 4
66794	ethanol fermentation	50	1 of 2
66794	lactate fermentation	50	2 of 4
66794	denitrification	50	1 of 2
66794	glycine metabolism	50	5 of 10
66794	toluene degradation	50	2 of 4
66794	phenylmercury acetate degradation	50	1 of 2
66794	arginine metabolism	50	12 of 24
66794	4-hydroxyphenylacetate degradation	50	5 of 10
66794	histidine metabolism	48.28	14 of 29
66794	degradation of hexoses	44.44	8 of 18
66794	polyamine pathway	43.48	10 of 23
66794	glutathione metabolism	42.86	6 of 14
66794	degradation of aromatic, nitrogen containing compounds	41.67	5 of 12
66794	arachidonate biosynthesis	40	2 of 5
66794	glycine betaine biosynthesis	40	2 of 5
66794	factor 420 biosynthesis	40	2 of 5
66794	lipoate biosynthesis	40	2 of 5
66794	ethylmalonyl-CoA pathway	40	2 of 5
66794	ketogluconate metabolism	37.5	3 of 8
66794	dTDPLrhamnose biosynthesis	37.5	3 of 8
66794	ascorbate metabolism	36.36	8 of 22
66794	pentose phosphate pathway	36.36	4 of 11
66794	enterobactin biosynthesis	33.33	1 of 3
66794	acetyl CoA biosynthesis	33.33	1 of 3
66794	(5R)-carbapenem carboxylate biosynthesis	33.33	1 of 3
66794	IAA biosynthesis	33.33	1 of 3
66794	degradation of pentoses	32.14	9 of 28
66794	phenol degradation	30	6 of 20
66794	Entner Doudoroff pathway	30	3 of 10
66794	myo-inositol biosynthesis	30	3 of 10
66794	coenzyme M biosynthesis	30	3 of 10
66794	metabolism of disaccharids	27.27	3 of 11
66794	androgen and estrogen metabolism	25	4 of 16
66794	methanogenesis from CO2	25	3 of 12
66794	degradation of sugar alcohols	25	4 of 16
66794	cyclohexanol degradation	25	1 of 4
66794	phenylpropanoid biosynthesis	23.08	3 of 13
66794	allantoin degradation	22.22	2 of 9

Isolation, sampling and environmental information

Isolation source categories

Cat1	Cat2	Cat3
#Engineered	#Industrial	#Oil reservoir

Isolation

@ref	Sample type	Country	Country ISO 3 Code	Continent
4832	oil reservoir model column	Norway	NOR	Europe

Taxonmaps

69479

Global distribution of 16S sequence AF146526 (>99% sequence identity) for Denitrovibrio acetiphilus subclade from Microbeatlas

Aquatic Samples	557
Soil Samples	36
Animal Samples	128
Plant Samples	41
Total Samples	762

Interaction and safety

Risk assessment

@ref	Biosafety level	Biosafety level comment
4832	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	ASM2572v1 assembly for Denitrovibrio acetiphilus DSM 12809	complete	GCA_000025725	522772.6	646564527	522772	98.91

16S sequences

@ref	Description	Accession	Length	Database	NCBI tax ID
4832	Denitrovibrio acetophilus 16S ribosomal RNA gene, partial sequence	AF146526	1516		522772

GC content

@ref	GC-content (mol%)	Method
4832	42.6	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: Denitrovibrio acetiphilus DSM 12809
PATRIC: 522772.6

@ref	Trait	Model	Prediction	Confidence in %	In training data
125439	spore_formation	BacteriaNetⓘ	no	99.70	no
125439	motility	BacteriaNetⓘ	no	56.30	no
125439	gram_stain	BacteriaNetⓘ	negative	99.80	no
125439	oxygen_tolerance	BacteriaNetⓘ	obligate anaerobe	69.60	no

Predictions from bacterial phenotypic traits through improved machine learning using high-quality, curated datasets based on: Denitrovibrio acetiphilus DSM 12809 DSM 12809
NCBI: GCA_000025725.1

@ref	Trait	Model	Prediction	Confidence in %	In training data
125438	gram-positive	gram-positiveⓘ	no	96.55	no
125438	anaerobic	anaerobicⓘ	yes	74.32	yes
125438	aerobic	aerobicⓘ	no	88.05	yes
125438	spore-forming	spore-formingⓘ	no	89.51	no
125438	thermophilic	thermophileⓘ	no	84.50	no
125438	flagellated	motile2+ⓘ	yes	71.20	no

Literature

Topic	Title	Authors	Journal	DOI	Year
	Reshaping UDP-binding pocket of bacterial sucrose synthase to improve efficiency of UDP-glucose production.	Li J, Li M, Yong C, Zhou Z, Han L, Liu Z.	Bioresour Technol	10.1016/j.biortech.2025.132396	2025
	Machine Learning Predicts Biogeochemistry from Microbial Community Structure in a Complex Model System.	Dutta A, Goldman T, Keating J, Burke E, Williamson N, Dirmeier R, Bowman JS.	Microbiol Spectr	10.1128/spectrum.01909-21	2022
Metabolism	Recent Origin of the Methacrylate Redox System in Geobacter sulfurreducens AM-1 through Horizontal Gene Transfer.	Arkhipova OV, Meer MV, Mikoulinskaia GV, Zakharova MV, Galushko AS, Akimenko VK, Kondrashov FA.	PLoS One	10.1371/journal.pone.0125888	2015
	Impact of Antibiotic-Induced Depletion of Gut Microbiota and Selenium Supplementation on Plasma Selenoproteome and Metal Homeostasis in a Mice Model.	Callejon-Leblic B, Selma-Royo M, Collado MC, Abril N, Garcia-Barrera T.	J Agric Food Chem	10.1021/acs.jafc.1c02622	2021
Metabolism	Identification of Residues in the Lipopolysaccharide ABC Transporter That Coordinate ATPase Activity with Extractor Function.	Simpson BW, Owens TW, Orabella MJ, Davis RM, May JM, Trauger SA, Kahne D, Ruiz N.	mBio	10.1128/mbio.01729-16	2016
Metabolism	Identification of an enzyme system for daidzein-to-equol conversion in Slackia sp. strain NATTS.	Tsuji H, Moriyama K, Nomoto K, Akaza H.	Appl Environ Microbiol	10.1128/aem.06779-11	2012
	nifPred: Proteome-Wide Identification and Categorization of Nitrogen-Fixation Proteins of Diaztrophs Based on Composition-Transition-Distribution Features Using Support Vector Machine.	Meher PK, Sahu TK, Mohanty J, Gahoi S, Purru S, Grover M, Rao AR.	Front Microbiol	10.3389/fmicb.2018.01100	2018
Metabolism	Distribution of glucan-branching enzymes among prokaryotes.	Suzuki E, Suzuki R.	Cell Mol Life Sci	10.1007/s00018-016-2243-9	2016
	Evolution of endonuclease IV protein family: an in silico analysis.	Kanchan S, Sharma P, Chowdhury S.	3 Biotech	10.1007/s13205-019-1696-6	2019
	Complete genome sequence of Dehalogenimonas lykanthroporepellens type strain (BL-DC-9(T)) and comparison to "Dehalococcoides" strains.	Siddaramappa S, Challacombe JF, Delano SF, Green LD, Daligault H, Bruce D, Detter C, Tapia R, Han S, Goodwin L, Han J, Woyke T, Pitluck S, Pennacchio L, Nolan M, Land M, Chang YJ, Kyrpides NC, Ovchinnikova G, Hauser L, Lapidus A, Yan J, Bowman KS, da Costa MS, Rainey FA, Moe WM.	Stand Genomic Sci	10.4056/sigs.2806097	2012
	The zinc-ribbon domain of Helicobacter pylori HP0958: requirement for RpoN accumulation and possible roles of homologs in other bacteria.	Pereira LE, Tsang J, Mrazek J, Hoover TR.	Microb Inform Exp	10.1186/2042-5783-1-8	2011
	Veillonella, Firmicutes: Microbes disguised as Gram negatives.	Vesth T, Ozen A, Andersen SC, Kaas RS, Lukjancenko O, Bohlin J, Nookaew I, Wassenaar TM, Ussery DW.	Stand Genomic Sci	10.4056/sigs.2981345	2013
Genetics	Genomic Analysis of Caldithrix abyssi, the Thermophilic Anaerobic Bacterium of the Novel Bacterial Phylum Calditrichaeota.	Kublanov IV, Sigalova OM, Gavrilov SN, Lebedinsky AV, Rinke C, Kovaleva O, Chernyh NA, Ivanova N, Daum C, Reddy TB, Klenk HP, Spring S, Goker M, Reva ON, Miroshnichenko ML, Kyrpides NC, Woyke T, Gelfand MS, Bonch-Osmolovskaya EA.	Front Microbiol	10.3389/fmicb.2017.00195	2017
Metabolism	Emergence of cytochrome bc complexes in the context of photosynthesis.	Dibrova DV, Shalaeva DN, Galperin MY, Mulkidjanian AY.	Physiol Plant	10.1111/ppl.12586	2017
Genetics	Pre_GI: a global map of ontological links between horizontally transferred genomic islands in bacterial and archaeal genomes.	Pierneef R, Cronje L, Bezuidt O, Reva ON.	Database (Oxford)	10.1093/database/bav058	2015
Metabolism	Evolution and multiplicity of arginine decarboxylases in polyamine biosynthesis and essential role in Bacillus subtilis biofilm formation.	Burrell M, Hanfrey CC, Murray EJ, Stanley-Wall NR, Michael AJ.	J Biol Chem	10.1074/jbc.m110.163154	2010
	Annotation of Protein Domains Reveals Remarkable Conservation in the Functional Make up of Proteomes Across Superkingdoms.	Nasir A, Naeem A, Khan MJ, Nicora HD, Caetano-Anolles G.	Genes (Basel)	10.3390/genes2040869	2011
	Genomic analyses of bacterial porin-cytochrome gene clusters.	Shi L, Fredrickson JK, Zachara JM	Front Microbiol	10.3389/fmicb.2014.00657	2014
Enzymology	Identification of a possible respiratory arsenate reductase in Denitrovibrio acetiphilus, a member of the phylum Deferribacteres.	Denton K, Atkinson MM, Borenstein SP, Carlson A, Carroll T, Cullity K, Demarsico C, Ellowitz D, Gialtouridis A, Gore R, Herleikson A, Ling AY, Martin R, McMahan K, Naksukpaiboon P, Seiz A, Yearwood K, O'Neill J, Wiatrowski H	Arch Microbiol	10.1007/s00203-013-0915-5	2013
Metabolism	Precipitation of alacranite (As8S9) by a novel As(V)-respiring anaerobe strain MPA-C3.	Mumford AC, Yee N, Young LY	Environ Microbiol	10.1111/1462-2920.12136	2013
Genetics	Complete genome sequence of Denitrovibrio acetiphilus type strain (N2460).	Kiss H, Lang E, Lapidus A, Copeland A, Nolan M, Glavina Del Rio T, Chen F, Lucas S, Tice H, Cheng JF, Han C, Goodwin L, Pitluck S, Liolios K, Pati A, Ivanova N, Mavromatis K, Chen A, Palaniappan K, Land M, Hauser L, Chang YJ, Jeffries CD, Detter JC, Brettin T, Spring S, Rohde M, Goker M, Woyke T, Bristow J, Eisen JA, Markowitz V, Hugenholtz P, Kyrpides NC, Klenk HP	Stand Genomic Sci	10.4056/sigs.892105	2010
Phylogeny	Denitrovibrio acetiphilus, a novel genus and species of dissimilatory nitrate-reducing bacterium isolated from an oil reservoir model column.	Myhr S, Torsvik T	Int J Syst Evol Microbiol	10.1099/00207713-50-4-1611	2000

References

#4832	Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 12809
#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) .
#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 )
#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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Denitrovibrio acetiphilus (DSM 12809, NBRC 114555, N2460)

Name and taxonomic classification

Morphology

Cell morphology

Multimedia

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_000025725

16S sequences

GC content

Genome-based predictions

Predictions

Literature

Literature

References

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