Nitratidesulfovibrio oxamicus (DSM 1925, ATCC 33405, NCIMB 9442)

Name: Nitratidesulfovibrio oxamicus (DSM 1925, ATCC 33405, NCIMB 9442)
Creator: BacDive
License: http://creativecommons.org/licenses/by/4.0/

BacDive ID 4104

Type strain

Culture col. no. DSM 1925 ATCC 33405 NCIMB 9442 VKM B-1766 Monticello 2

NCBI tax ID(s) 32016

Special Collections DSMZ

History DSMZ <- NCIB <- J.R. Postgate, strain Monticello 2

Links

Nitratidesulfovibrio oxamicus DSM 1925 is an anaerobe bacterium that was isolated from mud.

anaerobe genome sequence 16S sequence Bacteria

Name and taxonomic classification

SI-ID 311074

ATCC 33405,NCIB 9442,DSM 1925,VKM B-1766,NCIMB 9442

@ref 20215

Last LPSN update 2026-05-29 08:25:51

Domain Bacteria

Phylum Thermodesulfobacteriota

Class Desulfovibrionia

Order Desulfovibrionales

Family Desulfovibrionaceae

Genus Nitratidesulfovibrio

Species Nitratidesulfovibrio oxamicus

Full scientific name Nitratidesulfovibrio oxamicus (Postgate and Campbell 1966) Waite et al. 2020

Synonyms (3)

Desulfovibrio vulgaris subsp. oxamicus
Desulfovibrio oxamicus
Cupidesulfovibrio oxamicus

Morphology

Cell morphology

@ref	Gram stain	Confidence
125438	negative	95.691

Culture and growth conditions

Culture medium

@ref	Name	Growth	Medium link	Composition
669	DESULFOVIBRIO (POSTGATE) MEDIUM (DSMZ Medium 63)		Medium recipe at MediaDive	Name: DESULFOVIBRIO (POSTGATE) MEDIUM (DSMZ Medium 63) Composition: MgSO4 x 7 H2O 2.0 g/l Na-DL-lactate 2.0 g/l NH4Cl 1.0 g/l Yeast extract 1.0 g/l Na2SO4 1.0 g/l FeSO4 x 7 H2O 0.5 g/l K2HPO4 0.5 g/l CaCl2 x 2 H2O 0.1 g/l Na-thioglycolate 0.1 g/l Ascorbic acid 0.1 g/l Sodium resazurin 0.0005 g/l Distilled water

Culture temp

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

Physiology and metabolism

Oxygen tolerance

@ref	Oxygen tolerance	Confidence
669	anaerobe
125439	facultative anaerobe	92.641

Spore formation

@ref	Spore formation	Confidence
125439		97.658

Isolation, sampling and environmental information

Isolation source categories

Cat1	Cat2	Cat3
#Environmental	#Terrestrial	#Mud (Sludge)

Isolation

@ref	Sample type	Geographic location	Country	Country ISO 3 Code	Continent
669	mud	Illinois, Monticello near Urbana	USA	USA	North America

Taxonmaps

69479

Global distribution of 16S sequence DQ122124 (>99% sequence identity) for Desulfovibrionaceae from Microbeatlas

Aquatic Samples	25
Soil Samples	1
Animal Samples	6
Plant Samples	3
Total Samples	35

Interaction and safety

Risk assessment

@ref	Biosafety level	Biosafety level comment
669	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	ASM1573176v1 assembly for Nitratidesulfovibrio oxamicus NCIMB 9442	contig	GCA_015731765	32016.3	8063188021	32016	0

16S sequences

@ref	Description	Accession	Length	Database	NCBI tax ID
20218	Desulfovibrio oxamicus partial 16S rRNA gene, type strain DSM 1925T	AJ295677	1189		32016
669	Desulfovibrio oxamicus strain DSM 1925 16S ribosomal RNA gene, partial sequence	DQ122124	1513		32016

Genome-based predictions

Predictions

Predictions from Deep Learning for Genome Sequence Data. R package version 0.3.1 based on: ASM1573176v1 assembly for Nitratidesulfovibrio oxamicus NCIMB 9442
BV-BRC: 32016.3

@ref	Trait	Model	Prediction	Confidence in %	In training data
125439	oxygen_tolerance	BacteriaNetⓘ	facultative anaerobe	92.64	no
125439	gram_stain	BacteriaNetⓘ	negative	76.57	no
125439	motility	BacteriaNetⓘ	yes	58.36	no
125439	spore_formation	BacteriaNetⓘ	no	97.66	no

Predictions from bacterial phenotypic traits through improved machine learning using high-quality, curated datasets based on: Desulfovibrio oxamicus strain NCIMB 9442 strain not collected
PATRIC: 32016.3

@ref	Trait	Model	Prediction	Confidence in %	In training data
125438	gram-positive	gram-positiveⓘ	no	95.69	no
125438	anaerobic	anaerobicⓘ	yes	79.46	yes
125438	spore-forming	spore-formingⓘ	no	86.18	no
125438	aerobic	aerobicⓘ	no	87.23	yes
125438	thermophilic	thermophileⓘ	no	92.84	yes
125438	flagellated	motile2+ⓘ	yes	78.18	no

Literature

Topic	Title	Authors	Journal	DOI	Year
Genetics	Establishment of Genome Based Criteria for Classification of the Family Desulfovibrionaceae and Proposal of Two Novel Genera, Alkalidesulfovibrio gen. nov. and Salidesulfovibrio gen. nov.	Park MJ, Kim YJ, Park M, Yu J, Namirimu T, Roh YR, Kwon KK.	Front Microbiol	10.3389/fmicb.2022.738205	2022
Metabolism	Microbial ecology of arsenic-mobilizing Cambodian sediments: lithological controls uncovered by stable-isotope probing.	Hery M, Rizoulis A, Sanguin H, Cooke DA, Pancost RD, Polya DA, Lloyd JR	Environ Microbiol	10.1111/1462-2920.12412	2014
Phylogeny	Cupidesulfovibrio liaohensis gen. nov., sp. nov., a novel sulphate-reducing bacterium isolated from an oil reservoir and reclassification of Desulfovibrio oxamicus and Desulfovibrio termitidis as Cupidesulfovibrio oxamicus comb. nov. and Cupidesulfovibrio termitidis comb. nov.	Wan YY, Luo N, Liu XL, Lai QL, Goodfellow M	Int J Syst Evol Microbiol	10.1099/ijsem.0.004618	2021
Phylogeny	Reclassification of the sulfate- and nitrate-reducing bacterium Desulfovibrio vulgaris subsp. oxamicus as Desulfovibrio oxamicus sp. nov., comb. nov.	Lopez-Cortes A, Fardeau ML, Fauque G, Joulian C, Ollivier B	Int J Syst Evol Microbiol	10.1099/ijs.0.64074-0	2006

References

#669	Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 1925
#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 )
#20218	Verslyppe, B., De Smet, W., De Baets, B., De Vos, P., Dawyndt P.: StrainInfo introduces electronic passports for microorganisms.. Syst Appl Microbiol. 37: 42 - 50 2014 ( DOI 10.1016/j.syapm.2013.11.002 , PubMed 24321274 )
#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) .
#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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Nitratidesulfovibrio oxamicus (DSM 1925, ATCC 33405, NCIMB 9442)

Name and taxonomic classification

Morphology

Cell morphology

Culture and growth conditions

Culture medium

Culture temp

Physiology and metabolism

Oxygen tolerance

Spore formation

Isolation, sampling and environmental information

Isolation source categories

Isolation

Taxonmaps

Interaction and safety

Risk assessment

Sequence information

Genome sequences

Genome browser: GCA_015731765

16S sequences

Genome-based predictions

Predictions

Literature

Literature

References

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