Name: Nitratidesulfovibrio oxamicus DSM 1925
Creator: BacDive
License: https://creativecommons.org/licenses/by/4.0/

Strain identifier

BacDive ID: 4104

Type strain:

Species: Nitratidesulfovibrio oxamicus

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

Strain history: <- NCIB <- J.R. Postgate, strain Monticello 2

NCBI tax ID(s): 32016 (species)

SI-ID 311074

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

Special Collections

DSMZ

Section

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

motile
anaerobe
16S sequence
Bacteria
genome sequence

Information on the name and the taxonomic classification. Name and taxonomic classification

	Last LPSN update	14-12-2023 (DD-MM-YYYY)
	Domain	"Bacteria"
	Phylum	*Pseudomonadota*
	Class	*Deltaproteobacteria*
	Order	*Desulfovibrionales*
	Family	*Desulfovibrionaceae*
	Genus	*Nitratidesulfovibrio*
	Species	**Nitratidesulfovibrio oxamicus**
	Full Scientific Name (LPSN)	Nitratidesulfovibrio oxamicus (Postgate and Campbell 1966) Waite et al. 2020

	Synonym	Cupidesulfovibrio oxamicus
	Synonym	Desulfovibrio vulgaris subsp. oxamicus
	Synonym	Desulfovibrio oxamicus

Information on morphological and physiological properties Morphology

[Ref.: #69480]	Gram stain	negative Confidence in %95.691

Information on culture and growth conditions Culture and growth conditions

[Ref.: #669]

Culture medium

DESULFOVIBRIO (POSTGATE) MEDIUM (DSMZ Medium 63)

[Ref.: #669]

Culture medium growth

[Ref.: #669]

Culture medium link

Medium recipe at MediaDive

[Ref.: #669]

Culture medium composition

expand / minimize

	Temperatures	Kind of temperature		Temperature
[Ref.: #669]			growth	30 °C

Information on physiology and metabolism Physiology and metabolism

[Ref.: #669]

Oxygen tolerance

anaerobe

Information on isolation source, the sampling and environmental conditions Isolation, sampling and environmental information

[Ref.: #669]	Sample type/isolated from	mud
[Ref.: #669]	Geographic location (country and/or sea, region)	Illinois, Monticello near Urbana
[Ref.: #669]	Country	USA
[Ref.: #669]	Country ISO 3 Code	USA
[Ref.: #669]	Continent	North America
* marker position based on {}

Isolation sources categories

#Environmental

#Terrestrial

#Mud (Sludge)

What are isolation sources categories?

[Ref.: #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

Information on possible application of the strain and its possible interaction with e.g. potential hosts Safety information

[Ref.: #669]

Biosafety level

Risk group (German classification)
According to TRBA 466

Information on genomic background e.g. entries in nucleic sequence databass Sequence information

16S Sequence information:

	Sequence accession description	Seq. accession number	Sequence length (bp)	Sequence database	Associated NCBI tax ID
[Ref.: #669]	Desulfovibrio oxamicus strain DSM 1925 16S ribosomal RNA gene, partial sequence	DQ122124	1513	GenBank ENA	32016 tax ID
[Ref.: #20218]	Desulfovibrio oxamicus partial 16S rRNA gene, type strain DSM 1925T	AJ295677	1189	GenBank ENA	32016 tax ID	*

Genome sequence information:

	Sequence accession description	Seq. accession number	Assembly level	Sequence database	Associated NCBI tax ID
[Ref.: #66792]	Cupidesulfovibrio oxamicus NCIMB 9442	GCA_015731765	contig	GenBank ENA	32016 tax ID	*
[Ref.: #66792]	Desulfovibrio oxamicus strain NCIMB 9442 strain not collected	32016.3	wgs	PATRIC	32016 tax ID	*

Data predicted using genome information as a basis Genome-based predictions

	Trait	Model	Prediction	Confidence in %	In training data
	Predictions from GenomeNet Sporulation v. 1 based on: Desulfovibrio oxamicus strain NCIMB 9442 strain not collected PATRIC: 32016.3
[Ref.: #69481]	spore-forming	spore-formingⓘ	no	79	no

	Trait	Model	Prediction	Confidence in %	In training data
	Predictions from Diaspora project based on: Desulfovibrio oxamicus strain NCIMB 9442 strain not collected PATRIC: 32016.3
[Ref.: #69480]	gram-positive	gram-positiveⓘ	no	95.691	no
[Ref.: #69480]	anaerobic	anaerobicⓘ	yes	79.457	yes
[Ref.: #69480]	spore-forming	spore-formingⓘ	no	86.182	no
[Ref.: #69480]	aerobic	aerobicⓘ	no	87.23	yes
[Ref.: #69480]	thermophilic	thermophileⓘ	no	92.841	yes
[Ref.: #69480]	flagellated	motile2+ⓘ	yes	78.175	no

Availability in culture collections External links

[Ref.: #669]

Culture collection no.

DSM 1925, ATCC 33405, NCIMB 9442, VKM B-1766, Monticello 2

[Ref.: #73607]

SI-ID 311074

Literature:

Topic	Title	Authors	Journal	DOI	Year
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	*
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	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 .

#69480

Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmann: Predictions based on genome sequence made in the Diaspora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information) .

#69481

Xiao-Yin To, René Mreches, Martin Binder, Alice C. McHardy, Philipp C. Münch: Predictions based on the model GenomeNet Sporulation v. 1 . ( DOI 10.21203/rs.3.rs-2527258/v1 )

#73607

Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.: StrainInfo: A central database for resolving microbial strain identifiers . ( DOI 10.60712/SI-ID311074.1 )

* These data were automatically processed and therefore are not curated

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Desulfovibrio oxamicus strain NCIMB 9442 strain not collected

Desulfovibrio oxamicus strain NCIMB 9442 strain not collected

Change proposal

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