Name: Desulfomicrobium orale NY678
Creator: BacDive
License: http://creativecommons.org/licenses/by-nc/4.0/

Strain identifier

BacDive ID: 4059

Type strain:

Species: Desulfomicrobium orale

Strain Designation: NY678

Culture col. no.: DSM 12838, JCM 17150

Strain history: DSM 12838 <-- P. S. Langendijk NY678.

NCBI tax ID(s): 888061 (strain), 132132 (species)

SI-ID 49378

DSM 12838, JCM 17150

Section

Desulfomicrobium orale NY678 is an anaerobe, mesophilic, motile bacterium that was isolated from subgingival plaque of a patient with periodontitis.

motile
anaerobe
mesophilic
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	*Desulfomicrobiaceae*
	Genus	*Desulfomicrobium*
	Species	**Desulfomicrobium orale**
	Full Scientific Name (LPSN)	Desulfomicrobium orale Langendijk et al. 2001

Information on morphological and physiological properties Morphology

[Ref.: #69480]	Gram stain	negative Confidence in %99.999

[Ref.: #69480]	Motility	yes Confidence in %96.556

Information on culture and growth conditions Culture and growth conditions

[Ref.: #4846]

Culture medium

DESULFOVIBRIO (POSTGATE) MEDIUM (DSMZ Medium 63)

[Ref.: #4846]

Culture medium growth

[Ref.: #4846]

Culture medium link

Medium recipe at MediaDive

[Ref.: #4846]

Culture medium composition

expand / minimize

	Temperatures	Kind of temperature		Temperature
[Ref.: #4846]			growth	37 °C
[Ref.: #67770]			growth	37 °C

[Ref.: #4846]	Temperature range	mesophilic
[Ref.: #67770]	Temperature range	mesophilic

Information on physiology and metabolism Physiology and metabolism

[Ref.: #4846]	Oxygen tolerance	anaerobe
[Ref.: #69480]	Oxygen tolerance	anaerobe Confidence in %100

[Ref.: #69481]	Ability of spore formation	no Confidence in %100
[Ref.: #69480]	Ability of spore formation	no Confidence in %99.983

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

[Ref.: #4846]	Sample type/isolated from	subgingival plaque of a patient with periodontitis
[Ref.: #4846]	Country	Netherlands
[Ref.: #4846]	Country ISO 3 Code	NLD
[Ref.: #4846]	Continent	Europe

[Ref.: #67770]	Sample type/isolated from	Subgingival plaque of a patient with periodontitis
* marker position based on {}

Isolation sources categories

#Infection	#Inflammation	-
#Infection	#Patient	-
#Host Body-Site	#Oral cavity and airways	#Subgingival plaque

What are isolation sources categories?

[Ref.: #69479]

Global distribution of 16S sequence AJ251623 (>99% sequence identity) for Desulfomicrobium orale subclade from Microbeatlas

Aquatic Samples	470
Soil Samples	199
Animal Samples	5462
Plant Samples	63
Total Samples	6194

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

[Ref.: #4846]

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.: #4846]	Desulfomicrobium orale 16S rRNA gene, strain DSM12838	AJ251623	1475	ENA	888061 tax ID
[Ref.: #20218]	Desulfomicrobium orale gene for 16S ribosomal RNA, partial sequence, strain: JCM 17150	AB573871	1513	ENA	132132 tax ID	*

Genome sequence information:

	Sequence accession description	Seq. accession number	Assembly level	Sequence database	Associated NCBI tax ID
[Ref.: #66792]	Desulfomicrobium orale DSM 12838	GCA_001553625	complete	GenBank	888061 tax ID	*
[Ref.: #66792]	Desulfomicrobium orale DSM 12838	888061.5	complete	PATRIC	888061 tax ID	*
[Ref.: #66792]	Desulfomicrobium orale DSM 12838	2684623057	complete	JGI IMG/M	888061 tax ID	*

[Ref.: #4846]	GC-content	59.7 mol%	high performance liquid chromatography (HPLC)
[Ref.: #67770]	GC-content	59.5 mol%	high performance liquid chromatography (HPLC)

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

	Trait	Prediction	Confidence in %	In training data
	Predictions from GenomeNet Sporulation v. 1 based on: Desulfomicrobium orale DSM 12838 DSM 12838 NCBI: GCA_001553625.1
[Ref.: #69481]	spore-forming	no	100	no

	Trait	Prediction	Confidence in %	In training data
	Predictions from Diaspora project based on: Desulfomicrobium orale DSM 12838 DSM 12838 NCBI: GCA_001553625.1
[Ref.: #69480]	flagellated	no	57.282	no
[Ref.: #69480]	gram-positive	no	99.145	no
[Ref.: #69480]	anaerobic	yes	99.457	yes
[Ref.: #69480]	halophile	no	72.566	no
[Ref.: #69480]	spore-forming	no	96.242	no
[Ref.: #69480]	thermophile	no	75.804	yes
[Ref.: #69480]	glucose-util	no	72.026	no
[Ref.: #69480]	motile	yes	88.042	no
[Ref.: #69480]	aerobic	no	98.661	yes
[Ref.: #69480]	glucose-ferment	no	77.048	no

Availability in culture collections External links

[Ref.: #4846]

Culture collection no.

DSM 12838, JCM 17150

[Ref.: #73564]

SI-ID 49378

Literature:

Topic	Title	Authors	Journal	DOI	Year
Phylogeny	Oligoflexus tunisiensis gen. nov., sp. nov., a Gram-negative, aerobic, filamentous bacterium of a novel proteobacterial lineage, and description of Oligoflexaceae fam. nov., Oligoflexales ord. nov. and Oligoflexia classis nov.	Nakai R, Nishijima M, Tazato N, Handa Y, Karray F, Sayadi S, Isoda H, Naganuma T	Int J Syst Evol Microbiol	10.1099/ijs.0.060798-0	2014	*
Phylogeny	Isolation of Desulfomicrobium orale sp. nov. and Desulfovibrio strain NY682, oral sulfate-reducing bacteria involved in human periodontal disease.	Langendijk PS, Kulik EM, Sandmeier H, Meyer J, van der Hoeven JS	Int J Syst Evol Microbiol	10.1099/00207713-51-3-1035	2001	*

References

#4846

Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 12838

#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) .

#67770 Japan Collection of Microorganism (JCM) ; Curators of the JCM;

#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 )

#73564

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-ID49378.1 )

* These data were automatically processed and therefore are not curated

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Desulfomicrobium orale DSM 12838 DSM 12838

Desulfomicrobium orale DSM 12838 DSM 12838

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