Name: Dysgonomonas oryzarvi Dy73
Creator: BacDive
License: http://creativecommons.org/licenses/by-nc/4.0/

Strain identifier

BacDive ID: 140047

Type strain:

Species: Dysgonomonas oryzarvi

Strain Designation: Dy73

Culture col. no.: DSM 105828, JCM 16859, KCTC 5936

Strain history: <- Yumiko Kodama Univ. of Tokyo, Dy73

NCBI tax ID(s): 722737 (species)

SI-ID 398352

DSM 105828

Other strains from Dysgonomonas oryzarvi

D. oryzarvi

Section

Dysgonomonas oryzarvi Dy73 is a facultative anaerobe, mesophilic, Gram-negative bacterium that was isolated from broth sample of microbial fuel cell.

Gram-negative
ovoid-shaped
facultative anaerobe
mesophilic
16S sequence
Bacteria

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

	Last LPSN update	14-12-2023 (DD-MM-YYYY)
	Domain	"Bacteria"
	Phylum	*Bacteroidota*
	Class	*Bacteroidia*
	Order	*Bacteroidales*
	Family	*Dysgonomonadaceae*
	Genus	*Dysgonomonas*
	Species	**Dysgonomonas oryzarvi**
	Full Scientific Name (LPSN)	Dysgonomonas oryzarvi Kodama et al. 2012

Information on morphological and physiological properties Morphology

[Ref.: #30573]	Gram stain	negative
[Ref.: #67771]	Gram stain	negative

[Ref.: #30573]	Cell shape	ovoid-shaped
[Ref.: #67771]	Cell shape	rod-shaped

[Ref.: #30573]	Motility	no
[Ref.: #67771]	Motility	no

Information on culture and growth conditions Culture and growth conditions

[Ref.: #42654]

Culture medium

COLUMBIA BLOOD MEDIUM (DSMZ Medium 693)

[Ref.: #42654]

Culture medium growth

[Ref.: #42654]

Culture medium link

Medium recipe at MediaDive

[Ref.: #42654]

Culture medium composition

expand / minimize

[Ref.: #42654]

Culture medium

PYG MEDIUM (MODIFIED) (DSMZ Medium 104)

[Ref.: #42654]

Culture medium growth

[Ref.: #42654]

Culture medium link

Medium recipe at MediaDive

[Ref.: #42654]

Culture medium composition

expand / minimize

		Temperature
[Ref.: #42654]	growth	37 °C
[Ref.: #67770]	growth	37 °C
[Ref.: #67771]	growth	37 °C

[Ref.: #42654]	Temperature range	mesophilic
[Ref.: #67770]	Temperature range	mesophilic
[Ref.: #67771]	Temperature range	mesophilic

Information on physiology and metabolism Physiology and metabolism

[Ref.: #30573]	Oxygen tolerance	facultative anaerobe
[Ref.: #67771]	Oxygen tolerance	anaerobe

	Metabolite	Utilization activity	Kind of utilization tested
[Ref.: #30573]	arabinose ChEBI	+	carbon source
[Ref.: #30573]	cellobiose ChEBI	+	carbon source
[Ref.: #30573]	fructose ChEBI	+	carbon source
[Ref.: #30573]	galactose ChEBI	+	carbon source
[Ref.: #30573]	glucose ChEBI	+	carbon source
[Ref.: #30573]	lactose ChEBI	+	carbon source
[Ref.: #30573]	maltose ChEBI	+	carbon source
[Ref.: #30573]	mannose ChEBI	+	carbon source
[Ref.: #30573]	raffinose ChEBI	+	carbon source
[Ref.: #30573]	rhamnose ChEBI	+	carbon source
[Ref.: #30573]	ribose ChEBI	+	carbon source
[Ref.: #30573]	sucrose ChEBI	+	carbon source
[Ref.: #30573]	xylose ChEBI	+	carbon source
	Only first 10 entries are displayed. Click here to see all.

	Enzymes	Enzyme	Enzyme activity	EC number
[Ref.: #30573]		alkaline phosphatase	+	3.1.3.1
[Ref.: #30573]		alpha-galactosidase	+	3.2.1.22

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

[Ref.: #42654]	Sample type/isolated from	broth sample of microbial fuel cell
[Ref.: #42654]	Country	Japan
[Ref.: #42654]	Country ISO 3 Code	JPN
[Ref.: #42654]	Continent	Asia

[Ref.: #67770]	Sample type/isolated from	Microbial fuel cell

[Ref.: #67771]	Sample type/isolated from	From broth, cassette-electrode microbial fuel cell
[Ref.: #67771]	Country	Japan
[Ref.: #67771]	Country ISO 3 Code	JPN
[Ref.: #67771]	Continent	Asia
* marker position based on {}

Isolation sources categories

#Engineered	#Bioreactor	-
#Host	#Microbial	-

What are isolation sources categories?

[Ref.: #69479]

Global distribution of 16S sequence AB547446 (>99% sequence identity) for Dysgonomonas from Microbeatlas

Aquatic Samples	5965
Soil Samples	933
Animal Samples	4917
Plant Samples	388
Total Samples	12203

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

[Ref.: #42654]

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.: #42654]	Dysgonomonas oryzarvi gene for 16S rRNA, partial sequence	AB547446	1429	ENA	722737 tax ID

[Ref.: #42654]	GC-content	37.5 mol%	high performance liquid chromatography (HPLC)
[Ref.: #67771]	GC-content	37.5 mol%

Availability in culture collections External links

[Ref.: #42654]

Culture collection no.

DSM 105828, JCM 16859, KCTC 5936

[Ref.: #96466]

SI-ID 398352

Literature:

Topic	Title	Authors	Journal	DOI	Year
Phylogeny	Dysgonomonas oryzarvi sp. nov., isolated from a microbial fuel cell.	Kodama Y, Shimoyama T, Watanabe K	Int J Syst Evol Microbiol	10.1099/ijs.0.039040-0	2012	*

References

#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 )

#30573

Barberan A, Caceres Velazquez H, Jones S, Fierer N.: Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information. mSphere 2: 2017 ( DOI 10.1128/mSphere.00237-17 , PubMed 28776041 ) - originally annotated from #26904 (see below)

#42654

Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 105828

#67770 Japan Collection of Microorganism (JCM) ; Curators of the JCM;
#67771 Korean Collection for Type Cultures (KCTC) ; Curators of the KCTC;

#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 .

#96466

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-ID398352.1 )

#26904

IJSEM 3055 2012 ( DOI 10.1099/ijs.0.039040-0 , PubMed 22307505 )

* These data were automatically processed and therefore are not curated

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