Name: Pseudovibrio denitrificans DN34
Creator: BacDive
License: http://creativecommons.org/licenses/by-nc/4.0/

Strain identifier

BacDive ID: 13737

Type strain:

Species: Pseudovibrio denitrificans

Strain Designation: DN34

Culture col. no.: DSM 17465, BCRC 17323, JCM 12308, CIP 108640, IAM 15184, NBRC 100825

Strain history: CIP <- 2005, JCM <- 2003, W.Y. Shieh: strain DN34

NCBI tax ID(s): 1236962 (strain), 258256 (species)

SI-ID 134447

BCRC 17323, JCM 12308, NBRC 100825, CCRC 17323, CIP 108640, IAM 15184, DSM 17465

Other strains from Pseudovibrio denitrificans

P. denitrificans Fo-BEG1, DSM 100123

Section

Pseudovibrio denitrificans DN34 is a facultative anaerobe, mesophilic, Gram-negative bacterium that was isolated from sea water.

Gram-negative
motile
rod-shaped
facultative 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	*Alphaproteobacteria*
	Order	*Hyphomicrobiales*
	Family	*Stappiaceae*
	Genus	*Pseudovibrio*
	Species	**Pseudovibrio denitrificans**
	Full Scientific Name (LPSN)	Pseudovibrio denitrificans Shieh et al. 2004

Information on morphological and physiological properties Morphology

[Ref.: #31236]	Gram stain	negative
[Ref.: #118904]	Gram stain	negative
[Ref.: #69480]	Gram stain	negative Confidence in %99.994

[Ref.: #31236]	Cell length	3.25 µm

[Ref.: #31236]	Cell width	0.7 µm

[Ref.: #31236]	Cell shape	rod-shaped
[Ref.: #118904]	Cell shape	rod-shaped

[Ref.: #31236]	Motility	yes
[Ref.: #69480]	Motility	yes Confidence in %92.823

Information on culture and growth conditions Culture and growth conditions

[Ref.: #7004]

Culture medium

BACTO MARINE BROTH (DIFCO 2216) (DSMZ Medium 514)

[Ref.: #7004]

Culture medium growth

[Ref.: #7004]

Culture medium link

Medium recipe at MediaDive

[Ref.: #7004]

Culture medium composition

expand / minimize

[Ref.: #7004]

Culture medium

PY-BROTH (DSMZ Medium 1071)

[Ref.: #7004]

Culture medium growth

[Ref.: #7004]

Culture medium link

Medium recipe at MediaDive

[Ref.: #7004]

Culture medium composition

expand / minimize

[Ref.: #37444]

Culture medium

Marine agar (MA)

[Ref.: #37444]

Culture medium growth

[Ref.: #37444]

Culture medium composition

expand / minimize

[Ref.: #118904]

Culture medium

CIP Medium 13

[Ref.: #118904]

Culture medium growth

[Ref.: #118904]

Culture medium link

Medium recipe provided by DSMZ

	Kind of temperature		Temperature
[Ref.: #7004]		growth	28 °C
[Ref.: #31236]		optimum	30 °C
[Ref.: #37444]		growth	30 °C
[Ref.: #67770]		growth	30 °C
[Ref.: #118904]		growth	5-37 °C
[Ref.: #118904]	no	growth	41 °C
[Ref.: #118904]	no	growth	45 °C

[Ref.: #7004]	Temperature range	mesophilic
[Ref.: #31236]	Temperature range	mesophilic
[Ref.: #37444]	Temperature range	mesophilic
[Ref.: #67770]	Temperature range	mesophilic
[Ref.: #118904]	Temperature range	thermophilic

	pH	Kind of pH		pH
[Ref.: #31236]			optimum	8

Information on physiology and metabolism Physiology and metabolism

[Ref.: #31236]

Oxygen tolerance

facultative anaerobe

[Ref.: #69481]	Ability of spore formation	no Confidence in %100
[Ref.: #69480]	Ability of spore formation	no Confidence in %99.992

	Salt	Tested relation		Salt conc.
[Ref.: #31236]	NaCl		optimum	3	%
[Ref.: #118904]	NaCl		growth	2-8	%
[Ref.: #118904]	NaCl	no	growth	0	%
[Ref.: #118904]	NaCl	no	growth	10	%

	Metabolite	Utilization activity	Kind of utilization tested
[Ref.: #118904]	citrate ChEBI	-	carbon source
[Ref.: #118904]	esculin ChEBI	-	hydrolysis
[Ref.: #31236]	galactose ChEBI	+	carbon source
[Ref.: #31236]	glucose ChEBI	+	carbon source
[Ref.: #118904]	glucose ChEBI	+	degradation
[Ref.: #118904]	hippurate ChEBI	+	hydrolysis
[Ref.: #118904]	malonate ChEBI	-	assimilation
[Ref.: #31236]	mannose ChEBI	+	carbon source
[Ref.: #31236]	nitrate ChEBI	+	reduction
[Ref.: #118904]	nitrate ChEBI	+	builds gas from
[Ref.: #118904]	nitrate ChEBI	+	reduction
[Ref.: #118904]	nitrite ChEBI	+	builds gas from
[Ref.: #118904]	nitrite ChEBI	+	reduction
[Ref.: #31236]	sucrose ChEBI	+	carbon source
[Ref.: #31236]	trehalose ChEBI	+	carbon source
	Only first 10 entries are displayed. Click here to see all.

	Metabolite production	Metabolite	Production
[Ref.: #118904]		indole ChEBI	yes

	Physiological tests	Metabolite	Voges-Proskauer-test	Methylred-test
[Ref.: #118904]		acetoin ChEBI	-
[Ref.: #118904]		glucose ChEBI		-

	Enzyme	Enzyme activity	EC number
[Ref.: #68382]	acid phosphatase	+	3.1.3.2	* from API zym
[Ref.: #118904]	alcohol dehydrogenase	-	1.1.1.1
[Ref.: #68382]	alkaline phosphatase	+	3.1.3.1	* from API zym
[Ref.: #68382]	alpha-chymotrypsin	+	3.4.21.1	* from API zym
[Ref.: #68382]	alpha-fucosidase	-	3.2.1.51	* from API zym
[Ref.: #68382]	alpha-galactosidase	+	3.2.1.22	* from API zym
[Ref.: #68382]	alpha-glucosidase	+	3.2.1.20	* from API zym
[Ref.: #68382]	alpha-mannosidase	-	3.2.1.24	* from API zym
[Ref.: #118904]	amylase	-
[Ref.: #118904]	beta-galactosidase	+	3.2.1.23
[Ref.: #68382]	beta-galactosidase	-	3.2.1.23	* from API zym
[Ref.: #68382]	beta-glucosidase	-	3.2.1.21	* from API zym
[Ref.: #68382]	beta-glucuronidase	-	3.2.1.31	* from API zym
[Ref.: #118904]	caseinase	+	3.4.21.50
[Ref.: #31236]	catalase	+	1.11.1.6
[Ref.: #118904]	catalase	+	1.11.1.6
[Ref.: #68382]	cystine arylamidase	+	3.4.11.3	* from API zym
[Ref.: #31236]	cytochrome oxidase	+	1.9.3.1
[Ref.: #68382]	esterase (C 4)	+		* from API zym
[Ref.: #68382]	esterase lipase (C 8)	+		* from API zym
[Ref.: #118904]	gamma-glutamyltransferase	+	2.3.2.2
[Ref.: #31236]	gelatinase	+
[Ref.: #118904]	gelatinase	+
[Ref.: #118904]	lecithinase	-
[Ref.: #68382]	leucine arylamidase	+	3.4.11.1	* from API zym
[Ref.: #118904]	lipase	-
[Ref.: #68382]	lipase (C 14)	+		* from API zym
[Ref.: #118904]	lysine decarboxylase	+	4.1.1.18
[Ref.: #68382]	N-acetyl-beta-glucosaminidase	+	3.2.1.52	* from API zym
[Ref.: #68382]	naphthol-AS-BI-phosphohydrolase	+		* from API zym
[Ref.: #118904]	ornithine decarboxylase	-	4.1.1.17
[Ref.: #118904]	oxidase	+
[Ref.: #118904]	phenylalanine ammonia-lyase	-	4.3.1.24
[Ref.: #68382]	trypsin	+	3.4.21.4	* from API zym
[Ref.: #118904]	tryptophan deaminase	-
[Ref.: #118904]	tween esterase	-
[Ref.: #118904]	urease	-	3.5.1.5
[Ref.: #68382]	valine arylamidase	+		* from API zym
	Only first 10 entries are displayed. Click here to see all.

API® zym:

Note that the displayed test results represent raw data and therefore may deviate!

	API ID	Control	2-naphthyl phosphateAlkaline phosphatase	2-naphthyl butyrateEsterase (C 4)	2-naphtyl caprylateEsterase Lipase (C 8)	2-naphthyl myristateLipase (C 14)	L-leucyl-2-naphthylamideLeucine arylamidase	L-valyl-2-naphthylamideValine arylamidase	L-cystyl-2-naphthylamideCystine arylamidase	N-benzoyl-DL-arginine-2-naphthylamideTrypsin	N-glutaryl-phenylalanine-2-naphthylamidealpha- Chymotrypsin	2-naphthyl phosphateAcid phosphatase	Naphthol-AS-BI-phosphateNaphthol-AS-BI-phosphohydrolase	6-Br-2-naphthyl-alphaD-galactpyranosidealpha- Galactosidase	2-naphthyl-betaD-galactpyranosidebeta- Galactosidase	Naphthol-AS-BI-betaD-glucuronidebeta- Glucuronidase	2-naphthyl-alphaD-glucopyranosidealpha- Glucosidase	6-Br-2-naphthyl-betaD-glucopyranosidebeta- Glucosidase	1-naphthyl-N-acetyl-betaD-glucosaminideN-acetyl-beta- glucosaminidase	6-Br-2-naphthyl-alphaD-mannopyranosidealpha- Mannosidase	2-naphthyl-alphaL-fucopyranosidealpha- Fucosidase
[Ref.: #118904]	11352	-	+	+	+	+	+	+	+	+	+	+	+	+	-	-	+	-	+	-	-

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

[Ref.: #7004]	Sample type/isolated from	sea water
[Ref.: #7004]	Geographic location (country and/or sea, region)	Nanwan Bay
[Ref.: #7004]	Country	Taiwan
[Ref.: #7004]	Country ISO 3 Code	TWN
[Ref.: #7004]	Continent	Asia

[Ref.: #67770]	Sample type/isolated from	Seawater samples collected in Nanwan Bay
[Ref.: #67770]	Geographic location (country and/or sea, region)	Kenting National Park
[Ref.: #67770]	Country	Taiwan
[Ref.: #67770]	Country ISO 3 Code	TWN
[Ref.: #67770]	Continent	Asia

[Ref.: #118904]	Sample type/isolated from	Environment, Sea water
[Ref.: #118904]	Geographic location (country and/or sea, region)	Kenting National Park , Nanwan bay
[Ref.: #118904]	Country	Taiwan
[Ref.: #118904]	Country ISO 3 Code	TWN
[Ref.: #118904]	Continent	Asia
* marker position based on {}

Isolation sources categories

#Environmental

#Aquatic

#Marine

What are isolation sources categories?

[Ref.: #69479]

Global distribution of 16S sequence AY486423 (>99% sequence identity) for Pseudovibrio from Microbeatlas

Aquatic Samples	4843
Soil Samples	120
Animal Samples	523
Plant Samples	19
Total Samples	5505

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

[Ref.: #7004]	Biosafety level	1	Risk group (German classification) According to TRBA 466
[Ref.: #118904]	Biosafety level	2	Risk group (French classification)

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.: #7004]	Pseudovibrio denitrificans strain DN34 16S ribosomal RNA gene, partial sequence	AY486423	1434	ENA	258256 tax ID

Genome sequence information:

Only first 5 entries are displayed. Click here to see all.

	Sequence accession description	Seq. accession number	Assembly level	Sequence database	Associated NCBI tax ID
[Ref.: #67770]	Pseudovibrio denitrificans JCM 12308	GCA_001310815	contig	GenBank	1236962 tax ID
[Ref.: #67770]	Pseudovibrio denitrificans DSM 17465	GCA_900116575	contig	GenBank	258256 tax ID
[Ref.: #66792]	Pseudovibrio denitrificans JCM 12308	1236962.4	wgs	PATRIC	1236962 tax ID	*
[Ref.: #66792]	Pseudovibrio denitrificans strain DSM 17465	258256.6	wgs	PATRIC	258256 tax ID	*
[Ref.: #66792]	Pseudovibrio denitrificans DSM 17465	2693429873	draft	JGI IMG/M	258256 tax ID	*
[Ref.: #66792]	Pseudovibrio denitrificans JCM 12308	2681812989	draft	JGI IMG/M	1236962 tax ID	*

[Ref.: #7004]

GC-content

51.7 mol%

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: Pseudovibrio denitrificans JCM 12308 PATRIC: 1236962.4
[Ref.: #69481]	spore-forming	no	100	no

	Trait	Prediction	Confidence in %	In training data
	Predictions from Diaspora project based on: Pseudovibrio denitrificans JCM 12308 PATRIC: 1236962.4
[Ref.: #69480]	motile	yes	90.988	no
[Ref.: #69480]	gram-positive	no	98.217	yes
[Ref.: #69480]	anaerobic	no	98.292	yes
[Ref.: #69480]	aerobic	yes	86.429	yes
[Ref.: #69480]	halophile	yes	63.617	no
[Ref.: #69480]	spore-forming	no	94.529	no
[Ref.: #69480]	thermophile	no	97.822	yes
[Ref.: #69480]	glucose-util	yes	91.453	yes
[Ref.: #69480]	flagellated	yes	58.55	no
[Ref.: #69480]	glucose-ferment	no	83.458	no

Availability in culture collections External links

[Ref.: #7004]

Culture collection no.

DSM 17465, BCRC 17323, JCM 12308, CIP 108640, IAM 15184, NBRC 100825

[Ref.: #82919]

SI-ID 134447

Literature:

Topic	Title	Authors	Journal	DOI	Year
Phylogeny	Pseudovibrio denitrificans gen. nov., sp. nov., a marine, facultatively anaerobic, fermentative bacterium capable of denitrification.	Shieh WY, Lin YT, Jean WD	Int J Syst Evol Microbiol	10.1099/ijs.0.63107-0	2004	*

References

#7004

Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 17465

#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 )

#31236

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 #27560 (see below)

#37444 ; Curators of the CIP;

#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;

#68382

Automatically annotated from API zym .

#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 )

#82919

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-ID134447.1 )

#118904 Collection of Institut Pasteur ; Curators of the CIP; CIP 108640

#27560

IJSEM 2307 2004 ( DOI 10.1099/ijs.0.63107-0 , PubMed 15545476 )

* These data were automatically processed and therefore are not curated

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Pseudovibrio denitrificans JCM 12308

Pseudovibrio denitrificans JCM 12308

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