Name: Pseudophaeobacter leonis 306
Creator: BacDive
License: https://creativecommons.org/licenses/by/4.0/

Strain identifier

BacDive ID: 24494

Type strain:

Species: Pseudophaeobacter leonis

Strain Designation: 306

Culture col. no.: DSM 25627, CIP 110369, UBOCC 3187

Strain history: CIP <- 2012, F. Gaboyer, IUER, Plouzane, France: strain 306

NCBI tax ID(s): 1144477 (species)

SI-ID 402045

DSM 25627, CIP 110369

Special Collections

Section

When using BacDive for research please cite our paper

Pseudophaeobacter leonis 306 is an aerobe, mesophilic, Gram-negative bacterium that was isolated from anoxic marine sediment beneath the sea floor.

Gram-negative
motile
rod-shaped
aerobe
mesophilic
16S sequence
Bacteria
genome sequence

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

	Last LPSN update	09-12-2024 (DD-MM-YYYY)
	Domain	*Bacteria*
	Phylum	*Pseudomonadota*
	Class	*Alphaproteobacteria*
	Order	*Rhodobacterales*
	Family	*Roseobacteraceae*
	Genus	*Pseudophaeobacter*
	Species	**Pseudophaeobacter leonis**
	Full Scientific Name (LPSN)	Pseudophaeobacter leonis (Gaboyer et al. 2013) Breider et al. 2014

Synonym

Phaeobacter leonis

Information on morphological and physiological properties Morphology

[Ref.: #30861]	Gram stain	negative
[Ref.: #120586]	Gram stain	negative
[Ref.: #125439]	Gram stain	negative Confidence in %98.8

[Ref.: #30861]	Cell length	1.6 µm

[Ref.: #30861]	Cell width	0.7 µm

[Ref.: #30861]	Cell shape	rod-shaped
[Ref.: #120586]	Cell shape	rod-shaped

[Ref.: #30861]	Motility	yes
[Ref.: #120586]	Motility	no

[Ref.: #20730]

Incubation period

2-3 days

[Ref.: #30861]

Pigment production

yes

Information on culture and growth conditions Culture and growth conditions

[Ref.: #36561]

Culture medium

Marine agar (MA)

[Ref.: #36561]

Culture medium growth

[Ref.: #36561]

Culture medium composition

expand / minimize

[Ref.: #20730]

Culture medium

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

[Ref.: #20730]

Culture medium growth

[Ref.: #20730]

Culture medium link

Medium recipe at MediaDive

[Ref.: #20730]

Culture medium composition

expand / minimize

[Ref.: #120586]

Culture medium

CIP Medium 13

[Ref.: #120586]

Culture medium growth

[Ref.: #120586]

Culture medium link

Medium recipe provided by DSMZ

		Temperature
[Ref.: #20730]	growth	25 °C
[Ref.: #30861]	growth	04-32 °C
[Ref.: #30861]	optimum	19.5 °C
[Ref.: #36561]	growth	30 °C

	pH	Kind of pH		pH
[Ref.: #30861]			optimum	8.5
[Ref.: #30861]			growth	6.5-9

Information on physiology and metabolism Physiology and metabolism

[Ref.: #30861]	Oxygen tolerance	aerobe
[Ref.: #125439]	Oxygen tolerance	obligate aerobe Confidence in %93.3

[Ref.: #30861]	Ability of spore formation	no
[Ref.: #125439]	Ability of spore formation	no Confidence in %98.7

	Halophily	Salt	Tested relation		Salt conc.
[Ref.: #30861]		NaCl		growth	0.5-6	%
[Ref.: #30861]		NaCl		optimum	2	%

[Ref.: #30861]

Observation

aggregates in clumps

	Metabolite	Utilization activity	Kind of utilization tested
[Ref.: #30861]	alanine ChEBI	+	carbon source
[Ref.: #30861]	arabinose ChEBI	+	carbon source
[Ref.: #30861]	arginine ChEBI	+	carbon source
[Ref.: #68369]	arginine ChEBI	-	hydrolysis	* from API 20NE
[Ref.: #30861]	asparagine ChEBI	+	carbon source
[Ref.: #30861]	citrate ChEBI	+	carbon source
[Ref.: #68369]	D-glucose ChEBI	-	assimilation	* from API 20NE
[Ref.: #68369]	D-glucose ChEBI	-	fermentation	* from API 20NE
[Ref.: #68369]	D-mannitol ChEBI	-	assimilation	* from API 20NE
[Ref.: #68369]	D-mannose ChEBI	-	assimilation	* from API 20NE
[Ref.: #30861]	D-tryptophan ChEBI	+	carbon source
[Ref.: #68369]	decanoate ChEBI	-	assimilation	* from API 20NE
[Ref.: #68369]	esculin ChEBI	-	hydrolysis	* from API 20NE
[Ref.: #30861]	ethanol ChEBI	+	carbon source
[Ref.: #30861]	fructose ChEBI	+	carbon source
[Ref.: #68369]	gelatin ChEBI	-	hydrolysis	* from API 20NE
[Ref.: #68369]	gluconate ChEBI	-	assimilation	* from API 20NE
[Ref.: #30861]	glutamate ChEBI	+	carbon source
[Ref.: #30861]	glycine ChEBI	+	carbon source
[Ref.: #68369]	L-arabinose ChEBI	-	assimilation	* from API 20NE
[Ref.: #30861]	leucine ChEBI	+	carbon source
[Ref.: #68369]	malate ChEBI	-	assimilation	* from API 20NE
[Ref.: #68369]	maltose ChEBI	-	assimilation	* from API 20NE
[Ref.: #30861]	mannitol ChEBI	+	carbon source
[Ref.: #30861]	mannose ChEBI	+	carbon source
[Ref.: #68369]	N-acetylglucosamine ChEBI	-	assimilation	* from API 20NE
[Ref.: #120586]	nitrate ChEBI	-	reduction
[Ref.: #68369]	nitrate ChEBI	-	reduction	* from API 20NE
[Ref.: #120586]	nitrite ChEBI	-	reduction
[Ref.: #30861]	phenylalanine ChEBI	+	carbon source
[Ref.: #30861]	proline ChEBI	+	carbon source
[Ref.: #30861]	propionate ChEBI	+	carbon source
[Ref.: #30861]	rhamnose ChEBI	+	carbon source
[Ref.: #30861]	ribose ChEBI	+	carbon source
[Ref.: #30861]	serine ChEBI	+	carbon source
[Ref.: #30861]	succinate ChEBI	+	carbon source
[Ref.: #30861]	sucrose ChEBI	+	carbon source
[Ref.: #30861]	threonine ChEBI	+	carbon source
[Ref.: #30861]	trehalose ChEBI	+	carbon source
[Ref.: #68369]	tryptophan ChEBI	-	energy source	* from API 20NE
[Ref.: #68369]	urea ChEBI	-	hydrolysis	* from API 20NE
	Only first 10 entries are displayed. Click here to see all.

	Metabolite production	Metabolite	Production
[Ref.: #120586]		indole ChEBI	no
[Ref.: #68369]		indole ChEBI	no	* from API 20NE

	Physiological tests	Metabolite	Indole test
[Ref.: #68369]		indole ChEBI	-	* from API 20NE

	Enzyme	Enzyme activity	EC number
[Ref.: #68382]	acid phosphatase	+	3.1.3.2	* from API zym
[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.: #68369]	arginine dihydrolase	-	3.5.3.6	* from API 20NE
[Ref.: #68382]	beta-galactosidase	-	3.2.1.23	* from API zym
[Ref.: #68382]	beta-glucosidase	-	3.2.1.21	* from API zym, API 20NE
[Ref.: #68382]	beta-glucuronidase	-	3.2.1.31	* from API zym
[Ref.: #20730]	catalase	+	1.11.1.6
[Ref.: #30861]	catalase	+	1.11.1.6
[Ref.: #120586]	catalase	-	1.11.1.6
[Ref.: #68382]	cystine arylamidase	-	3.4.11.3	* from API zym
[Ref.: #30861]	cytochrome oxidase	+	1.9.3.1
[Ref.: #68369]	cytochrome oxidase	+	1.9.3.1	* from API 20NE
[Ref.: #20730]	cytochrome-c oxidase	+	1.9.3.1
[Ref.: #68382]	esterase (C 4)	+		* from API zym
[Ref.: #68382]	esterase lipase (C 8)	-		* from API zym
[Ref.: #68369]	gelatinase	-		* from API 20NE
[Ref.: #68382]	leucine arylamidase	-	3.4.11.1	* from API zym
[Ref.: #68382]	lipase (C 14)	-		* from API zym
[Ref.: #68382]	N-acetyl-beta-glucosaminidase	-	3.2.1.52	* from API zym
[Ref.: #68382]	naphthol-AS-BI-phosphohydrolase	-		* from API zym
[Ref.: #120586]	oxidase	-
[Ref.: #68382]	trypsin	-	3.4.21.4	* from API zym
[Ref.: #120586]	urease	-	3.5.1.5
[Ref.: #68369]	urease	-	3.5.1.5	* from API 20NE
[Ref.: #68382]	valine arylamidase	-		* from API zym
	Only first 10 entries are displayed. Click here to see all.

API® 20NE:

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

	API ID	Reduction of nitratesNO3	Indole productionTRP	Fermentation of D-glucoseGLU_ Ferm	Arginine dihydrolaseADH (Arg)	Urease/urea hydrolysisURE	Esculin hydrolysis/beta-GlucosidaseESC	Gelatinase/gelatin hydrolysisGEL	beta-GalactosidasePNPG	Assimilation of D-glucoseGLU_ Assim	Assimilation of L-arabinoseARA	Assimilation of D-mannoseMNE	Assimilation of D-mannitolMAN	Assimilation of N-acetyl-glucosamineNAG	Assimilation of maltoseMAL	Assimilation of gluconateGNT	Assimilation of capric acidCAP	Assimilation adipic acidADI	Assimilation of malic acidMLT	Assimilation of citric acidCIT	Assimilation of phenyl-acetic acidPAC	Cytochrome oxidaseOX
[Ref.: #20730]	27009	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	+/-	-	-	-	+
[Ref.: #20730]	26587	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	not determinedn.d.

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.: #120586]	12556	-	+	+	-	-	-	-	-	-	-	+	-	-	-	-	-	-	-	-	-

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

[Ref.: #20730]	Sample type/isolated from	anoxic marine sediment beneath the sea floor
[Ref.: #20730]	Geographic location (country and/or sea, region)	Mediterranean Sea, Gulf of Lions (42° 41.596' N, 03° 50.493' E) water depth: 291 m, 109 cm below the sea floor
[Ref.: #20730]	Country	France
[Ref.: #20730]	Country ISO 3 Code	FRA
[Ref.: #20730]	Continent	Europe
[Ref.: #20730]	Geographic location	42.6933°/3.8416°

[Ref.: #120586]	Sample type/isolated from	Environment, Sea sediment
[Ref.: #120586]	Geographic location (country and/or sea, region)	Mediterranean Sea
[Ref.: #120586]	Country	France
[Ref.: #120586]	Country ISO 3 Code	FRA
[Ref.: #120586]	Continent	Europe
[Ref.: #120586]	Isolation date	2010
* marker position based on {}

Isolation sources categories

#Environmental	#Aquatic	#Marine
#Environmental	#Aquatic	#Sediment
#Condition	#Anoxic (anaerobic)	-

What are isolation sources categories?

[Ref.: #69479]

Global distribution of 16S sequence HE661585 (>99% sequence identity) for Pseudophaeobacter leonis from Microbeatlas

Aquatic Samples	316
Soil Samples	5
Animal Samples	15
Plant Samples	1
Total Samples	337

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

[Ref.: #20730]	Biosafety level	1	Risk group (German classification) According to TRBA 466
[Ref.: #120586]	Biosafety level	1	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.: #20730]	Pseudophaeobacter leonis partial 16S rRNA gene, strain 306	HE661585	1355	GenBank ENA	1144477 tax ID
[Ref.: #124043]	Pseudophaeobacter leonis strain 306 16S ribosomal RNA gene, partial sequence; 16S-23S intergenic spacer, tRNA-Ile and tRNA-Ala genes, complete sequence; and 23S ribosomal RNA gene, partial sequence.	KC907729	1318	GenBank ENA	1144477 tax ID	*

Genome sequence information:

	Sequence accession description	Seq. accession number	Assembly level	Sequence database	Associated NCBI tax ID
[Ref.: #66792]	Pseudophaeobacter leonis 306	GCA_002087335	contig	GenBank ENA	1144477 tax ID	*
[Ref.: #66792]	Pseudophaeobacter leonis 306	2791354898	draft	JGI IMG/M	1144477 tax ID	*

[Ref.: #20730]	GC-content	58.8 mol%	high performance liquid chromatography (HPLC)
[Ref.: #30861]	GC-content	59 mol%

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

	Model	Trait	Prediction	Confidence in %
	Predictions from Deep Learning for Genome Sequence Data. R package version 0.3.1 based on: Pseudophaeobacter leonis 306 NCBI: GCA_002087335
[Ref.: #125439]	BacteriaNet	spore_formationⓘ	no	98.7
[Ref.: #125439]	BacteriaNet	motilityⓘ	yes	75.3
[Ref.: #125439]	BacteriaNet	gram_stainⓘ	negative	98.8
[Ref.: #125439]	BacteriaNet	oxygen_toleranceⓘ	obligate aerobe	93.3

Availability in culture collections External links

[Ref.: #20730]

Culture collection no.

DSM 25627, CIP 110369, UBOCC 3187

[Ref.: #88353]

SI-ID 402045

Literature:

Topic	Title	Authors	Journal	DOI	Year
Phylogeny	Pseudophaeobacter flagellatus sp. nov., isolated from coastal water.	Guan Y, Jiang Y, Kim YM, Yu SY, Choi SH, Choe H, Li Z, Lee MK	Int J Syst Evol Microbiol	10.1099/ijsem.0.005399	2022	*
Phylogeny	Phaeobacter leonis sp. nov., an alphaproteobacterium from Mediterranean Sea sediments.	Gaboyer F, Tindall BJ, Ciobanu MC, Duthoit F, Le Romancer M, Alain K	Int J Syst Evol Microbiol	10.1099/ijs.0.046128-0	2013	*

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 )

#20730

Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 25627

#30861

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 #27191 (see below)

#36561 ; 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) .

#68369

Automatically annotated from API 20NE .

#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 .

#88353

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-ID402045.1 )

#120586 Collection of Institut Pasteur ; Curators of the CIP; CIP 110369

#124043

Isabel Schober, Julia Koblitz: Data extracted from sequence databases, automatically matched based on designation and taxonomy .

#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 .

#27191

IJSEM 3301 2013 ( DOI 10.1099/ijs.0.046128-0 , PubMed 23475346 )

* These data were automatically processed and therefore are not curated

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