Name: Yoonia rosea Fg36
Creator: BacDive
License: https://creativecommons.org/licenses/by/4.0/

Strain identifier

BacDive ID: 130606

Type strain:

Species: Yoonia rosea

Strain Designation: Fg36

Culture col. no.: DSM 29591, CIP 107851, KMM 6003, LMG 22534

Strain history: CIP <- 2003, E. Ivanova, Swinburne Inst, Victoria, Autralia: strain Fg 36, Sulfitobacter sp. <- N. Gorshkova

NCBI tax ID(s): 287098 (species)

SI-ID 131997

LMG 22534, CIP 107851

Special Collections

Section

When using BacDive for research please cite our paper

Yoonia rosea Fg36 is an aerobe, spore-forming, mesophilic bacterium that was isolated from sediments.

Gram-negative
rod-shaped
spore-forming
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	*Yoonia*
	Species	**Yoonia rosea**
	Full Scientific Name (LPSN)	Yoonia rosea (Ivanova et al. 2005) Wirth and Whitman 2018

Synonym

Loktanella rosea

Information on morphological and physiological properties Morphology

[Ref.: #31393]	Gram stain	negative
[Ref.: #122255]	Gram stain	negative
[Ref.: #125438]	Gram stain	negative Confidence in %98.833
[Ref.: #125439]	Gram stain	negative Confidence in %99.3

[Ref.: #31393]	Cell width	0.8 µm

[Ref.: #31393]	Cell shape	rod-shaped
[Ref.: #122255]	Cell shape	rod-shaped

[Ref.: #31393]	Motility	no
[Ref.: #122255]	Motility	no

[Ref.: #21633]

Incubation period

1-2 days

[Ref.: #31393]

Pigment production

yes

Information on culture and growth conditions Culture and growth conditions

[Ref.: #21633]

Culture medium

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

[Ref.: #21633]

Culture medium growth

[Ref.: #21633]

Culture medium link

Medium recipe at MediaDive

[Ref.: #21633]

Culture medium composition

expand / minimize

[Ref.: #36653]

Culture medium

Marine agar (MA)

[Ref.: #36653]

Culture medium growth

[Ref.: #36653]

Culture medium composition

expand / minimize

[Ref.: #36660]

Culture medium

Marine agar (MA)

[Ref.: #36660]

Culture medium growth

[Ref.: #36660]

Culture medium composition

expand / minimize

[Ref.: #122255]

Culture medium

CIP Medium 13

[Ref.: #122255]

Culture medium growth

[Ref.: #122255]

Culture medium link

Medium recipe provided by DSMZ

	Kind of temperature		Temperature
[Ref.: #21633]		growth	30 °C
[Ref.: #31393]		growth	04-35 °C
[Ref.: #31393]		optimum	25 °C
[Ref.: #36653]		growth	25 °C
[Ref.: #36660]		growth	25 °C
[Ref.: #122255]		growth	15-35 °C
[Ref.: #122255]	negative	growth	5 °C
[Ref.: #122255]	negative	growth	41 °C
[Ref.: #122255]	negative	growth	45 °C

	pH	Kind of pH		pH
[Ref.: #31393]			optimum	7.75
[Ref.: #31393]			growth	6.0-10.0

Information on physiology and metabolism Physiology and metabolism

[Ref.: #31393]	Oxygen tolerance	aerobe
[Ref.: #125439]	Oxygen tolerance	obligate aerobe Confidence in %97

[Ref.: #31393]	Ability of spore formation	yes
[Ref.: #125439]	Ability of spore formation	no Confidence in %99

	Salt	Tested relation		Salt conc.
[Ref.: #31393]	NaCl		growth	01-12	%
[Ref.: #31393]	NaCl		optimum	6.5	%
[Ref.: #122255]	NaCl		growth	0	%
[Ref.: #122255]	NaCl	no	growth	2	%
[Ref.: #122255]	NaCl	no	growth	4	%
[Ref.: #122255]	NaCl	no	growth	6	%
[Ref.: #122255]	NaCl	no	growth	8	%
[Ref.: #122255]	NaCl	no	growth	10	%

[Ref.: #31393]

Observation

aggregates in clumps

	Metabolite	Utilization activity	Kind of utilization tested
[Ref.: #68369]	adipate ChEBI	-	assimilation	* from API 20NE
[Ref.: #68369]	arginine ChEBI	-	hydrolysis	* from API 20NE
[Ref.: #122255]	citrate ChEBI	-	carbon source
[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.: #68369]	decanoate ChEBI	-	assimilation	* from API 20NE
[Ref.: #122255]	esculin ChEBI	+	hydrolysis
[Ref.: #68369]	esculin ChEBI	+	hydrolysis	* from API 20NE
[Ref.: #68369]	gelatin ChEBI	-	hydrolysis	* from API 20NE
[Ref.: #68369]	gluconate ChEBI	-	assimilation	* from API 20NE
[Ref.: #122255]	glucose ChEBI	-	degradation
[Ref.: #31393]	glucuronamide ChEBI	+	carbon source
[Ref.: #31393]	glycine ChEBI	+	carbon source
[Ref.: #122255]	hippurate ChEBI	-	hydrolysis
[Ref.: #31393]	L-alaninamide ChEBI	+	carbon source
[Ref.: #68369]	L-arabinose ChEBI	-	assimilation	* from API 20NE
[Ref.: #122255]	malonate ChEBI	-	assimilation
[Ref.: #68369]	maltose ChEBI	-	assimilation	* from API 20NE
[Ref.: #68369]	N-acetylglucosamine ChEBI	-	assimilation	* from API 20NE
[Ref.: #122255]	nitrate ChEBI	-	builds gas from
[Ref.: #122255]	nitrate ChEBI	-	reduction
[Ref.: #68369]	nitrate ChEBI	-	reduction	* from API 20NE
[Ref.: #122255]	nitrite ChEBI	-	builds gas from
[Ref.: #122255]	nitrite ChEBI	-	reduction
[Ref.: #68369]	tryptophan ChEBI	-	energy source	* from API 20NE
[Ref.: #31393]	tween 80 ChEBI	+	carbon source
[Ref.: #68369]	urea ChEBI	-	hydrolysis	* from API 20NE
	Only first 10 entries are displayed. Click here to see all.

	Metabolite production	Metabolite	Production
[Ref.: #122255]		indole ChEBI	no
[Ref.: #68369]		indole ChEBI	no	* from API 20NE

	Metabolite	Voges-Proskauer-test	Methylred-test	Indole test
[Ref.: #122255]	acetoin ChEBI	-
[Ref.: #122255]	glucose ChEBI		-
[Ref.: #68369]	indole ChEBI			-	* from API 20NE

	Enzyme	Enzyme activity	EC number
[Ref.: #68382]	acid phosphatase	+	3.1.3.2	* from API zym
[Ref.: #122255]	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.: #122255]	amylase	-
[Ref.: #68369]	arginine dihydrolase	-	3.5.3.6	* from API 20NE
[Ref.: #122255]	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, API 20NE
[Ref.: #68382]	beta-glucuronidase	-	3.2.1.31	* from API zym
[Ref.: #122255]	caseinase	-	3.4.21.50
[Ref.: #21633]	catalase	+	1.11.1.6
[Ref.: #31393]	catalase	+	1.11.1.6
[Ref.: #122255]	catalase	+	1.11.1.6
[Ref.: #68382]	cystine arylamidase	-	3.4.11.3	* from API zym
[Ref.: #21633]	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.: #122255]	gamma-glutamyltransferase	-	2.3.2.2
[Ref.: #122255]	gelatinase	+/-
[Ref.: #68369]	gelatinase	-		* from API 20NE
[Ref.: #122255]	lecithinase	-
[Ref.: #68382]	leucine arylamidase	+	3.4.11.1	* from API zym
[Ref.: #122255]	lipase	-
[Ref.: #68382]	lipase (C 14)	-		* from API zym
[Ref.: #122255]	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.: #122255]	ornithine decarboxylase	-	4.1.1.17
[Ref.: #122255]	oxidase	+
[Ref.: #122255]	phenylalanine ammonia-lyase	-	4.3.1.24
[Ref.: #122255]	protease	+
[Ref.: #68382]	trypsin	-	3.4.21.4	* from API zym
[Ref.: #122255]	tryptophan deaminase	-
[Ref.: #122255]	tween esterase	+
[Ref.: #122255]	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.: #21633]	26742	-	-	-	-	-	+	-	+	+/-	-	-	+	-	-	-	-	-	+/-	-	-	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.: #122255]	10697	-	+	+	+	-	+	-	-	-	-	+	+	-	+	-	-	+	-	-	-

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

[Ref.: #21633]	Sample type/isolated from	sediments
[Ref.: #21633]	Geographic location (country and/or sea, region)	Pacific Ocean, Sea of Japan, Chazma Bay
[Ref.: #21633]	Country	Japan
[Ref.: #21633]	Country ISO 3 Code	JPN
[Ref.: #21633]	Continent	Asia

[Ref.: #122255]	Sample type/isolated from	Environment, Sediment sample
[Ref.: #122255]	Country	Japan
[Ref.: #122255]	Country ISO 3 Code	JPN
[Ref.: #122255]	Continent	Asia
[Ref.: #122255]	Isolation date	2002
* marker position based on {}

Isolation sources categories

#Environmental

#Terrestrial

#Sediment

What are isolation sources categories?

[Ref.: #69479]

Global distribution of 16S sequence AY682199 (>99% sequence identity) for Yoonia from Microbeatlas

Aquatic Samples	352
Soil Samples	11
Animal Samples	21
Plant Samples	8
Total Samples	392

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

[Ref.: #21633]	Biosafety level	1	Risk group (German classification) According to TRBA 466
[Ref.: #122255]	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.: #21633]	Loktanella rosea 16S ribosomal RNA gene, partial sequence	AY682199	1398	GenBank ENA	287098 tax ID

Genome sequence information:

	Sequence accession description	Seq. accession number	Assembly level	Sequence database	Associated NCBI tax ID
[Ref.: #66792]	Yoonia rosea DSM 29591	GCA_900156505	contig	GenBank ENA	287098 tax ID	*
[Ref.: #66792]	Loktanella rosea strain DSM 29591	287098.3	wgs	PATRIC	287098 tax ID	*
[Ref.: #66792]	Yoonia rosea DSM 29591	2681812930	draft	JGI IMG/M	287098 tax ID	*

[Ref.: #31393]

GC-content

60.5-61.8 mol%

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

	Model	Trait	Prediction	Confidence in %	In training data
	Predictions from bacterial phenotypic traits through improved machine learning using high-quality, curated datasets based on: Loktanella rosea strain DSM 29591 PATRIC: 287098.3
[Ref.: #125438]	gram-positive	gram-positiveⓘ	no	98.833	yes
[Ref.: #125438]	anaerobic	anaerobicⓘ	no	94.357	no
[Ref.: #125438]	spore-forming	spore-formingⓘ	no	77.486	yes
[Ref.: #125438]	thermophile	thermophilicⓘ	no	96.447	yes
[Ref.: #125438]	aerobic	aerobicⓘ	yes	87.022	no
[Ref.: #125438]	motile2+	flagellatedⓘ	yes	58.053	no

	Model	Trait	Prediction	Confidence in %
	Predictions from Deep Learning for Genome Sequence Data. R package version 0.3.1 based on: Yoonia rosea DSM 29591 NCBI: GCA_900156505
[Ref.: #125439]	BacteriaNet	spore_formationⓘ	no	99
[Ref.: #125439]	BacteriaNet	motilityⓘ	yes	80.8
[Ref.: #125439]	BacteriaNet	gram_stainⓘ	negative	99.3
[Ref.: #125439]	BacteriaNet	oxygen_toleranceⓘ	obligate aerobe	97

Availability in culture collections External links

[Ref.: #21633]

Culture collection no.

DSM 29591, CIP 107851, KMM 6003, LMG 22534

[Ref.: #89120]

SI-ID 131997

Literature:

Topic	Title	Authors	Journal	DOI	Year
Phylogeny	Loktanella sediminilitoris sp. nov., isolated from tidal flat sediment.	Park S, Jung YT, Yoon JH	Int J Syst Evol Microbiol	10.1099/ijs.0.049841-0	2013	*
Phylogeny	Loktanella agnita sp. nov. and Loktanella rosea sp. nov., from the north-west Pacific Ocean.	Ivanova EP, Zhukova NV, Lysenko AM, Gorshkova NM, Sergeev AF, Mikhailov VV, Bowman JP	Int J Syst Evol Microbiol	10.1099/ijs.0.63461-0	2005	*

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 )

#21633

Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 29591

#31393

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 #27704 (see below)

#36653 ; Curators of the CIP;
#36660 ; 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 .

#89120

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-ID131997.1 )

#122255 Collection of Institut Pasteur ; Curators of the CIP; CIP 107851

#125438

Julia Koblitz, Lorenz Christian Reimer, Rüdiger Pukall, Jörg Overmann: Predicting bacterial phenotypic traits through improved machine learning using high-quality, curated datasets. 2024 ( DOI 10.1101/2024.08.12.607695 )

#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 .

#27704

IJSEM 2203 2005 ( DOI 10.1099/ijs.0.63461-0 , PubMed 16166733 )

* These data were automatically processed and therefore are not curated

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Loktanella rosea strain DSM 29591

Yoonia rosea DSM 29591

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