Leisingera daeponensis (DSM 23529, JCM 13606, KCTC 12794)

Name: Leisingera daeponensis (DSM 23529, JCM 13606, KCTC 12794)
Creator: BacDive
License: http://creativecommons.org/licenses/by/4.0/

BacDive ID 13732

Type strain

Strain Designation TF-218

Culture col. no. DSM 23529 JCM 13606 KCTC 12794 TF-218 LMG 24139 2 more

NCBI tax ID(s) 999547 405746

Special Collections DSMZ JCM KCTC CIP Literature strains

History <- KCTC <- J.-H. Yoon, Korea Res. Inst. Biosci. & Biotechnol. (KRIBB), Taejon, South Korea J.-H. Yoon TF-218. <- JH Yoon, KRIBB CIP <- 2007, JCM <- 2006, J. H. Yoon, KRIBB, Korea: strain TF-218

Links

Leisingera daeponensis TF-218 is an anaerobe, Gram-negative, motile bacterium that was isolated from tidal flat sediment.

Gram-negative motile ovoid-shaped anaerobe genome sequence 16S sequence Bacteria

Name and taxonomic classification

SI-ID 302771

JCM 13606,KCTC 12794,LMG 24139,CECT 7309,CIP 109576,DSM 23529

@ref 20215

Last LPSN update 2026-02-09 11:21:13

Domain Bacteria

Phylum Pseudomonadota

Class Alphaproteobacteria

Order Rhodobacterales

Family Roseobacteraceae

Genus Leisingera

Species Leisingera daeponensis

Full scientific name Leisingera daeponensis (Yoon et al. 2007) Breider et al. 2014

Synonyms (1)

Phaeobacter daeponensis

Morphology

Cell morphology

@ref	Gram stain	Cell length	Cell width	Cell shape	Confidence
31996	negative	1.35 µm	0.65 µm	ovoid-shaped
67771	negative
118848	negative			rod-shaped
125438	negative				99.5
125439	negative				98

Colony morphology

17260

Incubation period3-7 days

Pigmentation

31996

Productionno

Multimedia

@ref:	66793
multimedia content:	EM_DSM_23529_1.jpg
multimedia.multimedia content:	EM_DSM_23529_1.jpg
caption:	electron microscopic image
intellectual property rights:	© HZI/Manfred Rohde
manual_annotation:	1

Culture and growth conditions

Culture medium

@ref	Name	Medium link	Composition
17260	BACTO MARINE BROTH (DIFCO 2216) (DSMZ Medium 514)	Medium recipe at MediaDive	Name: BACTO MARINE BROTH (DIFCO 2216) (DSMZ Medium 514) Composition: NaCl 19.45 g/l MgCl2 5.9 g/l Bacto peptone 5.0 g/l Na2SO4 3.24 g/l CaCl2 1.8 g/l Yeast extract 1.0 g/l KCl 0.55 g/l NaHCO3 0.16 g/l Fe(III) citrate 0.1 g/l KBr 0.08 g/l SrCl2 0.034 g/l H3BO3 0.022 g/l Na2HPO4 0.008 g/l Na-silicate 0.004 g/l NaF 0.0024 g/l (NH4)NO3 0.0016 g/l Distilled water
36607	Marine agar (MA)		Distilled water make up to (1000.000 ml);Marine agar (55.100 g)
118848	CIP Medium 13	Medium recipe at CIP

Culture temp

@ref	Growth	Type	Temperature (°C)
17260	positive	growth	37
31996	positive	growth	04-42
31996	positive	optimum	37
36607	positive	growth	37
67770	positive	growth	37
67771	positive	growth	37

Culture pH

@ref	Ability	Type	PH
31996	positive	optimum	07-08
31996	positive	growth	5.5-8

Physiology and metabolism

Oxygen tolerance

@ref	Oxygen tolerance	Confidence
31996	anaerobe
67771	aerobe
125439	aerobe	92.5

Spore formation

@ref	Spore formation	Confidence
125439		97.9

Halophily

@ref	Salt	Growth	Tested relation	Concentration
31996	NaCl	positive	growth	01-08 %
31996	NaCl	positive	optimum	2 %

Observation

67770

Observationquinones: Q-10

Metabolite utilization

@ref	Chebi-ID	Metabolite	Utilization activity	Kind of utilization tested
31996	30089 ChEBI	acetate	+	carbon source
68368	27613 ChEBI	amygdalin	-	fermentation	from API 20E
68368	29016 ChEBI	arginine	-	hydrolysis	from API 20E
31996	16947 ChEBI	citrate	+	carbon source
68368	16947 ChEBI	citrate	-	assimilation	from API 20E
68368	17634 ChEBI	D-glucose	-	fermentation	from API 20E
68368	16899 ChEBI	D-mannitol	-	fermentation	from API 20E
68368	5291 ChEBI	gelatin	-	hydrolysis	from API 20E
68368	30849 ChEBI	L-arabinose	-	fermentation	from API 20E
68368	62345 ChEBI	L-rhamnose	-	fermentation	from API 20E
31996	25017 ChEBI	leucine	+	carbon source
68368	25094 ChEBI	lysine	-	degradation	from API 20E
31996	25115 ChEBI	malate	+	carbon source
68368	28053 ChEBI	melibiose	-	fermentation	from API 20E
68368	17268 ChEBI	myo-inositol	-	fermentation	from API 20E
31996	17632 ChEBI	nitrate	+	reduction
118848	17632 ChEBI	nitrate	-	reduction
118848	16301 ChEBI	nitrite	-	reduction
68368	18257 ChEBI	ornithine	-	degradation	from API 20E
31996	15361 ChEBI	pyruvate	+	carbon source
31996	33942 ChEBI	ribose	+	carbon source
31996	17822 ChEBI	serine	+	carbon source
68368	30911 ChEBI	sorbitol	-	fermentation	from API 20E
31996	30031 ChEBI	succinate	+	carbon source
68368	17992 ChEBI	sucrose	-	fermentation	from API 20E
68368	27897 ChEBI	tryptophan	-	energy source	from API 20E
68368	16199 ChEBI	urea	-	hydrolysis	from API 20E

Metabolite production

@ref	Chebi-ID	Metabolite
68368	15688 ChEBI	acetoin	from API 20E
68368	16136 ChEBI	hydrogen sulfide	from API 20E
118848	35581 ChEBI	indole
68368	35581 ChEBI	indole	from API 20E

Metabolite tests

@ref	Chebi-ID	Metabolite	Voges-proskauer-test	Indole test
68368	15688 ChEBI	acetoin	-		from API 20E
68368	35581 ChEBI	indole		-	from API 20E

Enzymes

@ref	Value	Activity	Ec
68382	acid phosphatase	+	3.1.3.2	from API zym
31996	alkaline phosphatase	+	3.1.3.1
68382	alkaline phosphatase	+	3.1.3.1	from API zym
68382	alpha-chymotrypsin	-	3.4.21.1	from API zym
68382	alpha-fucosidase	-	3.2.1.51	from API zym
68382	alpha-galactosidase	-	3.2.1.22	from API zym
68382	alpha-glucosidase	-	3.2.1.20	from API zym
68382	alpha-mannosidase	-	3.2.1.24	from API zym
68368	arginine dihydrolase	-	3.5.3.6	from API 20E
68382	beta-galactosidase	-	3.2.1.23	from API zym
68368	beta-galactosidase	-	3.2.1.23	from API 20E
68382	beta-glucosidase	-	3.2.1.21	from API zym
68382	beta-glucuronidase	-	3.2.1.31	from API zym
17260	catalase	+	1.11.1.6
31996	catalase	+	1.11.1.6
118848	catalase	+	1.11.1.6
68382	cystine arylamidase	-	3.4.11.3	from API zym
31996	cytochrome oxidase	+	1.9.3.1
17260	cytochrome-c oxidase	+	1.9.3.1
68382	esterase (C 4)	+		from API zym
68382	esterase lipase (C 8)	-		from API zym
68368	gelatinase	-		from API 20E
68382	leucine arylamidase	+	3.4.11.1	from API zym
68382	lipase (C 14)	-		from API zym
68368	lysine decarboxylase	-	4.1.1.18	from API 20E
68382	N-acetyl-beta-glucosaminidase	-	3.2.1.52	from API zym
68382	naphthol-AS-BI-phosphohydrolase	-		from API zym
68368	ornithine decarboxylase	-	4.1.1.17	from API 20E
118848	oxidase	+
68382	trypsin	-	3.4.21.4	from API zym
68368	tryptophan deaminase	-	4.1.99.1	from API 20E
118848	urease	-	3.5.1.5
68368	urease	-	3.5.1.5	from API 20E
68382	valine arylamidase	+		from API zym

API 20E

@ref	ONPG	ADH (Arg)	LDC (Lys)	ODC	CIT	H2S productionH2S	URE	TDA (Trp)	IND	Acetoin production (Voges Proskauer test)VP	GEL	GLU	MAN	INO	Sor	RHA	SAC	MEL	AMY	ARA	OX	Nitrite productionNO2	Reduction to N2N2	MotilityMOB	Growth on MacConkey mediumMAC	OF-O	OF-F
17260	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	not determinedn.d.	not determinedn.d.	not determinedn.d.	not determinedn.d.	not determinedn.d.	not determinedn.d.	not determinedn.d.

API zym

@ref	Control	Alkaline phosphatase	Esterase (C 4)	2-naphtyl caprylateEsterase Lipase (C 8)	Lipase (C 14)	L-leucyl-2-naphthylamideLeucine arylamidase	L-valyl-2-naphthylamideValine arylamidase	L-cystyl-2-naphthylamideCystine arylamidase	Trypsin	alpha- Chymotrypsin	Acid phosphatase	Naphthol-AS-BI-phosphateNaphthol-AS-BI-phosphohydrolase	alpha- Galactosidase	beta- Galactosidase	beta- Glucuronidase	alpha- Glucosidase	beta- Glucosidase	N-acetyl-beta- glucosaminidase	alpha- Mannosidase	alpha- Fucosidase
118848	-	+	+	-	-	+	+	-	-	-	+	-	-	-	-	-	-	-	-	-

Isolation, sampling and environmental information

Isolation source categories

Cat1	Cat2	Cat3
#Environmental	#Terrestrial	#Tidal flat
#Environmental	#Terrestrial	#Sediment

Isolation

@ref	Sample type	Geographic location	Country	Country ISO 3 Code	Continent
17260	tidal flat sediment	Daepo Beach, Yellow Sea	Republic of Korea	KOR	Asia
67770	Tidal flat at Daepo Beach (Yellow Sea)		Republic of Korea	KOR	Asia
67771	From gaetbul	the Yellow Sea	Republic of Korea	KOR	Asia
118848	Environment, Tidal flat	Yellow sea	Republic of Korea	KOR	Asia

Taxonmaps

69479

Global distribution of 16S sequence DQ981486 (>99% sequence identity) for Leisingera daeponensis from Microbeatlas

Aquatic Samples	371
Soil Samples	14
Animal Samples	43
Plant Samples	5
Total Samples	433

Interaction and safety

Risk assessment

@ref	Biosafety level	Biosafety level comment
17260	1	Risk group (German classification) According to TRBA 466
118848	1	Risk group (French classification) According to TRBA 466

Sequence information

Genome sequences

@ref	Description	Assembly level	INSDC accession	BV-BRC accession	IMG accession	NCBI tax ID	Score
67770	ASM47314v1 assembly for Leisingera daeponensis DSM 23529	scaffold	GCA_000473145	999547.5	2521172619	999547	74.04

16S sequences

@ref	Description	Accession	Length	Database	NCBI tax ID
17260	Phaeobacter daeponensis strain TF-218 16S ribosomal RNA gene, partial sequence	DQ981486	1419		999547

GC content

@ref	GC-content (mol%)	Method
17260	64.9	high performance liquid chromatography (HPLC)
31996	64.9

Genome-based predictions

Predictions

Predictions from Deep Learning for Genome Sequence Data. R package version 0.3.1 based on: Leisingera daeponensis DSM 23529
NCBI: GCA_000473145

@ref	Trait	Model	Prediction	Confidence in %	In training data
125439	spore_formation	BacteriaNetⓘ	no	97.90	no
125439	motility	BacteriaNetⓘ	yes	76.90	no
125439	gram_stain	BacteriaNetⓘ	negative	98.00	no
125439	oxygen_tolerance	BacteriaNetⓘ	aerobe	92.50	no

Predictions from bacterial phenotypic traits through improved machine learning using high-quality, curated datasets based on: Phaeobacter daeponensis DSM 23529
PATRIC: 999547.5

@ref	Trait	Model	Prediction	Confidence in %	In training data
125438	gram-positive	gram-positiveⓘ	no	99.50	yes
125438	anaerobic	anaerobicⓘ	no	93.91	no
125438	aerobic	aerobicⓘ	yes	82.69	no
125438	spore-forming	spore-formingⓘ	no	89.61	no
125438	thermophilic	thermophileⓘ	no	96.64	no
125438	flagellated	motile2+ⓘ	yes	70.27	no

Literature

Topic	Title	Authors	Journal	DOI	Year
	Genome Sequences and Metagenome-Assembled Genome Sequences of Microbial Communities Enriched on Phytoplankton Exometabolites.	Fu H, Smith CB, Sharma S, Moran MA.	Microbiol Resour Announc	10.1128/mra.00724-20	2020
Enzymology	Cultivable microbiota associated with Aurelia aurita and Mnemiopsis leidyi.	Weiland-Brauer N, Prasse D, Brauer A, Jaspers C, Reusch TBH, Schmitz RA.	Microbiologyopen	10.1002/mbo3.1094	2020
	Evolutionary Timeline and Genomic Plasticity Underlying the Lifestyle Diversity in Rhizobiales.	Wang S, Meade A, Lam HM, Luo H.	mSystems	10.1128/msystems.00438-20	2020
Genetics	Genome sequence of Phaeobacter daeponensis type strain (DSM 23529(T)), a facultatively anaerobic bacterium isolated from marine sediment, and emendation of Phaeobacter daeponensis.	Dogs M, Teshima H, Petersen J, Fiebig A, Chertkov O, Dalingault H, Chen A, Pati A, Goodwin LA, Chain P, Detter JC, Ivanova N, Lapidus A, Rohde M, Gronow S, Kyrpides NC, Woyke T, Simon M, Goker M, Klenk HP, Brinkhoff T	Stand Genomic Sci	10.4056/sigs.4287962	2013
	Leisingera thetidis sp. nov., isolated from coastal water.	Kim MJ, Guan Y, Choe H, Li Z, Chung N, Kang YH, Lee MK.	Int J Syst Evol Microbiol	10.1099/ijsem.0.005945	2023
Phylogeny	Cribrihabitans neustonicus sp. nov., isolated from coastal surface seawater, and emended description of the genus Cribrihabitans Chen et al. 2014.	Hameed A, Shahina M, Lin SY, Lai WA, Liu YC, Hsu YH, Young CC	Int J Syst Evol Microbiol	10.1099/ijs.0.066142-0	2014
Phylogeny	Phaeobacter aquaemixtae sp. nov., isolated from the junction between the ocean and a freshwater spring.	Park S, Park DS, Bae KS, Yoon JH	Int J Syst Evol Microbiol	10.1099/ijs.0.057646-0	2014
Phylogeny	Phaeobacter daeponensis sp. nov., isolated from a tidal flat of the Yellow Sea in Korea.	Yoon JH, Kang SJ, Lee SY, Oh TK	Int J Syst Evol Microbiol	10.1099/ijs.0.64779-0	2007

References

#17260	Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 23529
#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 )
#28250	IJSEM 856 2007 ( DOI 10.1099/ijs.0.64779-0 , PubMed 17392219 )
#31996	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 #28250
#36607	; Curators of the CIP;
#66793	Mukherjee et al.: GEBA: 1,003 reference genomes of bacterial and archaeal isolates expand coverage of the tree of life. 35: 676 - 683 2017 ( DOI 10.1038/nbt.3886 , PubMed 28604660 )
#67770	Japan Collection of Microorganism (JCM) ; Curators of the JCM;
#67771	Korean Collection for Type Cultures (KCTC) ; Curators of the KCTC;
#68368	Automatically annotated from API 20E .
#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 .
#118848	Collection of Institut Pasteur ; Curators of the CIP; CIP 109576
#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 .
#126262	A. Lissin, I. Schober, J. F. Witte, H. Lüken, A. Podstawka, J. Koblitz, B. Bunk, P. Dawyndt, P. Vandamme, P. de Vos, J. Overmann, L. C. Reimer: StrainInfo—the central database for linked microbial strain identifiers. ( DOI 10.1093/database/baaf059 )

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Leisingera daeponensis (DSM 23529, JCM 13606, KCTC 12794)

Name and taxonomic classification

Morphology

Cell morphology

Colony morphology

Pigmentation

Multimedia

Culture and growth conditions

Culture medium

Culture temp

Culture pH

Physiology and metabolism

Oxygen tolerance

Spore formation

Halophily

Observation

Metabolite utilization

Metabolite production

Metabolite tests

Enzymes

API 20E

API zym

Isolation, sampling and environmental information

Isolation source categories

Isolation

Taxonmaps

Interaction and safety

Risk assessment

Sequence information

Genome sequences

Genome browser: GCA_000473145

16S sequences

GC content

Genome-based predictions

Predictions

Literature

Literature

References

BacDive

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