Paracoccus aestuarii (DSM 19484, JCM 15119, KCTC 22049)

Name: Paracoccus aestuarii (DSM 19484, JCM 15119, KCTC 22049)
Creator: BacDive
License: http://creativecommons.org/licenses/by/4.0/

BacDive ID 13727

Type strain

Strain Designation B7

Culture col. no. DSM 19484 JCM 15119 KCTC 22049 B7 BCRC 80158

NCBI tax ID(s) 453842

Special Collections DSMZ JCM KCTC Literature strains

History <- S. W. Roh, Korea Res. Inst. Biosci. & Biotechnol. (KRIBB), Taejon, South Korea; B7 S. W. Roh B7. <- SW Roh, KRIBB

Links

Paracoccus aestuarii B7 is an aerobe, Gram-negative, rod-shaped bacterium that was isolated from tidal flat sediment.

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

Name and taxonomic classification

SI-ID 406104

KCTC 22049,JCM 15119,DSM 19484

@ref 20215

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

Domain Bacteria

Phylum Pseudomonadota

Class Alphaproteobacteria

Order Rhodobacterales

Family Paracoccaceae

Genus Paracoccus

Species Paracoccus aestuarii

Full scientific name Paracoccus aestuarii Roh et al. 2009

Morphology

Cell morphology

@ref	Gram stain	Cell length	Cell width	Cell shape	Confidence
32603	negative	1.75 µm	0.9 µm	rod-shaped
67771	negative
125439	negative				91.5
125438	negative				97.5

Pigmentation

32603

Productionyes

Culture and growth conditions

Culture medium

@ref	Name	Growth	Medium link	Composition
8046	TRYPTONE SOYA BROTH (TSB) (DSMZ Medium 545)		Medium recipe at MediaDive	Name: TRYPTONE SOYA BROTH (TSB) (DSMZ Medium 545) Composition: Casein peptone 17.0 g/l NaCl 5.0 g/l Soy peptone 3.0 g/l D(+)-Glucose 2.5 g/l K2HPO4 2.5 g/l Distilled water

Culture temp

@ref	Growth	Type	Temperature (°C)
8046	positive	growth	28
32603	positive	growth	15-37
32603	positive	optimum	26
67770	positive	growth	30
67771	positive	growth	37

Culture pH

@ref	Ability	Type	PH	PH range
32603	positive	optimum	9
32603	positive	growth	7.5-9.5	alkaliphile

Physiology and metabolism

Oxygen tolerance

@ref	Oxygen tolerance	Confidence
32603	aerobe
67771	aerobe
125439	obligate aerobe	93.1

Spore formation

@ref	Spore formation	Confidence
125439		95
125438		92.883

Halophily

@ref	Salt	Growth	Tested relation	Concentration
32603	NaCl	positive	growth	<5 %

Observation

@ref	Observation
32603	aggregates in clumps
67770	quinones: Q-10

Metabolite utilization

@ref	Chebi-ID	Metabolite	Utilization activity	Kind of utilization tested
32603	16808 ChEBI	2-dehydro-D-gluconate	+	carbon source
32603	58143 ChEBI	5-dehydro-D-gluconate	+	carbon source
32603	4853 ChEBI	esculin	+	hydrolysis
32603	17234 ChEBI	glucose	+	carbon source
32603	18403 ChEBI	L-arabitol	+	carbon source
32603	25115 ChEBI	malate	+	carbon source
32603	17306 ChEBI	maltose	+	carbon source
32603	29864 ChEBI	mannitol	+	carbon source
32603	37684 ChEBI	mannose	+	carbon source
32603	506227 ChEBI	N-acetylglucosamine	+	carbon source
32603	15963 ChEBI	ribitol	+	carbon source
32603	33942 ChEBI	ribose	+	carbon source
32603	53258 ChEBI	sodium citrate	+	carbon source
32603	18222 ChEBI	xylose	+	carbon source

Enzymes

@ref	Value	Activity	Ec
32603	acid phosphatase	+	3.1.3.2
32603	alkaline phosphatase	+	3.1.3.1
32603	alpha-galactosidase	+	3.2.1.22
32603	catalase	+	1.11.1.6
32603	cytochrome oxidase	+	1.9.3.1

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	Latitude	Longitude
8046	tidal flat sediment	Yeosu (34° 47' 26'' N 127° 34' 01'' E)	Republic of Korea	KOR	Asia	34.7906	127.567 34.7906/127.567
67770	Tidal flat sediment in Yeosu (34° 47' 26" N 127° 34' 01" E)		Republic of Korea	KOR	Asia	34.7906	127.567 34.7906/127.567
67771	From flat tidal		Republic of Korea	KOR	Asia

Interaction and safety

Risk assessment

@ref	Biosafety level	Biosafety level comment
8046	1	Risk group (German classification) According to TRBA 466

Sequence information

Genome sequences

@ref	Description	Assembly level	INSDC accession	BV-BRC accession	IMG accession	NCBI tax ID	Score
66792	ASM2855388v1 assembly for Paracoccus aestuarii DSM 19484	complete	GCA_028553885	453842.10	8114114138	453842	95.86
67770	ASM359481v1 assembly for Paracoccus aestuarii DSM 19484	contig	GCA_003594815	453842.8	2901860463	453842	23.22

16S sequences

@ref	Description	Accession	Length	Database	NCBI tax ID
8046	Paracoccus aestuarii strain B7 16S ribosomal RNA gene, partial sequence	EF660757	1300		453842
124043	Paracoccus aestuarii strain DSM 19484 16S ribosomal RNA gene, partial sequence.	MZ276321	1358		453842

GC content

@ref	GC-content (mol%)	Method
8046	62.0	high performance liquid chromatography (HPLC)
32603	62
67770	62	high performance liquid chromatography (HPLC)

Genome-based predictions

Predictions

Predictions from Deep Learning for Genome Sequence Data. R package version 0.3.1 based on: Paracoccus aestuarii DSM 19484
NCBI: GCA_003594815

@ref	Trait	Model	Prediction	Confidence in %	In training data
125439	spore_formation	BacteriaNetⓘ	no	95.00	no
125439	motility	BacteriaNetⓘ	no	51.40	no
125439	gram_stain	BacteriaNetⓘ	negative	91.50	no
125439	oxygen_tolerance	BacteriaNetⓘ	obligate aerobe	93.10	no

Predictions from bacterial phenotypic traits through improved machine learning using high-quality, curated datasets based on: Paracoccus aestuarii DSM 19484
NCBI: GCA_028553885.1

@ref	Trait	Model	Prediction	Confidence in %	In training data
125438	gram-positive	gram-positiveⓘ	no	97.50	yes
125438	anaerobic	anaerobicⓘ	no	94.79	yes
125438	aerobic	aerobicⓘ	yes	86.68	yes
125438	spore-forming	spore-formingⓘ	no	92.88	no
125438	thermophilic	thermophileⓘ	no	97.20	no
125438	flagellated	motile2+ⓘ	yes	67.78	no

Literature

Topic	Title	Authors	Journal	DOI	Year
	Paracoccus onchidii sp. nov., a moderately halophilic bacterium isolated from a marine invertebrate from the South China Sea.	Xu SS, Lai QL, Liu ZZ, Xu Y.	Antonie Van Leeuwenhoek	10.1007/s10482-023-01848-7	2023
Phylogeny	Paracoccus amoyensis sp. nov., isolated from the surface seawater along the coast of Xiamen Island, China.	Lyu L, Lai Q, Li J, Yu Z, Shao Z	Int J Syst Evol Microbiol	10.1099/ijsem.0.004685	2021
Phylogeny	Paracoccus pueri sp. nov., isolated from Pu'er tea.	Wang YS, Yan ZF, Lin P, Gao W, Yi TH	Antonie Van Leeuwenhoek	10.1007/s10482-018-1041-9	2018
Phylogeny	Paracoccus rhizosphaerae sp. nov., isolated from the rhizosphere of the plant Crossostephium chinense (L.) Makino (Seremban).	Kampfer P, Lai WA, Arun AB, Young CC, Rekha PD, Martin K, Busse HJ, Chen WM	Int J Syst Evol Microbiol	10.1099/ijs.0.039057-0	2012
Phylogeny	Paracoccus aestuarii sp. nov., isolated from tidal flat sediment.	Roh SW, Nam YD, Chang HW, Kim KH, Kim MS, Shin KS, Yoon JH, Oh HM, Bae JW	Int J Syst Evol Microbiol	10.1099/ijs.0.65759-0	2009

References

#8046	Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 19484
#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 )
#28816	IJSEM 790 2009 ( DOI 10.1099/ijs.0.65759-0 , PubMed 19329608 )
#32603	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 #28816
#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;
#67771	Korean Collection for Type Cultures (KCTC) ; Curators of the KCTC;
#124043	Isabel Schober, Julia Koblitz: Data extracted from sequence databases, automatically matched based on designation and taxonomy .
#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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Paracoccus aestuarii (DSM 19484, JCM 15119, KCTC 22049)

Name and taxonomic classification

Morphology

Cell morphology

Pigmentation

Culture and growth conditions

Culture medium

Culture temp

Culture pH

Physiology and metabolism

Oxygen tolerance

Spore formation

Halophily

Observation

Metabolite utilization

Enzymes

Isolation, sampling and environmental information

Isolation source categories

Isolation

Interaction and safety

Risk assessment

Sequence information

Genome sequences

Genome browser: GCA_028553885

16S sequences

GC content

Genome-based predictions

Predictions

Literature

Literature

References

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