Pelagibius litoralis (KCCM 42323, JCM 15426, DSM 21314)

Name: Pelagibius litoralis (KCCM 42323, JCM 15426, DSM 21314)
Creator: BacDive
License: http://creativecommons.org/licenses/by/4.0/

BacDive ID 133435

Type strain

Strain Designation CL-UU02

Culture col. no. KCCM 42323 JCM 15426 DSM 21314 CL-UU02

NCBI tax ID(s) 374515

Special Collections DSMZ JCM Literature strains

History <- B. C. Cho, Seoul Natl. Univ., Republic of Korea; CL-UU02 B. C. Cho CL-UU02.

Links

Pelagibius litoralis CL-UU02 is an aerobe, Gram-negative, motile bacterium that was isolated from seawater.

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

Name and taxonomic classification

SI-ID 398076

JCM 15426,DSM 21314

@ref 20215

Last LPSN update 2026-02-09 11:31:57

Domain Bacteria

Phylum Pseudomonadota

Class Alphaproteobacteria

Order Rhodospirillales

Family Kiloniellaceae

Genus Pelagibius

Species Pelagibius litoralis

Full scientific name Pelagibius litoralis Choi et al. 2009

Morphology

Cell morphology

@ref	Gram stain	Cell length	Cell width	Cell shape	Confidence
28965	negative	1.85 µm	0.75 µm	rod-shaped
125439	negative				99.5
125438	negative				97.5

Culture and growth conditions

Culture medium

@ref	Name	Growth	Medium link	Composition
64728	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

Culture temp

@ref	Growth	Type	Temperature (°C)
28965	positive	growth	15-33
28965	positive	optimum	29
64728	positive	growth	28
67770	positive	growth	30

Culture pH

@ref	Ability	Type	PH	PH range
28965	positive	optimum	7.5
28965	positive	growth	06-11	alkaliphile

Physiology and metabolism

Oxygen tolerance

28965

Oxygen toleranceaerobe

Spore formation

@ref	Spore formation	Confidence
125439		99.3

Halophily

@ref	Salt	Growth	Tested relation	Concentration
28965	NaCl	positive	growth	02-06 %
28965	NaCl	positive	optimum	3.5 %

Observation

@ref	Observation
28965	aggregates in clumps
67770	quinones: Q-10

Metabolite utilization

@ref	Chebi-ID	Metabolite	Utilization activity	Kind of utilization tested
28965	22599 ChEBI	arabinose	+	carbon source
28965	4853 ChEBI	esculin	+	hydrolysis
28965	28260 ChEBI	galactose	+	carbon source
28965	17234 ChEBI	glucose	+	carbon source
28965	29864 ChEBI	mannitol	+	carbon source
28965	37684 ChEBI	mannose	+	carbon source
28965	17632 ChEBI	nitrate	+	reduction
28965	15361 ChEBI	pyruvate	+	carbon source
28965	30031 ChEBI	succinate	+	carbon source
28965	18222 ChEBI	xylose	+	carbon source

Enzymes

@ref	Value	Activity	Ec
28965	acid phosphatase	+	3.1.3.2
28965	alkaline phosphatase	+	3.1.3.1

Isolation, sampling and environmental information

Isolation source categories

Cat1	Cat2	Cat3
#Environmental	#Aquatic	#Marine

Isolation

@ref	Sample type	Geographic location	Country	Country ISO 3 Code	Continent
28965	seawater
64728	seawater	JooMoonjin harbor	Republic of Korea	KOR	Asia
67770	Coastal seawater off the east coast of Korea

Taxonmaps

69479

Global distribution of 16S sequence DQ401091 (>99% sequence identity) for Pelagibius litoralis subclade from Microbeatlas

Aquatic Samples	59
Soil Samples	3
Animal Samples	26
Plant Samples	1
Total Samples	89

Interaction and safety

Risk assessment

@ref	Biosafety level	Biosafety level comment
64728	1	Risk group (German classification)

Sequence information

Genome sequences

@ref	Description	Assembly level	INSDC accession	BV-BRC accession	IMG accession	NCBI tax ID	Score
67770	ASM1168391v1 assembly for Pelagibius litoralis DSM 21314	contig	GCA_011683915	374515.3	2989044555	374515	64.94

16S sequences

@ref	Description	Accession	Length	Database	NCBI tax ID
64728	Pelagibius litoralis strain CL-UU02 16S ribosomal RNA gene, partial sequence	DQ401091	1422		374515

GC content

@ref	GC-content (mol%)	Method
64728	66.3
67770	66.3	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: Pelagibius litoralis DSM 21314
NCBI: GCA_011683915

@ref	Trait	Model	Prediction	Confidence in %	In training data
125439	spore_formation	BacteriaNetⓘ	no	99.30	no
125439	motility	BacteriaNetⓘ	yes	77.10	no
125439	gram_stain	BacteriaNetⓘ	negative	99.50	no
125439	oxygen_tolerance	BacteriaNetⓘ	aerobe	76.30	no

Predictions from bacterial phenotypic traits through improved machine learning using high-quality, curated datasets based on: Pelagibius litoralis strain DSM 21314
PATRIC: 374515.3

@ref	Trait	Model	Prediction	Confidence in %	In training data
125438	gram-positive	gram-positiveⓘ	no	97.50	yes
125438	anaerobic	anaerobicⓘ	no	90.09	yes
125438	spore-forming	spore-formingⓘ	no	83.12	no
125438	aerobic	aerobicⓘ	yes	75.34	yes
125438	thermophilic	thermophileⓘ	no	95.10	yes
125438	flagellated	motile2+ⓘ	yes	73.95	no

Literature

Topic	Title	Authors	Journal	DOI	Year
Phylogeny	Limimonas halophila gen. nov., sp. nov., an extremely halophilic bacterium in the family Rhodospirillaceae.	Amoozegar MA, Makhdoumi-Kakhki A, Ramezani M, Nikou MM, Fazeli SAS, Schumann P, Ventosa A	Int J Syst Evol Microbiol	10.1099/ijs.0.041236-0	2012
Phylogeny	Pelagibius marinus sp. nov., a novel bacterium isolated from marine sediment, and emended description of the genus Pelagibius.	Yang C, Zhu S, Sun C, Ding L, Jung D, He S, Wang N, Zhang W	Int J Syst Evol Microbiol	10.1099/ijsem.0.005325	2022
Phylogeny	Denitrobaculum tricleocarpae gen. nov., sp. nov., a marine bacterium from coralline algae Tricleocarpa sp.	Wang G, Tang D, Li G, Xu S, Dang G, Su H, Liao Z, Chen B, Huang W, Liang J, Yu K	Int J Syst Evol Microbiol	10.1099/ijsem.0.004173	2020
Phylogeny	Marivibrio halodurans gen. nov., sp. nov., a marine bacterium in the family Rhodospirillaceae isolated from underground rock salt.	Chen S, Xu Y, Zheng C, Ke LX	Int J Syst Evol Microbiol	10.1099/ijsem.0.002309	2017
Phylogeny	Pelagibius litoralis gen. nov., sp. nov., a marine bacterium in the family Rhodospirillaceae isolated from coastal seawater.	Choi DH, Hwang CY, Cho BC	Int J Syst Evol Microbiol	10.1099/ijs.0.002774-0	2009

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 )
#25402	IJSEM 818 2009 ( DOI 10.1099/ijs.0.002774-0 , PubMed 19329613 )
#28965	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 #25402
#64728	Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 21314
#67770	Japan Collection of Microorganism (JCM) ; Curators of the JCM;
#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 .
#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 )

Rate our new design

Content

About us

Pelagibius litoralis (KCCM 42323, JCM 15426, DSM 21314)

Name and taxonomic classification

Morphology

Cell morphology

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

Taxonmaps

Interaction and safety

Risk assessment

Sequence information

Genome sequences

Genome browser: GCA_011683915

16S sequences

GC content

Genome-based predictions

Predictions

Literature

Literature

References

BacDive

Help

Social Media