Name: Pelagibius litoralis CL-UU02
Creator: BacDive
License: http://creativecommons.org/licenses/by-nc/4.0/

Strain identifier

BacDive ID: 133435

Type strain:

Species: Pelagibius litoralis

Strain Designation: CL-UU02

Culture col. no.: KCCM 42323, JCM 15426, DSM 21314

Strain history: B. C. Cho CL-UU02.

NCBI tax ID(s): 374515 (species)

SI-ID 398076

DSM 21314

Section

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

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	14-12-2023 (DD-MM-YYYY)
	Domain	"Bacteria"
	Phylum	*Pseudomonadota*
	Class	*Alphaproteobacteria*
	Order	*Rhodospirillales*
	Family	*Rhodovibrionaceae*
	Genus	*Pelagibius*
	Species	**Pelagibius litoralis**
	Full Scientific Name (LPSN)	Pelagibius litoralis Choi et al. 2009

Information on morphological and physiological properties Morphology

[Ref.: #28965]	Gram stain	negative
[Ref.: #69480]	Gram stain	negative Confidence in %99.953

[Ref.: #28965]	Cell length	1.85 µm

[Ref.: #28965]	Cell width	0.75 µm

[Ref.: #28965]	Cell shape	rod-shaped

[Ref.: #28965]	Motility	yes
[Ref.: #69480]	Motility	yes Confidence in %95.264

Information on culture and growth conditions Culture and growth conditions

[Ref.: #64728]

Culture medium

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

[Ref.: #64728]

Culture medium growth

[Ref.: #64728]

Culture medium link

Medium recipe at MediaDive

[Ref.: #64728]

Culture medium composition

expand / minimize

		Temperature
[Ref.: #28965]	growth	15-33 °C
[Ref.: #28965]	optimum	29 °C
[Ref.: #64728]	growth	28 °C
[Ref.: #67770]	growth	30 °C

[Ref.: #28965]	Temperature range	mesophilic
[Ref.: #64728]	Temperature range	mesophilic
[Ref.: #67770]	Temperature range	mesophilic

	pH	Kind of pH		pH
[Ref.: #28965]			optimum	7.5
[Ref.: #28965]			growth	06-11

Information on physiology and metabolism Physiology and metabolism

[Ref.: #28965]

Oxygen tolerance

aerobe

[Ref.: #69481]	Ability of spore formation	no Confidence in %100
[Ref.: #69480]	Ability of spore formation	no Confidence in %99.93

	Halophily	Salt	Tested relation		Salt conc.
[Ref.: #28965]		NaCl		growth	02-06	%
[Ref.: #28965]		NaCl		optimum	3.5	%

[Ref.: #28965]	Observation	aggregates in clumps
[Ref.: #67770]	Observation	quinones: Q-10

	Metabolite	Utilization activity	Kind of utilization tested
[Ref.: #28965]	arabinose ChEBI	+	carbon source
[Ref.: #28965]	esculin ChEBI	+	hydrolysis
[Ref.: #28965]	galactose ChEBI	+	carbon source
[Ref.: #28965]	glucose ChEBI	+	carbon source
[Ref.: #28965]	mannitol ChEBI	+	carbon source
[Ref.: #28965]	mannose ChEBI	+	carbon source
[Ref.: #28965]	nitrate ChEBI	+	reduction
[Ref.: #28965]	pyruvate ChEBI	+	carbon source
[Ref.: #28965]	succinate ChEBI	+	carbon source
[Ref.: #28965]	xylose ChEBI	+	carbon source

	Enzymes	Enzyme	Enzyme activity	EC number
[Ref.: #28965]		acid phosphatase	+	3.1.3.2
[Ref.: #28965]		alkaline phosphatase	+	3.1.3.1

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

[Ref.: #28965]	Sample type/isolated from	seawater

[Ref.: #64728]	Sample type/isolated from	seawater
[Ref.: #64728]	Geographic location (country and/or sea, region)	JooMoonjin harbor
[Ref.: #64728]	Country	Republic of Korea
[Ref.: #64728]	Country ISO 3 Code	KOR
[Ref.: #64728]	Continent	Asia

[Ref.: #67770]	Sample type/isolated from	Coastal seawater off the east coast of Korea
* marker position based on {}

Isolation sources categories

#Environmental

#Aquatic

#Marine

What are isolation sources categories?

[Ref.: #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

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

[Ref.: #64728]

Biosafety level

Risk group (German classification)
According to TRBA 466

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.: #64728]	Pelagibius litoralis strain CL-UU02 16S ribosomal RNA gene, partial sequence	DQ401091	1422	ENA	374515 tax ID

Genome sequence information:

	Sequence accession description	Seq. accession number	Assembly level	Sequence database	Associated NCBI tax ID
[Ref.: #67770]	Pelagibius litoralis DSM 21314	GCA_011683915	contig	GenBank	374515 tax ID
[Ref.: #66792]	Pelagibius litoralis strain DSM 21314	374515.3	wgs	PATRIC	374515 tax ID	*

[Ref.: #64728]	GC-content	66.3 mol%
[Ref.: #67770]	GC-content	66.3 mol%	high performance liquid chromatography (HPLC)

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

	Trait	Prediction	Confidence in %	In training data
	Predictions from GenomeNet Sporulation v. 1 based on: Pelagibius litoralis strain DSM 21314 PATRIC: 374515.3
[Ref.: #69481]	spore-forming	no	100	no

	Trait	Prediction	Confidence in %	In training data
	Predictions from Diaspora project based on: Pelagibius litoralis strain DSM 21314 PATRIC: 374515.3
[Ref.: #69480]	gram-positive	no	98.318	yes
[Ref.: #69480]	anaerobic	no	97.544	yes
[Ref.: #69480]	halophile	no	59.457	no
[Ref.: #69480]	spore-forming	no	93.901	no
[Ref.: #69480]	glucose-util	yes	87.797	yes
[Ref.: #69480]	aerobic	yes	68.849	no
[Ref.: #69480]	motile	yes	86.684	yes
[Ref.: #69480]	flagellated	no	57.905	no
[Ref.: #69480]	thermophile	no	97.344	yes
[Ref.: #69480]	glucose-ferment	no	89.526	no

Availability in culture collections External links

[Ref.: #64728]

Culture collection no.

KCCM 42323, JCM 15426, DSM 21314

[Ref.: #91439]

SI-ID 398076

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 )

#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 (see below)

#64728

Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 21314

#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;

#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 .

#69480

Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmann: Predictions based on genome sequence made in the Diaspora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information) .

#69481

Xiao-Yin To, René Mreches, Martin Binder, Alice C. McHardy, Philipp C. Münch: Predictions based on the model GenomeNet Sporulation v. 1 . ( DOI 10.21203/rs.3.rs-2527258/v1 )

#91439

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-ID398076.1 )

#25402

IJSEM 818 2009 ( DOI 10.1099/ijs.0.002774-0 , PubMed 19329613 )

* These data were automatically processed and therefore are not curated

Change proposal

You found an error in BacDive? Please tell us about it!

Note that changes will be reviewed and judged. If your changes are legitimate, changes will occur within the next BacDive update. Only proposed changes supported by the according reference will be reviewed. The BacDive team reserves the right to reject proposed changes.

Search for species Pelagibius litoralis in external resources:
SILVA
BRENDA
PANGAEA
StrainInfo
GBIF

Pelagibius litoralis strain DSM 21314

Pelagibius litoralis strain DSM 21314

Change proposal

Change proposal