Name: Paracoccus limosus KEMC5401-184
Creator: BacDive
License: http://creativecommons.org/licenses/by-nc/4.0/

Strain identifier

BacDive ID: 133753

Type strain:

Species: Paracoccus limosus

Strain Designation: KEMC5401-184, NB88

Culture col. no.: JCM 17370, KEMC 5401-184

Strain history: S.-S. Lee NB88.

NCBI tax ID(s): 913252 (species)

Section

Paracoccus limosus KEMC5401-184 is a Gram-negative, rod-shaped bacterium that was isolated from wastewater.

Gram-negative
rod-shaped
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	*Rhodobacterales*
	Family	*Paracoccaceae*
	Genus	*Paracoccus*
	Species	**Paracoccus limosus**
	Full Scientific Name (LPSN)	Paracoccus limosus Lee and Lee 2013

Information on morphological and physiological properties Morphology

[Ref.: #30401]	Gram stain	negative
[Ref.: #69480]	Gram stain	negative Confidence in %99.997

[Ref.: #30401]	Cell length	1 µm

[Ref.: #30401]	Cell width	0.85 µm

[Ref.: #30401]	Cell shape	rod-shaped

[Ref.: #30401]	Motility	no

[Ref.: #30401]

Pigment production

yes

Information on culture and growth conditions Culture and growth conditions

		Temperature
[Ref.: #30401]	growth	20-37 °C
[Ref.: #30401]	optimum	30 °C
[Ref.: #67770]	growth	30 °C

[Ref.: #30401]	Temperature range	mesophilic
[Ref.: #67770]	Temperature range	mesophilic

	pH	Kind of pH		pH
[Ref.: #30401]			optimum	7
[Ref.: #30401]			growth	06-09

Information on physiology and metabolism Physiology and metabolism

[Ref.: #30401]	Ability of spore formation	no
[Ref.: #69481]	Ability of spore formation	no Confidence in %100
[Ref.: #69480]	Ability of spore formation	no Confidence in %99.993

	Halophily	Salt	Tested relation		Salt conc.
[Ref.: #30401]		NaCl		growth	0-4	%

[Ref.: #30401]	Observation	aggregates in clumps
[Ref.: #67770]	Observation	quinones: Q-10

	Metabolite	Utilization activity	Kind of utilization tested
[Ref.: #30401]	4-hydroxybenzoate ChEBI	+	carbon source
[Ref.: #30401]	acetate ChEBI	+	carbon source
[Ref.: #30401]	alanine ChEBI	+	carbon source
[Ref.: #30401]	fucose ChEBI	+	carbon source
[Ref.: #30401]	glucose ChEBI	+	carbon source
[Ref.: #30401]	histidine ChEBI	+	carbon source
[Ref.: #30401]	lactate ChEBI	+	carbon source
[Ref.: #30401]	malate ChEBI	+	carbon source
[Ref.: #30401]	mannitol ChEBI	+	carbon source
[Ref.: #30401]	mannose ChEBI	+	carbon source
[Ref.: #30401]	myo-inositol ChEBI	+	carbon source
[Ref.: #30401]	nitrate ChEBI	+	reduction
[Ref.: #30401]	propionate ChEBI	+	carbon source
[Ref.: #30401]	ribose ChEBI	+	carbon source
[Ref.: #30401]	serine ChEBI	+	carbon source
[Ref.: #30401]	sorbitol ChEBI	+	carbon source
[Ref.: #30401]	sucrose ChEBI	+	carbon source
	Only first 10 entries are displayed. Click here to see all.

	Enzyme	Enzyme activity	EC number
[Ref.: #30401]	acid phosphatase	+	3.1.3.2
[Ref.: #30401]	alkaline phosphatase	+	3.1.3.1
[Ref.: #30401]	catalase	+	1.11.1.6
[Ref.: #30401]	cytochrome oxidase	+	1.9.3.1

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

[Ref.: #30401]	Sample type/isolated from	wastewater

[Ref.: #67770]	Sample type/isolated from	Activated sludge in the Mae-san sewage treatment plant
[Ref.: #67770]	Country	Republic of Korea
[Ref.: #67770]	Country ISO 3 Code	KOR
[Ref.: #67770]	Continent	Asia
* marker position based on {}

Isolation sources categories

#Engineered

#Waste

#Wastewater

What are isolation sources categories?

[Ref.: #69479]

Global distribution of 16S sequence HQ336256 (>99% sequence identity) for Paracoccus limosus from Microbeatlas

Aquatic Samples	362
Soil Samples	235
Animal Samples	170
Plant Samples	76
Total Samples	843

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.: #30401]	Paracoccus limosus strain NB88 16S ribosomal RNA gene, partial sequence	HQ336256	1400	GenBank	913252 tax ID

Genome sequence information:

	Sequence accession description	Seq. accession number	Assembly level	Sequence database	Associated NCBI tax ID
[Ref.: #67770]	Paracoccus limosus JCM 17370	GCA_009711185	scaffold	GenBank	913252 tax ID
[Ref.: #66792]	Paracoccus limosus strain JCM 17370	913252.3	wgs	PATRIC	913252 tax ID	*

[Ref.: #30401]	GC-content	66.4 mol%
[Ref.: #67770]	GC-content	66.4 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: Paracoccus limosus JCM 17370 NCBI: GCA_009711185.1
[Ref.: #69481]	spore-forming	no	100	no

	Trait	Prediction	Confidence in %	In training data
	Predictions from Diaspora project based on: Paracoccus limosus strain JCM 17370 PATRIC: 913252.3
[Ref.: #69480]	motile	no	70.129	yes
[Ref.: #69480]	flagellated	no	82.453	no
[Ref.: #69480]	gram-positive	no	98.473	yes
[Ref.: #69480]	anaerobic	no	98.369	no
[Ref.: #69480]	halophile	no	86.789	no
[Ref.: #69480]	spore-forming	no	95.949	yes
[Ref.: #69480]	glucose-util	yes	92.728	no
[Ref.: #69480]	aerobic	yes	90.322	no
[Ref.: #69480]	thermophile	no	98.396	yes
[Ref.: #69480]	glucose-ferment	no	88.807	no

Availability in culture collections External links

[Ref.: #30401]

Culture collection no.

JCM 17370, KEMC 5401-184

Literature:

Topic	Title	Authors	Journal	DOI	Year
Phylogeny	Paracoccus limosus sp. nov., isolated from activated sludge in a sewage treatment plant.	Lee MJ, Lee SS	Int J Syst Evol Microbiol	10.1099/ijs.0.035212-0	2012	*

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 )

#30401

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 #26738 (see below)

#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 )

#26738

IJSEM 1311 2013 ( DOI 10.1099/ijs.0.035212-0 , PubMed 22798648 )

* These data were automatically processed and therefore are not curated

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Paracoccus limosus JCM 17370

Paracoccus limosus strain JCM 17370

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