Name: Paracoccus litorisediminis GHD-05
Creator: BacDive
License: https://creativecommons.org/licenses/by/4.0/

Strain identifier

BacDive ID: 158752

Type strain:

Species: Paracoccus litorisediminis

Strain Designation: GHD-05

Culture col. no.: KCTC 52978, NBRC 112902

Strain history: <- Jung-Hoon YOON, Sungkyunkwan Univ.

NCBI tax ID(s): 2006130 (species)

Special Collections

Section

Paracoccus litorisediminis GHD-05 is an aerobe, Gram-negative, rod-shaped bacterium that forms circular colonies and was isolated from from tidal flat sediment.

colony-forming
Gram-negative
rod-shaped
aerobe
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 litorisediminis**
	Full Scientific Name (LPSN)	Paracoccus litorisediminis Park et al. 2017

Information on morphological and physiological properties Morphology

[Ref.: #65504]	Gram stain	negative
[Ref.: #69480]	Gram stain	negative Confidence in %97.482

[Ref.: #65504]	Cell length	0.4-2.0 µm

[Ref.: #65504]	Cell width	0.4-0.8 µm

[Ref.: #65504]	Cell shape	rod-shaped
[Ref.: #65504]	Cell shape	coccus-shaped
[Ref.: #65504]	Cell shape	ovoid-shaped

[Ref.: #65504]	Motility	no

[Ref.: #65504]	Colony size	1.0-2.0 mm
[Ref.: #65504]	Colony color	yellowish white
[Ref.: #65504]	Colony shape	circular
[Ref.: #65504]	Incubation period	3 days
[Ref.: #65504]	Cultivation medium used	MA

Information on culture and growth conditions Culture and growth conditions

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Culture medium

Marine agar (MA)

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Culture medium growth

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Culture medium

Marine agar (MA)

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Culture medium growth

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Culture medium composition

expand / minimize

	Kind of temperature		Temperature
[Ref.: #65504]		optimum	30 °C
[Ref.: #65504]		growth	10-40 °C
[Ref.: #65504]	no	growth	4 °C
[Ref.: #65504]	no	growth	45 °C
[Ref.: #67771]		growth	30 °C

	Kind of pH		pH
[Ref.: #65504]		optimum	7.0-8.0
[Ref.: #65504]		growth	5.5
[Ref.: #65504]	no	growth	5.0

Information on physiology and metabolism Physiology and metabolism

[Ref.: #65504]	Oxygen tolerance	aerobe
[Ref.: #65504]	Oxygen tolerance	anaerobe
[Ref.: #67771]	Oxygen tolerance	aerobe

[Ref.: #65504]	Ability of spore formation	no
[Ref.: #69481]	Ability of spore formation	no Confidence in %100

	Salt		Salt conc.
[Ref.: #65504]	NaCl	growth	0-5.0	%(w/v)
[Ref.: #65504]	NaCl	optimum	2.0	%(w/v)
[Ref.: #65504]	MgCl2	growth	0	%

	Metabolite	Utilization activity	Kind of utilization tested
[Ref.: #65504]	acetate ChEBI	+	carbon source
[Ref.: #65504]	acetate ChEBI	+	energy source
[Ref.: #65504]	benzoate ChEBI	-	carbon source
[Ref.: #65504]	benzoate ChEBI	-	energy source
[Ref.: #65504]	casein	+	hydrolysis
[Ref.: #65504]	cellobiose ChEBI	+	carbon source
[Ref.: #65504]	cellobiose ChEBI	+	energy source
[Ref.: #65504]	citrate ChEBI	+	carbon source
[Ref.: #65504]	citrate ChEBI	+	energy source
[Ref.: #65504]	D-fructose ChEBI	+	carbon source
[Ref.: #65504]	D-fructose ChEBI	+	energy source
[Ref.: #65504]	D-galactose ChEBI	+	carbon source
[Ref.: #65504]	D-galactose ChEBI	+	energy source
[Ref.: #65504]	D-glucose ChEBI	+	carbon source
[Ref.: #65504]	D-glucose ChEBI	+	energy source
[Ref.: #65504]	D-mannose ChEBI	+	carbon source
[Ref.: #65504]	D-mannose ChEBI	+	energy source
[Ref.: #65504]	D-xylose ChEBI	+	carbon source
[Ref.: #65504]	D-xylose ChEBI	+	energy source
[Ref.: #65504]	esculin ChEBI	-	hydrolysis
[Ref.: #65504]	formate ChEBI	-	carbon source
[Ref.: #65504]	formate ChEBI	-	energy source
[Ref.: #65504]	gelatin ChEBI	-	hydrolysis
[Ref.: #65504]	hypoxanthine ChEBI	+	hydrolysis
[Ref.: #65504]	L-arabinose ChEBI	+	carbon source
[Ref.: #65504]	L-arabinose ChEBI	+	energy source
[Ref.: #65504]	L-glutamate ChEBI	-	carbon source
[Ref.: #65504]	L-glutamate ChEBI	-	energy source
[Ref.: #65504]	L-malate ChEBI	+	carbon source
[Ref.: #65504]	L-malate ChEBI	+	energy source
[Ref.: #65504]	L-tyrosine ChEBI	+	hydrolysis
[Ref.: #65504]	maltose ChEBI	-	carbon source
[Ref.: #65504]	maltose ChEBI	-	energy source
[Ref.: #65504]	nitrate ChEBI	+	reduction
[Ref.: #65504]	pyruvate ChEBI	+	carbon source
[Ref.: #65504]	pyruvate ChEBI	+	energy source
[Ref.: #65504]	salicin ChEBI	+	carbon source
[Ref.: #65504]	salicin ChEBI	+	energy source
[Ref.: #65504]	starch ChEBI	-	hydrolysis
[Ref.: #65504]	succinate ChEBI	+	carbon source
[Ref.: #65504]	succinate ChEBI	+	energy source
[Ref.: #65504]	sucrose ChEBI	-	carbon source
[Ref.: #65504]	sucrose ChEBI	-	energy source
[Ref.: #65504]	trehalose ChEBI	-	carbon source
[Ref.: #65504]	trehalose ChEBI	-	energy source
[Ref.: #65504]	tween 80 ChEBI	-	hydrolysis
[Ref.: #65504]	xanthine ChEBI	+	hydrolysis
	Only first 10 entries are displayed. Click here to see all.

	Metabolite	Antibiotic sensitivity	Concentration		Antibiotic resistance	Concentration
[Ref.: #65504]	ampicillin ChEBI				yes	10	µg (disc)
[Ref.: #65504]	carbenicillin ChEBI	yes	100	µg (disc)
[Ref.: #65504]	cephalothin ChEBI	yes	30	µg (disc)
[Ref.: #65504]	chloramphenicol ChEBI	yes	100	µg (disc)
[Ref.: #65504]	gentamicin ChEBI	yes	30	µg (disc)
[Ref.: #65504]	kanamycin ChEBI	yes	30	µg (disc)
[Ref.: #65504]	lincomycin ChEBI				yes	15	µg (disc)
[Ref.: #65504]	neomycin ChEBI	yes	30	µg (disc)
[Ref.: #65504]	novobiocin ChEBI	yes	5	µg (disc)
[Ref.: #65504]	oleandomycin ChEBI				yes	15	µg (disc)
[Ref.: #65504]	penicillin g ChEBI				yes	20	Unit (disc)
[Ref.: #65504]	polymyxin b ChEBI	yes	100	Unit (disc)
[Ref.: #65504]	streptomycin ChEBI	yes	50	µg (disc)
[Ref.: #65504]	tetracycline ChEBI	yes	30	µg (disc)
	Only first 10 entries are displayed. Click here to see all.

	Metabolite production	Metabolite	Production
[Ref.: #65504]		hydrogen sulfide ChEBI	no

	Enzyme	Enzyme activity	EC number
[Ref.: #65504]	acid phosphatase	+	3.1.3.2
[Ref.: #65504]	alkaline phosphatase	+	3.1.3.1
[Ref.: #65504]	alpha-chymotrypsin	-	3.4.21.1
[Ref.: #65504]	alpha-fucosidase	-	3.2.1.51
[Ref.: #65504]	alpha-galactosidase	-	3.2.1.22
[Ref.: #65504]	alpha-glucosidase	+	3.2.1.20
[Ref.: #65504]	alpha-mannosidase	-	3.2.1.24
[Ref.: #65504]	beta-galactosidase	-	3.2.1.23
[Ref.: #65504]	beta-glucosidase	-	3.2.1.21
[Ref.: #65504]	beta-glucuronidase	-	3.2.1.31
[Ref.: #65504]	catalase	+	1.11.1.6
[Ref.: #65504]	cystine arylamidase	+	3.4.11.3
[Ref.: #65504]	cytochrome oxidase	+	1.9.3.1
[Ref.: #65504]	esterase (C 4)	+
[Ref.: #65504]	esterase Lipase (C 8)	+
[Ref.: #65504]	leucine arylamidase	+	3.4.11.1
[Ref.: #65504]	lipase (C 14)	-
[Ref.: #65504]	N-acetyl-beta-glucosaminidase	+	3.2.1.52
[Ref.: #65504]	naphthol-AS-BI-phosphohydrolase	+
[Ref.: #65504]	trypsin	-	3.4.21.4
[Ref.: #65504]	valine arylamidase	+
	Only first 10 entries are displayed. Click here to see all.

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

[Ref.: #65504]	Sample type/isolated from	from tidal flat sediment
[Ref.: #65504]	Geographic location (country and/or sea, region)	Gangwha Island, Yellow Sea
[Ref.: #65504]	Country	Republic of Korea
[Ref.: #65504]	Country ISO 3 Code	KOR
[Ref.: #65504]	Continent	Asia
[Ref.: #65504]	Enrichment culture	MA
[Ref.: #65504]	Enrichment culture temperature	25 ̊C
[Ref.: #65504]	Isolation/enrichment procedure	standard dilution plating technique

[Ref.: #67771]	Sample type/isolated from	From mud flat
[Ref.: #67771]	Geographic location (country and/or sea, region)	Ganghwado Island
[Ref.: #67771]	Country	Republic of Korea
[Ref.: #67771]	Country ISO 3 Code	KOR
[Ref.: #67771]	Continent	Asia
* marker position based on {}

Isolation sources categories

#Environmental	#Aquatic	#Sediment
#Environmental	#Terrestrial	#Tidal flat

What are isolation sources categories?

[Ref.: #69479]

Global distribution of 16S sequence MF193602 (>99% sequence identity) for Paracoccus from Microbeatlas

Aquatic Samples	92
Soil Samples	43
Animal Samples	63
Plant Samples	129
Total Samples	327

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.: #65504]	Paracoccus litorisediminis strain GHD-05 16S ribosomal RNA gene, partial sequence	MF193602		GenBank ENA

Genome sequence information:

	Sequence accession description	Seq. accession number	Assembly level	Sequence database	Associated NCBI tax ID
[Ref.: #66792]	Paracoccus litorisediminis NBRC 112902	GCA_009711205	contig	GenBank ENA	2006130 tax ID	*
[Ref.: #66792]	Paracoccus litorisediminis strain NBRC 112902	2006130.3	wgs	PATRIC	2006130 tax ID	*

[Ref.: #65504]

GC-content

64.1 mol%

high performance liquid chromatography (HPLC)

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

	Trait	Model	Prediction	Confidence in %	In training data
	Predictions from GenomeNet Sporulation v. 1 based on: Paracoccus litorisediminis strain NBRC 112902 PATRIC: 2006130.3
[Ref.: #69481]	spore-forming	spore-formingⓘ	no	100	no

	Trait	Model	Prediction	Confidence in %	In training data
	Predictions from Diaspora project based on: Paracoccus litorisediminis strain NBRC 112902 PATRIC: 2006130.3
[Ref.: #69480]	gram-positive	gram-positiveⓘ	no	97.482	yes
[Ref.: #69480]	anaerobic	anaerobicⓘ	no	94.422	no
[Ref.: #69480]	spore-forming	spore-formingⓘ	no	88.564	yes
[Ref.: #69480]	aerobic	aerobicⓘ	yes	82.41	no
[Ref.: #69480]	thermophilic	thermophileⓘ	no	97.75	yes
[Ref.: #69480]	flagellated	motile2+ⓘ	no	54.385	no

Availability in culture collections External links

[Ref.: #65504]

Culture collection no.

KCTC 52978, NBRC 112902

Literature:

Topic	Title	Authors	Journal	DOI	Year
Phylogeny	Paracoccus litorisediminis sp. nov., isolated from a tidal flat.	Park S, Choi J, Choi SJ, Yoon JH	Int J Syst Evol Microbiol	10.1099/ijsem.0.002373	2017	*

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 )

#65504

Sooyeon Park, Jeehyun Choi, Su Jung Choi and Jung-Hoon Yoon: Paracoccus litorisediminis sp. nov., isolated from a tidal flat. IJSEM 67: 4760 - 4766 2017 ( DOI 10.1099/ijsem.0.002373 , PubMed 28984555 )

#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) .

#67771 Korean Collection for Type Cultures (KCTC) ; Curators of the KCTC;

#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 )

* These data were automatically processed and therefore are not curated

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Paracoccus litorisediminis strain NBRC 112902

Paracoccus litorisediminis strain NBRC 112902

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