Name: Paracoccus isoporae SW-3
Creator: BacDive
License: http://creativecommons.org/licenses/by-nc/4.0/

Strain identifier

BacDive ID: 13729

Type strain:

Species: Paracoccus isoporae

Strain Designation: SW-3

Culture col. no.: DSM 22220, BCRC 17967, LMG 25205

Strain history: <- J.-H. Chou, Natl. Kaohsiung Marine Univ. Taiwan <- W.-M. Chen; SW-3

NCBI tax ID(s): 591205 (species)

SI-ID 360699

LMG 25205, BCRC 17967, DSM 22220

Section

Paracoccus isoporae SW-3 is an aerobe, mesophilic, Gram-negative bacterium that was isolated from reef-building coral Isopora palifera.

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	*Rhodobacterales*
	Family	*Paracoccaceae*
	Genus	*Paracoccus*
	Species	**Paracoccus isoporae**
	Full Scientific Name (LPSN)	Paracoccus isoporae Chen et al. 2011

Information on morphological and physiological properties Morphology

[Ref.: #29870]	Gram stain	negative
[Ref.: #69480]	Gram stain	negative Confidence in %99.995

[Ref.: #29870]	Cell length	1.1 µm

[Ref.: #29870]	Cell width	0.6 µm

[Ref.: #29870]	Cell shape	rod-shaped

[Ref.: #29870]	Motility	yes

Information on culture and growth conditions Culture and growth conditions

[Ref.: #16210]

Culture medium

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

[Ref.: #16210]

Culture medium growth

[Ref.: #16210]

Culture medium link

Medium recipe at MediaDive

[Ref.: #16210]

Culture medium composition

expand / minimize

		Temperature
[Ref.: #16210]	growth	25 °C
[Ref.: #29870]	growth	04-40 °C
[Ref.: #29870]	optimum	27.5 °C

[Ref.: #16210]	Temperature range	mesophilic
[Ref.: #29870]	Temperature range	mesophilic

	pH	Kind of pH		pH
[Ref.: #29870]			optimum	9.5
[Ref.: #29870]			growth	07-10

Information on physiology and metabolism Physiology and metabolism

[Ref.: #29870]

Oxygen tolerance

aerobe

[Ref.: #69480]

Ability of spore formation

no Confidence in %99.997

	Halophily	Salt	Tested relation		Salt conc.
[Ref.: #29870]		NaCl		growth	0-12	%
[Ref.: #29870]		NaCl		optimum	4	%

	Metabolite	Utilization activity	Kind of utilization tested
[Ref.: #29870]	2,3-butanediol ChEBI	+	carbon source
[Ref.: #29870]	esculin ChEBI	+	hydrolysis
[Ref.: #29870]	fucose ChEBI	+	carbon source
[Ref.: #29870]	galactose ChEBI	+	carbon source
[Ref.: #29870]	glucose ChEBI	+	carbon source
[Ref.: #29870]	glycerol ChEBI	+	carbon source
[Ref.: #29870]	lactose ChEBI	+	carbon source
[Ref.: #29870]	maltose ChEBI	+	carbon source
[Ref.: #29870]	mannitol ChEBI	+	carbon source
[Ref.: #29870]	methyl pyruvate ChEBI	+	carbon source
[Ref.: #29870]	sucrose ChEBI	+	carbon source
[Ref.: #29870]	trehalose ChEBI	+	carbon source
[Ref.: #29870]	tween 20 ChEBI	+	carbon source
[Ref.: #29870]	tween 40 ChEBI	+	carbon source
[Ref.: #29870]	tween 60 ChEBI	+	carbon source
[Ref.: #29870]	tween 80 ChEBI	+	carbon source
	Only first 10 entries are displayed. Click here to see all.

	Enzyme	Enzyme activity	EC number
[Ref.: #29870]	acid phosphatase	+	3.1.3.2
[Ref.: #29870]	alkaline phosphatase	+	3.1.3.1
[Ref.: #29870]	alpha-galactosidase	+	3.2.1.22
[Ref.: #29870]	catalase	+	1.11.1.6
[Ref.: #29870]	cytochrome oxidase	+	1.9.3.1

	Pathway	Enzyme coverage	Annotated reactions
	Pathway annotation	Computationally determined by
[Ref.: #66794]	CDP-diacylglycerol biosynthesis	100	2 of 2
[Ref.: #66794]	gluconeogenesis	100	8 of 8
[Ref.: #66794]	C4 and CAM-carbon fixation	100	8 of 8
[Ref.: #66794]	suberin monomers biosynthesis	100	2 of 2
[Ref.: #66794]	UDP-GlcNAc biosynthesis	100	3 of 3
[Ref.: #66794]	coenzyme A metabolism	100	4 of 4
[Ref.: #66794]	adipate degradation	100	2 of 2
[Ref.: #66794]	methylglyoxal degradation	100	5 of 5
[Ref.: #66794]	Entner Doudoroff pathway	100	10 of 10
[Ref.: #66794]	valine metabolism	100	9 of 9
[Ref.: #66794]	ppGpp biosynthesis	100	4 of 4
[Ref.: #66794]	denitrification	100	2 of 2
[Ref.: #66794]	ribulose monophosphate pathway	100	2 of 2
[Ref.: #66794]	phenylacetate degradation (aerobic)	100	5 of 5
[Ref.: #66794]	formaldehyde oxidation	100	3 of 3
[Ref.: #66794]	folate polyglutamylation	100	1 of 1
[Ref.: #66794]	anapleurotic synthesis of oxalacetate	100	1 of 1
[Ref.: #66794]	octane oxidation	100	3 of 3
[Ref.: #66794]	pentose phosphate pathway	100	11 of 11
[Ref.: #66794]	glycogen biosynthesis	100	4 of 4
[Ref.: #66794]	palmitate biosynthesis	95.45	21 of 22
[Ref.: #66794]	citric acid cycle	92.86	13 of 14
[Ref.: #66794]	molybdenum cofactor biosynthesis	88.89	8 of 9
[Ref.: #66794]	lipid A biosynthesis	88.89	8 of 9
[Ref.: #66794]	serine metabolism	88.89	8 of 9
[Ref.: #66794]	4-hydroxymandelate degradation	88.89	8 of 9
[Ref.: #66794]	chorismate metabolism	88.89	8 of 9
[Ref.: #66794]	ketogluconate metabolism	87.5	7 of 8
[Ref.: #66794]	reductive acetyl coenzyme A pathway	85.71	6 of 7
[Ref.: #66794]	glutathione metabolism	85.71	12 of 14
[Ref.: #66794]	vitamin B1 metabolism	84.62	11 of 13
[Ref.: #66794]	leucine metabolism	84.62	11 of 13
[Ref.: #66794]	degradation of sugar acids	84	21 of 25
[Ref.: #66794]	glutamate and glutamine metabolism	82.14	23 of 28
[Ref.: #66794]	proline metabolism	81.82	9 of 11
[Ref.: #66794]	purine metabolism	80.85	76 of 94
[Ref.: #66794]	threonine metabolism	80	8 of 10
[Ref.: #66794]	pyrimidine metabolism	80	36 of 45
[Ref.: #66794]	glycogen metabolism	80	4 of 5
[Ref.: #66794]	ethylmalonyl-CoA pathway	80	4 of 5
[Ref.: #66794]	peptidoglycan biosynthesis	80	12 of 15
[Ref.: #66794]	photosynthesis	78.57	11 of 14
[Ref.: #66794]	CO2 fixation in Crenarchaeota	77.78	7 of 9
[Ref.: #66794]	NAD metabolism	77.78	14 of 18
[Ref.: #66794]	phenylalanine metabolism	76.92	10 of 13
[Ref.: #66794]	isoleucine metabolism	75	6 of 8
[Ref.: #66794]	6-hydroxymethyl-dihydropterin diphosphate biosynthesis	75	6 of 8
[Ref.: #66794]	CMP-KDO biosynthesis	75	3 of 4
[Ref.: #66794]	acetate fermentation	75	3 of 4
[Ref.: #66794]	degradation of sugar alcohols	75	12 of 16
[Ref.: #66794]	butanoate fermentation	75	3 of 4
[Ref.: #66794]	sulfopterin metabolism	75	3 of 4
[Ref.: #66794]	methionine metabolism	73.08	19 of 26
[Ref.: #66794]	tyrosine metabolism	71.43	10 of 14
[Ref.: #66794]	ubiquinone biosynthesis	71.43	5 of 7
[Ref.: #66794]	cardiolipin biosynthesis	71.43	5 of 7
[Ref.: #66794]	propanol degradation	71.43	5 of 7
[Ref.: #66794]	oxidative phosphorylation	69.23	63 of 91
[Ref.: #66794]	tryptophan metabolism	68.42	26 of 38
[Ref.: #66794]	flavin biosynthesis	66.67	10 of 15
[Ref.: #66794]	aspartate and asparagine metabolism	66.67	6 of 9
[Ref.: #66794]	cyanate degradation	66.67	2 of 3
[Ref.: #66794]	methane metabolism	66.67	2 of 3
[Ref.: #66794]	selenocysteine biosynthesis	66.67	4 of 6
[Ref.: #66794]	acetyl CoA biosynthesis	66.67	2 of 3
[Ref.: #66794]	sulfoquinovose degradation	66.67	2 of 3
[Ref.: #66794]	L-lactaldehyde degradation	66.67	2 of 3
[Ref.: #66794]	acetoin degradation	66.67	2 of 3
[Ref.: #66794]	allantoin degradation	66.67	6 of 9
[Ref.: #66794]	d-mannose degradation	66.67	6 of 9
[Ref.: #66794]	lysine metabolism	66.67	28 of 42
[Ref.: #66794]	alanine metabolism	65.52	19 of 29
[Ref.: #66794]	histidine metabolism	65.52	19 of 29
[Ref.: #66794]	glycolysis	64.71	11 of 17
[Ref.: #66794]	tetrahydrofolate metabolism	64.29	9 of 14
[Ref.: #66794]	heme metabolism	64.29	9 of 14
[Ref.: #66794]	vitamin B6 metabolism	63.64	7 of 11
[Ref.: #66794]	non-pathway related	63.16	24 of 38
[Ref.: #66794]	arginine metabolism	62.5	15 of 24
[Ref.: #66794]	urea cycle	61.54	8 of 13
[Ref.: #66794]	cysteine metabolism	61.11	11 of 18
[Ref.: #66794]	propionate fermentation	60	6 of 10
[Ref.: #66794]	O-antigen biosynthesis	60	3 of 5
[Ref.: #66794]	myo-inositol biosynthesis	60	6 of 10
[Ref.: #66794]	metabolism of amino sugars and derivatives	60	3 of 5
[Ref.: #66794]	lipid metabolism	58.06	18 of 31
[Ref.: #66794]	isoprenoid biosynthesis	57.69	15 of 26
[Ref.: #66794]	degradation of hexoses	55.56	10 of 18
[Ref.: #66794]	nitrate assimilation	55.56	5 of 9
[Ref.: #66794]	degradation of pentoses	53.57	15 of 28
[Ref.: #66794]	3-phenylpropionate degradation	53.33	8 of 15
[Ref.: #66794]	ethanol fermentation	50	1 of 2
[Ref.: #66794]	dolichol and dolichyl phosphate biosynthesis	50	1 of 2
[Ref.: #66794]	biotin biosynthesis	50	2 of 4
[Ref.: #66794]	toluene degradation	50	2 of 4
[Ref.: #66794]	phenylmercury acetate degradation	50	1 of 2
[Ref.: #66794]	glycolate and glyoxylate degradation	50	3 of 6
[Ref.: #66794]	cis-vaccenate biosynthesis	50	1 of 2
[Ref.: #66794]	phenol degradation	50	10 of 20
[Ref.: #66794]	quinate degradation	50	1 of 2
[Ref.: #66794]	ascorbate metabolism	50	11 of 22
[Ref.: #66794]	cyclohexanol degradation	50	2 of 4
[Ref.: #66794]	lactate fermentation	50	2 of 4
[Ref.: #66794]	dTDPLrhamnose biosynthesis	50	4 of 8
[Ref.: #66794]	carnitine metabolism	50	4 of 8
[Ref.: #66794]	glycine metabolism	50	5 of 10
[Ref.: #66794]	sulfate reduction	46.15	6 of 13
[Ref.: #66794]	benzoyl-CoA degradation	42.86	3 of 7
[Ref.: #66794]	degradation of aromatic, nitrogen containing compounds	41.67	5 of 12
[Ref.: #66794]	starch degradation	40	4 of 10
[Ref.: #66794]	cellulose degradation	40	2 of 5
[Ref.: #66794]	3-chlorocatechol degradation	40	2 of 5
[Ref.: #66794]	glycine betaine biosynthesis	40	2 of 5
[Ref.: #66794]	lipoate biosynthesis	40	2 of 5
[Ref.: #66794]	vitamin K metabolism	40	2 of 5
[Ref.: #66794]	coenzyme M biosynthesis	40	4 of 10
[Ref.: #66794]	gallate degradation	40	2 of 5
[Ref.: #66794]	arachidonic acid metabolism	38.89	7 of 18
[Ref.: #66794]	polyamine pathway	34.78	8 of 23
[Ref.: #66794]	sphingosine metabolism	33.33	2 of 6
[Ref.: #66794]	enterobactin biosynthesis	33.33	1 of 3
[Ref.: #66794]	IAA biosynthesis	33.33	1 of 3
[Ref.: #66794]	(5R)-carbapenem carboxylate biosynthesis	33.33	1 of 3
[Ref.: #66794]	ginsenoside metabolism	31.25	5 of 16
[Ref.: #66794]	androgen and estrogen metabolism	31.25	5 of 16
[Ref.: #66794]	phosphatidylethanolamine bioynthesis	30.77	4 of 13
[Ref.: #66794]	4-hydroxyphenylacetate degradation	30	3 of 10
[Ref.: #66794]	metabolism of disaccharids	27.27	3 of 11
[Ref.: #66794]	d-xylose degradation	27.27	3 of 11
[Ref.: #66794]	alginate biosynthesis	25	1 of 4
		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.: #16210]	Sample type/isolated from	reef-building coral Isopora palifera
[Ref.: #16210]	Host species	Isopora palifera
[Ref.: #16210]	Geographic location (country and/or sea, region)	Pingtung County, off the coast of Kenting (21°56' 29'' N 120° 44' 70'' E)
[Ref.: #16210]	Country	Taiwan
[Ref.: #16210]	Country ISO 3 Code	TWN
[Ref.: #16210]	Continent	Asia
* marker position based on {}

Isolation sources categories

#Host

#Invertebrates (Other)

#Cnidaria (Corals)

What are isolation sources categories?

[Ref.: #69479]

Global distribution of 16S sequence FJ593906 (>99% sequence identity) for Paracoccus isoporae subclade from Microbeatlas

Aquatic Samples	37
Soil Samples	3
Animal Samples	27
Plant Samples
Total Samples	67

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

[Ref.: #16210]

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.: #16210]	Paracoccus isoporae strain SW-3 16S ribosomal RNA gene, partial sequence	FJ593906	1426	ENA	591205 tax ID

Genome sequence information:

	Sequence accession description	Seq. accession number	Assembly level	Sequence database	Associated NCBI tax ID
[Ref.: #66792]	Paracoccus isoporae DSM 22220	GCA_900101865	contig	GenBank	591205 tax ID	*
[Ref.: #66792]	Paracoccus isoporae strain DSM 22220	591205.3	wgs	PATRIC	591205 tax ID	*
[Ref.: #66792]	Paracoccus isoporae DSM 22220	2675903152	draft	JGI IMG/M	591205 tax ID	*

[Ref.: #16210]

GC-content

63.7 mol%

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 isoporae strain DSM 22220 PATRIC: 591205.3
[Ref.: #69481]	spore-forming	no	72	no

	Trait	Prediction	Confidence in %	In training data
	Predictions from Diaspora project based on: Paracoccus isoporae strain DSM 22220 PATRIC: 591205.3
[Ref.: #69480]	gram-positive	no	97.433	no
[Ref.: #69480]	anaerobic	no	98.954	yes
[Ref.: #69480]	halophile	yes	55.783	no
[Ref.: #69480]	spore-forming	no	96.913	no
[Ref.: #69480]	glucose-util	yes	87.351	yes
[Ref.: #69480]	flagellated	no	83.842	no
[Ref.: #69480]	aerobic	yes	92.78	yes
[Ref.: #69480]	thermophile	no	93.513	yes
[Ref.: #69480]	motile	yes	65.895	yes
[Ref.: #69480]	glucose-ferment	no	91.997	no

Availability in culture collections External links

[Ref.: #16210]

Culture collection no.

DSM 22220, BCRC 17967, LMG 25205

[Ref.: #82912]

SI-ID 360699

Literature:

Topic	Title	Authors	Journal	DOI	Year
Phylogeny	Paracoccus xiamenensis sp. nov., isolated from seawater on the Xiamen.	Lyu L, Zhi B, Lai Q, Shao Z, Yu Z	Int J Syst Evol Microbiol	10.1099/ijsem.0.004284	2020	*
Phylogeny	Paracoccus isoporae sp. nov., isolated from the reef-building coral Isopora palifera.	Chen MH, Sheu SY, Chen CA, Wang JT, Chen WM	Int J Syst Evol Microbiol	10.1099/ijs.0.023333-0	2010	*

References

#16210

Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 22220

#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 )

#29870

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 #26244 (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) .

#66794

Antje Chang, Lisa Jeske, Sandra Ulbrich, Julia Hofmann, Julia Koblitz, Ida Schomburg, Meina Neumann-Schaal, Dieter Jahn, Dietmar Schomburg: BRENDA, the ELIXIR core data resource in 2021: new developments and updates. Nucleic Acids Res. 49: D498 - D508 2020 ( DOI 10.1093/nar/gkaa1025 , PubMed 33211880 )

#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 )

#82912

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-ID360699.1 )

#26244

IJSEM 1138 2011 ( DOI 10.1099/ijs.0.023333-0 , PubMed 20543151 )

* These data were automatically processed and therefore are not curated

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Paracoccus isoporae strain DSM 22220

Paracoccus isoporae strain DSM 22220

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