Name: Parasphingopyxis lamellibrachiae DSM 26725
Creator: BacDive
License: https://creativecommons.org/licenses/by/4.0/

Strain identifier

BacDive ID: 14299

Type strain:

Species: Parasphingopyxis lamellibrachiae

Culture col. no.: DSM 26725, JCM 15549, NCIMB 14486, JAMH 0132

Strain history: M. Miyazaki JAMH 0132.

NCBI tax ID(s): 680125 (species)

SI-ID 401434

DSM 26725

Special Collections

Section

Parasphingopyxis lamellibrachiae DSM 26725 is an aerobe, Gram-negative, motile bacterium that was isolated from Trophosome of annelid worm Lamellibrachia satsuma.

Gram-negative
motile
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	*Sphingomonadales*
	Family	*Sphingomonadaceae*
	Genus	*Parasphingopyxis*
	Species	**Parasphingopyxis lamellibrachiae**
	Full Scientific Name (LPSN)	Parasphingopyxis lamellibrachiae Uchida et al. 2012

Information on morphological and physiological properties Morphology

[Ref.: #30347]	Gram stain	negative
[Ref.: #69480]	Gram stain	negative Confidence in %96.833

[Ref.: #30347]	Cell length	1.5 µm

[Ref.: #30347]	Cell width	0.55 µm

[Ref.: #30347]	Cell shape	rod-shaped

[Ref.: #30347]	Motility	yes

[Ref.: #18275]

Incubation period

2-3 days

[Ref.: #30347]

Pigment production

yes

Information on culture and growth conditions Culture and growth conditions

[Ref.: #18275]

Culture medium

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

[Ref.: #18275]

Culture medium growth

[Ref.: #18275]

Culture medium link

Medium recipe at MediaDive

[Ref.: #18275]

Culture medium composition

expand / minimize

		Temperature
[Ref.: #18275]	growth	28 °C
[Ref.: #30347]	growth	05-36 °C
[Ref.: #30347]	optimum	29 °C
[Ref.: #67770]	growth	30 °C

	pH	Kind of pH		pH
[Ref.: #30347]			optimum	7
[Ref.: #30347]			growth	6-9.5

Information on physiology and metabolism Physiology and metabolism

[Ref.: #30347]

Oxygen tolerance

aerobe

[Ref.: #30347]	Ability of spore formation	no
[Ref.: #69480]	Ability of spore formation	no Confidence in %90.124
[Ref.: #69481]	Ability of spore formation	no Confidence in %100

	Halophily	Salt	Tested relation		Salt conc.
[Ref.: #30347]		NaCl		growth	0.5-5	%
[Ref.: #30347]		NaCl		optimum	2	%

[Ref.: #67770]

Observation

quinones: Q-10

	Metabolite	Utilization activity	Kind of utilization tested
[Ref.: #68369]	adipate ChEBI	-	assimilation	* from API 20NE
[Ref.: #30347]	arabinose ChEBI	+	carbon source
[Ref.: #68369]	arginine ChEBI	-	hydrolysis	* from API 20NE
[Ref.: #68369]	D-glucose ChEBI	-	assimilation	* from API 20NE
[Ref.: #68369]	D-glucose ChEBI	-	fermentation	* from API 20NE
[Ref.: #68369]	D-mannitol ChEBI	-	assimilation	* from API 20NE
[Ref.: #68369]	D-mannose ChEBI	-	assimilation	* from API 20NE
[Ref.: #68369]	decanoate ChEBI	-	assimilation	* from API 20NE
[Ref.: #68369]	esculin ChEBI	-	hydrolysis	* from API 20NE
[Ref.: #68369]	gelatin ChEBI	-	hydrolysis	* from API 20NE
[Ref.: #68369]	gluconate ChEBI	-	assimilation	* from API 20NE
[Ref.: #30347]	glucose ChEBI	+	carbon source
[Ref.: #68369]	L-arabinose ChEBI	-	assimilation	* from API 20NE
[Ref.: #68369]	malate ChEBI	-	assimilation	* from API 20NE
[Ref.: #68369]	maltose ChEBI	-	assimilation	* from API 20NE
[Ref.: #68369]	N-acetylglucosamine ChEBI	-	assimilation	* from API 20NE
[Ref.: #30347]	nitrate ChEBI	+	reduction
[Ref.: #68369]	nitrate ChEBI	+	reduction	* from API 20NE
[Ref.: #68369]	tryptophan ChEBI	-	energy source	* from API 20NE
[Ref.: #68369]	urea ChEBI	-	hydrolysis	* from API 20NE
	Only first 10 entries are displayed. Click here to see all.

	Metabolite production	Metabolite	Production
[Ref.: #68369]		indole ChEBI	no	* from API 20NE

	Physiological tests	Metabolite	Indole test
[Ref.: #68369]		indole ChEBI	-	* from API 20NE

	Enzyme	Enzyme activity	EC number
[Ref.: #68369]	arginine dihydrolase	-	3.5.3.6	* from API 20NE
[Ref.: #68369]	beta-glucosidase	-	3.2.1.21	* from API 20NE
[Ref.: #30347]	cytochrome oxidase	+	1.9.3.1
[Ref.: #68369]	cytochrome oxidase	+	1.9.3.1	* from API 20NE
[Ref.: #30347]	gelatinase	+
[Ref.: #68369]	gelatinase	-		* from API 20NE
[Ref.: #68369]	urease	-	3.5.1.5	* from API 20NE

API® 20NE:

Note that the displayed test results represent raw data and therefore may deviate!

	API ID	Reduction of nitratesNO3	Indole productionTRP	Fermentation of D-glucoseGLU_ Ferm	Arginine dihydrolaseADH (Arg)	Urease/urea hydrolysisURE	Esculin hydrolysis/beta-GlucosidaseESC	Gelatinase/gelatin hydrolysisGEL	beta-GalactosidasePNPG	Assimilation of D-glucoseGLU_ Assim	Assimilation of L-arabinoseARA	Assimilation of D-mannoseMNE	Assimilation of D-mannitolMAN	Assimilation of N-acetyl-glucosamineNAG	Assimilation of maltoseMAL	Assimilation of gluconateGNT	Assimilation of capric acidCAP	Assimilation adipic acidADI	Assimilation of malic acidMLT	Assimilation of citric acidCIT	Assimilation of phenyl-acetic acidPAC	Cytochrome oxidaseOX
[Ref.: #18275]	23405	+	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	+

	Pathway	Enzyme coverage	Annotated reactions
	Pathway annotation	Computationally determined by
[Ref.: #66794]	UDP-GlcNAc biosynthesis	100	3 of 3
[Ref.: #66794]	gluconeogenesis	100	8 of 8
[Ref.: #66794]	C4 and CAM-carbon fixation	100	8 of 8
[Ref.: #66794]	ppGpp biosynthesis	100	4 of 4
[Ref.: #66794]	methylglyoxal degradation	100	5 of 5
[Ref.: #66794]	coenzyme A metabolism	100	4 of 4
[Ref.: #66794]	formaldehyde oxidation	100	3 of 3
[Ref.: #66794]	octane oxidation	100	3 of 3
[Ref.: #66794]	adipate degradation	100	2 of 2
[Ref.: #66794]	ethylmalonyl-CoA pathway	100	5 of 5
[Ref.: #66794]	CDP-diacylglycerol biosynthesis	100	2 of 2
[Ref.: #66794]	folate polyglutamylation	100	1 of 1
[Ref.: #66794]	anapleurotic synthesis of oxalacetate	100	1 of 1
[Ref.: #66794]	valine metabolism	100	9 of 9
[Ref.: #66794]	quinate degradation	100	2 of 2
[Ref.: #66794]	taurine degradation	100	1 of 1
[Ref.: #66794]	suberin monomers biosynthesis	100	2 of 2
[Ref.: #66794]	palmitate biosynthesis	95.45	21 of 22
[Ref.: #66794]	citric acid cycle	92.86	13 of 14
[Ref.: #66794]	threonine metabolism	90	9 of 10
[Ref.: #66794]	chorismate metabolism	88.89	8 of 9
[Ref.: #66794]	serine metabolism	88.89	8 of 9
[Ref.: #66794]	molybdenum cofactor biosynthesis	88.89	8 of 9
[Ref.: #66794]	photosynthesis	85.71	12 of 14
[Ref.: #66794]	leucine metabolism	84.62	11 of 13
[Ref.: #66794]	phenylalanine metabolism	84.62	11 of 13
[Ref.: #66794]	peptidoglycan biosynthesis	80	12 of 15
[Ref.: #66794]	phenylacetate degradation (aerobic)	80	4 of 5
[Ref.: #66794]	gallate degradation	80	4 of 5
[Ref.: #66794]	propionate fermentation	80	8 of 10
[Ref.: #66794]	NAD metabolism	77.78	14 of 18
[Ref.: #66794]	aspartate and asparagine metabolism	77.78	7 of 9
[Ref.: #66794]	CO2 fixation in Crenarchaeota	77.78	7 of 9
[Ref.: #66794]	vitamin B1 metabolism	76.92	10 of 13
[Ref.: #66794]	methionine metabolism	76.92	20 of 26
[Ref.: #66794]	alanine metabolism	75.86	22 of 29
[Ref.: #66794]	CMP-KDO biosynthesis	75	3 of 4
[Ref.: #66794]	sulfopterin metabolism	75	3 of 4
[Ref.: #66794]	acetate fermentation	75	3 of 4
[Ref.: #66794]	isoleucine metabolism	75	6 of 8
[Ref.: #66794]	butanoate fermentation	75	3 of 4
[Ref.: #66794]	purine metabolism	74.47	70 of 94
[Ref.: #66794]	vitamin B6 metabolism	72.73	8 of 11
[Ref.: #66794]	pentose phosphate pathway	72.73	8 of 11
[Ref.: #66794]	histidine metabolism	72.41	21 of 29
[Ref.: #66794]	heme metabolism	71.43	10 of 14
[Ref.: #66794]	propanol degradation	71.43	5 of 7
[Ref.: #66794]	tetrahydrofolate metabolism	71.43	10 of 14
[Ref.: #66794]	glutamate and glutamine metabolism	71.43	20 of 28
[Ref.: #66794]	reductive acetyl coenzyme A pathway	71.43	5 of 7
[Ref.: #66794]	ubiquinone biosynthesis	71.43	5 of 7
[Ref.: #66794]	tryptophan metabolism	71.05	27 of 38
[Ref.: #66794]	Entner Doudoroff pathway	70	7 of 10
[Ref.: #66794]	acetyl CoA biosynthesis	66.67	2 of 3
[Ref.: #66794]	flavin biosynthesis	66.67	10 of 15
[Ref.: #66794]	lipid A biosynthesis	66.67	6 of 9
[Ref.: #66794]	methane metabolism	66.67	2 of 3
[Ref.: #66794]	d-mannose degradation	66.67	6 of 9
[Ref.: #66794]	acetoin degradation	66.67	2 of 3
[Ref.: #66794]	L-lactaldehyde degradation	66.67	2 of 3
[Ref.: #66794]	cyanate degradation	66.67	2 of 3
[Ref.: #66794]	glycolysis	64.71	11 of 17
[Ref.: #66794]	tyrosine metabolism	64.29	9 of 14
[Ref.: #66794]	glutathione metabolism	64.29	9 of 14
[Ref.: #66794]	proline metabolism	63.64	7 of 11
[Ref.: #66794]	6-hydroxymethyl-dihydropterin diphosphate biosynthesis	62.5	5 of 8
[Ref.: #66794]	cysteine metabolism	61.11	11 of 18
[Ref.: #66794]	3-phenylpropionate degradation	60	9 of 15
[Ref.: #66794]	arginine metabolism	58.33	14 of 24
[Ref.: #66794]	lipid metabolism	58.06	18 of 31
[Ref.: #66794]	non-pathway related	57.89	22 of 38
[Ref.: #66794]	pyrimidine metabolism	57.78	26 of 45
[Ref.: #66794]	isoprenoid biosynthesis	57.69	15 of 26
[Ref.: #66794]	urea cycle	53.85	7 of 13
[Ref.: #66794]	biotin biosynthesis	50	2 of 4
[Ref.: #66794]	lysine metabolism	50	21 of 42
[Ref.: #66794]	toluene degradation	50	2 of 4
[Ref.: #66794]	ribulose monophosphate pathway	50	1 of 2
[Ref.: #66794]	selenocysteine biosynthesis	50	3 of 6
[Ref.: #66794]	cis-vaccenate biosynthesis	50	1 of 2
[Ref.: #66794]	cyclohexanol degradation	50	2 of 4
[Ref.: #66794]	degradation of sugar alcohols	50	8 of 16
[Ref.: #66794]	ethanol fermentation	50	1 of 2
[Ref.: #66794]	glycogen biosynthesis	50	2 of 4
[Ref.: #66794]	phenylmercury acetate degradation	50	1 of 2
[Ref.: #66794]	phenol degradation	50	10 of 20
[Ref.: #66794]	bile acid biosynthesis, neutral pathway	47.06	8 of 17
[Ref.: #66794]	androgen and estrogen metabolism	43.75	7 of 16
[Ref.: #66794]	cardiolipin biosynthesis	42.86	3 of 7
[Ref.: #66794]	degradation of aromatic, nitrogen containing compounds	41.67	5 of 12
[Ref.: #66794]	oxidative phosphorylation	40.66	37 of 91
[Ref.: #66794]	lipoate biosynthesis	40	2 of 5
[Ref.: #66794]	3-chlorocatechol degradation	40	2 of 5
[Ref.: #66794]	metabolism of amino sugars and derivatives	40	2 of 5
[Ref.: #66794]	glycine betaine biosynthesis	40	2 of 5
[Ref.: #66794]	hydrogen production	40	2 of 5
[Ref.: #66794]	glycine metabolism	40	4 of 10
[Ref.: #66794]	D-cycloserine biosynthesis	40	2 of 5
[Ref.: #66794]	arachidonic acid metabolism	38.89	7 of 18
[Ref.: #66794]	sulfate reduction	38.46	5 of 13
[Ref.: #66794]	phosphatidylethanolamine bioynthesis	38.46	5 of 13
[Ref.: #66794]	carnitine metabolism	37.5	3 of 8
[Ref.: #66794]	ketogluconate metabolism	37.5	3 of 8
[Ref.: #66794]	dTDPLrhamnose biosynthesis	37.5	3 of 8
[Ref.: #66794]	metabolism of disaccharids	36.36	4 of 11
[Ref.: #66794]	carotenoid biosynthesis	36.36	8 of 22
[Ref.: #66794]	degradation of pentoses	35.71	10 of 28
[Ref.: #66794]	glycolate and glyoxylate degradation	33.33	2 of 6
[Ref.: #66794]	sphingosine metabolism	33.33	2 of 6
[Ref.: #66794]	degradation of hexoses	33.33	6 of 18
[Ref.: #66794]	pantothenate biosynthesis	33.33	2 of 6
[Ref.: #66794]	(5R)-carbapenem carboxylate biosynthesis	33.33	1 of 3
[Ref.: #66794]	enterobactin biosynthesis	33.33	1 of 3
[Ref.: #66794]	IAA biosynthesis	33.33	1 of 3
[Ref.: #66794]	ascorbate metabolism	31.82	7 of 22
[Ref.: #66794]	myo-inositol biosynthesis	30	3 of 10
[Ref.: #66794]	coenzyme M biosynthesis	30	3 of 10
[Ref.: #66794]	4-hydroxyphenylacetate degradation	30	3 of 10
[Ref.: #66794]	benzoyl-CoA degradation	28.57	2 of 7
[Ref.: #66794]	aclacinomycin biosynthesis	28.57	2 of 7
[Ref.: #66794]	chlorophyll metabolism	27.78	5 of 18
[Ref.: #66794]	d-xylose degradation	27.27	3 of 11
[Ref.: #66794]	lactate fermentation	25	1 of 4
[Ref.: #66794]	catecholamine biosynthesis	25	1 of 4
[Ref.: #66794]	vitamin E metabolism	25	1 of 4
[Ref.: #66794]	4-hydroxymandelate degradation	22.22	2 of 9
		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.: #18275]	Sample type/isolated from	Trophosome of annelid worm Lamellibrachia satsuma
[Ref.: #18275]	Host species	Lamellibrachia satsuma
[Ref.: #18275]	Geographic location (country and/or sea, region)	Kagoshima Bay
[Ref.: #18275]	Country	Japan
[Ref.: #18275]	Country ISO 3 Code	JPN
[Ref.: #18275]	Continent	Asia

[Ref.: #67770]	Sample type/isolated from	Trophosome of a tubeworm (Lamellibrachia satsuma) in Kagoshima Bay
[Ref.: #67770]	Host species	Lamellibrachia satsuma
[Ref.: #67770]	Country	Japan
[Ref.: #67770]	Country ISO 3 Code	JPN
[Ref.: #67770]	Continent	Asia
* marker position based on {}

Isolation sources categories

#Host	#Invertebrates (Other)	#Annelida
#Host Body-Site	#Organ	-

What are isolation sources categories?

[Ref.: #69479]

Global distribution of 16S sequence AB524074 (>99% sequence identity) for Parasphingopyxis lamellibrachiae subclade from Microbeatlas

Aquatic Samples	1886
Soil Samples	190
Animal Samples	86
Plant Samples	46
Total Samples	2208

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

[Ref.: #18275]

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.: #18275]	Parasphingopyxis lamellibrachiae gene for 16S ribosomal RNA, partial sequence	AB524074	1447	GenBank ENA	680125 tax ID

Genome sequence information:

	Sequence accession description	Seq. accession number	Assembly level	Sequence database	Associated NCBI tax ID
[Ref.: #67770]	Parasphingopyxis lamellibrachiae DSM 26725	GCA_003385775	scaffold	GenBank ENA	680125 tax ID
[Ref.: #66792]	Parasphingopyxis lamellibrachiae strain DSM 26725	680125.3	wgs	PATRIC	680125 tax ID	*
[Ref.: #66792]	Parasphingopyxis lamellibrachiae DSM 26725	2770939550	draft	JGI IMG/M	680125 tax ID	*

[Ref.: #30347]	GC-content	60.1 mol%
[Ref.: #67770]	GC-content	60.1 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: Parasphingopyxis lamellibrachiae DSM 26725 NCBI: GCA_003385775.1
[Ref.: #69481]	spore-forming	spore-formingⓘ	no	100	no

	Trait	Model	Prediction	Confidence in %	In training data
	Predictions from Diaspora project based on: Parasphingopyxis lamellibrachiae strain DSM 26725 PATRIC: 680125.3
[Ref.: #69480]	gram-positive	gram-positiveⓘ	no	96.833	no
[Ref.: #69480]	anaerobic	anaerobicⓘ	no	94.223	yes
[Ref.: #69480]	spore-forming	spore-formingⓘ	no	90.124	no
[Ref.: #69480]	thermophilic	thermophileⓘ	no	93.509	no
[Ref.: #69480]	aerobic	aerobicⓘ	yes	86.265	yes
[Ref.: #69480]	flagellated	motile2+ⓘ	no	68.9	no

Availability in culture collections External links

[Ref.: #18275]

Culture collection no.

DSM 26725, JCM 15549, NCIMB 14486, JAMH 0132

[Ref.: #83452]

SI-ID 401434

Literature:

Topic	Title	Authors	Journal	DOI	Year
Phylogeny	Parasphingopyxis marina sp. nov. isolated from coastal seawater.	Choi SY, Oh JS, Roh DH	Int J Syst Evol Microbiol	10.1099/ijsem.0.005049	2021	*
Phylogeny	Parasphingopyxis algicola sp. nov., isolated from a marine red alga Asparagopsis taxiformis and emended description of the genus Parasphingopyxis Uchida et al. 2012.	Jeong SE, Kim KH, Baek K, Jeon CO	Int J Syst Evol Microbiol	10.1099/ijsem.0.002215	2017	*
Phylogeny	Parasphingopyxis lamellibrachiae gen. nov., sp. nov., isolated from a marine annelid worm.	Uchida H, Hamana K, Miyazaki M, Yoshida T, Nogi Y	Int J Syst Evol Microbiol	10.1099/ijs.0.034033-0	2011	*

References

#18275

Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 26725

#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 )

#30347

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 #26688 (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 )

#67770 Japan Collection of Microorganism (JCM) ; Curators of the JCM;

#68369

Automatically annotated from API 20NE .

#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 )

#83452

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-ID401434.1 )

#26688

IJSEM 2224 2012 ( DOI 10.1099/ijs.0.034033-0 , PubMed 22081711 )

* These data were automatically processed and therefore are not curated

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Parasphingopyxis lamellibrachiae DSM 26725

Parasphingopyxis lamellibrachiae strain DSM 26725

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