Name: Roseivirga pacifica DY53
Creator: BacDive
License: http://creativecommons.org/licenses/by-nc/4.0/

Strain identifier

BacDive ID: 131264

Type strain:

Species: Roseivirga pacifica

Strain Designation: DY53

Culture col. no.: DSM 100771, CGMCC 1.12402, JCM 18885

Strain history: X.-W. Xu DY53.

NCBI tax ID(s): 1267423 (species)

SI-ID 398197

DSM 100771

Section

Roseivirga pacifica DY53 is an aerobe, mesophilic, Gram-negative bacterium that was isolated from seawater from 2672 m depth.

Gram-negative
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	*Bacteroidota*
	Class	*Cytophagia*
	Order	*Cytophagales*
	Family	*Roseivirgaceae*
	Genus	*Roseivirga*
	Species	**Roseivirga pacifica**
	Full Scientific Name (LPSN)	Roseivirga pacifica (Huo et al. 2013) García-López et al. 2020

Synonym

Fabibacter pacificus

Information on morphological and physiological properties Morphology

[Ref.: #31070]	Gram stain	negative

[Ref.: #31070]	Cell length	3.25 µm

[Ref.: #31070]	Cell width	0.6 µm

[Ref.: #31070]	Cell shape	rod-shaped

[Ref.: #31070]

Pigment production

yes

Information on culture and growth conditions Culture and growth conditions

[Ref.: #22491]

Culture medium

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

[Ref.: #22491]

Culture medium growth

[Ref.: #22491]

Culture medium link

Medium recipe at MediaDive

[Ref.: #22491]

Culture medium composition

expand / minimize

		Temperature
[Ref.: #22491]	growth	37 °C
[Ref.: #31070]	growth	15-40 °C
[Ref.: #31070]	optimum	36 °C
[Ref.: #67770]	growth	35 °C

[Ref.: #22491]	Temperature range	mesophilic
[Ref.: #31070]	Temperature range	mesophilic
[Ref.: #67770]	Temperature range	mesophilic

	pH	Kind of pH		pH
[Ref.: #31070]			optimum	7.5
[Ref.: #31070]			growth	6.5-8.5

Information on physiology and metabolism Physiology and metabolism

[Ref.: #31070]

Oxygen tolerance

aerobe

	Halophily	Salt	Tested relation		Salt conc.
[Ref.: #31070]		NaCl		growth	0.5-15	%
[Ref.: #31070]		NaCl		optimum	2	%

[Ref.: #31070]	Observation	aggregates in clumps
[Ref.: #67770]	Observation	quinones: MK-7

	Metabolite	Utilization activity	Kind of utilization tested
[Ref.: #68369]	adipate ChEBI	-	assimilation	* from API 20NE
[Ref.: #31070]	alanine ChEBI	+	carbon source
[Ref.: #31070]	arginine ChEBI	+	carbon source
[Ref.: #68369]	arginine ChEBI	-	hydrolysis	* from API 20NE
[Ref.: #31070]	aspartate ChEBI	+	carbon source
[Ref.: #31070]	cellobiose ChEBI	+	carbon source
[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.: #31070]	esculin ChEBI	+	hydrolysis
[Ref.: #68369]	esculin ChEBI	+	hydrolysis	* from API 20NE
[Ref.: #31070]	fructose ChEBI	+	carbon source
[Ref.: #31070]	galactose ChEBI	+	carbon source
[Ref.: #68369]	gelatin ChEBI	-	hydrolysis	* from API 20NE
[Ref.: #31070]	gluconate ChEBI	+	carbon source
[Ref.: #68369]	gluconate ChEBI	-	assimilation	* from API 20NE
[Ref.: #31070]	glucose ChEBI	+	carbon source
[Ref.: #31070]	glutamate ChEBI	+	carbon source
[Ref.: #31070]	glycerol ChEBI	+	carbon source
[Ref.: #31070]	histidine ChEBI	+	carbon source
[Ref.: #68369]	L-arabinose ChEBI	-	assimilation	* from API 20NE
[Ref.: #31070]	lactose ChEBI	+	carbon source
[Ref.: #68369]	malate ChEBI	-	assimilation	* from API 20NE
[Ref.: #31070]	maltose ChEBI	+	carbon source
[Ref.: #68369]	maltose ChEBI	+	assimilation	* from API 20NE
[Ref.: #31070]	mannose ChEBI	+	carbon source
[Ref.: #68369]	N-acetylglucosamine ChEBI	-	assimilation	* from API 20NE
[Ref.: #68369]	nitrate ChEBI	-	reduction	* from API 20NE
[Ref.: #31070]	ornithine ChEBI	+	carbon source
[Ref.: #31070]	pyruvate ChEBI	+	carbon source
[Ref.: #31070]	raffinose ChEBI	+	carbon source
[Ref.: #31070]	salicin ChEBI	+	carbon source
[Ref.: #31070]	succinate ChEBI	+	carbon source
[Ref.: #31070]	sucrose ChEBI	+	carbon source
[Ref.: #31070]	trehalose ChEBI	+	carbon source
[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.: #31070]	acid phosphatase	+	3.1.3.2
[Ref.: #31070]	alkaline phosphatase	+	3.1.3.1
[Ref.: #68369]	arginine dihydrolase	-	3.5.3.6	* from API 20NE
[Ref.: #68369]	beta-glucosidase	+	3.2.1.21	* from API 20NE
[Ref.: #31070]	catalase	+	1.11.1.6
[Ref.: #31070]	cytochrome oxidase	+	1.9.3.1
[Ref.: #68369]	cytochrome oxidase	+	1.9.3.1	* from API 20NE
[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.: #22491]	23525	-	-	-	-	-	+	-	+	-	-	-	-	-	+	-	-	-	-	-	-	+

	Pathway	Enzyme coverage	Annotated reactions
	Pathway annotation	Computationally determined by
[Ref.: #66794]	adipate degradation	100	2 of 2
[Ref.: #66794]	cis-vaccenate biosynthesis	100	2 of 2
[Ref.: #66794]	gluconeogenesis	100	8 of 8
[Ref.: #66794]	reductive acetyl coenzyme A pathway	100	7 of 7
[Ref.: #66794]	CMP-KDO biosynthesis	100	4 of 4
[Ref.: #66794]	ethanol fermentation	100	2 of 2
[Ref.: #66794]	octane oxidation	100	3 of 3
[Ref.: #66794]	palmitate biosynthesis	100	22 of 22
[Ref.: #66794]	ppGpp biosynthesis	100	4 of 4
[Ref.: #66794]	methylglyoxal degradation	100	5 of 5
[Ref.: #66794]	biotin biosynthesis	100	4 of 4
[Ref.: #66794]	kanosamine biosynthesis II	100	2 of 2
[Ref.: #66794]	molybdenum cofactor biosynthesis	100	9 of 9
[Ref.: #66794]	folate polyglutamylation	100	1 of 1
[Ref.: #66794]	anapleurotic synthesis of oxalacetate	100	1 of 1
[Ref.: #66794]	mannosylglycerate biosynthesis	100	2 of 2
[Ref.: #66794]	UDP-GlcNAc biosynthesis	100	3 of 3
[Ref.: #66794]	CDP-diacylglycerol biosynthesis	100	2 of 2
[Ref.: #66794]	sulfopterin metabolism	100	4 of 4
[Ref.: #66794]	coenzyme A metabolism	100	4 of 4
[Ref.: #66794]	vitamin K metabolism	100	5 of 5
[Ref.: #66794]	phenylacetate degradation (aerobic)	100	5 of 5
[Ref.: #66794]	suberin monomers biosynthesis	100	2 of 2
[Ref.: #66794]	leucine metabolism	92.31	12 of 13
[Ref.: #66794]	serine metabolism	88.89	8 of 9
[Ref.: #66794]	NAD metabolism	88.89	16 of 18
[Ref.: #66794]	lipid A biosynthesis	88.89	8 of 9
[Ref.: #66794]	chorismate metabolism	88.89	8 of 9
[Ref.: #66794]	C4 and CAM-carbon fixation	87.5	7 of 8
[Ref.: #66794]	tetrahydrofolate metabolism	85.71	12 of 14
[Ref.: #66794]	heme metabolism	85.71	12 of 14
[Ref.: #66794]	phenylalanine metabolism	84.62	11 of 13
[Ref.: #66794]	tryptophan metabolism	84.21	32 of 38
[Ref.: #66794]	glycolate and glyoxylate degradation	83.33	5 of 6
[Ref.: #66794]	histidine metabolism	82.76	24 of 29
[Ref.: #66794]	glutamate and glutamine metabolism	82.14	23 of 28
[Ref.: #66794]	pentose phosphate pathway	81.82	9 of 11
[Ref.: #66794]	threonine metabolism	80	8 of 10
[Ref.: #66794]	starch degradation	80	8 of 10
[Ref.: #66794]	3-chlorocatechol degradation	80	4 of 5
[Ref.: #66794]	peptidoglycan biosynthesis	80	12 of 15
[Ref.: #66794]	Entner Doudoroff pathway	80	8 of 10
[Ref.: #66794]	photosynthesis	78.57	11 of 14
[Ref.: #66794]	tyrosine metabolism	78.57	11 of 14
[Ref.: #66794]	valine metabolism	77.78	7 of 9
[Ref.: #66794]	aspartate and asparagine metabolism	77.78	7 of 9
[Ref.: #66794]	CO2 fixation in Crenarchaeota	77.78	7 of 9
[Ref.: #66794]	d-mannose degradation	77.78	7 of 9
[Ref.: #66794]	purine metabolism	77.66	73 of 94
[Ref.: #66794]	alanine metabolism	75.86	22 of 29
[Ref.: #66794]	acetate fermentation	75	3 of 4
[Ref.: #66794]	glycogen biosynthesis	75	3 of 4
[Ref.: #66794]	6-hydroxymethyl-dihydropterin diphosphate biosynthesis	75	6 of 8
[Ref.: #66794]	isoleucine metabolism	75	6 of 8
[Ref.: #66794]	flavin biosynthesis	73.33	11 of 15
[Ref.: #66794]	pyrimidine metabolism	73.33	33 of 45
[Ref.: #66794]	proline metabolism	72.73	8 of 11
[Ref.: #66794]	cardiolipin biosynthesis	71.43	5 of 7
[Ref.: #66794]	propanol degradation	71.43	5 of 7
[Ref.: #66794]	glycolysis	70.59	12 of 17
[Ref.: #66794]	propionate fermentation	70	7 of 10
[Ref.: #66794]	isoprenoid biosynthesis	69.23	18 of 26
[Ref.: #66794]	lysine metabolism	69.05	29 of 42
[Ref.: #66794]	cysteine metabolism	66.67	12 of 18
[Ref.: #66794]	IAA biosynthesis	66.67	2 of 3
[Ref.: #66794]	acetoin degradation	66.67	2 of 3
[Ref.: #66794]	formaldehyde oxidation	66.67	2 of 3
[Ref.: #66794]	L-lactaldehyde degradation	66.67	2 of 3
[Ref.: #66794]	citric acid cycle	64.29	9 of 14
[Ref.: #66794]	d-xylose degradation	63.64	7 of 11
[Ref.: #66794]	arginine metabolism	62.5	15 of 24
[Ref.: #66794]	ketogluconate metabolism	62.5	5 of 8
[Ref.: #66794]	methionine metabolism	61.54	16 of 26
[Ref.: #66794]	urea cycle	61.54	8 of 13
[Ref.: #66794]	non-pathway related	60.53	23 of 38
[Ref.: #66794]	coenzyme M biosynthesis	60	6 of 10
[Ref.: #66794]	glycogen metabolism	60	3 of 5
[Ref.: #66794]	cellulose degradation	60	3 of 5
[Ref.: #66794]	metabolism of amino sugars and derivatives	60	3 of 5
[Ref.: #66794]	lipid metabolism	58.06	18 of 31
[Ref.: #66794]	glutathione metabolism	57.14	8 of 14
[Ref.: #66794]	ubiquinone biosynthesis	57.14	4 of 7
[Ref.: #66794]	carotenoid biosynthesis	54.55	12 of 22
[Ref.: #66794]	pantothenate biosynthesis	50	3 of 6
[Ref.: #66794]	butanoate fermentation	50	2 of 4
[Ref.: #66794]	phenol degradation	50	10 of 20
[Ref.: #66794]	dTDPLrhamnose biosynthesis	50	4 of 8
[Ref.: #66794]	catecholamine biosynthesis	50	2 of 4
[Ref.: #66794]	selenocysteine biosynthesis	50	3 of 6
[Ref.: #66794]	cyclohexanol degradation	50	2 of 4
[Ref.: #66794]	phenylmercury acetate degradation	50	1 of 2
[Ref.: #66794]	degradation of aromatic, nitrogen containing compounds	50	6 of 12
[Ref.: #66794]	4-hydroxyphenylacetate degradation	50	5 of 10
[Ref.: #66794]	quinate degradation	50	1 of 2
[Ref.: #66794]	3-phenylpropionate degradation	46.67	7 of 15
[Ref.: #66794]	degradation of pentoses	46.43	13 of 28
[Ref.: #66794]	vitamin B1 metabolism	46.15	6 of 13
[Ref.: #66794]	sulfate reduction	46.15	6 of 13
[Ref.: #66794]	oxidative phosphorylation	46.15	42 of 91
[Ref.: #66794]	vitamin B6 metabolism	45.45	5 of 11
[Ref.: #66794]	metabolism of disaccharids	45.45	5 of 11
[Ref.: #66794]	4-hydroxymandelate degradation	44.44	4 of 9
[Ref.: #66794]	degradation of hexoses	44.44	8 of 18
[Ref.: #66794]	ascorbate metabolism	40.91	9 of 22
[Ref.: #66794]	glycine betaine biosynthesis	40	2 of 5
[Ref.: #66794]	gallate degradation	40	2 of 5
[Ref.: #66794]	factor 420 biosynthesis	40	2 of 5
[Ref.: #66794]	D-cycloserine biosynthesis	40	2 of 5
[Ref.: #66794]	glycine metabolism	40	4 of 10
[Ref.: #66794]	myo-inositol biosynthesis	40	4 of 10
[Ref.: #66794]	bacilysin biosynthesis	40	2 of 5
[Ref.: #66794]	arachidonate biosynthesis	40	2 of 5
[Ref.: #66794]	lipoate biosynthesis	40	2 of 5
[Ref.: #66794]	arachidonic acid metabolism	38.89	7 of 18
[Ref.: #66794]	phenylpropanoid biosynthesis	38.46	5 of 13
[Ref.: #66794]	androgen and estrogen metabolism	37.5	6 of 16
[Ref.: #66794]	degradation of sugar acids	36	9 of 25
[Ref.: #66794]	(5R)-carbapenem carboxylate biosynthesis	33.33	1 of 3
[Ref.: #66794]	acetyl CoA biosynthesis	33.33	1 of 3
[Ref.: #66794]	enterobactin biosynthesis	33.33	1 of 3
[Ref.: #66794]	cyanate degradation	33.33	1 of 3
[Ref.: #66794]	vitamin B12 metabolism	32.35	11 of 34
[Ref.: #66794]	degradation of sugar alcohols	31.25	5 of 16
[Ref.: #66794]	polyamine pathway	30.43	7 of 23
[Ref.: #66794]	chlorophyll metabolism	27.78	5 of 18
[Ref.: #66794]	toluene degradation	25	1 of 4
[Ref.: #66794]	carnitine metabolism	25	2 of 8
[Ref.: #66794]	lactate fermentation	25	1 of 4
[Ref.: #66794]	phosphatidylethanolamine bioynthesis	23.08	3 of 13
[Ref.: #66794]	allantoin 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.: #22491]	Sample type/isolated from	seawater from 2672 m depth
[Ref.: #22491]	Geographic location (country and/or sea, region)	East
[Ref.: #22491]	Geographic location	5.3004°/106.4870°

[Ref.: #67770]	Sample type/isolated from	Deep-seawater sample from the eastern Pacific Ocean
* marker position based on {}

Isolation sources categories

#Environmental	#Aquatic	#Marine
#Environmental	#Terrestrial	#Core sample

What are isolation sources categories?

[Ref.: #69479]

Global distribution of 16S sequence KC005305 (>99% sequence identity) for Roseivirga pacifica subclade from Microbeatlas

Aquatic Samples	448
Soil Samples	5
Animal Samples	16
Plant Samples	3
Total Samples	472

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

[Ref.: #22491]

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.: #22491]	Fabibacter pacificus strain DY53 16S ribosomal RNA gene, partial sequence	KC005305	1442	ENA	1267423 tax ID

Genome sequence information:

Only first 5 entries are displayed. Click here to see all.

	Sequence accession description	Seq. accession number	Assembly level	Sequence database	Associated NCBI tax ID
[Ref.: #67770]	Roseivirga pacifica CGMCC 1.12402	GCA_900111145	contig	GenBank	1267423 tax ID
[Ref.: #67770]	Roseivirga pacifica DSM 100771	GCA_003633845	scaffold	GenBank	1267423 tax ID
[Ref.: #66792]	Fabibacter pacificus strain CGMCC 1.12402	1267423.4	wgs	PATRIC	1267423 tax ID	*
[Ref.: #66792]	Fabibacter pacificus strain DSM 100771	1267423.11	wgs	PATRIC	1267423 tax ID	*
[Ref.: #66792]	Fabibacter pacificus DSM 100771	2728369263	draft	JGI IMG/M	1267423 tax ID	*
[Ref.: #66792]	Fabibacter pacificus CGMCC 1.12402	2667527390	draft	JGI IMG/M	1267423 tax ID	*

[Ref.: #31070]	GC-content	40.8 mol%
[Ref.: #22491]	GC-content	40.8 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 Diaspora project based on: Fabibacter pacificus strain CGMCC 1.12402 PATRIC: 1267423.4
[Ref.: #69480]	motile	no	92.508	no
[Ref.: #69480]	gram-positive	no	97.654	yes
[Ref.: #69480]	anaerobic	no	99.112	no
[Ref.: #69480]	aerobic	yes	92.488	yes
[Ref.: #69480]	halophile	no	85.864	no
[Ref.: #69480]	spore-forming	no	95.719	no
[Ref.: #69480]	glucose-util	yes	88.609	no
[Ref.: #69480]	flagellated	no	97.354	no
[Ref.: #69480]	thermophile	no	97.715	yes
[Ref.: #69480]	glucose-ferment	no	91.382	yes

Availability in culture collections External links

[Ref.: #22491]

Culture collection no.

DSM 100771, CGMCC 1.12402, JCM 18885

[Ref.: #89708]

SI-ID 398197

Literature:

Topic	Title	Authors	Journal	DOI	Year
Phylogeny	Fabibacter pacificus sp. nov., a moderately halophilic bacterium isolated from seawater.	Huo YY, Xu L, Wang CS, Yang JY, You H, Oren A, Xu XW	Int J Syst Evol Microbiol	10.1099/ijs.0.051276-0	2013	*

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 )

#22491

Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 100771

#31070

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 #27399 (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) .

#89708

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-ID398197.1 )

#27399

IJSEM 3710 2013 ( DOI 10.1099/ijs.0.051276-0 , PubMed 23625263 )

* These data were automatically processed and therefore are not curated

Change proposal

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Search for species Roseivirga pacifica in external resources:
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Fabibacter pacificus strain CGMCC 1.12402

Change proposal

Change proposal