Name: Flammeovirga pacifica WPAGA1
Creator: BacDive
License: http://creativecommons.org/licenses/by-nc/4.0/

Strain identifier

BacDive ID: 24012

Type strain:

Species: Flammeovirga pacifica

Strain Designation: WPAGA1

Culture col. no.: DSM 24597, CCTCC AB 2010364, LMG 26175, MCCC 1A06425

Strain history: <- H. Xu, Third Inst. Oceanography, State Oceanic Admin., China; WPAGA1 <- Z. Ding

NCBI tax ID(s): 915059 (species)

SI-ID 405555

DSM 24597

Section

Flammeovirga pacifica WPAGA1 is a mesophilic, Gram-negative, rod-shaped bacterium that was isolated from deep sea sediment.

Gram-negative
rod-shaped
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	*Flammeovirgaceae*
	Genus	*Flammeovirga*
	Species	**Flammeovirga pacifica**
	Full Scientific Name (LPSN)	Flammeovirga pacifica Xu et al. 2012

Information on morphological and physiological properties Morphology

[Ref.: #30204]	Gram stain	negative
[Ref.: #69480]	Gram stain	negative Confidence in %99.978

[Ref.: #30204]	Cell length	03-08 µm

[Ref.: #30204]	Cell width	0.5-0.8 µm

[Ref.: #30204]	Cell shape	rod-shaped

[Ref.: #30204]

Pigment production

yes

Information on culture and growth conditions Culture and growth conditions

[Ref.: #20564]

Culture medium

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

[Ref.: #20564]

Culture medium growth

[Ref.: #20564]

Culture medium link

Medium recipe at MediaDive

[Ref.: #20564]

Culture medium composition

expand / minimize

		Temperature
[Ref.: #20564]	growth	28 °C
[Ref.: #30204]	growth	04-42 °C
[Ref.: #30204]	optimum	32 °C

[Ref.: #20564]	Temperature range	mesophilic
[Ref.: #30204]	Temperature range	mesophilic

	pH	Kind of pH		pH
[Ref.: #30204]			optimum	07-09
[Ref.: #30204]			growth	06-10

Information on physiology and metabolism Physiology and metabolism

[Ref.: #69481]	Ability of spore formation	no Confidence in %100
[Ref.: #69480]	Ability of spore formation	no Confidence in %99.937

	Halophily	Salt	Tested relation		Salt conc.
[Ref.: #30204]		NaCl		growth	0-5	%
[Ref.: #30204]		NaCl		optimum	3	%

	Metabolite	Utilization activity	Kind of utilization tested
[Ref.: #30204]	adipate ChEBI	+	carbon source
[Ref.: #30204]	esculin ChEBI	+	hydrolysis
[Ref.: #30204]	malate ChEBI	+	carbon source
[Ref.: #30204]	maltose ChEBI	+	carbon source
[Ref.: #30204]	N-acetylglucosamine ChEBI	+	carbon source
[Ref.: #30204]	nitrate ChEBI	+	reduction

	Enzyme	Enzyme activity	EC number
[Ref.: #30204]	acid phosphatase	+	3.1.3.2
[Ref.: #30204]	alkaline phosphatase	+	3.1.3.1
[Ref.: #30204]	alpha-galactosidase	+	3.2.1.22
[Ref.: #30204]	cytochrome oxidase	+	1.9.3.1

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

[Ref.: #20564]	Sample type/isolated from	deep sea sediment
[Ref.: #20564]	Geographic location (country and/or sea, region)	West Pacific Ocean, site CM3MC04-1 (157° 24' 31''E 19°30' 30'' N)
[Ref.: #20564]	Country	China
[Ref.: #20564]	Country ISO 3 Code	CHN
[Ref.: #20564]	Continent	Asia
[Ref.: #20564]	Geographic location	19.5083°/157.4090°
* marker position based on {}

Isolation sources categories

#Environmental	#Aquatic	#Marine
#Environmental	#Aquatic	#Sediment

What are isolation sources categories?

[Ref.: #69479]

Global distribution of 16S sequence HQ412594 (>99% sequence identity) for Flammeovirga pacifica subclade from Microbeatlas

Aquatic Samples	1812
Soil Samples	305
Animal Samples	382
Plant Samples	94
Total Samples	2593

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

[Ref.: #20564]

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.: #20564]	Flammeovirga pacifica strain WPAGA1 16S ribosomal RNA gene, partial sequence	HQ412594	1489	ENA	915059 tax ID

Genome sequence information:

	Sequence accession description	Seq. accession number	Assembly level	Sequence database	Associated NCBI tax ID
[Ref.: #66792]	Flammeovirga pacifica WPAGA1	GCA_000807855	scaffold	GenBank	915059 tax ID	*
[Ref.: #66792]	Flammeovirga pacifica WPAGA1	915059.3	wgs	PATRIC	915059 tax ID	*
[Ref.: #66792]	Flammeovirga pacifica WPAGA1	2648501771	draft	JGI IMG/M	915059 tax ID	*

[Ref.: #20564]	GC-content	32.9 mol%	high performance liquid chromatography (HPLC)
[Ref.: #30204]	GC-content	32.9 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: Flammeovirga pacifica WPAGA1 NCBI: GCA_000807855.2
[Ref.: #69481]	spore-forming	no	100	no

	Trait	Prediction	Confidence in %	In training data
	Predictions from Diaspora project based on: Flammeovirga pacifica WPAGA1 NCBI: GCA_000807855.1
[Ref.: #69480]	motile	no	86.486	no
[Ref.: #69480]	flagellated	no	92.773	no
[Ref.: #69480]	gram-positive	no	98.517	yes
[Ref.: #69480]	anaerobic	no	97.154	no
[Ref.: #69480]	aerobic	yes	71.37	no
[Ref.: #69480]	halophile	no	79.985	no
[Ref.: #69480]	spore-forming	no	91.668	no
[Ref.: #69480]	glucose-util	yes	90.138	no
[Ref.: #69480]	thermophile	no	96.951	yes
[Ref.: #69480]	glucose-ferment	no	79.796	no
[Ref.: #69480]	motile	no	86.486	no
[Ref.: #69480]	flagellated	no	92.773	no
[Ref.: #69480]	gram-positive	no	98.517	yes
[Ref.: #69480]	anaerobic	no	97.154	no
[Ref.: #69480]	aerobic	yes	71.37	no
[Ref.: #69480]	halophile	no	79.985	no
[Ref.: #69480]	spore-forming	no	91.668	no
[Ref.: #69480]	glucose-util	yes	90.138	no
[Ref.: #69480]	thermophile	no	96.951	yes
[Ref.: #69480]	glucose-ferment	no	79.796	no

Availability in culture collections External links

[Ref.: #20564]

Culture collection no.

DSM 24597, CCTCC AB 2010364, LMG 26175, MCCC 1A06425

[Ref.: #87986]

SI-ID 405555

Literature:

Only first 10 entries are displayed. Click here to see all.

Topic	Title	Authors	Journal	DOI	Year
Metabolism	Amelioration of Androgenetic Alopecia by Algal Oligosaccharides Prepared by Deep-Sea Bacterium Biodegradation.	Jin M, Chen YL, He X, Hou Y, Chan Z, Zeng R	Front Microbiol	10.3389/fmicb.2020.567060	2020	*
Enzymology	Identification and Characterization of a Novel Thermostable and Salt-Tolerant beta-1,3 Xylanase from Flammeovirga pacifica Strain WPAGA1.	Yi Z, Cai Z, Zeng B, Zeng R, Zhang G	Biomolecules	10.3390/biom10091287	2020	*
Biotechnology	A Novel Strategy for Efficient Agaro-Oligosaccharide Production Based on the Enzymatic Degradation of Crude Agarose in Flammeovirga pacifica WPAGA1.	Gao B, Li L, Wu H, Zhu D, Jin M, Qu W, Zeng R	Front Microbiol	10.3389/fmicb.2019.01231	2019	*
Enzymology	Characterization of a novel psychrophilic and halophilic beta-1, 3-xylanase from deep-sea bacterium, Flammeovirga pacifica strain WPAGA1.	Cai ZW, Ge HH, Yi ZW, Zeng RY, Zhang GY	Int J Biol Macromol	10.1016/j.ijbiomac.2018.07.090	2018	*
Genetics	Draft genome sequence of an agar-degrading marine bacterium Flammeovirga pacifica WPAGA1.	Chan Z, Wang R, Liu S, Zhao C, Yang S, Zeng R	Mar Genomics	10.1016/j.margen.2014.12.001	2014	*
Phylogeny	Flammeovirga pacifica sp. nov., isolated from deep-sea sediment.	Xu H, Fu Y, Yang N, Ding Z, Lai Q, Zeng R	Int J Syst Evol Microbiol	10.1099/ijs.0.030676-0	2011	*
	Genome Sequencing Reveals the Complex Polysaccharide-Degrading Ability of Novel Deep-Sea Bacterium Flammeovirga pacifica WPAGA1.	Gao B, Jin M, Li L, Qu W, Zeng R	Front Microbiol	10.3389/fmicb.2017.00600	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 )

#20564

Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 24597

#30204

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 #26549 (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) .

#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 )

#87986

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-ID405555.1 )

#26549

IJSEM 937 2012 ( DOI 10.1099/ijs.0.030676-0 , PubMed 21669915 )

* These data were automatically processed and therefore are not curated

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