Name: Flammeovirga yaeyamensis IR25-3
Creator: BacDive
License: http://creativecommons.org/licenses/by-nc/4.0/

Strain identifier

BacDive ID: 24010

Type strain:

Species: Flammeovirga yaeyamensis

Strain Designation: IR25-3

Culture col. no.: DSM 25626, CIP 109099, NBRC 100898

Strain history: CIP <- 2006, NBRC <- Y. Nakagawa, IFO: strain IR25-3

NCBI tax ID(s): 367791 (species)

SI-ID 297160

CIP 109099, NBRC 100898, DSM 25626

Section

Flammeovirga yaeyamensis IR25-3 is an obligate aerobe, mesophilic, Gram-negative bacterium that was isolated from seaweed Digenea simplex.

Gram-negative
mesophilic
obligate 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	*Bacteroidota*
	Class	*Cytophagia*
	Order	*Cytophagales*
	Family	*Flammeovirgaceae*
	Genus	*Flammeovirga*
	Species	**Flammeovirga yaeyamensis**
	Full Scientific Name (LPSN)	Flammeovirga yaeyamensis Takahashi et al. 2006

Information on morphological and physiological properties Morphology

[Ref.: #124007]	Gram stain	negative
[Ref.: #69480]	Gram stain	negative Confidence in %99.991

[Ref.: #124007]	Cell shape	rod-shaped

[Ref.: #124007]	Motility	no

Information on culture and growth conditions Culture and growth conditions

[Ref.: #20562]

Culture medium

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

[Ref.: #20562]

Culture medium growth

[Ref.: #20562]

Culture medium link

Medium recipe at MediaDive

[Ref.: #20562]

Culture medium composition

expand / minimize

[Ref.: #40121]

Culture medium

Marine agar (MA)

[Ref.: #40121]

Culture medium growth

[Ref.: #40121]

Culture medium composition

expand / minimize

[Ref.: #124007]

Culture medium

CIP Medium 13

[Ref.: #124007]

Culture medium growth

[Ref.: #124007]

Culture medium link

Medium recipe provided by DSMZ

	Temperatures	Kind of temperature		Temperature
[Ref.: #20562]			growth	25 °C
[Ref.: #40121]			growth	30 °C

[Ref.: #20562]	Temperature range	mesophilic
[Ref.: #40121]	Temperature range	mesophilic

Information on physiology and metabolism Physiology and metabolism

[Ref.: #124007]

Oxygen tolerance

obligate aerobe

[Ref.: #69481]	Ability of spore formation	no Confidence in %97
[Ref.: #69480]	Ability of spore formation	no Confidence in %99.901

	Metabolite utilization	Metabolite	Utilization activity	Kind of utilization tested
[Ref.: #124007]		nitrate ChEBI	-	reduction
[Ref.: #124007]		nitrite ChEBI	-	reduction

	Metabolite production	Metabolite	Production
[Ref.: #124007]		indole ChEBI	no

	Enzyme	Enzyme activity	EC number
[Ref.: #68382]	acid phosphatase	+	3.1.3.2	* from API zym
[Ref.: #124007]	alcohol dehydrogenase	-	1.1.1.1
[Ref.: #68382]	alkaline phosphatase	+	3.1.3.1	* from API zym
[Ref.: #68382]	alpha-chymotrypsin	-	3.4.21.1	* from API zym
[Ref.: #68382]	alpha-fucosidase	-	3.2.1.51	* from API zym
[Ref.: #68382]	alpha-galactosidase	+	3.2.1.22	* from API zym
[Ref.: #68382]	alpha-glucosidase	+	3.2.1.20	* from API zym
[Ref.: #68382]	alpha-mannosidase	-	3.2.1.24	* from API zym
[Ref.: #68382]	beta-galactosidase	-	3.2.1.23	* from API zym
[Ref.: #68382]	beta-glucosidase	-	3.2.1.21	* from API zym
[Ref.: #68382]	beta-glucuronidase	-	3.2.1.31	* from API zym
[Ref.: #124007]	catalase	+	1.11.1.6
[Ref.: #68382]	cystine arylamidase	-	3.4.11.3	* from API zym
[Ref.: #68382]	esterase (C 4)	+		* from API zym
[Ref.: #68382]	esterase lipase (C 8)	+		* from API zym
[Ref.: #68382]	leucine arylamidase	+	3.4.11.1	* from API zym
[Ref.: #68382]	lipase (C 14)	-		* from API zym
[Ref.: #124007]	lysine decarboxylase	-	4.1.1.18
[Ref.: #68382]	N-acetyl-beta-glucosaminidase	-	3.2.1.52	* from API zym
[Ref.: #68382]	naphthol-AS-BI-phosphohydrolase	+		* from API zym
[Ref.: #124007]	ornithine decarboxylase	-	4.1.1.17
[Ref.: #124007]	oxidase	+
[Ref.: #68382]	trypsin	+	3.4.21.4	* from API zym
[Ref.: #124007]	urease	-	3.5.1.5
[Ref.: #68382]	valine arylamidase	+		* from API zym
	Only first 10 entries are displayed. Click here to see all.

API® zym:

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

	API ID	Control	2-naphthyl phosphateAlkaline phosphatase	2-naphthyl butyrateEsterase (C 4)	2-naphtyl caprylateEsterase Lipase (C 8)	2-naphthyl myristateLipase (C 14)	L-leucyl-2-naphthylamideLeucine arylamidase	L-valyl-2-naphthylamideValine arylamidase	L-cystyl-2-naphthylamideCystine arylamidase	N-benzoyl-DL-arginine-2-naphthylamideTrypsin	N-glutaryl-phenylalanine-2-naphthylamidealpha- Chymotrypsin	2-naphthyl phosphateAcid phosphatase	Naphthol-AS-BI-phosphateNaphthol-AS-BI-phosphohydrolase	6-Br-2-naphthyl-alphaD-galactpyranosidealpha- Galactosidase	2-naphthyl-betaD-galactpyranosidebeta- Galactosidase	Naphthol-AS-BI-betaD-glucuronidebeta- Glucuronidase	2-naphthyl-alphaD-glucopyranosidealpha- Glucosidase	6-Br-2-naphthyl-betaD-glucopyranosidebeta- Glucosidase	1-naphthyl-N-acetyl-betaD-glucosaminideN-acetyl-beta- glucosaminidase	6-Br-2-naphthyl-alphaD-mannopyranosidealpha- Mannosidase	2-naphthyl-alphaL-fucopyranosidealpha- Fucosidase
[Ref.: #124007]	11667	-	+	+	+	-	+	+	-	+	-	+	+	+	-	-	+	-	-	-	-

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

[Ref.: #20562]	Sample type/isolated from	seaweed Digenea simplex
[Ref.: #20562]	Host species	Digenea simplex
[Ref.: #20562]	Geographic location (country and/or sea, region)	Okinawa Pref., Yaeyama Islands
[Ref.: #20562]	Country	Japan
[Ref.: #20562]	Country ISO 3 Code	JPN
[Ref.: #20562]	Continent	Asia

[Ref.: #124007]	Sample type/isolated from	Seaweed, Digenea simplex
[Ref.: #124007]	Geographic location (country and/or sea, region)	Uehara, Iriomote Island, Okinawa
[Ref.: #124007]	Country	Japan
[Ref.: #124007]	Country ISO 3 Code	JPN
[Ref.: #124007]	Continent	Asia
[Ref.: #124007]	Isolation date	2001
* marker position based on {}

Isolation sources categories

#Host

#Plants

#Aquatic plant

What are isolation sources categories?

[Ref.: #69479]

Global distribution of 16S sequence AB247554 (>99% sequence identity) for Flammeovirga yaeyamensis subclade from Microbeatlas

Aquatic Samples	1080
Soil Samples	58
Animal Samples	614
Plant Samples	5
Total Samples	1757

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

[Ref.: #20562]	Biosafety level	1	Risk group (German classification) According to TRBA 466
[Ref.: #124007]	Biosafety level	1	Risk group (French classification)

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.: #20562]	Flammeovirga yaeyamensis gene for 16S ribosomal RNA, partial sequence, strain: NBRC 100898	AB247554	1451	ENA	367791 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.: #66792]	Flammeovirga yaeyamensis NBRC:100898	GCA_018736045	complete	GenBank	367791 tax ID	*
[Ref.: #66792]	Flammeovirga yaeyamensis DSM 25626	GCA_014195575	scaffold	GenBank	367791 tax ID	*
[Ref.: #66792]	Flammeovirga yaeyamensis NBRC 100898	GCA_012844325	scaffold	GenBank	367791 tax ID	*
[Ref.: #66792]	Flammeovirga yaeyamensis strain DSM 25626	367791.5	wgs	PATRIC	367791 tax ID	*
[Ref.: #66792]	Flammeovirga yaeyamensis strain NBRC 100898	367791.4	wgs	PATRIC	367791 tax ID	*
[Ref.: #66792]	Flammeovirga yaeyamensis strain NBRC:100898	367791.6	complete	PATRIC	367791 tax ID	*

[Ref.: #20562]

GC-content

33.4-35.7 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: Flammeovirga yaeyamensis NBRC:100898 NCBI: GCA_018736045.1
[Ref.: #69481]	spore-forming	no	97	no

	Trait	Prediction	Confidence in %	In training data
	Predictions from Diaspora project based on: Flammeovirga yaeyamensis NBRC:100898 NCBI: GCA_018736045.1
[Ref.: #69480]	flagellated	no	92.806	no
[Ref.: #69480]	gram-positive	no	98.051	no
[Ref.: #69480]	anaerobic	no	97.936	no
[Ref.: #69480]	aerobic	yes	76.393	no
[Ref.: #69480]	halophile	no	76.986	no
[Ref.: #69480]	spore-forming	no	91.145	no
[Ref.: #69480]	thermophile	no	97.997	yes
[Ref.: #69480]	motile	no	86.284	no
[Ref.: #69480]	glucose-util	yes	89.718	no
[Ref.: #69480]	glucose-ferment	no	81.594	no

Availability in culture collections External links

[Ref.: #20562]

Culture collection no.

DSM 25626, CIP 109099, NBRC 100898

[Ref.: #87984]

SI-ID 297160

Literature:

Topic	Title	Authors	Journal	DOI	Year
Phylogeny	Emendation of the genus Flammeovirga and Flammeovirga aprica with the proposal of Flammeovirga arenaria nom. rev., comb. nov. and Flammeovirga yaeyamensis sp. nov.	Takahashi M, Suzuki KI, Nakagawa Y	Int J Syst Evol Microbiol	10.1099/ijs.0.64324-0	2006	*
Phylogeny	Flammeovirga agarivorans sp. nov., an agar-digesting marine bacterium isolated from surface seawater.	Wang X, Guo F, Tian P, Yu S, Xue CX, Wang W, Xiao J, Niu W	Int J Syst Evol Microbiol	10.1099/ijsem.0.004497	2020	*
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	*
Phylogeny	Perexilibacter aurantiacus gen. nov., sp. nov., a novel member of the family 'Flammeovirgaceae' isolated from sediment.	Yoon J, Ishikawa S, Kasai H, Yokota A	Int J Syst Evol Microbiol	10.1099/ijs.0.64845-0	2007	*

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 )

#20562

Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 25626

#40121 ; Curators of the CIP;

#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) .

#68382

Automatically annotated from API zym .

#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 )

#87984

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-ID297160.1 )

#124007 Collection of Institut Pasteur ; Curators of the CIP; CIP 109099
* These data were automatically processed and therefore are not curated

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Flammeovirga yaeyamensis NBRC:100898

Flammeovirga yaeyamensis NBRC:100898

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