Name: Flavobacterium rakeshii FCS-5
Creator: BacDive
License: https://creativecommons.org/licenses/by/4.0/

Strain identifier

BacDive ID: 133758

Type strain:

Species: Flavobacterium rakeshii

Strain Designation: FCS-5

Culture col. no.: MTCC 10967, JCM 17928, CIP 110368

Strain history: CIP <- 2012, JCM <- IMTECH, Chandigarh, India: strain FCS-5

NCBI tax ID(s): 1038845 (species)

SI-ID 382385

JCM 17928, CIP 110368

Special Collections

Section

Flavobacterium rakeshii FCS-5 is an aerobe, Gram-negative, rod-shaped bacterium that was isolated from Marine sediment from the Fort Cochin area.

Gram-negative
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	*Bacteroidota*
	Class	*Flavobacteriia*
	Order	*Flavobacteriales*
	Family	*Flavobacteriaceae*
	Genus	*Flavobacterium*
	Species	**Flavobacterium rakeshii**
	Full Scientific Name (LPSN)	Flavobacterium rakeshii Kaur et al. 2012

Information on morphological and physiological properties Morphology

[Ref.: #30420]	Gram stain	negative
[Ref.: #122133]	Gram stain	negative
[Ref.: #69480]	Gram stain	negative Confidence in %97.727

[Ref.: #30420]	Cell length	3 µm

[Ref.: #30420]	Cell width	1.4 µm

[Ref.: #30420]	Cell shape	rod-shaped
[Ref.: #122133]	Cell shape	rod-shaped

[Ref.: #30420]	Motility	no
[Ref.: #122133]	Motility	no
[Ref.: #69480]	Motility	no Confidence in %91.5

[Ref.: #30420]

Pigment production

yes

Information on culture and growth conditions Culture and growth conditions

[Ref.: #37597]

Culture medium

MEDIUM 72- for trypto casein soja agar

[Ref.: #37597]

Culture medium growth

[Ref.: #37597]

Culture medium composition

expand / minimize

[Ref.: #122133]

Culture medium

CIP Medium 72

[Ref.: #122133]

Culture medium growth

[Ref.: #122133]

Culture medium link

Medium recipe provided by DSMZ

		Temperature
[Ref.: #30420]	growth	20-37 °C
[Ref.: #30420]	optimum	30 °C
[Ref.: #37597]	growth	30 °C
[Ref.: #67770]	growth	30 °C

	pH	Kind of pH		pH
[Ref.: #30420]			optimum	8
[Ref.: #30420]			growth	05-12

Information on physiology and metabolism Physiology and metabolism

[Ref.: #30420]	Oxygen tolerance	aerobe
[Ref.: #122133]	Oxygen tolerance	obligate aerobe

[Ref.: #69480]	Ability of spore formation	no Confidence in %92.803
[Ref.: #69481]	Ability of spore formation	no Confidence in %100

	Halophily	Salt	Tested relation		Salt conc.
[Ref.: #30420]		NaCl		growth	0-3	%
[Ref.: #30420]		NaCl		optimum	2	%

[Ref.: #67770]

Observation

quinones: MK-6

	Metabolite	Utilization activity	Kind of utilization tested
[Ref.: #30420]	arabinose ChEBI	+	carbon source
[Ref.: #30420]	cellobiose ChEBI	+	carbon source
[Ref.: #30420]	esculin ChEBI	+	hydrolysis
[Ref.: #30420]	fructose ChEBI	+	carbon source
[Ref.: #30420]	galactose ChEBI	+	carbon source
[Ref.: #30420]	lactose ChEBI	+	carbon source
[Ref.: #30420]	mannitol ChEBI	+	carbon source
[Ref.: #30420]	mannose ChEBI	+	carbon source
[Ref.: #30420]	myo-inositol ChEBI	+	carbon source
[Ref.: #30420]	nitrate ChEBI	+	reduction
[Ref.: #122133]	nitrate ChEBI	-	reduction
[Ref.: #122133]	nitrite ChEBI	-	reduction
[Ref.: #30420]	rhamnose ChEBI	+	carbon source
[Ref.: #30420]	salicin ChEBI	+	carbon source
[Ref.: #30420]	sucrose ChEBI	+	carbon source
[Ref.: #30420]	trehalose ChEBI	+	carbon source
	Only first 10 entries are displayed. Click here to see all.

	Metabolite production	Metabolite	Production
[Ref.: #122133]		indole ChEBI	no

	Enzyme	Enzyme activity	EC number
[Ref.: #30420]	acid phosphatase	+	3.1.3.2
[Ref.: #68382]	acid phosphatase	+	3.1.3.2	* from API zym
[Ref.: #30420]	alkaline phosphatase	+	3.1.3.1
[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.: #30420]	catalase	+	1.11.1.6
[Ref.: #122133]	catalase	+	1.11.1.6
[Ref.: #68382]	cystine arylamidase	-	3.4.11.3	* from API zym
[Ref.: #30420]	cytochrome oxidase	+	1.9.3.1
[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.: #68382]	N-acetyl-beta-glucosaminidase	-	3.2.1.52	* from API zym
[Ref.: #68382]	naphthol-AS-BI-phosphohydrolase	+		* from API zym
[Ref.: #122133]	oxidase	-
[Ref.: #68382]	trypsin	-	3.4.21.4	* from API zym
[Ref.: #122133]	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.: #122133]	12555	-	+	+	+	-	+	-	-	-	-	+	+	-	-	-	+	-	-	-	-

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

[Ref.: #67770]	Sample type/isolated from	Marine sediment from the Fort Cochin area
[Ref.: #67770]	Geographic location (country and/or sea, region)	coastal Arabian Sea, state of Kerala
[Ref.: #67770]	Country	India
[Ref.: #67770]	Country ISO 3 Code	IND
[Ref.: #67770]	Continent	Asia

[Ref.: #122133]	Sample type/isolated from	Environment, Marine sediment sample
[Ref.: #122133]	Geographic location (country and/or sea, region)	Fort Kochi, coastal Arabian Sea, Kerala
[Ref.: #122133]	Country	India
[Ref.: #122133]	Country ISO 3 Code	IND
[Ref.: #122133]	Continent	Asia
* marker position based on {}

[Ref.: #69479]

Global distribution of 16S sequence JF830803 (>99% sequence identity) for Flavobacterium rakeshii from Microbeatlas

Aquatic Samples	85
Soil Samples	133
Animal Samples	23
Plant Samples	11
Total Samples	252

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

[Ref.: #122133]

Biosafety level

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.: #30420]	Flavobacterium rakeshii strain FCS-5 16S ribosomal RNA gene, partial sequence	JF830803	1459	GenBank ENA	1038845 tax ID

Genome sequence information:

	Sequence accession description	Seq. accession number	Assembly level	Sequence database	Associated NCBI tax ID
[Ref.: #67770]	Flavobacterium rakeshii JCM 17928	GCA_009741375	contig	GenBank ENA	1038845 tax ID
[Ref.: #66792]	Flavobacterium rakeshii strain JCM 17928	1038845.3	wgs	PATRIC	1038845 tax ID	*

[Ref.: #30420]	GC-content	32.4 mol%
[Ref.: #67770]	GC-content	32.4 mol%	thermal denaturation, midpoint method (Tm)

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: Flavobacterium rakeshii strain JCM 17928 PATRIC: 1038845.3
[Ref.: #69481]	spore-forming	spore-formingⓘ	no	100	no

	Trait	Model	Prediction	Confidence in %	In training data
	Predictions from Diaspora project based on: Flavobacterium rakeshii strain JCM 17928 PATRIC: 1038845.3
[Ref.: #69480]	gram-positive	gram-positiveⓘ	no	97.727	yes
[Ref.: #69480]	anaerobic	anaerobicⓘ	no	97.731	yes
[Ref.: #69480]	spore-forming	spore-formingⓘ	no	92.803	no
[Ref.: #69480]	aerobic	aerobicⓘ	yes	86.573	yes
[Ref.: #69480]	thermophilic	thermophileⓘ	no	94.351	no
[Ref.: #69480]	flagellated	motile2+ⓘ	no	91.5	yes

Availability in culture collections External links

[Ref.: #30420]

Culture collection no.

MTCC 10967, JCM 17928, CIP 110368

[Ref.: #91587]

SI-ID 382385

Literature:

Topic	Title	Authors	Journal	DOI	Year
Phylogeny	Flavobacterium alkalisoli sp. nov., isolated from rhizosphere soil of Suaeda salsa.	Xu L, Wang HT, Zhang JX, Zhang H, Wang S, Sun JQ	Int J Syst Evol Microbiol	10.1099/ijsem.0.004255	2020	*
Phylogeny	Flavobacterium suaedae sp. nov., an endophyte isolated from the root of Suaeda corniculata.	Sun JQ, Xu L, Liu M, Wang XY, Wu XL	Int J Syst Evol Microbiol	10.1099/ijsem.0.000967	2016	*
Phylogeny	Flavobacterium rakeshii sp. nov., isolated from marine sediment, and emended description of Flavobacterium beibuense Fu et al. 2011.	Kaur I, Kaur C, Khan F, Mayilraj S	Int J Syst Evol Microbiol	10.1099/ijs.0.035691-0	2012	*

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 )

#30420

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 #26756 (see below)

#37597 ; 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) .

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

#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 )

#91587

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-ID382385.1 )

#122133 Collection of Institut Pasteur ; Curators of the CIP; CIP 110368

#26756

IJSEM 2897 2012 ( DOI 10.1099/ijs.0.035691-0 , PubMed 22247214 )

* These data were automatically processed and therefore are not curated

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Flavobacterium rakeshii strain JCM 17928

Flavobacterium rakeshii strain JCM 17928

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