Name: Flavobacterium indicum GPTSA100-9
Creator: BacDive
License: http://creativecommons.org/licenses/by-nc/4.0/

Strain identifier

BacDive ID: 5563

Type strain:

Species: Flavobacterium indicum

Strain Designation: GPTSA100-9

Culture col. no.: DSM 17447, CIP 109464, MTCC 6936, CCUG 58932

Strain history: CIP <- 2007, DSMZ <- MTCC <- P. Saha and T. Chakrabarti, strain: GPTSA100-9

NCBI tax ID(s): 1094466 (strain), 312277 (species)

SI-ID 297202

DSM 17447, CIP 109464, CCUG 58932

Section

Flavobacterium indicum GPTSA100-9 is an aerobe, mesophilic, Gram-negative bacterium that was isolated from warmspring water.

Gram-negative
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	*Flavobacteriia*
	Order	*Flavobacteriales*
	Family	*Flavobacteriaceae*
	Genus	*Flavobacterium*
	Species	**Flavobacterium indicum**
	Full Scientific Name (LPSN)	Flavobacterium indicum Saha and Chakrabarti 2006

Information on morphological and physiological properties Morphology

[Ref.: #120080]	Gram stain	negative
[Ref.: #69480]	Gram stain	negative Confidence in %99.998

[Ref.: #120080]	Cell shape	rod-shaped

[Ref.: #120080]	Motility	no

Information on culture and growth conditions Culture and growth conditions

[Ref.: #6988]

Culture medium

TRYPTONE SOYA BROTH (TSB) (DSMZ Medium 545)

[Ref.: #6988]

Culture medium growth

[Ref.: #6988]

Culture medium link

Medium recipe at MediaDive

[Ref.: #6988]

Culture medium composition

expand / minimize

[Ref.: #34002]

Culture medium

MEDIUM 566- Reasoner's 2A agar for Flavobacterium micromati

[Ref.: #34002]

Culture medium growth

[Ref.: #34002]

Culture medium composition

expand / minimize

[Ref.: #120080]

Culture medium

CIP Medium 566

[Ref.: #120080]

Culture medium growth

[Ref.: #120080]

Culture medium link

Medium recipe provided by DSMZ

		Temperature
[Ref.: #6988]	growth	30 °C
[Ref.: #34002]	growth	37 °C
[Ref.: #61779]	growth	30 °C

[Ref.: #6988]	Temperature range	mesophilic
[Ref.: #34002]	Temperature range	mesophilic
[Ref.: #61779]	Temperature range	mesophilic

Information on physiology and metabolism Physiology and metabolism

[Ref.: #61779]	Oxygen tolerance	aerobe
[Ref.: #120080]	Oxygen tolerance	obligate aerobe

[Ref.: #69481]	Ability of spore formation	no Confidence in %100
[Ref.: #69480]	Ability of spore formation	no Confidence in %99.999

	Metabolite utilization	Metabolite	Utilization activity	Kind of utilization tested
[Ref.: #120080]		nitrate ChEBI	-	reduction
[Ref.: #120080]		nitrite ChEBI	-	reduction

	Metabolite production	Metabolite	Production
[Ref.: #120080]		indole ChEBI	no

	Enzyme	Enzyme activity	EC number
[Ref.: #68382]	acid phosphatase	+	3.1.3.2	* from API zym
[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.: #120080]	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.: #68382]	N-acetyl-beta-glucosaminidase	-	3.2.1.52	* from API zym
[Ref.: #68382]	naphthol-AS-BI-phosphohydrolase	+		* from API zym
[Ref.: #120080]	oxidase	+
[Ref.: #68382]	trypsin	+	3.4.21.4	* from API zym
[Ref.: #120080]	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.: #120080]	11883	-	+	+	+	-	+	+	+	+	-	+	+	-	-	-	+	-	-	-	-

	Pathway	Enzyme coverage	Annotated reactions
	Pathway annotation	Computationally determined by
[Ref.: #66794]	adipate degradation	100	2 of 2
[Ref.: #66794]	biotin biosynthesis	100	4 of 4
[Ref.: #66794]	starch degradation	100	10 of 10
[Ref.: #66794]	vitamin K metabolism	100	5 of 5
[Ref.: #66794]	ppGpp biosynthesis	100	4 of 4
[Ref.: #66794]	palmitate biosynthesis	100	22 of 22
[Ref.: #66794]	cis-vaccenate biosynthesis	100	2 of 2
[Ref.: #66794]	cyanate degradation	100	3 of 3
[Ref.: #66794]	suberin monomers biosynthesis	100	2 of 2
[Ref.: #66794]	anapleurotic synthesis of oxalacetate	100	1 of 1
[Ref.: #66794]	UDP-GlcNAc biosynthesis	100	3 of 3
[Ref.: #66794]	folate polyglutamylation	100	1 of 1
[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]	chorismate metabolism	88.89	8 of 9
[Ref.: #66794]	lipid A biosynthesis	88.89	8 of 9
[Ref.: #66794]	d-mannose degradation	88.89	8 of 9
[Ref.: #66794]	C4 and CAM-carbon fixation	87.5	7 of 8
[Ref.: #66794]	gluconeogenesis	87.5	7 of 8
[Ref.: #66794]	leucine metabolism	84.62	11 of 13
[Ref.: #66794]	peptidoglycan biosynthesis	80	12 of 15
[Ref.: #66794]	cellulose degradation	80	4 of 5
[Ref.: #66794]	methylglyoxal degradation	80	4 of 5
[Ref.: #66794]	glycine betaine biosynthesis	80	4 of 5
[Ref.: #66794]	propionate fermentation	80	8 of 10
[Ref.: #66794]	citric acid cycle	78.57	11 of 14
[Ref.: #66794]	tetrahydrofolate metabolism	78.57	11 of 14
[Ref.: #66794]	photosynthesis	78.57	11 of 14
[Ref.: #66794]	NAD metabolism	77.78	14 of 18
[Ref.: #66794]	CO2 fixation in Crenarchaeota	77.78	7 of 9
[Ref.: #66794]	aspartate and asparagine metabolism	77.78	7 of 9
[Ref.: #66794]	serine metabolism	77.78	7 of 9
[Ref.: #66794]	CMP-KDO biosynthesis	75	3 of 4
[Ref.: #66794]	glycogen biosynthesis	75	3 of 4
[Ref.: #66794]	isoleucine metabolism	75	6 of 8
[Ref.: #66794]	6-hydroxymethyl-dihydropterin diphosphate biosynthesis	75	6 of 8
[Ref.: #66794]	acetate fermentation	75	3 of 4
[Ref.: #66794]	tryptophan metabolism	73.68	28 of 38
[Ref.: #66794]	propanol degradation	71.43	5 of 7
[Ref.: #66794]	cardiolipin biosynthesis	71.43	5 of 7
[Ref.: #66794]	ubiquinone biosynthesis	71.43	5 of 7
[Ref.: #66794]	glutamate and glutamine metabolism	67.86	19 of 28
[Ref.: #66794]	purine metabolism	67.02	63 of 94
[Ref.: #66794]	IAA biosynthesis	66.67	2 of 3
[Ref.: #66794]	valine metabolism	66.67	6 of 9
[Ref.: #66794]	pyrimidine metabolism	66.67	30 of 45
[Ref.: #66794]	acetoin degradation	66.67	2 of 3
[Ref.: #66794]	octane oxidation	66.67	2 of 3
[Ref.: #66794]	flavin biosynthesis	66.67	10 of 15
[Ref.: #66794]	L-lactaldehyde degradation	66.67	2 of 3
[Ref.: #66794]	histidine metabolism	65.52	19 of 29
[Ref.: #66794]	lipid metabolism	64.52	20 of 31
[Ref.: #66794]	dTDPLrhamnose biosynthesis	62.5	5 of 8
[Ref.: #66794]	lysine metabolism	61.9	26 of 42
[Ref.: #66794]	phenylalanine metabolism	61.54	8 of 13
[Ref.: #66794]	threonine metabolism	60	6 of 10
[Ref.: #66794]	arachidonate biosynthesis	60	3 of 5
[Ref.: #66794]	glycogen metabolism	60	3 of 5
[Ref.: #66794]	glycolysis	58.82	10 of 17
[Ref.: #66794]	alanine metabolism	58.62	17 of 29
[Ref.: #66794]	non-pathway related	57.89	22 of 38
[Ref.: #66794]	reductive acetyl coenzyme A pathway	57.14	4 of 7
[Ref.: #66794]	cysteine metabolism	55.56	10 of 18
[Ref.: #66794]	proline metabolism	54.55	6 of 11
[Ref.: #66794]	methionine metabolism	53.85	14 of 26
[Ref.: #66794]	quinate degradation	50	1 of 2
[Ref.: #66794]	phenylmercury acetate degradation	50	1 of 2
[Ref.: #66794]	butanoate fermentation	50	2 of 4
[Ref.: #66794]	tyrosine metabolism	50	7 of 14
[Ref.: #66794]	ketogluconate metabolism	50	4 of 8
[Ref.: #66794]	ethanol fermentation	50	1 of 2
[Ref.: #66794]	kanosamine biosynthesis II	50	1 of 2
[Ref.: #66794]	heme metabolism	50	7 of 14
[Ref.: #66794]	vitamin B1 metabolism	46.15	6 of 13
[Ref.: #66794]	isoprenoid biosynthesis	46.15	12 of 26
[Ref.: #66794]	oxidative phosphorylation	46.15	42 of 91
[Ref.: #66794]	vitamin B6 metabolism	45.45	5 of 11
[Ref.: #66794]	mevalonate metabolism	42.86	3 of 7
[Ref.: #66794]	degradation of aromatic, nitrogen containing compounds	41.67	5 of 12
[Ref.: #66794]	carotenoid biosynthesis	40.91	9 of 22
[Ref.: #66794]	bacilysin biosynthesis	40	2 of 5
[Ref.: #66794]	Entner Doudoroff pathway	40	4 of 10
[Ref.: #66794]	metabolism of amino sugars and derivatives	40	2 of 5
[Ref.: #66794]	lipoate biosynthesis	40	2 of 5
[Ref.: #66794]	coenzyme M biosynthesis	40	4 of 10
[Ref.: #66794]	glycine metabolism	40	4 of 10
[Ref.: #66794]	3-chlorocatechol degradation	40	2 of 5
[Ref.: #66794]	pentose phosphate pathway	36.36	4 of 11
[Ref.: #66794]	(5R)-carbapenem carboxylate biosynthesis	33.33	1 of 3
[Ref.: #66794]	pantothenate biosynthesis	33.33	2 of 6
[Ref.: #66794]	formaldehyde oxidation	33.33	1 of 3
[Ref.: #66794]	acetyl CoA biosynthesis	33.33	1 of 3
[Ref.: #66794]	glycolate and glyoxylate degradation	33.33	2 of 6
[Ref.: #66794]	molybdenum cofactor biosynthesis	33.33	3 of 9
[Ref.: #66794]	enterobactin biosynthesis	33.33	1 of 3
[Ref.: #66794]	selenocysteine biosynthesis	33.33	2 of 6
[Ref.: #66794]	degradation of sugar alcohols	31.25	5 of 16
[Ref.: #66794]	phenylpropanoid biosynthesis	30.77	4 of 13
[Ref.: #66794]	polyamine pathway	30.43	7 of 23
[Ref.: #66794]	arginine metabolism	29.17	7 of 24
[Ref.: #66794]	glutathione metabolism	28.57	4 of 14
[Ref.: #66794]	degradation of hexoses	27.78	5 of 18
[Ref.: #66794]	ascorbate metabolism	27.27	6 of 22
[Ref.: #66794]	dolichyl-diphosphooligosaccharide biosynthesis	27.27	3 of 11
[Ref.: #66794]	metabolism of disaccharids	27.27	3 of 11
[Ref.: #66794]	3-phenylpropionate degradation	26.67	4 of 15
[Ref.: #66794]	vitamin B12 metabolism	26.47	9 of 34
[Ref.: #66794]	androgen and estrogen metabolism	25	4 of 16
[Ref.: #66794]	lactate fermentation	25	1 of 4
[Ref.: #66794]	cyclohexanol degradation	25	1 of 4
[Ref.: #66794]	toluene degradation	25	1 of 4
[Ref.: #66794]	catecholamine biosynthesis	25	1 of 4
[Ref.: #66794]	alginate biosynthesis	25	1 of 4
[Ref.: #66794]	phenol degradation	25	5 of 20
[Ref.: #66794]	sulfate reduction	23.08	3 of 13
[Ref.: #66794]	arachidonic acid metabolism	22.22	4 of 18
[Ref.: #66794]	nitrate assimilation	22.22	2 of 9
[Ref.: #66794]	degradation of pentoses	21.43	6 of 28
		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.: #6988]	Sample type/isolated from	warmspring water
[Ref.: #6988]	Geographic location (country and/or sea, region)	Assam, Jorhat
[Ref.: #6988]	Country	India
[Ref.: #6988]	Country ISO 3 Code	IND
[Ref.: #6988]	Continent	Asia

[Ref.: #61779]	Sample type/isolated from	Water,warmspring
[Ref.: #61779]	Geographic location (country and/or sea, region)	Assam
[Ref.: #61779]	Country	India
[Ref.: #61779]	Country ISO 3 Code	IND
[Ref.: #61779]	Continent	Asia

[Ref.: #120080]	Sample type/isolated from	Environment, Water, warmspring
[Ref.: #120080]	Geographic location (country and/or sea, region)	Assam, Johrat
[Ref.: #120080]	Country	India
[Ref.: #120080]	Country ISO 3 Code	IND
[Ref.: #120080]	Continent	Asia
* marker position based on {}

Isolation sources categories

#Environmental

#Aquatic

#Thermal spring

What are isolation sources categories?

[Ref.: #69479]

Global distribution of 16S sequence AY904351 (>99% sequence identity) for Flavobacterium indicum subclade from Microbeatlas

Aquatic Samples	2946
Soil Samples	156
Animal Samples	415
Plant Samples	50
Total Samples	3567

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

[Ref.: #6988]	Biosafety level	1	Risk group (German classification) According to TRBA 466
[Ref.: #120080]	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.: #6988]	Flavobacterium indicum strain GPTSA100-9 16S ribosomal RNA gene, partial sequence	AY904351	1396	ENA	1094466 tax ID

Genome sequence information:

	Sequence accession description	Seq. accession number	Assembly level	Sequence database	Associated NCBI tax ID
[Ref.: #66792]	Flavobacterium indicum GPTSA100-9 = DSM 17447	GCA_000455605	complete	GenBank	1094466 tax ID	*
[Ref.: #66792]	Flavobacterium indicum GPTSA100-9 = DSM 17447	1094466.20		PATRIC	1094466 tax ID	*
[Ref.: #66792]	Flavobacterium indicum GPTSA100-9	2540341066	complete	JGI IMG/M	1094466 tax ID	*

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: Flavobacterium indicum GPTSA100-9 = DSM 17447 GPTSA100-9 NCBI: GCA_000455605.1
[Ref.: #69481]	spore-forming	no	100	no

	Trait	Prediction	Confidence in %	In training data
	Predictions from Diaspora project based on: Flavobacterium indicum GPTSA100-9 = DSM 17447 GPTSA100-9 NCBI: GCA_000455605.1
[Ref.: #69480]	motile	no	89.357	no
[Ref.: #69480]	flagellated	no	95.453	no
[Ref.: #69480]	gram-positive	no	98.824	no
[Ref.: #69480]	anaerobic	no	99.149	yes
[Ref.: #69480]	aerobic	yes	92.13	yes
[Ref.: #69480]	halophile	no	97.399	no
[Ref.: #69480]	spore-forming	no	95.527	no
[Ref.: #69480]	thermophile	no	98.666	no
[Ref.: #69480]	glucose-util	yes	74.587	no
[Ref.: #69480]	glucose-ferment	no	92.697	no

Availability in culture collections External links

[Ref.: #6988]

Culture collection no.

DSM 17447, CIP 109464, MTCC 6936, CCUG 58932

[Ref.: #75045]

SI-ID 297202

Literature:

Topic	Title	Authors	Journal	DOI	Year
Enzymology	Alkaline active cyanide dihydratase of Flavobacterium indicum MTCC 6936: Growth optimization, purification, characterization and in silico analysis.	Kumar V, Kumar V, Bhalla TC	Int J Biol Macromol	10.1016/j.ijbiomac.2018.05.075	2018	*
Genetics	Complete genome sequence of Flavobacterium indicum GPSTA100-9T, isolated from warm spring water.	Barbier P, Houel A, Loux V, Poulain J, Bernardet JF, Touchon M, Duchaud E	J Bacteriol	10.1128/JB.00420-12	2012	*
Phylogeny	Flavobacterium haoranii sp. nov., a cypermethrin-degrading bacterium isolated from a wastewater treatment system.	Zhang J, Jiang RB, Zhang XX, Hang BJ, He J, Li SP	Int J Syst Evol Microbiol	10.1099/ijs.0.020776-0	2010	*
Phylogeny	Flavobacterium indicum sp. nov., isolated from warm spring water in Assam, India.	Saha P, Chakrabarti T	Int J Syst Evol Microbiol	10.1099/ijs.0.64309-0	2006	*

References

#6988

Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 17447

#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 )

#34002 ; Curators of the CIP;
#61779 Culture Collection University of Gothenburg (CCUG) ; Curators of the CCUG; CCUG 58932

#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 )

#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 )

#75045

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-ID297202.1 )

#120080 Collection of Institut Pasteur ; Curators of the CIP; CIP 109464
* These data were automatically processed and therefore are not curated

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Flavobacterium indicum GPTSA100-9 = DSM 17447 GPTSA100-9

Flavobacterium indicum GPTSA100-9 = DSM 17447 GPTSA100-9

Change proposal

Change proposal