Flavobacterium gilvum (KACC 18113, JCM 30144, EM1308)

Name: Flavobacterium gilvum (KACC 18113, JCM 30144, EM1308)
Creator: BacDive
License: http://creativecommons.org/licenses/by/4.0/

BacDive ID 133319

Type strain

Strain Designation EM1308

Culture col. no. KACC 18113 JCM 30144 EM1308

NCBI tax ID(s) 1492737

Special Collections JCM Literature strains

History JCM <-- H. Yi; Korea Univ., South Korea; EM1308.

Links

Flavobacterium gilvum EM1308 is an aerobe, Gram-negative, rod-shaped bacterium that forms circular colonies and was isolated from stream water in Bukhansan National Park, Seoul.

Gram-negative rod-shaped colony-forming aerobe genome sequence 16S sequence Bacteria

Name and taxonomic classification

SI-ID 132201

JCM 30144

@ref 20215

Last LPSN update 2026-05-29 08:38:03

Domain Bacteria

Phylum Bacteroidota

Class Flavobacteriia

Order Flavobacteriales

Family Flavobacteriaceae

Genus Flavobacterium

Species Flavobacterium gilvum

Full scientific name Flavobacterium gilvum Shin et al. 2017

Morphology

Cell morphology

@ref	Gram stain	Cell length	Cell width	Cell shape	Confidence
25165	negative	0.5-1.2 µm	0.3-0.7 µm	rod-shaped
125439	negative				90.104
125438					93.5
125438	negative				97.811

Colony morphology

@ref	Colony size	Colony color	Colony shape	Incubation period	Medium used
25165	2.0-3.0 mm	cream-coloured	circular	2 days	R2A

Pigmentation

@ref	Production	Name
25165		flexirubin type pigments

Culture and growth conditions

Culture medium

@ref	Name	Growth
25165	Reasoner's 2A agar (R2A)

Culture temp

@ref	Growth	Type	Temperature (°C)
25165	positive	growth	4-30
25165	positive	optimum	28
25165	negative	growth	37
25165	negative	growth	42
67770	positive	growth	30

Culture pH

@ref	Ability	Type	PH
25165	positive	optimum	6.5-7.5
25165	positive	growth	5.5-8.0

Physiology and metabolism

Oxygen tolerance

@ref	Oxygen tolerance	Confidence
25165	aerobe
125439	facultative anaerobe	99.316

Spore formation

@ref	Spore formation	Confidence
125439		99.985
125438		91.933

Halophily

@ref	Salt	Growth	Tested relation	Concentration
25165	NaCl	positive	growth	0-1 %(w/v)

Metabolite utilization

@ref	Chebi-ID	Metabolite	Utilization activity	Kind of utilization tested
25165	16708 ChEBI	adenine	-	hydrolysis
25165	17128 ChEBI	adipate	-	assimilation
25165	27613 ChEBI	amygdalin	-	carbon source
25165	85146 ChEBI	carboxymethylcellulose	-	hydrolysis
25165		casein	+	hydrolysis
25165	17634 ChEBI	D-glucose	-	carbon source
25165	16899 ChEBI	D-mannitol	-	carbon source
25165	16024 ChEBI	D-mannose	-	carbon source
25165	17924 ChEBI	D-sorbitol	-	carbon source
25165	27689 ChEBI	decanoate	-	assimilation
25165	16991 ChEBI	dna	+	hydrolysis
25165	4853 ChEBI	esculin	+	hydrolysis
25165	5291 ChEBI	gelatin	-	hydrolysis
25165	17234 ChEBI	glucose	-	fermentation
25165	17368 ChEBI	hypoxanthine	-	hydrolysis
25165	30849 ChEBI	L-arabinose	-	carbon source
25165	62345 ChEBI	L-rhamnose	-	carbon source
25165	17895 ChEBI	L-tyrosine	-	hydrolysis
25165	25115 ChEBI	malate	-	assimilation
25165	17306 ChEBI	maltose	-	carbon source
25165	28053 ChEBI	melibiose	-	carbon source
25165	17268 ChEBI	myo-inositol	-	carbon source
25165	506227 ChEBI	N-acetylglucosamine	-	carbon source
25165	17632 ChEBI	nitrate	+	reduction
25165	18401 ChEBI	phenylacetate	-	assimilation
25165	32032 ChEBI	potassium gluconate	-	assimilation
25165	53258 ChEBI	sodium citrate	-	assimilation
25165	28017 ChEBI	starch	+	hydrolysis
25165	17992 ChEBI	sucrose	-	carbon source
25165	53424 ChEBI	tween 20	-	hydrolysis
25165	53423 ChEBI	tween 40	-	hydrolysis
25165	53425 ChEBI	tween 60	-	hydrolysis
25165	53426 ChEBI	tween 80	-	hydrolysis
25165	15318 ChEBI	xanthine	-	hydrolysis

Metabolite production

@ref	Chebi-ID	Metabolite	Production
25165	16136 ChEBI	hydrogen sulfide
25165	35581 ChEBI	indole

Enzymes

@ref	Value	Activity	Ec
25165	acid phosphatase	+	3.1.3.2
25165	alkaline phosphatase	+	3.1.3.1
25165	alpha-chymotrypsin	+	3.4.21.1
25165	alpha-fucosidase	+	3.2.1.51
25165	alpha-galactosidase	-	3.2.1.22
25165	alpha-galactosidase	+	3.2.1.22
25165	alpha-glucosidase	+	3.2.1.20
25165	alpha-mannosidase	-	3.2.1.24
25165	arginine dihydrolase	-	3.5.3.6
25165	beta-galactosidase	+	3.2.1.23
25165	beta-glucosidase	-	3.2.1.21
25165	beta-glucuronidase	-	3.2.1.31
25165	catalase	+	1.11.1.6
25165	cystine arylamidase	-	3.4.11.3
25165	cytochrome oxidase	+	1.9.3.1
25165	esterase (C 4)	+
25165	esterase Lipase (C 8)	+
25165	gelatinase	-
25165	leucine arylamidase	+	3.4.11.1
25165	lipase (C 14)	-
25165	N-acetyl-beta-glucosaminidase	+	3.2.1.52
25165	naphthol-AS-BI-phosphohydrolase	+
25165	trypsin	-	3.4.21.4
25165	urease	-	3.5.1.5
25165	valine arylamidase	+

Pathway annotation

Computationally determined by

@ref	pathway	enzyme coverage	annotated reactions
66794	palmitate biosynthesis	100	22 of 22
66794	methylglyoxal degradation	100	5 of 5
66794	cis-vaccenate biosynthesis	100	2 of 2
66794	sulfopterin metabolism	100	4 of 4
66794	coenzyme A metabolism	100	4 of 4
66794	glycogen metabolism	100	5 of 5
66794	biotin biosynthesis	100	4 of 4
66794	glycine betaine biosynthesis	100	5 of 5
66794	adipate degradation	100	2 of 2
66794	vitamin K metabolism	100	5 of 5
66794	L-lactaldehyde degradation	100	3 of 3
66794	kanosamine biosynthesis II	100	2 of 2
66794	gluconeogenesis	100	8 of 8
66794	UDP-GlcNAc biosynthesis	100	3 of 3
66794	CDP-diacylglycerol biosynthesis	100	2 of 2
66794	anapleurotic synthesis of oxalacetate	100	1 of 1
66794	ppGpp biosynthesis	100	4 of 4
66794	teichoic acid biosynthesis	100	1 of 1
66794	folate polyglutamylation	100	1 of 1
66794	denitrification	100	2 of 2
66794	tetrahydrofolate metabolism	92.86	13 of 14
66794	threonine metabolism	90	9 of 10
66794	molybdenum cofactor biosynthesis	88.89	8 of 9
66794	chorismate metabolism	88.89	8 of 9
66794	lipid A biosynthesis	88.89	8 of 9
66794	C4 and CAM-carbon fixation	87.5	7 of 8
66794	heme metabolism	85.71	12 of 14
66794	photosynthesis	85.71	12 of 14
66794	reductive acetyl coenzyme A pathway	85.71	6 of 7
66794	vitamin B1 metabolism	84.62	11 of 13
66794	lipid metabolism	83.87	26 of 31
66794	NAD metabolism	83.33	15 of 18
66794	degradation of hexoses	83.33	15 of 18
66794	Entner Doudoroff pathway	80	8 of 10
66794	starch degradation	80	8 of 10
66794	peptidoglycan biosynthesis	80	12 of 15
66794	purine metabolism	78.72	74 of 94
66794	valine metabolism	77.78	7 of 9
66794	d-mannose degradation	77.78	7 of 9
66794	serine metabolism	77.78	7 of 9
66794	leucine metabolism	76.92	10 of 13
66794	phenylalanine metabolism	76.92	10 of 13
66794	glycogen biosynthesis	75	3 of 4
66794	isoleucine metabolism	75	6 of 8
66794	butanoate fermentation	75	3 of 4
66794	CMP-KDO biosynthesis	75	3 of 4
66794	acetate fermentation	75	3 of 4
66794	glutamate and glutamine metabolism	75	21 of 28
66794	flavin biosynthesis	73.33	11 of 15
66794	pentose phosphate pathway	72.73	8 of 11
66794	propanol degradation	71.43	5 of 7
66794	alanine metabolism	68.97	20 of 29
66794	degradation of sugar acids	68	17 of 25
66794	acetyl CoA biosynthesis	66.67	2 of 3
66794	formaldehyde oxidation	66.67	2 of 3
66794	aspartate and asparagine metabolism	66.67	6 of 9
66794	pyrimidine metabolism	66.67	30 of 45
66794	acetoin degradation	66.67	2 of 3
66794	CO2 fixation in Crenarchaeota	66.67	6 of 9
66794	histidine metabolism	65.52	19 of 29
66794	tyrosine metabolism	64.29	9 of 14
66794	degradation of pentoses	64.29	18 of 28
66794	lysine metabolism	64.29	27 of 42
66794	citric acid cycle	64.29	9 of 14
66794	d-xylose degradation	63.64	7 of 11
66794	vitamin B6 metabolism	63.64	7 of 11
66794	proline metabolism	63.64	7 of 11
66794	tryptophan metabolism	63.16	24 of 38
66794	degradation of sugar alcohols	62.5	10 of 16
66794	6-hydroxymethyl-dihydropterin diphosphate biosynthesis	62.5	5 of 8
66794	ketogluconate metabolism	62.5	5 of 8
66794	methionine metabolism	61.54	16 of 26
66794	cysteine metabolism	61.11	11 of 18
66794	3-chlorocatechol degradation	60	3 of 5
66794	O-antigen biosynthesis	60	3 of 5
66794	cellulose degradation	60	3 of 5
66794	hydrogen production	60	3 of 5
66794	myo-inositol biosynthesis	60	6 of 10
66794	metabolism of amino sugars and derivatives	60	3 of 5
66794	arachidonate biosynthesis	60	3 of 5
66794	propionate fermentation	60	6 of 10
66794	glycolysis	58.82	10 of 17
66794	non-pathway related	57.89	22 of 38
66794	ubiquinone biosynthesis	57.14	4 of 7
66794	mevalonate metabolism	57.14	4 of 7
66794	nitrate assimilation	55.56	5 of 9
66794	arginine metabolism	54.17	13 of 24
66794	sulfate reduction	53.85	7 of 13
66794	ribulose monophosphate pathway	50	1 of 2
66794	dolichol and dolichyl phosphate biosynthesis	50	1 of 2
66794	pantothenate biosynthesis	50	3 of 6
66794	cyclohexanol degradation	50	2 of 4
66794	quinate degradation	50	1 of 2
66794	suberin monomers biosynthesis	50	1 of 2
66794	dTDPLrhamnose biosynthesis	50	4 of 8
66794	vitamin E metabolism	50	2 of 4
66794	ethanol fermentation	50	1 of 2
66794	phenylpropanoid biosynthesis	46.15	6 of 13
66794	isoprenoid biosynthesis	46.15	12 of 26
66794	metabolism of disaccharids	45.45	5 of 11
66794	cardiolipin biosynthesis	42.86	3 of 7
66794	degradation of aromatic, nitrogen containing compounds	41.67	5 of 12
66794	glycine metabolism	40	4 of 10
66794	lipoate biosynthesis	40	2 of 5
66794	coenzyme M biosynthesis	40	4 of 10
66794	oxidative phosphorylation	39.56	36 of 91
66794	ascorbate metabolism	36.36	8 of 22
66794	selenocysteine biosynthesis	33.33	2 of 6
66794	IAA biosynthesis	33.33	1 of 3
66794	enterobactin biosynthesis	33.33	1 of 3
66794	cyanate degradation	33.33	1 of 3
66794	arachidonic acid metabolism	33.33	6 of 18
66794	glycolate and glyoxylate degradation	33.33	2 of 6
66794	octane oxidation	33.33	1 of 3
66794	(5R)-carbapenem carboxylate biosynthesis	33.33	1 of 3
66794	vitamin B12 metabolism	32.35	11 of 34
66794	androgen and estrogen metabolism	31.25	5 of 16
66794	urea cycle	30.77	4 of 13
66794	polyamine pathway	30.43	7 of 23
66794	phenol degradation	30	6 of 20
66794	dolichyl-diphosphooligosaccharide biosynthesis	27.27	3 of 11
66794	3-phenylpropionate degradation	26.67	4 of 15
66794	lactate fermentation	25	1 of 4
66794	catecholamine biosynthesis	25	1 of 4
66794	phosphatidylethanolamine bioynthesis	23.08	3 of 13
66794	4-hydroxymandelate degradation	22.22	2 of 9
66794	glutathione metabolism	21.43	3 of 14

Isolation, sampling and environmental information

Isolation source categories

Cat1	Cat2
#Environmental	#Aquatic

Isolation

@ref	Sample type	Geographic location	Country	Country ISO 3 Code	Continent	Latitude	Longitude
25165	stream water in Bukhansan National Park, Seoul	Bukhansan National Park, Seoul	Republic of Korea	KOR	Asia	37.66	126.99 37.66/126.99
67770	Stream water

Taxonmaps

69479

Global distribution of 16S sequence KX037100 (>99% sequence identity) for Flavobacterium gilvum subclade from Microbeatlas

Aquatic Samples	900
Soil Samples	151
Animal Samples	148
Plant Samples	544
Total Samples	1743

Interaction and safety

Sequence information

Genome sequences

@ref	Description	Assembly level	INSDC accession	BV-BRC accession	IMG accession	NCBI tax ID	Score
66792	ASM176146v1 assembly for Flavobacterium gilvum EM1308	complete	GCA_001761465		2718217955	1492737	98.41
66792	ASM73553v1 assembly for Flavobacterium gilvum EM1308	contig	GCA_000735535	1492737.3	2609460187	1492737	35.24

16S sequences

@ref	Description	Accession	Length	Database	NCBI tax ID
25165	Flavobacterium gilvum strain EM1308 16S ribosomal RNA gene, partial sequence	KX037100	1470		1492737

GC content

@ref	GC-content (mol%)	Method
25165	35.2
67770	35.2	genome sequence analysis

Genome-based predictions

Predictions

Predictions from Deep Learning for Genome Sequence Data. R package version 0.3.1 based on: ASM176146v1 assembly for Flavobacterium gilvum EM1308
NCBI: GCA_001761465

@ref	Trait	Model	Prediction	Confidence in %	In training data
125439	oxygen_tolerance	BacteriaNetⓘ	facultative anaerobe	99.32	no
125439	gram_stain	BacteriaNetⓘ	negative	90.10	no
125439	spore_formation	BacteriaNetⓘ	no	99.99	no
125439	motility	BacteriaNetⓘ	yes	40.44	no

Predictions from bacterial phenotypic traits through improved machine learning using high-quality, curated datasets based on: Flavobacterium gilvum EM1308
NCBI: GCA_001761465.1

@ref	Trait	Model	Prediction	Confidence in %	In training data
125438	gram-positive	gram-positiveⓘ	no	97.81	yes
125438	anaerobic	anaerobicⓘ	no	95.67	yes
125438	aerobic	aerobicⓘ	yes	75.42	yes
125438	spore-forming	spore-formingⓘ	no	91.93	no
125438	thermophilic	thermophileⓘ	no	97.22	yes
125438	flagellated	motile2+ⓘ	no	93.50	yes

Literature

Topic	Title	Authors	Journal	DOI	Year
Phylogeny	Flavobacterium gilvum sp. nov., isolated from stream water.	Shin SK, Ha Y, Cho YJ, Kwon S, Yong D, Yi H	Int J Syst Evol Microbiol	10.1099/ijsem.0.001594	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 )
#25165	S.-K. H. Shin, Yongheon,Cho, Yong-Joon,Kwon, Soonsung,Yong, Dongeun,Yi, Hana: Flavobacterium gilvum sp. nov., isolated from stream water. IJSEM 67: 153 - 157 2017 ( DOI 10.1099/ijsem.0.001594 , PubMed 27902216 )
#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;
#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 .
#125438	Julia Koblitz, Lorenz Christian Reimer, Rüdiger Pukall, Jörg Overmann: Predicting bacterial phenotypic traits through improved machine learning using high-quality, curated datasets. 2024 ( DOI 10.1101/2024.08.12.607695 )
#125439	Philipp Münch, René Mreches, Martin Binder, Hüseyin Anil Gündüz, Xiao-Yin To, Alice McHardy: deepG: Deep Learning for Genome Sequence Data. R package version 0.3.1 .
#126262	A. Lissin, I. Schober, J. F. Witte, H. Lüken, A. Podstawka, J. Koblitz, B. Bunk, P. Dawyndt, P. Vandamme, P. de Vos, J. Overmann, L. C. Reimer: StrainInfo—the central database for linked microbial strain identifiers. ( DOI 10.1093/database/baaf059 )

Content

About us

Flavobacterium gilvum (KACC 18113, JCM 30144, EM1308)

Name and taxonomic classification

Morphology

Cell morphology

Colony morphology

Pigmentation

Culture and growth conditions

Culture medium

Culture temp

Culture pH

Physiology and metabolism

Oxygen tolerance

Spore formation

Halophily

Metabolite utilization

Metabolite production

Enzymes

Pathway annotation

Isolation, sampling and environmental information

Isolation source categories

Isolation

Taxonmaps

Interaction and safety

Sequence information

Genome sequences

Genome browser: GCA_001761465

16S sequences

GC content

Genome-based predictions

Predictions

Literature

Literature

References

BacDive

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