Name: Fluviicoccus keumensis 4DR5
Creator: BacDive
License: http://creativecommons.org/licenses/by-nc/4.0/

Strain identifier

BacDive ID: 132964

Type strain:

Species: Fluviicoccus keumensis

Strain Designation: 4DR5

Culture col. no.: DSM 105135, JCM 19370, KCTC 32475

Strain history: S. B. Kim 4DR5.

NCBI tax ID(s): 1435465 (species)

SI-ID 401246

DSM 105135

Section

Fluviicoccus keumensis 4DR5 is an aerobe, Gram-negative, coccus-shaped bacterium that forms circular colonies and was isolated from freshwater.

coccus-shaped
colony-forming
Gram-negative
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	*Pseudomonadota*
	Class	*Gammaproteobacteria*
	Order	*Pseudomonadales*
	Family	*Moraxellaceae*
	Genus	*Fluviicoccus*
	Species	**Fluviicoccus keumensis**
	Full Scientific Name (LPSN)	Fluviicoccus keumensis Kim et al. 2016

Information on morphological and physiological properties Morphology

[Ref.: #44050]	Gram stain	negative
[Ref.: #69480]	Gram stain	negative Confidence in %99.998

[Ref.: #44050]	Cell length	0.8-1.3 µm

[Ref.: #44050]	Cell width	0.8-1.3 µm

[Ref.: #44050]	Cell shape	coccus-shaped

[Ref.: #44050]	Motility	no

[Ref.: #44050]	Colony size	0.6-1.6 mm
[Ref.: #44050]	Colony color	white
[Ref.: #44050]	Colony shape	circular
[Ref.: #44050]	Incubation period	3 days
[Ref.: #44050]	Cultivation medium used	R2A agar

Information on culture and growth conditions Culture and growth conditions

[Ref.: #44050]

Culture medium

Reasoner's 2A agar (R2A)

[Ref.: #44050]

Culture medium growth

[Ref.: #24752]

Culture medium

R2A MEDIUM (DSMZ Medium 830)

[Ref.: #24752]

Culture medium growth

[Ref.: #24752]

Culture medium link

Medium recipe at MediaDive

[Ref.: #24752]

Culture medium composition

expand / minimize

		Temperature
[Ref.: #24752]	growth	28 °C
[Ref.: #44050]	growth	10-40 °C
[Ref.: #44050]	optimum	30 °C
[Ref.: #67770]	growth	37 °C

[Ref.: #24752]	Temperature range	mesophilic
[Ref.: #44050]	Temperature range	mesophilic
[Ref.: #67770]	Temperature range	mesophilic

	pH	Kind of pH		pH
[Ref.: #44050]			growth	6-9

Information on physiology and metabolism Physiology and metabolism

[Ref.: #44050]

Oxygen tolerance

aerobe

[Ref.: #44050]	Type of spore	spore
[Ref.: #44050]	Ability of spore formation	no
[Ref.: #69481]	Ability of spore formation	no Confidence in %100
[Ref.: #69480]	Ability of spore formation	no Confidence in %99.991

[Ref.: #44050]

Halophily / tolerance level

non-halophilic

	Halophily	Salt	Tested relation		Salt conc.
[Ref.: #44050]		NaCl		growth	0-0.4	%(w/v)
[Ref.: #44050]		NaCl		optimum	0	%(w/v)

[Ref.: #67770]

Observation

quinones: Q-10

	Metabolite	Utilization activity	Kind of utilization tested
[Ref.: #44050]	adipate ChEBI	-	assimilation
[Ref.: #44050]	casein	-	hydrolysis
[Ref.: #44050]	cellulose ChEBI	-	hydrolysis
[Ref.: #44050]	D-glucose ChEBI	-	assimilation
[Ref.: #44050]	D-mannitol ChEBI	-	assimilation
[Ref.: #44050]	D-mannose ChEBI	-	assimilation
[Ref.: #44050]	decanoate ChEBI	-	assimilation
[Ref.: #44050]	dna ChEBI	-	hydrolysis
[Ref.: #44050]	esculin ChEBI	+	hydrolysis
[Ref.: #44050]	gelatin ChEBI	-	hydrolysis
[Ref.: #44050]	L-arabinose ChEBI	-	assimilation
[Ref.: #44050]	malate ChEBI	-	assimilation
[Ref.: #44050]	maltose ChEBI	-	assimilation
[Ref.: #44050]	N-acetylglucosamine ChEBI	-	assimilation
[Ref.: #44050]	nitrate ChEBI	-	reduction
[Ref.: #44050]	phenylacetate ChEBI	-	assimilation
[Ref.: #44050]	potassium gluconate ChEBI	-	assimilation
[Ref.: #44050]	sodium citrate ChEBI	-	assimilation
[Ref.: #44050]	starch ChEBI	-	hydrolysis
	Only first 10 entries are displayed. Click here to see all.

	Metabolite production	Metabolite	Production
[Ref.: #44050]		indole ChEBI	no

	Enzyme	Enzyme activity	EC number
[Ref.: #44050]	acid phosphatase	+	3.1.3.2
[Ref.: #44050]	alkaline phosphatase	-	3.1.3.1
[Ref.: #44050]	alpha-chymotrypsin	-	3.4.21.1
[Ref.: #44050]	alpha-fucosidase	-	3.2.1.51
[Ref.: #44050]	alpha-galactosidase	-	3.2.1.22
[Ref.: #44050]	alpha-glucosidase	-	3.2.1.20
[Ref.: #44050]	alpha-mannosidase	-	3.2.1.24
[Ref.: #44050]	beta-galactosidase	-	3.2.1.23
[Ref.: #44050]	beta-glucosidase	-	3.2.1.21
[Ref.: #44050]	beta-glucuronidase	-	3.2.1.31
[Ref.: #44050]	catalase	+	1.11.1.6
[Ref.: #44050]	cystine arylamidase	-	3.4.11.3
[Ref.: #44050]	cytochrome oxidase	+	1.9.3.1
[Ref.: #44050]	esterase (C 4)	+
[Ref.: #44050]	esterase Lipase (C 8)	+
[Ref.: #44050]	leucine arylamidase	+	3.4.11.1
[Ref.: #44050]	lipase (C 14)	+
[Ref.: #44050]	N-acetyl-beta-glucosaminidase	-	3.2.1.52
[Ref.: #44050]	naphthol-AS-BI-phosphohydrolase	+
[Ref.: #44050]	trypsin	-	3.4.21.4
[Ref.: #44050]	valine arylamidase	+/-
	Only first 10 entries are displayed. Click here to see all.

	Pathway	Enzyme coverage	Annotated reactions
	Pathway annotation	Computationally determined by
[Ref.: #66794]	suberin monomers biosynthesis	100	2 of 2
[Ref.: #66794]	CDP-diacylglycerol biosynthesis	100	2 of 2
[Ref.: #66794]	palmitate biosynthesis	100	22 of 22
[Ref.: #66794]	L-lactaldehyde degradation	100	3 of 3
[Ref.: #66794]	denitrification	100	2 of 2
[Ref.: #66794]	aspartate and asparagine metabolism	100	9 of 9
[Ref.: #66794]	biotin biosynthesis	100	4 of 4
[Ref.: #66794]	octane oxidation	100	3 of 3
[Ref.: #66794]	coenzyme A metabolism	100	4 of 4
[Ref.: #66794]	formaldehyde oxidation	100	3 of 3
[Ref.: #66794]	UDP-GlcNAc biosynthesis	100	3 of 3
[Ref.: #66794]	cis-vaccenate biosynthesis	100	2 of 2
[Ref.: #66794]	ubiquinone biosynthesis	100	7 of 7
[Ref.: #66794]	methylglyoxal degradation	100	5 of 5
[Ref.: #66794]	anapleurotic synthesis of oxalacetate	100	1 of 1
[Ref.: #66794]	folate polyglutamylation	100	1 of 1
[Ref.: #66794]	ceramide biosynthesis	100	1 of 1
[Ref.: #66794]	ppGpp biosynthesis	100	4 of 4
[Ref.: #66794]	adipate degradation	100	2 of 2
[Ref.: #66794]	valine metabolism	100	9 of 9
[Ref.: #66794]	tetrahydrofolate metabolism	92.86	13 of 14
[Ref.: #66794]	molybdenum cofactor biosynthesis	88.89	8 of 9
[Ref.: #66794]	isoleucine metabolism	87.5	7 of 8
[Ref.: #66794]	photosynthesis	85.71	12 of 14
[Ref.: #66794]	reductive acetyl coenzyme A pathway	85.71	6 of 7
[Ref.: #66794]	phenylalanine metabolism	84.62	11 of 13
[Ref.: #66794]	glutamate and glutamine metabolism	82.14	23 of 28
[Ref.: #66794]	vitamin B6 metabolism	81.82	9 of 11
[Ref.: #66794]	peptidoglycan biosynthesis	80	12 of 15
[Ref.: #66794]	cellulose degradation	80	4 of 5
[Ref.: #66794]	propionate fermentation	80	8 of 10
[Ref.: #66794]	phenylacetate degradation (aerobic)	80	4 of 5
[Ref.: #66794]	heme metabolism	78.57	11 of 14
[Ref.: #66794]	chorismate metabolism	77.78	7 of 9
[Ref.: #66794]	serine metabolism	77.78	7 of 9
[Ref.: #66794]	CO2 fixation in Crenarchaeota	77.78	7 of 9
[Ref.: #66794]	lipid A biosynthesis	77.78	7 of 9
[Ref.: #66794]	lipid metabolism	77.42	24 of 31
[Ref.: #66794]	vitamin B1 metabolism	76.92	10 of 13
[Ref.: #66794]	alanine metabolism	75.86	22 of 29
[Ref.: #66794]	acetate fermentation	75	3 of 4
[Ref.: #66794]	CMP-KDO biosynthesis	75	3 of 4
[Ref.: #66794]	toluene degradation	75	3 of 4
[Ref.: #66794]	gluconeogenesis	75	6 of 8
[Ref.: #66794]	sulfopterin metabolism	75	3 of 4
[Ref.: #66794]	proline metabolism	72.73	8 of 11
[Ref.: #66794]	purine metabolism	72.34	68 of 94
[Ref.: #66794]	NAD metabolism	72.22	13 of 18
[Ref.: #66794]	cardiolipin biosynthesis	71.43	5 of 7
[Ref.: #66794]	pyrimidine metabolism	71.11	32 of 45
[Ref.: #66794]	threonine metabolism	70	7 of 10
[Ref.: #66794]	leucine metabolism	69.23	9 of 13
[Ref.: #66794]	methionine metabolism	69.23	18 of 26
[Ref.: #66794]	flavin biosynthesis	66.67	10 of 15
[Ref.: #66794]	d-mannose degradation	66.67	6 of 9
[Ref.: #66794]	acetoin degradation	66.67	2 of 3
[Ref.: #66794]	glycolysis	64.71	11 of 17
[Ref.: #66794]	citric acid cycle	64.29	9 of 14
[Ref.: #66794]	C4 and CAM-carbon fixation	62.5	5 of 8
[Ref.: #66794]	6-hydroxymethyl-dihydropterin diphosphate biosynthesis	62.5	5 of 8
[Ref.: #66794]	ketogluconate metabolism	62.5	5 of 8
[Ref.: #66794]	degradation of sugar alcohols	62.5	10 of 16
[Ref.: #66794]	cysteine metabolism	61.11	11 of 18
[Ref.: #66794]	lipoate biosynthesis	60	3 of 5
[Ref.: #66794]	Entner Doudoroff pathway	60	6 of 10
[Ref.: #66794]	gallate degradation	60	3 of 5
[Ref.: #66794]	arginine metabolism	58.33	14 of 24
[Ref.: #66794]	propanol degradation	57.14	4 of 7
[Ref.: #66794]	nitrate assimilation	55.56	5 of 9
[Ref.: #66794]	tryptophan metabolism	55.26	21 of 38
[Ref.: #66794]	non-pathway related	55.26	21 of 38
[Ref.: #66794]	lysine metabolism	54.76	23 of 42
[Ref.: #66794]	sulfate reduction	53.85	7 of 13
[Ref.: #66794]	urea cycle	53.85	7 of 13
[Ref.: #66794]	3-phenylpropionate degradation	53.33	8 of 15
[Ref.: #66794]	histidine metabolism	51.72	15 of 29
[Ref.: #66794]	oxidative phosphorylation	50.55	46 of 91
[Ref.: #66794]	dTDPLrhamnose biosynthesis	50	4 of 8
[Ref.: #66794]	cyclohexanol degradation	50	2 of 4
[Ref.: #66794]	glycine metabolism	50	5 of 10
[Ref.: #66794]	selenocysteine biosynthesis	50	3 of 6
[Ref.: #66794]	starch degradation	50	5 of 10
[Ref.: #66794]	ethanol fermentation	50	1 of 2
[Ref.: #66794]	glycogen biosynthesis	50	2 of 4
[Ref.: #66794]	glutathione metabolism	50	7 of 14
[Ref.: #66794]	tyrosine metabolism	50	7 of 14
[Ref.: #66794]	polyamine pathway	47.83	11 of 23
[Ref.: #66794]	isoprenoid biosynthesis	46.15	12 of 26
[Ref.: #66794]	phosphatidylethanolamine bioynthesis	46.15	6 of 13
[Ref.: #66794]	androgen and estrogen metabolism	43.75	7 of 16
[Ref.: #66794]	degradation of aromatic, nitrogen containing compounds	41.67	5 of 12
[Ref.: #66794]	vitamin K metabolism	40	2 of 5
[Ref.: #66794]	glycine betaine biosynthesis	40	2 of 5
[Ref.: #66794]	phenol degradation	40	8 of 20
[Ref.: #66794]	factor 420 biosynthesis	40	2 of 5
[Ref.: #66794]	3-chlorocatechol degradation	40	2 of 5
[Ref.: #66794]	arachidonate biosynthesis	40	2 of 5
[Ref.: #66794]	degradation of hexoses	38.89	7 of 18
[Ref.: #66794]	arachidonic acid metabolism	38.89	7 of 18
[Ref.: #66794]	ginsenoside metabolism	37.5	6 of 16
[Ref.: #66794]	pentose phosphate pathway	36.36	4 of 11
[Ref.: #66794]	cyanate degradation	33.33	1 of 3
[Ref.: #66794]	glycolate and glyoxylate degradation	33.33	2 of 6
[Ref.: #66794]	sphingosine metabolism	33.33	2 of 6
[Ref.: #66794]	pantothenate biosynthesis	33.33	2 of 6
[Ref.: #66794]	(5R)-carbapenem carboxylate biosynthesis	33.33	1 of 3
[Ref.: #66794]	methane metabolism	33.33	1 of 3
[Ref.: #66794]	IAA biosynthesis	33.33	1 of 3
[Ref.: #66794]	acetyl CoA biosynthesis	33.33	1 of 3
[Ref.: #66794]	degradation of pentoses	32.14	9 of 28
[Ref.: #66794]	bile acid biosynthesis, neutral pathway	29.41	5 of 17
[Ref.: #66794]	benzoyl-CoA degradation	28.57	2 of 7
[Ref.: #66794]	metabolism of disaccharids	27.27	3 of 11
[Ref.: #66794]	alginate biosynthesis	25	1 of 4
[Ref.: #66794]	butanoate fermentation	25	1 of 4
[Ref.: #66794]	lactate fermentation	25	1 of 4
[Ref.: #66794]	vitamin E metabolism	25	1 of 4
[Ref.: #66794]	carnitine metabolism	25	2 of 8
[Ref.: #66794]	carotenoid biosynthesis	22.73	5 of 22
[Ref.: #66794]	ascorbate metabolism	22.73	5 of 22
[Ref.: #66794]	chlorophyll metabolism	22.22	4 of 18
[Ref.: #66794]	4-hydroxymandelate degradation	22.22	2 of 9
		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.: #24752]	Sample type/isolated from	freshwater
[Ref.: #24752]	Geographic location (country and/or sea, region)	Keum River
[Ref.: #24752]	Country	Republic of Korea
[Ref.: #24752]	Country ISO 3 Code	KOR
[Ref.: #24752]	Continent	Asia

[Ref.: #44050]	Sample type/isolated from	freshwater sample from river
[Ref.: #44050]	Geographic location (country and/or sea, region)	Keum River
[Ref.: #44050]	Country	Republic of Korea
[Ref.: #44050]	Country ISO 3 Code	KOR
[Ref.: #44050]	Continent	Asia
[Ref.: #44050]	Enrichment culture	R2A broth and agar
[Ref.: #44050]	Enrichment culture duration	7 + 7 days
[Ref.: #44050]	Enrichment culture temperature	25 ̊C
[Ref.: #44050]	Isolation/enrichment procedure	sample filtered using a 0.2 µm hydrophilic membrane

[Ref.: #67770]	Sample type/isolated from	Freshwater from Keum River
[Ref.: #67770]	Country	Republic of Korea
[Ref.: #67770]	Country ISO 3 Code	KOR
[Ref.: #67770]	Continent	Asia
* marker position based on {}

Isolation sources categories

#Environmental	#Aquatic	#Freshwater
#Environmental	#Aquatic	#River (Creek)

What are isolation sources categories?

[Ref.: #69479]

Global distribution of 16S sequence KF891388 (>99% sequence identity) for Fluviicoccus keumensis subclade from Microbeatlas

Aquatic Samples	542
Soil Samples	20
Animal Samples	8
Plant Samples	11
Total Samples	581

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

[Ref.: #24752]

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.: #24752]	Fluviicoccus keumensis strain 4DR5 16S ribosomal RNA gene, partial sequence	KF891388	1405	ENA	1435465 tax ID

Genome sequence information:

	Sequence accession description	Seq. accession number	Assembly level	Sequence database	Associated NCBI tax ID
[Ref.: #67770]	Fluviicoccus keumensis DSM 105135	GCA_004217445	scaffold	GenBank	1435465 tax ID
[Ref.: #66792]	Fluviicoccus keumensis strain DSM 105135	1435465.3	wgs	PATRIC	1435465 tax ID	*
[Ref.: #66792]	Fluviicoccus keumensis DSM 105135	2802429732	draft	JGI IMG/M	1435465 tax ID	*

[Ref.: #44050]

GC-content

61.2 mol%

thermal denaturation, midpoint method (Tm)

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: Fluviicoccus keumensis DSM 105135 NCBI: GCA_004217445.1
[Ref.: #69481]	spore-forming	no	100	no

	Trait	Prediction	Confidence in %	In training data
	Predictions from Diaspora project based on: Fluviicoccus keumensis strain DSM 105135 PATRIC: 1435465.3
[Ref.: #69480]	motile	no	50.746	yes
[Ref.: #69480]	gram-positive	no	99.072	yes
[Ref.: #69480]	anaerobic	no	97.328	yes
[Ref.: #69480]	halophile	no	93.212	yes
[Ref.: #69480]	spore-forming	no	96.484	yes
[Ref.: #69480]	thermophile	no	98.44	yes
[Ref.: #69480]	glucose-util	no	81.473	yes
[Ref.: #69480]	aerobic	yes	64.963	no
[Ref.: #69480]	flagellated	no	82.781	yes
[Ref.: #69480]	glucose-ferment	no	92.286	no

Availability in culture collections External links

[Ref.: #24752]

Culture collection no.

DSM 105135, JCM 19370, KCTC 32475

[Ref.: #91241]

SI-ID 401246

Literature:

Topic	Title	Authors	Journal	DOI	Year
Phylogeny	Fluviicoccus keumensis gen. nov., sp. nov., isolated from freshwater.	Kim MK, Kim TW, Kim TS, Joung Y, Han JH, Kim SB	Int J Syst Evol Microbiol	10.1099/ijsem.0.000694	2015	*

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 )

#24752

Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 105135

#44050

Min-Kyeong Kim, Tae-Woon Kim, Tae-Su Kim, Yochan Joung, Ji-Hye Han and Seung Bum Kim: Fluviicoccus keumensis gen. nov., sp. nov., isolated from freshwater. IJSEM 66: 201 - 205 2016 ( DOI 10.1099/ijsem.0.000694 , PubMed 26498187 )

#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 .

#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 )

#91241

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-ID401246.1 )

* These data were automatically processed and therefore are not curated

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Fluviicoccus keumensis DSM 105135

Fluviicoccus keumensis strain DSM 105135

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