Name: Flavobacterium urocaniciphilum DSM 27078
Creator: BacDive
License: http://creativecommons.org/licenses/by-nc/4.0/

Strain identifier

BacDive ID: 24026

Type strain:

Species: Flavobacterium urocaniciphilum

Culture col. no.: DSM 27078, JCM 19142, YIT 12746, BCRC 81228, NRIC 0940

Strain history: D. Fujii strain 95 (=YIT 12746).

NCBI tax ID(s): 1299341 (species)

SI-ID 407649

DSM 27078

Section

Flavobacterium urocaniciphilum DSM 27078 is a mesophilic, Gram-negative bacterium that was isolated from sludge from wastewater treatment plant associated with a facility, that produces a fermented milk drink.

Gram-negative
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 urocaniciphilum**
	Full Scientific Name (LPSN)	Flavobacterium urocaniciphilum Fujii et al. 2014

Information on morphological and physiological properties Morphology

[Ref.: #69480]	Gram stain	negative Confidence in %99.997

Information on culture and growth conditions Culture and growth conditions

[Ref.: #20573]

Culture medium

R2A MEDIUM (DSMZ Medium 830)

[Ref.: #20573]

Culture medium growth

[Ref.: #20573]

Culture medium link

Medium recipe at MediaDive

[Ref.: #20573]

Culture medium composition

expand / minimize

	Temperatures	Kind of temperature		Temperature
[Ref.: #20573]			growth	25 °C
[Ref.: #67770]			growth	25 °C

[Ref.: #20573]	Temperature range	mesophilic
[Ref.: #67770]	Temperature range	mesophilic

Information on physiology and metabolism Physiology and metabolism

[Ref.: #69481]	Ability of spore formation	no Confidence in %100
[Ref.: #69480]	Ability of spore formation	no Confidence in %99.998

[Ref.: #67770]

Observation

quinones: MK-6

	Pathway	Enzyme coverage	Annotated reactions
	Pathway annotation	Computationally determined by
[Ref.: #66794]	adipate degradation	100	2 of 2
[Ref.: #66794]	coenzyme A metabolism	100	4 of 4
[Ref.: #66794]	sulfopterin metabolism	100	4 of 4
[Ref.: #66794]	biotin biosynthesis	100	4 of 4
[Ref.: #66794]	CDP-diacylglycerol biosynthesis	100	2 of 2
[Ref.: #66794]	vitamin K metabolism	100	5 of 5
[Ref.: #66794]	UDP-GlcNAc biosynthesis	100	3 of 3
[Ref.: #66794]	cis-vaccenate biosynthesis	100	2 of 2
[Ref.: #66794]	suberin monomers biosynthesis	100	2 of 2
[Ref.: #66794]	anapleurotic synthesis of oxalacetate	100	1 of 1
[Ref.: #66794]	palmitate biosynthesis	100	22 of 22
[Ref.: #66794]	ppGpp biosynthesis	100	4 of 4
[Ref.: #66794]	folate polyglutamylation	100	1 of 1
[Ref.: #66794]	chorismate metabolism	88.89	8 of 9
[Ref.: #66794]	lipid A biosynthesis	88.89	8 of 9
[Ref.: #66794]	gluconeogenesis	87.5	7 of 8
[Ref.: #66794]	C4 and CAM-carbon fixation	87.5	7 of 8
[Ref.: #66794]	tetrahydrofolate metabolism	85.71	12 of 14
[Ref.: #66794]	vitamin B1 metabolism	84.62	11 of 13
[Ref.: #66794]	methylglyoxal degradation	80	4 of 5
[Ref.: #66794]	peptidoglycan biosynthesis	80	12 of 15
[Ref.: #66794]	cellulose degradation	80	4 of 5
[Ref.: #66794]	heme metabolism	78.57	11 of 14
[Ref.: #66794]	photosynthesis	78.57	11 of 14
[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]	acetate fermentation	75	3 of 4
[Ref.: #66794]	glycogen biosynthesis	75	3 of 4
[Ref.: #66794]	vitamin B6 metabolism	72.73	8 of 11
[Ref.: #66794]	propanol degradation	71.43	5 of 7
[Ref.: #66794]	citric acid cycle	71.43	10 of 14
[Ref.: #66794]	tryptophan metabolism	71.05	27 of 38
[Ref.: #66794]	propionate fermentation	70	7 of 10
[Ref.: #66794]	leucine metabolism	69.23	9 of 13
[Ref.: #66794]	alanine metabolism	68.97	20 of 29
[Ref.: #66794]	lipid metabolism	67.74	21 of 31
[Ref.: #66794]	d-mannose degradation	66.67	6 of 9
[Ref.: #66794]	flavin biosynthesis	66.67	10 of 15
[Ref.: #66794]	acetoin degradation	66.67	2 of 3
[Ref.: #66794]	formaldehyde oxidation	66.67	2 of 3
[Ref.: #66794]	NAD metabolism	66.67	12 of 18
[Ref.: #66794]	L-lactaldehyde degradation	66.67	2 of 3
[Ref.: #66794]	histidine metabolism	65.52	19 of 29
[Ref.: #66794]	pyrimidine metabolism	64.44	29 of 45
[Ref.: #66794]	lysine metabolism	64.29	27 of 42
[Ref.: #66794]	glutamate and glutamine metabolism	64.29	18 of 28
[Ref.: #66794]	6-hydroxymethyl-dihydropterin diphosphate biosynthesis	62.5	5 of 8
[Ref.: #66794]	purine metabolism	61.7	58 of 94
[Ref.: #66794]	non-pathway related	60.53	23 of 38
[Ref.: #66794]	arachidonate biosynthesis	60	3 of 5
[Ref.: #66794]	glycine betaine biosynthesis	60	3 of 5
[Ref.: #66794]	threonine metabolism	60	6 of 10
[Ref.: #66794]	glycolysis	58.82	10 of 17
[Ref.: #66794]	degradation of aromatic, nitrogen containing compounds	58.33	7 of 12
[Ref.: #66794]	mevalonate metabolism	57.14	4 of 7
[Ref.: #66794]	ubiquinone biosynthesis	57.14	4 of 7
[Ref.: #66794]	cysteine metabolism	55.56	10 of 18
[Ref.: #66794]	methionine metabolism	53.85	14 of 26
[Ref.: #66794]	phenylalanine metabolism	53.85	7 of 13
[Ref.: #66794]	butanoate fermentation	50	2 of 4
[Ref.: #66794]	isoprenoid biosynthesis	50	13 of 26
[Ref.: #66794]	kanosamine biosynthesis II	50	1 of 2
[Ref.: #66794]	isoleucine metabolism	50	4 of 8
[Ref.: #66794]	degradation of sugar alcohols	50	8 of 16
[Ref.: #66794]	starch degradation	50	5 of 10
[Ref.: #66794]	dTDPLrhamnose biosynthesis	50	4 of 8
[Ref.: #66794]	quinate degradation	50	1 of 2
[Ref.: #66794]	ketogluconate metabolism	50	4 of 8
[Ref.: #66794]	ethanol fermentation	50	1 of 2
[Ref.: #66794]	tyrosine metabolism	50	7 of 14
[Ref.: #66794]	carotenoid biosynthesis	45.45	10 of 22
[Ref.: #66794]	proline metabolism	45.45	5 of 11
[Ref.: #66794]	cardiolipin biosynthesis	42.86	3 of 7
[Ref.: #66794]	reductive acetyl coenzyme A pathway	42.86	3 of 7
[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]	oxidative phosphorylation	39.56	36 of 91
[Ref.: #66794]	sulfate reduction	38.46	5 of 13
[Ref.: #66794]	pentose phosphate pathway	36.36	4 of 11
[Ref.: #66794]	dolichyl-diphosphooligosaccharide biosynthesis	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]	3-phenylpropionate degradation	33.33	5 of 15
[Ref.: #66794]	glycolate and glyoxylate degradation	33.33	2 of 6
[Ref.: #66794]	sphingosine metabolism	33.33	2 of 6
[Ref.: #66794]	cyanate degradation	33.33	1 of 3
[Ref.: #66794]	acetyl CoA biosynthesis	33.33	1 of 3
[Ref.: #66794]	molybdenum cofactor biosynthesis	33.33	3 of 9
[Ref.: #66794]	IAA biosynthesis	33.33	1 of 3
[Ref.: #66794]	enterobactin biosynthesis	33.33	1 of 3
[Ref.: #66794]	octane oxidation	33.33	1 of 3
[Ref.: #66794]	selenocysteine biosynthesis	33.33	2 of 6
[Ref.: #66794]	arginine metabolism	33.33	8 of 24
[Ref.: #66794]	valine metabolism	33.33	3 of 9
[Ref.: #66794]	vitamin B12 metabolism	32.35	11 of 34
[Ref.: #66794]	ascorbate metabolism	31.82	7 of 22
[Ref.: #66794]	phenylpropanoid biosynthesis	30.77	4 of 13
[Ref.: #66794]	polyamine pathway	30.43	7 of 23
[Ref.: #66794]	Entner Doudoroff pathway	30	3 of 10
[Ref.: #66794]	degradation of hexoses	27.78	5 of 18
[Ref.: #66794]	metabolism of disaccharids	27.27	3 of 11
[Ref.: #66794]	degradation of pentoses	25	7 of 28
[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]	androgen and estrogen metabolism	25	4 of 16
[Ref.: #66794]	carnitine metabolism	25	2 of 8
[Ref.: #66794]	urea cycle	23.08	3 of 13
[Ref.: #66794]	nitrate assimilation	22.22	2 of 9
[Ref.: #66794]	arachidonic acid metabolism	22.22	4 of 18
[Ref.: #66794]	glutathione metabolism	21.43	3 of 14
		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.: #20573]	Sample type/isolated from	sludge from wastewater treatment plant associated with a facility, that produces a fermented milk drink
[Ref.: #20573]	Geographic location (country and/or sea, region)	Saga Prefecture, Yakult Honsha Co., Ltd.
[Ref.: #20573]	Country	Japan
[Ref.: #20573]	Country ISO 3 Code	JPN
[Ref.: #20573]	Continent	Asia

[Ref.: #67770]	Sample type/isolated from	Sludge from a wastewater treatment plant in Saga Pref.
[Ref.: #67770]	Country	Japan
[Ref.: #67770]	Country ISO 3 Code	JPN
[Ref.: #67770]	Continent	Asia
* marker position based on {}

Isolation sources categories

#Engineered	#Food production	-
#Engineered	#Waste	#Water treatment plant
#Environmental	#Terrestrial	#Mud (Sludge)
#Host Body Product	#Fluids	#Milk

What are isolation sources categories?

[Ref.: #69479]

Global distribution of 16S sequence AB795015 (>99% sequence identity) for Flavobacterium urocaniciphilum subclade from Microbeatlas

Aquatic Samples	1375
Soil Samples	418
Animal Samples	211
Plant Samples	79
Total Samples	2083

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

[Ref.: #20573]

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.: #20573]	Flavobacterium urocaniciphilum gene for 16S ribosomal RNA, partial sequence	AB795015	1468	ENA	1299341 tax ID

Genome sequence information:

	Sequence accession description	Seq. accession number	Assembly level	Sequence database	Associated NCBI tax ID
[Ref.: #67770]	Flavobacterium urocaniciphilum DSM 27078	GCA_900110615	contig	GenBank	1299341 tax ID
[Ref.: #66792]	Flavobacterium urocaniciphilum strain DSM 27078	1299341.3	wgs	PATRIC	1299341 tax ID	*
[Ref.: #66792]	Flavobacterium urocaniciphilum DSM 27078	2693429864	draft	JGI IMG/M	1299341 tax ID	*

[Ref.: #20573]

GC-content

30.9 mol%

high performance liquid chromatography (HPLC)

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 urocaniciphilum strain DSM 27078 PATRIC: 1299341.3
[Ref.: #69481]	spore-forming	no	100	no

	Trait	Prediction	Confidence in %	In training data
	Predictions from Diaspora project based on: Flavobacterium urocaniciphilum strain DSM 27078 PATRIC: 1299341.3
[Ref.: #69480]	motile	no	89.053	no
[Ref.: #69480]	gram-positive	no	99.229	no
[Ref.: #69480]	anaerobic	no	99.198	no
[Ref.: #69480]	aerobic	yes	89.521	no
[Ref.: #69480]	halophile	no	97.096	no
[Ref.: #69480]	spore-forming	no	95.58	no
[Ref.: #69480]	thermophile	no	98.647	no
[Ref.: #69480]	glucose-util	yes	75.136	no
[Ref.: #69480]	flagellated	no	95.933	no
[Ref.: #69480]	glucose-ferment	no	93.437	no

Availability in culture collections External links

[Ref.: #20573]

Culture collection no.

DSM 27078, JCM 19142, YIT 12746, BCRC 81228, NRIC 0940

[Ref.: #88000]

SI-ID 407649

Literature:

Topic	Title	Authors	Journal	DOI	Year
Phylogeny	Flavobacterium sediminis sp. nov., a starch-degrading bacterium isolated from tidal flat sediment.	Bae SS, Kim MR, Jung Y, Yang SH, Kwon KK, Baek K	Int J Syst Evol Microbiol	10.1099/ijsem.0.003081	2018	*
Phylogeny	Flavobacterium maris sp. nov. isolated from shallow sediments of the Sea of Japan.	Romanenko LA, Tanaka N, Svetashev VI, Kurilenko VV, Mikhailov VV	Arch Microbiol	10.1007/s00203-015-1128-x	2015	*
Phylogeny	Flavobacterium longum sp. nov. and Flavobacterium urocaniciphilum sp. nov., isolated from a wastewater treatment plant, and emended descriptions of Flavobacterium caeni and Flavobacterium terrigena.	Fujii D, Nagai F, Watanabe Y, Shirasawa Y	Int J Syst Evol Microbiol	10.1099/ijs.0.054312-0	2014	*

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 )

#20573

Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 27078

#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 )

#88000

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-ID407649.1 )

* These data were automatically processed and therefore are not curated

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Flavobacterium urocaniciphilum strain DSM 27078

Flavobacterium urocaniciphilum strain DSM 27078

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