Name: Filimonas lacunae YT21
Creator: BacDive
License: https://creativecommons.org/licenses/by/4.0/

Strain identifier

BacDive ID: 17763

Type strain:

Species: Filimonas lacunae

Strain Designation: YT21

Culture col. no.: DSM 21054, NBRC 104114

Strain history: <- K. Ueda, Nihon Univ., College of Bioresource Sci., Fujisawa, Japan; YT21 <- Y. Tagami

NCBI tax ID(s): 477680 (species)

SI-ID 400231

DSM 21054

Special Collections

Section

Filimonas lacunae YT21 is an aerobe, Gram-negative, motile bacterium that was isolated from shallow fresh water.

Gram-negative
motile
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	*Chitinophagia*
	Order	*Chitinophagales*
	Family	*Chitinophagaceae*
	Genus	*Filimonas*
	Species	**Filimonas lacunae**
	Full Scientific Name (LPSN)	Filimonas lacunae Shiratori et al. 2009

Information on morphological and physiological properties Morphology

[Ref.: #28958]	Gram stain	negative
[Ref.: #69480]	Gram stain	negative Confidence in %91.139

[Ref.: #28958]	Cell length	17.5 µm

[Ref.: #28958]	Cell width	0.4 µm

[Ref.: #28958]	Motility	yes

[Ref.: #28958]

Pigment production

yes

Information on culture and growth conditions Culture and growth conditions

[Ref.: #15537]

Culture medium

R2A MEDIUM (DSMZ Medium 830)

[Ref.: #15537]

Culture medium growth

[Ref.: #15537]

Culture medium link

Medium recipe at MediaDive

[Ref.: #15537]

Culture medium composition

expand / minimize

		Temperature
[Ref.: #15537]	growth	28 °C
[Ref.: #28958]	growth	10-35 °C
[Ref.: #28958]	optimum	29 °C

	pH	Kind of pH		pH
[Ref.: #28958]			optimum	6
[Ref.: #28958]			growth	05-09

Information on physiology and metabolism Physiology and metabolism

[Ref.: #28958]

Oxygen tolerance

aerobe

[Ref.: #28958]	Ability of spore formation	no
[Ref.: #69481]	Ability of spore formation	no Confidence in %91

	Halophily	Salt	Tested relation		Salt conc.
[Ref.: #28958]		NaCl		growth	<1	%

[Ref.: #28958]

Observation

aggregates in clumps

	Metabolite	Utilization activity	Kind of utilization tested
[Ref.: #28958]	arabinose ChEBI	+	carbon source
[Ref.: #28958]	dextrin ChEBI	+	carbon source
[Ref.: #28958]	esculin ChEBI	+	hydrolysis
[Ref.: #28958]	galactose ChEBI	+	carbon source
[Ref.: #28958]	glucose ChEBI	+	carbon source
[Ref.: #28958]	glycerol ChEBI	+	carbon source
[Ref.: #28958]	maltose ChEBI	+	carbon source
[Ref.: #28958]	mannose ChEBI	+	carbon source
[Ref.: #28958]	urea ChEBI	+	carbon source

	Enzyme	Enzyme activity	EC number
[Ref.: #28958]	acid phosphatase	+	3.1.3.2
[Ref.: #28958]	alkaline phosphatase	+	3.1.3.1
[Ref.: #28958]	catalase	+	1.11.1.6
[Ref.: #28958]	cytochrome oxidase	+	1.9.3.1
[Ref.: #28958]	gelatinase	+
[Ref.: #28958]	urease	+	3.5.1.5

	Pathway	Enzyme coverage	Annotated reactions
	Pathway annotation	Computationally determined by
[Ref.: #66794]	cellulose degradation	100	5 of 5
[Ref.: #66794]	gluconeogenesis	100	8 of 8
[Ref.: #66794]	starch degradation	100	10 of 10
[Ref.: #66794]	ppGpp biosynthesis	100	4 of 4
[Ref.: #66794]	phenylacetate degradation (aerobic)	100	5 of 5
[Ref.: #66794]	glycogen metabolism	100	5 of 5
[Ref.: #66794]	pentose phosphate pathway	100	11 of 11
[Ref.: #66794]	adipate degradation	100	2 of 2
[Ref.: #66794]	cis-vaccenate biosynthesis	100	2 of 2
[Ref.: #66794]	CMP-KDO biosynthesis	100	4 of 4
[Ref.: #66794]	palmitate biosynthesis	100	22 of 22
[Ref.: #66794]	ribulose monophosphate pathway	100	2 of 2
[Ref.: #66794]	formaldehyde oxidation	100	3 of 3
[Ref.: #66794]	threonine metabolism	100	10 of 10
[Ref.: #66794]	biotin biosynthesis	100	4 of 4
[Ref.: #66794]	aerobactin biosynthesis	100	1 of 1
[Ref.: #66794]	folate polyglutamylation	100	1 of 1
[Ref.: #66794]	suberin monomers biosynthesis	100	2 of 2
[Ref.: #66794]	UDP-GlcNAc biosynthesis	100	3 of 3
[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]	methylglyoxal degradation	100	5 of 5
[Ref.: #66794]	vitamin B1 metabolism	92.31	12 of 13
[Ref.: #66794]	propionate fermentation	90	9 of 10
[Ref.: #66794]	valine metabolism	88.89	8 of 9
[Ref.: #66794]	lipid A biosynthesis	88.89	8 of 9
[Ref.: #66794]	NAD metabolism	88.89	16 of 18
[Ref.: #66794]	chorismate metabolism	88.89	8 of 9
[Ref.: #66794]	C4 and CAM-carbon fixation	87.5	7 of 8
[Ref.: #66794]	tetrahydrofolate metabolism	85.71	12 of 14
[Ref.: #66794]	propanol degradation	85.71	6 of 7
[Ref.: #66794]	ubiquinone biosynthesis	85.71	6 of 7
[Ref.: #66794]	photosynthesis	85.71	12 of 14
[Ref.: #66794]	phenylalanine metabolism	84.62	11 of 13
[Ref.: #66794]	lipid metabolism	83.87	26 of 31
[Ref.: #66794]	proline metabolism	81.82	9 of 11
[Ref.: #66794]	Entner Doudoroff pathway	80	8 of 10
[Ref.: #66794]	flavin biosynthesis	80	12 of 15
[Ref.: #66794]	d-mannose degradation	77.78	7 of 9
[Ref.: #66794]	aspartate and asparagine metabolism	77.78	7 of 9
[Ref.: #66794]	molybdenum cofactor biosynthesis	77.78	7 of 9
[Ref.: #66794]	serine metabolism	77.78	7 of 9
[Ref.: #66794]	urea cycle	76.92	10 of 13
[Ref.: #66794]	purine metabolism	76.6	72 of 94
[Ref.: #66794]	6-hydroxymethyl-dihydropterin diphosphate biosynthesis	75	6 of 8
[Ref.: #66794]	ketogluconate metabolism	75	6 of 8
[Ref.: #66794]	glycogen biosynthesis	75	3 of 4
[Ref.: #66794]	acetate fermentation	75	3 of 4
[Ref.: #66794]	isoleucine metabolism	75	6 of 8
[Ref.: #66794]	peptidoglycan biosynthesis	73.33	11 of 15
[Ref.: #66794]	metabolism of disaccharids	72.73	8 of 11
[Ref.: #66794]	alanine metabolism	72.41	21 of 29
[Ref.: #66794]	cardiolipin biosynthesis	71.43	5 of 7
[Ref.: #66794]	citric acid cycle	71.43	10 of 14
[Ref.: #66794]	heme metabolism	71.43	10 of 14
[Ref.: #66794]	arginine metabolism	70.83	17 of 24
[Ref.: #66794]	glycolysis	70.59	12 of 17
[Ref.: #66794]	leucine metabolism	69.23	9 of 13
[Ref.: #66794]	lysine metabolism	69.05	29 of 42
[Ref.: #66794]	pyrimidine metabolism	68.89	31 of 45
[Ref.: #66794]	1,4-dihydroxy-6-naphthoate biosynthesis	66.67	4 of 6
[Ref.: #66794]	CO2 fixation in Crenarchaeota	66.67	6 of 9
[Ref.: #66794]	cyanate degradation	66.67	2 of 3
[Ref.: #66794]	octane oxidation	66.67	2 of 3
[Ref.: #66794]	acetoin degradation	66.67	2 of 3
[Ref.: #66794]	L-lactaldehyde degradation	66.67	2 of 3
[Ref.: #66794]	methionine metabolism	65.38	17 of 26
[Ref.: #66794]	isoprenoid biosynthesis	65.38	17 of 26
[Ref.: #66794]	tyrosine metabolism	64.29	9 of 14
[Ref.: #66794]	glutamate and glutamine metabolism	64.29	18 of 28
[Ref.: #66794]	vitamin B6 metabolism	63.64	7 of 11
[Ref.: #66794]	d-xylose degradation	63.64	7 of 11
[Ref.: #66794]	degradation of sugar alcohols	62.5	10 of 16
[Ref.: #66794]	histidine metabolism	62.07	18 of 29
[Ref.: #66794]	cysteine metabolism	61.11	11 of 18
[Ref.: #66794]	degradation of hexoses	61.11	11 of 18
[Ref.: #66794]	degradation of pentoses	60.71	17 of 28
[Ref.: #66794]	non-pathway related	60.53	23 of 38
[Ref.: #66794]	metabolism of amino sugars and derivatives	60	3 of 5
[Ref.: #66794]	gallate degradation	60	3 of 5
[Ref.: #66794]	coenzyme M biosynthesis	60	6 of 10
[Ref.: #66794]	tryptophan metabolism	57.89	22 of 38
[Ref.: #66794]	glutathione metabolism	57.14	8 of 14
[Ref.: #66794]	degradation of sugar acids	56	14 of 25
[Ref.: #66794]	carotenoid biosynthesis	54.55	12 of 22
[Ref.: #66794]	ascorbate metabolism	54.55	12 of 22
[Ref.: #66794]	dTDPLrhamnose biosynthesis	50	4 of 8
[Ref.: #66794]	degradation of aromatic, nitrogen containing compounds	50	6 of 12
[Ref.: #66794]	cyclohexanol degradation	50	2 of 4
[Ref.: #66794]	androgen and estrogen metabolism	50	8 of 16
[Ref.: #66794]	myo-inositol biosynthesis	50	5 of 10
[Ref.: #66794]	kanosamine biosynthesis II	50	1 of 2
[Ref.: #66794]	selenocysteine biosynthesis	50	3 of 6
[Ref.: #66794]	dolichol and dolichyl phosphate biosynthesis	50	1 of 2
[Ref.: #66794]	phenylmercury acetate degradation	50	1 of 2
[Ref.: #66794]	quinate degradation	50	1 of 2
[Ref.: #66794]	butanoate fermentation	50	2 of 4
[Ref.: #66794]	ethanol fermentation	50	1 of 2
[Ref.: #66794]	phenol degradation	50	10 of 20
[Ref.: #66794]	sulfate reduction	46.15	6 of 13
[Ref.: #66794]	phenylpropanoid biosynthesis	46.15	6 of 13
[Ref.: #66794]	arachidonic acid metabolism	44.44	8 of 18
[Ref.: #66794]	oxidative phosphorylation	43.96	40 of 91
[Ref.: #66794]	reductive acetyl coenzyme A pathway	42.86	3 of 7
[Ref.: #66794]	arachidonate biosynthesis	40	2 of 5
[Ref.: #66794]	glycine betaine biosynthesis	40	2 of 5
[Ref.: #66794]	glycine metabolism	40	4 of 10
[Ref.: #66794]	3-phenylpropionate degradation	40	6 of 15
[Ref.: #66794]	3-chlorocatechol degradation	40	2 of 5
[Ref.: #66794]	O-antigen biosynthesis	40	2 of 5
[Ref.: #66794]	lipoate biosynthesis	40	2 of 5
[Ref.: #66794]	4-hydroxyphenylacetate degradation	40	4 of 10
[Ref.: #66794]	carnitine metabolism	37.5	3 of 8
[Ref.: #66794]	dolichyl-diphosphooligosaccharide biosynthesis	36.36	4 of 11
[Ref.: #66794]	cholesterol biosynthesis	36.36	4 of 11
[Ref.: #66794]	polyamine pathway	34.78	8 of 23
[Ref.: #66794]	acetyl CoA biosynthesis	33.33	1 of 3
[Ref.: #66794]	IAA biosynthesis	33.33	1 of 3
[Ref.: #66794]	(5R)-carbapenem carboxylate biosynthesis	33.33	1 of 3
[Ref.: #66794]	sulfoquinovose degradation	33.33	1 of 3
[Ref.: #66794]	sphingosine metabolism	33.33	2 of 6
[Ref.: #66794]	enterobactin biosynthesis	33.33	1 of 3
[Ref.: #66794]	glycolate and glyoxylate degradation	33.33	2 of 6
[Ref.: #66794]	pantothenate biosynthesis	33.33	2 of 6
[Ref.: #66794]	lactate fermentation	25	1 of 4
[Ref.: #66794]	toluene degradation	25	1 of 4
[Ref.: #66794]	vitamin E metabolism	25	1 of 4
[Ref.: #66794]	alginate biosynthesis	25	1 of 4
[Ref.: #66794]	bile acid biosynthesis, neutral pathway	23.53	4 of 17
[Ref.: #66794]	phosphatidylethanolamine bioynthesis	23.08	3 of 13
[Ref.: #66794]	allantoin 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.: #15537]	Sample type/isolated from	shallow fresh water
[Ref.: #15537]	Country	Japan
[Ref.: #15537]	Country ISO 3 Code	JPN
[Ref.: #15537]	Continent	Asia
* marker position based on {}

Isolation sources categories

#Environmental

#Aquatic

#Freshwater

What are isolation sources categories?

[Ref.: #69479]

Global distribution of 16S sequence AB682148 (>99% sequence identity) for Filimonas lacunae subclade from Microbeatlas

Aquatic Samples	466
Soil Samples	441
Animal Samples	281
Plant Samples	148
Total Samples	1336

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

[Ref.: #15537]

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.: #15537]	Filimonas lacunae gene for 16S rRNA, partial sequence	AB362776	1493	GenBank ENA	477680 tax ID
[Ref.: #20218]	Filimonas lacunae gene for 16S rRNA, partial sequence, strain: NBRC 104114	AB682148	1454	GenBank ENA	477680 tax ID	*

Genome sequence information:

Only first 5 entries are displayed. Click here to see all.

	Sequence accession description	Seq. accession number	Assembly level	Sequence database	Associated NCBI tax ID
[Ref.: #66792]	Filimonas lacunae NBRC 104114	GCA_002355595	complete	GenBank ENA	477680 tax ID	*
[Ref.: #66792]	Filimonas lacunae DSM 21054	GCA_900156765	scaffold	GenBank ENA	477680 tax ID	*
[Ref.: #66792]	Filimonas lacunae strain DSM 21054	477680.4	wgs	PATRIC	477680 tax ID	*
[Ref.: #66792]	Filimonas lacunae strain NBRC 104114	477680.5	complete	PATRIC	477680 tax ID	*
[Ref.: #66792]	Filimonas lacunae DSM 21054	2681813554	draft	JGI IMG/M	477680 tax ID	*
[Ref.: #66792]	Filimonas lacunae NBRC 104114	2802429281	complete	JGI IMG/M	477680 tax ID	*

[Ref.: #15537]

GC-content

45.2 mol%

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: Filimonas lacunae NBRC 104114 NCBI: GCA_002355595.1
[Ref.: #69481]	spore-forming	spore-formingⓘ	no	91	no

	Trait	Model	Prediction	Confidence in %	In training data
	Predictions from Diaspora project based on: Filimonas lacunae NBRC 104114 NCBI: GCA_002355595.1
[Ref.: #69480]	gram-positive	gram-positiveⓘ	no	91.139	no
[Ref.: #69480]	anaerobic	anaerobicⓘ	no	98.93	no
[Ref.: #69480]	aerobic	aerobicⓘ	yes	87.401	yes
[Ref.: #69480]	spore-forming	spore-formingⓘ	no	81.017	yes
[Ref.: #69480]	thermophilic	thermophileⓘ	no	98.481	yes
[Ref.: #69480]	flagellated	motile2+ⓘ	no	86.75	no

Availability in culture collections External links

[Ref.: #15537]

Culture collection no.

DSM 21054, NBRC 104114

[Ref.: #86754]

SI-ID 400231

Literature:

Topic	Title	Authors	Journal	DOI	Year
Phylogeny	Filimonas zeae sp. nov., an endophytic bacterium isolated from maize root.	Gao JL, Sun P, Wang XM, Qiu TL, Lv FY, Yang MM, Lu M, Sun JG	Int J Syst Evol Microbiol	10.1099/ijsem.0.001116	2016	*
Phylogeny	Filimonas lacunae gen. nov., sp. nov., a member of the phylum Bacteroidetes isolated from fresh water.	Shiratori H, Tagami Y, Morishita T, Kamihara Y, Beppu T, Ueda K	Int J Syst Evol Microbiol	10.1099/ijs.0.002618-0	2009	*

References

#15537

Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 21054

#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 )

#20218

Verslyppe, B., De Smet, W., De Baets, B., De Vos, P., Dawyndt P.: StrainInfo introduces electronic passports for microorganisms.. Syst Appl Microbiol. 37: 42 - 50 2014 ( DOI 10.1016/j.syapm.2013.11.002 , PubMed 24321274 )

#28958

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 #25395 (see below)

#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 )

#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 )

#86754

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-ID400231.1 )

#25395

IJSEM 1137 2009 ( DOI 10.1099/ijs.0.002618-0 , PubMed 19406807 )

* These data were automatically processed and therefore are not curated

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Filimonas lacunae NBRC 104114

Filimonas lacunae NBRC 104114

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