Name: Prosthecobacter debontii FC3
Creator: BacDive
License: http://creativecommons.org/licenses/by-nc/4.0/

Strain identifier

BacDive ID: 17209

Type strain:

Species: Prosthecobacter debontii

Strain Designation: FC3

Culture col. no.: DSM 14044, ATCC 700200

Strain history: <- J. Dodsworth; FC3 <- B. P. Hedlund <- J. Lawrie

NCBI tax ID(s): 48467 (species)

SI-ID 43822

ATCC 700200, DSM 14044

Section

Prosthecobacter debontii FC3 is a mesophilic bacterium that was isolated from freshwater pond.

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	*Verrucomicrobiota*
	Class	*Verrucomicrobiia*
	Order	*Verrucomicrobiales*
	Family	*Verrucomicrobiaceae*
	Genus	*Prosthecobacter*
	Species	**Prosthecobacter debontii**
	Full Scientific Name (LPSN)	Prosthecobacter debontii Hedlund et al. 1998

Information on morphological and physiological properties Morphology

[Ref.: #69480]	Gram stain	negative Confidence in %99.991

[Ref.: #69480]	Motility	no Confidence in %93.725

Information on culture and growth conditions Culture and growth conditions

[Ref.: #5225]

Culture medium

MMB MEDIUM (DSMZ Medium 628)

[Ref.: #5225]

Culture medium growth

[Ref.: #5225]

Culture medium link

Medium recipe at MediaDive

[Ref.: #5225]

Culture medium composition

expand / minimize

[Ref.: #5225]

Culture medium

MMB MEDIUM (ATCC 2254) (DSMZ Medium 1728)

[Ref.: #5225]

Culture medium growth

[Ref.: #5225]

Culture medium link

Medium recipe at MediaDive

[Ref.: #5225]

Culture medium composition

expand / minimize

	Temperatures	Kind of temperature		Temperature
[Ref.: #5225]			growth	26 °C
[Ref.: #5225]			growth	25 °C

[Ref.: #5225]

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 %99.993

	Pathway	Enzyme coverage	Annotated reactions
	Pathway annotation	Computationally determined by
[Ref.: #66794]	anapleurotic synthesis of oxalacetate	100	1 of 1
[Ref.: #66794]	ppGpp biosynthesis	100	4 of 4
[Ref.: #66794]	CDP-diacylglycerol biosynthesis	100	2 of 2
[Ref.: #66794]	methylglyoxal degradation	100	5 of 5
[Ref.: #66794]	suberin monomers biosynthesis	100	2 of 2
[Ref.: #66794]	adipate degradation	100	2 of 2
[Ref.: #66794]	sulfopterin metabolism	100	4 of 4
[Ref.: #66794]	UDP-GlcNAc biosynthesis	100	3 of 3
[Ref.: #66794]	biotin biosynthesis	100	4 of 4
[Ref.: #66794]	octane oxidation	100	3 of 3
[Ref.: #66794]	formaldehyde oxidation	100	3 of 3
[Ref.: #66794]	folate polyglutamylation	100	1 of 1
[Ref.: #66794]	palmitate biosynthesis	95.45	21 of 22
[Ref.: #66794]	phenylalanine metabolism	92.31	12 of 13
[Ref.: #66794]	pentose phosphate pathway	90.91	10 of 11
[Ref.: #66794]	starch degradation	90	9 of 10
[Ref.: #66794]	Entner Doudoroff pathway	90	9 of 10
[Ref.: #66794]	chorismate metabolism	88.89	8 of 9
[Ref.: #66794]	valine metabolism	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]	reductive acetyl coenzyme A pathway	85.71	6 of 7
[Ref.: #66794]	tetrahydrofolate metabolism	85.71	12 of 14
[Ref.: #66794]	NAD metabolism	83.33	15 of 18
[Ref.: #66794]	glycolate and glyoxylate degradation	83.33	5 of 6
[Ref.: #66794]	gallate degradation	80	4 of 5
[Ref.: #66794]	glycogen metabolism	80	4 of 5
[Ref.: #66794]	cellulose degradation	80	4 of 5
[Ref.: #66794]	photosynthesis	78.57	11 of 14
[Ref.: #66794]	lipid A biosynthesis	77.78	7 of 9
[Ref.: #66794]	molybdenum cofactor biosynthesis	77.78	7 of 9
[Ref.: #66794]	vitamin B1 metabolism	76.92	10 of 13
[Ref.: #66794]	purine metabolism	76.6	72 of 94
[Ref.: #66794]	glycolysis	76.47	13 of 17
[Ref.: #66794]	coenzyme A metabolism	75	3 of 4
[Ref.: #66794]	degradation of sugar alcohols	75	12 of 16
[Ref.: #66794]	isoleucine metabolism	75	6 of 8
[Ref.: #66794]	ketogluconate metabolism	75	6 of 8
[Ref.: #66794]	acetate fermentation	75	3 of 4
[Ref.: #66794]	CMP-KDO biosynthesis	75	3 of 4
[Ref.: #66794]	glycogen biosynthesis	75	3 of 4
[Ref.: #66794]	lipid metabolism	74.19	23 of 31
[Ref.: #66794]	peptidoglycan biosynthesis	73.33	11 of 15
[Ref.: #66794]	flavin biosynthesis	73.33	11 of 15
[Ref.: #66794]	methionine metabolism	73.08	19 of 26
[Ref.: #66794]	cardiolipin biosynthesis	71.43	5 of 7
[Ref.: #66794]	degradation of pentoses	71.43	20 of 28
[Ref.: #66794]	threonine metabolism	70	7 of 10
[Ref.: #66794]	glutamate and glutamine metabolism	67.86	19 of 28
[Ref.: #66794]	acetyl CoA biosynthesis	66.67	2 of 3
[Ref.: #66794]	cyanate degradation	66.67	2 of 3
[Ref.: #66794]	d-mannose degradation	66.67	6 of 9
[Ref.: #66794]	acetoin degradation	66.67	2 of 3
[Ref.: #66794]	CO2 fixation in Crenarchaeota	66.67	6 of 9
[Ref.: #66794]	serine metabolism	66.67	6 of 9
[Ref.: #66794]	L-lactaldehyde degradation	66.67	2 of 3
[Ref.: #66794]	nitrate assimilation	66.67	6 of 9
[Ref.: #66794]	vitamin B6 metabolism	63.64	7 of 11
[Ref.: #66794]	proline metabolism	63.64	7 of 11
[Ref.: #66794]	6-hydroxymethyl-dihydropterin diphosphate biosynthesis	62.5	5 of 8
[Ref.: #66794]	isoprenoid biosynthesis	61.54	16 of 26
[Ref.: #66794]	phenylpropanoid biosynthesis	61.54	8 of 13
[Ref.: #66794]	leucine metabolism	61.54	8 of 13
[Ref.: #66794]	urea cycle	61.54	8 of 13
[Ref.: #66794]	cysteine metabolism	61.11	11 of 18
[Ref.: #66794]	non-pathway related	60.53	23 of 38
[Ref.: #66794]	metabolism of amino sugars and derivatives	60	3 of 5
[Ref.: #66794]	4-hydroxyphenylacetate degradation	60	6 of 10
[Ref.: #66794]	glycine betaine biosynthesis	60	3 of 5
[Ref.: #66794]	lipoate biosynthesis	60	3 of 5
[Ref.: #66794]	alanine metabolism	58.62	17 of 29
[Ref.: #66794]	histidine metabolism	58.62	17 of 29
[Ref.: #66794]	oxidative phosphorylation	58.24	53 of 91
[Ref.: #66794]	pyrimidine metabolism	57.78	26 of 45
[Ref.: #66794]	ubiquinone biosynthesis	57.14	4 of 7
[Ref.: #66794]	propanol degradation	57.14	4 of 7
[Ref.: #66794]	glutathione metabolism	57.14	8 of 14
[Ref.: #66794]	citric acid cycle	57.14	8 of 14
[Ref.: #66794]	lysine metabolism	57.14	24 of 42
[Ref.: #66794]	aspartate and asparagine metabolism	55.56	5 of 9
[Ref.: #66794]	tryptophan metabolism	55.26	21 of 38
[Ref.: #66794]	metabolism of disaccharids	54.55	6 of 11
[Ref.: #66794]	arginine metabolism	54.17	13 of 24
[Ref.: #66794]	polyamine pathway	52.17	12 of 23
[Ref.: #66794]	kanosamine biosynthesis II	50	1 of 2
[Ref.: #66794]	cis-vaccenate biosynthesis	50	1 of 2
[Ref.: #66794]	pantothenate biosynthesis	50	3 of 6
[Ref.: #66794]	ribulose monophosphate pathway	50	1 of 2
[Ref.: #66794]	cyclohexanol degradation	50	2 of 4
[Ref.: #66794]	heme metabolism	50	7 of 14
[Ref.: #66794]	dTDPLrhamnose biosynthesis	50	4 of 8
[Ref.: #66794]	mannosylglycerate biosynthesis	50	1 of 2
[Ref.: #66794]	ethanol fermentation	50	1 of 2
[Ref.: #66794]	glycine metabolism	50	5 of 10
[Ref.: #66794]	phenylmercury acetate degradation	50	1 of 2
[Ref.: #66794]	degradation of aromatic, nitrogen containing compounds	50	6 of 12
[Ref.: #66794]	quinate degradation	50	1 of 2
[Ref.: #66794]	resorcinol degradation	50	1 of 2
[Ref.: #66794]	alginate biosynthesis	50	2 of 4
[Ref.: #66794]	vitamin E metabolism	50	2 of 4
[Ref.: #66794]	sulfate reduction	46.15	6 of 13
[Ref.: #66794]	ascorbate metabolism	45.45	10 of 22
[Ref.: #66794]	degradation of hexoses	44.44	8 of 18
[Ref.: #66794]	arachidonic acid metabolism	44.44	8 of 18
[Ref.: #66794]	degradation of sugar acids	44	11 of 25
[Ref.: #66794]	tyrosine metabolism	42.86	6 of 14
[Ref.: #66794]	propionate fermentation	40	4 of 10
[Ref.: #66794]	3-chlorocatechol degradation	40	2 of 5
[Ref.: #66794]	myo-inositol biosynthesis	40	4 of 10
[Ref.: #66794]	3-phenylpropionate degradation	40	6 of 15
[Ref.: #66794]	d-xylose degradation	36.36	4 of 11
[Ref.: #66794]	dolichyl-diphosphooligosaccharide biosynthesis	36.36	4 of 11
[Ref.: #66794]	selenocysteine biosynthesis	33.33	2 of 6
[Ref.: #66794]	sphingosine metabolism	33.33	2 of 6
[Ref.: #66794]	enterobactin biosynthesis	33.33	1 of 3
[Ref.: #66794]	IAA biosynthesis	33.33	1 of 3
[Ref.: #66794]	phosphatidylethanolamine bioynthesis	30.77	4 of 13
[Ref.: #66794]	coenzyme M biosynthesis	30	3 of 10
[Ref.: #66794]	phenol degradation	30	6 of 20
[Ref.: #66794]	aclacinomycin biosynthesis	28.57	2 of 7
[Ref.: #66794]	carotenoid biosynthesis	27.27	6 of 22
[Ref.: #66794]	androgen and estrogen metabolism	25	4 of 16
[Ref.: #66794]	butanoate fermentation	25	1 of 4
[Ref.: #66794]	toluene degradation	25	1 of 4
[Ref.: #66794]	lactate fermentation	25	1 of 4
[Ref.: #66794]	vitamin B12 metabolism	23.53	8 of 34
[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.: #5225]	Sample type/isolated from	freshwater pond
[Ref.: #5225]	Geographic location (country and/or sea, region)	WA, Seattle
[Ref.: #5225]	Country	USA
[Ref.: #5225]	Country ISO 3 Code	USA
[Ref.: #5225]	Continent	North America
* marker position based on {}

Isolation sources categories

#Environmental	#Aquatic	#Freshwater
#Environmental	#Aquatic	#Pond (small)

What are isolation sources categories?

[Ref.: #69479]

Global distribution of 16S sequence AJ966882 (>99% sequence identity) for Prosthecobacter debontii subclade from Microbeatlas

Aquatic Samples	2262
Soil Samples	502
Animal Samples	2557
Plant Samples	61
Total Samples	5382

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

[Ref.: #5225]

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.: #20218]	Prosthecobacter debontii 16S rRNA gene (partial), 23S rRNA gene (partial), tRNA-Ala gene, tRNA-Ile gene and ITS1, strain DSM 14044	AJ966882	4881	ENA	48467 tax ID	*

Genome sequence information:

	Sequence accession description	Seq. accession number	Assembly level	Sequence database	Associated NCBI tax ID
[Ref.: #66792]	Prosthecobacter debontii ATCC 700200	GCA_900167535	scaffold	GenBank	48467 tax ID	*
[Ref.: #66792]	Prosthecobacter debontii strain ATCC 700200	48467.8	wgs	PATRIC	48467 tax ID	*
[Ref.: #66792]	Prosthecobacter debontii ATCC 700200	2590828807	draft	JGI IMG/M	48467 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: Prosthecobacter debontii ATCC 700200 NCBI: GCA_900167535.1
[Ref.: #69481]	spore-forming	no	100	no

	Trait	Prediction	Confidence in %	In training data
	Predictions from Diaspora project based on: Prosthecobacter debontii ATCC 700200 NCBI: GCA_900167535.1
[Ref.: #69480]	motile	no	91.219	no
[Ref.: #69480]	flagellated	no	96.056	no
[Ref.: #69480]	gram-positive	no	96.489	no
[Ref.: #69480]	anaerobic	no	98.358	no
[Ref.: #69480]	aerobic	yes	89.819	no
[Ref.: #69480]	halophile	no	87.401	no
[Ref.: #69480]	spore-forming	no	92.404	no
[Ref.: #69480]	thermophile	no	99.597	yes
[Ref.: #69480]	glucose-util	yes	88.109	no
[Ref.: #69480]	glucose-ferment	no	88.908	no

Availability in culture collections External links

[Ref.: #5225]

Culture collection no.

DSM 14044, ATCC 700200

[Ref.: #86208]

SI-ID 43822

Literature:

Topic	Title	Authors	Journal	DOI	Year
Phylogeny	Prosthecobacter algae sp. nov., isolated from activated sludge using algal metabolites.	Lee J, Park B, Woo SG, Lee J, Park J	Int J Syst Evol Microbiol	10.1099/ijs.0.052787-0	2013	*

References

#5225

Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 14044

#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 )

#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 )

#86208

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-ID43822.1 )

* These data were automatically processed and therefore are not curated

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Prosthecobacter debontii ATCC 700200

Prosthecobacter debontii ATCC 700200

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