Name: Ilyobacter polytropus DSM 2926
Creator: BacDive
License: http://creativecommons.org/licenses/by-nc/4.0/

Strain identifier

BacDive ID: 5777

Type strain:

Species: Ilyobacter polytropus

Culture col. no.: DSM 2926, CuHbu CuHBu1, CuHbu 1

Strain history: <- M. Stieb and B. Schink, CuHBu1

NCBI tax ID(s): 572544 (strain), 167642 (species)

SI-ID 47674

DSM 2926, ATCC 51220

Section

Ilyobacter polytropus DSM 2926 is an anaerobe, mesophilic, Gram-negative bacterium that was isolated from marine mud.

Gram-negative
anaerobe
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	*Fusobacteriota*
	Class	*Fusobacteriia*
	Order	*Fusobacteriales*
	Family	*Fusobacteriaceae*
	Genus	*Ilyobacter*
	Species	**Ilyobacter polytropus**
	Full Scientific Name (LPSN)	Ilyobacter polytropus Stieb and Schink 1985

Information on morphological and physiological properties Morphology

[Ref.: #69480]	Gram stain	negative Confidence in %99.983

Multimedia content

[Ref.: #66793]

Caption:

electron microscopic image

[Ref.: #66793]

Intellectual property rights:

Information on culture and growth conditions Culture and growth conditions

[Ref.: #1252]

Culture medium

ILYOBACTER POLYTROPUS MEDIUM (DSMZ Medium 314)

[Ref.: #1252]

Culture medium growth

[Ref.: #1252]

Culture medium link

Medium recipe at MediaDive

[Ref.: #1252]

Culture medium composition

expand / minimize

	Temperatures	Kind of temperature		Temperature
[Ref.: #1252]			growth	30 °C

[Ref.: #1252]

Temperature range

mesophilic

Information on physiology and metabolism Physiology and metabolism

[Ref.: #1252]	Oxygen tolerance	anaerobe
[Ref.: #69480]	Oxygen tolerance	anaerobe Confidence in %97.781

[Ref.: #69480]

Ability of spore formation

no Confidence in %99.999

	Pathway	Enzyme coverage	Annotated reactions
	Pathway annotation	Computationally determined by
[Ref.: #66794]	gluconeogenesis	100	8 of 8
[Ref.: #66794]	sulfopterin metabolism	100	4 of 4
[Ref.: #66794]	cardiolipin biosynthesis	100	7 of 7
[Ref.: #66794]	C4 and CAM-carbon fixation	100	8 of 8
[Ref.: #66794]	biotin biosynthesis	100	4 of 4
[Ref.: #66794]	L-lactaldehyde degradation	100	3 of 3
[Ref.: #66794]	coenzyme A metabolism	100	4 of 4
[Ref.: #66794]	d-mannose degradation	100	9 of 9
[Ref.: #66794]	adipate degradation	100	2 of 2
[Ref.: #66794]	palmitate biosynthesis	100	22 of 22
[Ref.: #66794]	CDP-diacylglycerol biosynthesis	100	2 of 2
[Ref.: #66794]	anapleurotic synthesis of oxalacetate	100	1 of 1
[Ref.: #66794]	cis-vaccenate biosynthesis	100	2 of 2
[Ref.: #66794]	folate polyglutamylation	100	1 of 1
[Ref.: #66794]	methylglyoxal degradation	100	5 of 5
[Ref.: #66794]	ppGpp biosynthesis	100	4 of 4
[Ref.: #66794]	suberin monomers biosynthesis	100	2 of 2
[Ref.: #66794]	isoleucine metabolism	100	8 of 8
[Ref.: #66794]	UDP-GlcNAc biosynthesis	100	3 of 3
[Ref.: #66794]	alanine metabolism	93.1	27 of 29
[Ref.: #66794]	glutamate and glutamine metabolism	92.86	26 of 28
[Ref.: #66794]	citric acid cycle	92.86	13 of 14
[Ref.: #66794]	tetrahydrofolate metabolism	92.86	13 of 14
[Ref.: #66794]	pentose phosphate pathway	90.91	10 of 11
[Ref.: #66794]	threonine metabolism	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]	chorismate metabolism	88.89	8 of 9
[Ref.: #66794]	serine metabolism	88.89	8 of 9
[Ref.: #66794]	aspartate and asparagine metabolism	88.89	8 of 9
[Ref.: #66794]	propanol degradation	85.71	6 of 7
[Ref.: #66794]	vitamin B12 metabolism	85.29	29 of 34
[Ref.: #66794]	vitamin B1 metabolism	84.62	11 of 13
[Ref.: #66794]	pyrimidine metabolism	84.44	38 of 45
[Ref.: #66794]	purine metabolism	84.04	79 of 94
[Ref.: #66794]	myo-inositol biosynthesis	80	8 of 10
[Ref.: #66794]	peptidoglycan biosynthesis	80	12 of 15
[Ref.: #66794]	propionate fermentation	80	8 of 10
[Ref.: #66794]	starch degradation	80	8 of 10
[Ref.: #66794]	hydrogen production	80	4 of 5
[Ref.: #66794]	photosynthesis	78.57	11 of 14
[Ref.: #66794]	molybdenum cofactor biosynthesis	77.78	7 of 9
[Ref.: #66794]	NAD metabolism	77.78	14 of 18
[Ref.: #66794]	CO2 fixation in Crenarchaeota	77.78	7 of 9
[Ref.: #66794]	phenylalanine metabolism	76.92	10 of 13
[Ref.: #66794]	glycogen biosynthesis	75	3 of 4
[Ref.: #66794]	acetate fermentation	75	3 of 4
[Ref.: #66794]	butanoate fermentation	75	3 of 4
[Ref.: #66794]	CMP-KDO biosynthesis	75	3 of 4
[Ref.: #66794]	flavin biosynthesis	73.33	11 of 15
[Ref.: #66794]	reductive acetyl coenzyme A pathway	71.43	5 of 7
[Ref.: #66794]	glycolysis	70.59	12 of 17
[Ref.: #66794]	Entner Doudoroff pathway	70	7 of 10
[Ref.: #66794]	urea cycle	69.23	9 of 13
[Ref.: #66794]	methionine metabolism	69.23	18 of 26
[Ref.: #66794]	degradation of sugar alcohols	68.75	11 of 16
[Ref.: #66794]	glycolate and glyoxylate degradation	66.67	4 of 6
[Ref.: #66794]	acetoin degradation	66.67	2 of 3
[Ref.: #66794]	octane oxidation	66.67	2 of 3
[Ref.: #66794]	selenocysteine biosynthesis	66.67	4 of 6
[Ref.: #66794]	methane metabolism	66.67	2 of 3
[Ref.: #66794]	cyanate degradation	66.67	2 of 3
[Ref.: #66794]	formaldehyde oxidation	66.67	2 of 3
[Ref.: #66794]	heme metabolism	64.29	9 of 14
[Ref.: #66794]	oxidative phosphorylation	62.64	57 of 91
[Ref.: #66794]	6-hydroxymethyl-dihydropterin diphosphate biosynthesis	62.5	5 of 8
[Ref.: #66794]	leucine metabolism	61.54	8 of 13
[Ref.: #66794]	cysteine metabolism	61.11	11 of 18
[Ref.: #66794]	glycogen metabolism	60	3 of 5
[Ref.: #66794]	factor 420 biosynthesis	60	3 of 5
[Ref.: #66794]	lipoate biosynthesis	60	3 of 5
[Ref.: #66794]	lipid metabolism	58.06	18 of 31
[Ref.: #66794]	non-pathway related	57.89	22 of 38
[Ref.: #66794]	glutathione metabolism	57.14	8 of 14
[Ref.: #66794]	lysine metabolism	57.14	24 of 42
[Ref.: #66794]	tryptophan metabolism	55.26	21 of 38
[Ref.: #66794]	histidine metabolism	55.17	16 of 29
[Ref.: #66794]	proline metabolism	54.55	6 of 11
[Ref.: #66794]	arginine metabolism	54.17	13 of 24
[Ref.: #66794]	aminopropanol phosphate biosynthesis	50	1 of 2
[Ref.: #66794]	ketogluconate metabolism	50	4 of 8
[Ref.: #66794]	ribulose monophosphate pathway	50	1 of 2
[Ref.: #66794]	phenylmercury acetate degradation	50	1 of 2
[Ref.: #66794]	dTDPLrhamnose biosynthesis	50	4 of 8
[Ref.: #66794]	ethanol fermentation	50	1 of 2
[Ref.: #66794]	glycine metabolism	50	5 of 10
[Ref.: #66794]	pantothenate biosynthesis	50	3 of 6
[Ref.: #66794]	degradation of aromatic, nitrogen containing compounds	50	6 of 12
[Ref.: #66794]	toluene degradation	50	2 of 4
[Ref.: #66794]	isoprenoid biosynthesis	50	13 of 26
[Ref.: #66794]	quinate degradation	50	1 of 2
[Ref.: #66794]	degradation of sugar acids	48	12 of 25
[Ref.: #66794]	degradation of pentoses	46.43	13 of 28
[Ref.: #66794]	sulfate reduction	46.15	6 of 13
[Ref.: #66794]	vitamin B6 metabolism	45.45	5 of 11
[Ref.: #66794]	metabolism of disaccharids	45.45	5 of 11
[Ref.: #66794]	nitrate assimilation	44.44	4 of 9
[Ref.: #66794]	tyrosine metabolism	42.86	6 of 14
[Ref.: #66794]	ubiquinone biosynthesis	42.86	3 of 7
[Ref.: #66794]	metabolism of amino sugars and derivatives	40	2 of 5
[Ref.: #66794]	O-antigen biosynthesis	40	2 of 5
[Ref.: #66794]	3-chlorocatechol degradation	40	2 of 5
[Ref.: #66794]	arachidonate biosynthesis	40	2 of 5
[Ref.: #66794]	ethylmalonyl-CoA pathway	40	2 of 5
[Ref.: #66794]	gallate degradation	40	2 of 5
[Ref.: #66794]	polyamine pathway	39.13	9 of 23
[Ref.: #66794]	degradation of hexoses	38.89	7 of 18
[Ref.: #66794]	phosphatidylethanolamine bioynthesis	38.46	5 of 13
[Ref.: #66794]	phenylpropanoid biosynthesis	38.46	5 of 13
[Ref.: #66794]	d-xylose degradation	36.36	4 of 11
[Ref.: #66794]	IAA biosynthesis	33.33	1 of 3
[Ref.: #66794]	acetyl CoA biosynthesis	33.33	1 of 3
[Ref.: #66794]	4-hydroxyphenylacetate degradation	30	3 of 10
[Ref.: #66794]	coenzyme M biosynthesis	30	3 of 10
[Ref.: #66794]	benzoyl-CoA degradation	28.57	2 of 7
[Ref.: #66794]	ascorbate metabolism	27.27	6 of 22
[Ref.: #66794]	phenol degradation	25	5 of 20
[Ref.: #66794]	cyclohexanol degradation	25	1 of 4
[Ref.: #66794]	lactate fermentation	25	1 of 4
[Ref.: #66794]	vitamin E metabolism	25	1 of 4
		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.: #1252]	Sample type/isolated from	marine mud
[Ref.: #1252]	Geographic location (country and/or sea, region)	Cuxhaven
[Ref.: #1252]	Country	Germany
[Ref.: #1252]	Country ISO 3 Code	DEU
[Ref.: #1252]	Continent	Europe
* marker position based on {}

Isolation sources categories

#Environmental	#Aquatic	#Marine
#Environmental	#Terrestrial	#Mud (Sludge)
#Environmental	#Aquatic	#Sediment

What are isolation sources categories?

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

[Ref.: #1252]

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.: #1252]	Ilyobacter polytropus 16S rRNA gene, DSM 2926 T	AJ307981	1516	ENA	572544 tax ID

Genome sequence information:

	Sequence accession description	Seq. accession number	Assembly level	Sequence database	Associated NCBI tax ID
[Ref.: #66792]	Ilyobacter polytropus DSM 2926	GCA_000165505	complete	GenBank	572544 tax ID	*
[Ref.: #66792]	Ilyobacter polytropus DSM 2926	572544.3	complete	PATRIC	572544 tax ID	*
[Ref.: #66792]	Ilyobacter polytropus DSM 2926	572544.12	plasmid	PATRIC	572544 tax ID	*
[Ref.: #66792]	Ilyobacter polytropus DSM 2926	572544.11	plasmid	PATRIC	572544 tax ID	*
[Ref.: #66792]	Ilyobacter polytropus CuHBu1, DSM 2926	649633056	complete	JGI IMG/M	572544 tax ID	*

[Ref.: #1252]

GC-content

32.2 mol%

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: Ilyobacter polytropus DSM 2926 DSM 2926 NCBI: GCA_000165505.1
[Ref.: #69481]	spore-forming	yes	53	no

	Trait	Prediction	Confidence in %	In training data
	Predictions from Diaspora project based on: Ilyobacter polytropus DSM 2926 DSM 2926 NCBI: GCA_000165505.1
[Ref.: #69480]	motile	no	88.675	no
[Ref.: #69480]	flagellated	no	93.761	no
[Ref.: #69480]	gram-positive	no	92.314	no
[Ref.: #69480]	anaerobic	yes	98.449	yes
[Ref.: #69480]	aerobic	no	94.949	no
[Ref.: #69480]	halophile	no	83.764	no
[Ref.: #69480]	spore-forming	no	93.189	no
[Ref.: #69480]	thermophile	no	65.373	no
[Ref.: #69480]	glucose-util	yes	88.195	no
[Ref.: #69480]	glucose-ferment	no	58.045	no

Availability in culture collections External links

[Ref.: #1252]

Culture collection no.

DSM 2926, CuHbu CuHBu1, CuHbu 1

[Ref.: #75256]

SI-ID 47674

Literature:

Topic	Title	Authors	Journal	DOI	Year
Genetics	Complete genome sequence of Ilyobacter polytropus type strain (CuHbu1).	Sikorski J, Chertkov O, Lapidus A, Nolan M, Lucas S, Del Rio TG, Tice H, Cheng JF, Tapia R, Han C, Goodwin L, Pitluck S, Liolios K, Ivanova N, Mavromatis K, Mikhailova N, Pati A, Chen A, Palaniappan K, Land M, Hauser L, Chang YJ, Jeffries CD, Brambilla E, Yasawong M, Rohde M, Pukall R, Spring S, Goker M, Woyke T, Bristow J, Eisen JA, Markowitz V, Hugenholtz P, Kyrpides NC, Klenk HP	Stand Genomic Sci	10.4056/sigs.1273360	2010	*

References

#1252

Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 2926

#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 )

#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) .

#66793

Mukherjee et al.: GEBA: 1,003 reference genomes of bacterial and archaeal isolates expand coverage of the tree of life. 35: 676 - 683 2017 ( DOI 10.1038/nbt.3886 , PubMed 28604660 )

#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 )

#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 )

#75256

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-ID47674.1 )

* These data were automatically processed and therefore are not curated

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Ilyobacter polytropus DSM 2926 DSM 2926

Ilyobacter polytropus DSM 2926 DSM 2926

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