Name: Desulfomonile tiedjei DCB-1
Creator: BacDive
License: http://creativecommons.org/licenses/by-nc/4.0/

Strain identifier

BacDive ID: 16666

Type strain:

Species: Desulfomonile tiedjei

Strain Designation: DCB-1

Culture col. no.: DSM 6799, ATCC 49306

Strain history: <- ATCC <- J.M. Tiedje, DCB-1

NCBI tax ID(s): 706587 (strain), 2358 (species)

SI-ID 42414

ATCC 49306, DSM 6799

Section

Desulfomonile tiedjei DCB-1 is an anaerobe, mesophilic, Gram-negative bacterium that was isolated from sewage sludge.

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	*Pseudomonadota*
	Class	*Deltaproteobacteria*
	Order	*Syntrophobacterales*
	Family	*Syntrophaceae*
	Genus	*Desulfomonile*
	Species	**Desulfomonile tiedjei**
	Full Scientific Name (LPSN)	Desulfomonile tiedjei De Weerd et al. 1991

Information on morphological and physiological properties Morphology

[Ref.: #69480]	Gram stain	negative Confidence in %99.14

[Ref.: #2827]

Incubation period

3-7 days

Multimedia content

[Ref.: #66793]

Caption:

electron microscopic image

[Ref.: #66793]

Intellectual property rights:

Information on culture and growth conditions Culture and growth conditions

[Ref.: #2827]

Culture medium

DESULFOMONILE MEDIUM (DSMZ Medium 521)

[Ref.: #2827]

Culture medium growth

[Ref.: #2827]

Culture medium link

Medium recipe at MediaDive

[Ref.: #2827]

Culture medium composition

expand / minimize

	Temperatures	Kind of temperature		Temperature
[Ref.: #2827]			growth	37 °C

[Ref.: #2827]

Temperature range

mesophilic

Information on physiology and metabolism Physiology and metabolism

[Ref.: #2827]	Oxygen tolerance	anaerobe
[Ref.: #69480]	Oxygen tolerance	anaerobe Confidence in %97.931

[Ref.: #69481]	Ability of spore formation	no Confidence in %99
[Ref.: #69480]	Ability of spore formation	no Confidence in %98.396

	Pathway	Enzyme coverage	Annotated reactions
	Pathway annotation	Computationally determined by
[Ref.: #66794]	sulfopterin metabolism	100	4 of 4
[Ref.: #66794]	acetoin degradation	100	3 of 3
[Ref.: #66794]	cis-vaccenate biosynthesis	100	2 of 2
[Ref.: #66794]	CO2 fixation in Crenarchaeota	100	9 of 9
[Ref.: #66794]	UDP-GlcNAc biosynthesis	100	3 of 3
[Ref.: #66794]	CDP-diacylglycerol biosynthesis	100	2 of 2
[Ref.: #66794]	biotin biosynthesis	100	4 of 4
[Ref.: #66794]	glycolate and glyoxylate degradation	100	6 of 6
[Ref.: #66794]	coenzyme A metabolism	100	4 of 4
[Ref.: #66794]	glycogen metabolism	100	5 of 5
[Ref.: #66794]	formaldehyde oxidation	100	3 of 3
[Ref.: #66794]	suberin monomers biosynthesis	100	2 of 2
[Ref.: #66794]	glycine betaine biosynthesis	100	5 of 5
[Ref.: #66794]	palmitate biosynthesis	100	22 of 22
[Ref.: #66794]	hydrogen production	100	5 of 5
[Ref.: #66794]	reductive acetyl coenzyme A pathway	100	7 of 7
[Ref.: #66794]	folate polyglutamylation	100	1 of 1
[Ref.: #66794]	methylglyoxal degradation	100	5 of 5
[Ref.: #66794]	adipate degradation	100	2 of 2
[Ref.: #66794]	anapleurotic synthesis of oxalacetate	100	1 of 1
[Ref.: #66794]	cyanate degradation	100	3 of 3
[Ref.: #66794]	valine metabolism	100	9 of 9
[Ref.: #66794]	CMP-KDO biosynthesis	100	4 of 4
[Ref.: #66794]	starch degradation	90	9 of 10
[Ref.: #66794]	propionate fermentation	90	9 of 10
[Ref.: #66794]	lipid A biosynthesis	88.89	8 of 9
[Ref.: #66794]	chorismate metabolism	88.89	8 of 9
[Ref.: #66794]	aspartate and asparagine metabolism	88.89	8 of 9
[Ref.: #66794]	nitrate assimilation	88.89	8 of 9
[Ref.: #66794]	molybdenum cofactor biosynthesis	88.89	8 of 9
[Ref.: #66794]	vitamin B12 metabolism	88.24	30 of 34
[Ref.: #66794]	isoleucine metabolism	87.5	7 of 8
[Ref.: #66794]	alanine metabolism	86.21	25 of 29
[Ref.: #66794]	propanol degradation	85.71	6 of 7
[Ref.: #66794]	benzoyl-CoA degradation	85.71	6 of 7
[Ref.: #66794]	ubiquinone biosynthesis	85.71	6 of 7
[Ref.: #66794]	leucine metabolism	84.62	11 of 13
[Ref.: #66794]	vitamin B1 metabolism	84.62	11 of 13
[Ref.: #66794]	selenocysteine biosynthesis	83.33	5 of 6
[Ref.: #66794]	glutamate and glutamine metabolism	82.14	23 of 28
[Ref.: #66794]	pentose phosphate pathway	81.82	9 of 11
[Ref.: #66794]	lipoate biosynthesis	80	4 of 5
[Ref.: #66794]	flavin biosynthesis	80	12 of 15
[Ref.: #66794]	cellulose degradation	80	4 of 5
[Ref.: #66794]	phenylacetate degradation (aerobic)	80	4 of 5
[Ref.: #66794]	citric acid cycle	78.57	11 of 14
[Ref.: #66794]	photosynthesis	78.57	11 of 14
[Ref.: #66794]	serine metabolism	77.78	7 of 9
[Ref.: #66794]	pyrimidine metabolism	77.78	35 of 45
[Ref.: #66794]	d-mannose degradation	77.78	7 of 9
[Ref.: #66794]	purine metabolism	77.66	73 of 94
[Ref.: #66794]	phenylalanine metabolism	76.92	10 of 13
[Ref.: #66794]	methionine metabolism	76.92	20 of 26
[Ref.: #66794]	acetate fermentation	75	3 of 4
[Ref.: #66794]	glycogen biosynthesis	75	3 of 4
[Ref.: #66794]	butanoate fermentation	75	3 of 4
[Ref.: #66794]	gluconeogenesis	75	6 of 8
[Ref.: #66794]	6-hydroxymethyl-dihydropterin diphosphate biosynthesis	75	6 of 8
[Ref.: #66794]	degradation of aromatic, nitrogen containing compounds	75	9 of 12
[Ref.: #66794]	C4 and CAM-carbon fixation	75	6 of 8
[Ref.: #66794]	ppGpp 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]	heme metabolism	71.43	10 of 14
[Ref.: #66794]	glycolysis	70.59	12 of 17
[Ref.: #66794]	threonine metabolism	70	7 of 10
[Ref.: #66794]	lysine metabolism	66.67	28 of 42
[Ref.: #66794]	enterobactin biosynthesis	66.67	2 of 3
[Ref.: #66794]	NAD metabolism	66.67	12 of 18
[Ref.: #66794]	octane oxidation	66.67	2 of 3
[Ref.: #66794]	L-lactaldehyde degradation	66.67	2 of 3
[Ref.: #66794]	IAA biosynthesis	66.67	2 of 3
[Ref.: #66794]	methane metabolism	66.67	2 of 3
[Ref.: #66794]	tetrahydrofolate metabolism	64.29	9 of 14
[Ref.: #66794]	proline metabolism	63.64	7 of 11
[Ref.: #66794]	arginine metabolism	62.5	15 of 24
[Ref.: #66794]	degradation of sugar alcohols	62.5	10 of 16
[Ref.: #66794]	oxidative phosphorylation	61.54	56 of 91
[Ref.: #66794]	factor 420 biosynthesis	60	3 of 5
[Ref.: #66794]	gallate degradation	60	3 of 5
[Ref.: #66794]	histidine metabolism	58.62	17 of 29
[Ref.: #66794]	tryptophan metabolism	57.89	22 of 38
[Ref.: #66794]	non-pathway related	57.89	22 of 38
[Ref.: #66794]	isoprenoid biosynthesis	57.69	15 of 26
[Ref.: #66794]	polyamine pathway	56.52	13 of 23
[Ref.: #66794]	cysteine metabolism	55.56	10 of 18
[Ref.: #66794]	d-xylose degradation	54.55	6 of 11
[Ref.: #66794]	urea cycle	53.85	7 of 13
[Ref.: #66794]	aminopropanol phosphate biosynthesis	50	1 of 2
[Ref.: #66794]	glycine metabolism	50	5 of 10
[Ref.: #66794]	pantothenate biosynthesis	50	3 of 6
[Ref.: #66794]	kanosamine biosynthesis II	50	1 of 2
[Ref.: #66794]	phenylmercury acetate degradation	50	1 of 2
[Ref.: #66794]	Entner Doudoroff pathway	50	5 of 10
[Ref.: #66794]	lactate fermentation	50	2 of 4
[Ref.: #66794]	ribulose monophosphate pathway	50	1 of 2
[Ref.: #66794]	degradation of pentoses	50	14 of 28
[Ref.: #66794]	coenzyme M biosynthesis	50	5 of 10
[Ref.: #66794]	denitrification	50	1 of 2
[Ref.: #66794]	toluene degradation	50	2 of 4
[Ref.: #66794]	mannosylglycerate biosynthesis	50	1 of 2
[Ref.: #66794]	4-hydroxyphenylacetate degradation	50	5 of 10
[Ref.: #66794]	ketogluconate metabolism	50	4 of 8
[Ref.: #66794]	quinate degradation	50	1 of 2
[Ref.: #66794]	tyrosine metabolism	50	7 of 14
[Ref.: #66794]	ethanol fermentation	50	1 of 2
[Ref.: #66794]	dTDPLrhamnose biosynthesis	50	4 of 8
[Ref.: #66794]	phosphatidylethanolamine bioynthesis	46.15	6 of 13
[Ref.: #66794]	sulfate reduction	46.15	6 of 13
[Ref.: #66794]	metabolism of disaccharids	45.45	5 of 11
[Ref.: #66794]	phenol degradation	45	9 of 20
[Ref.: #66794]	cardiolipin biosynthesis	42.86	3 of 7
[Ref.: #66794]	vitamin K metabolism	40	2 of 5
[Ref.: #66794]	bacilysin biosynthesis	40	2 of 5
[Ref.: #66794]	arachidonate biosynthesis	40	2 of 5
[Ref.: #66794]	metabolism of amino sugars and derivatives	40	2 of 5
[Ref.: #66794]	myo-inositol biosynthesis	40	4 of 10
[Ref.: #66794]	ethylmalonyl-CoA pathway	40	2 of 5
[Ref.: #66794]	3-chlorocatechol degradation	40	2 of 5
[Ref.: #66794]	vitamin B6 metabolism	36.36	4 of 11
[Ref.: #66794]	cholesterol biosynthesis	36.36	4 of 11
[Ref.: #66794]	degradation of sugar acids	36	9 of 25
[Ref.: #66794]	glutathione metabolism	35.71	5 of 14
[Ref.: #66794]	acetyl CoA biosynthesis	33.33	1 of 3
[Ref.: #66794]	4-hydroxymandelate degradation	33.33	3 of 9
[Ref.: #66794]	degradation of hexoses	33.33	6 of 18
[Ref.: #66794]	sulfoquinovose degradation	33.33	1 of 3
[Ref.: #66794]	methanogenesis from CO2	33.33	4 of 12
[Ref.: #66794]	3-phenylpropionate degradation	33.33	5 of 15
[Ref.: #66794]	(5R)-carbapenem carboxylate biosynthesis	33.33	1 of 3
[Ref.: #66794]	androgen and estrogen metabolism	31.25	5 of 16
[Ref.: #66794]	phenylpropanoid biosynthesis	30.77	4 of 13
[Ref.: #66794]	bile acid biosynthesis, neutral pathway	29.41	5 of 17
[Ref.: #66794]	aclacinomycin biosynthesis	28.57	2 of 7
[Ref.: #66794]	arachidonic acid metabolism	27.78	5 of 18
[Ref.: #66794]	ascorbate metabolism	27.27	6 of 22
[Ref.: #66794]	alginate biosynthesis	25	1 of 4
[Ref.: #66794]	cyclohexanol degradation	25	1 of 4
[Ref.: #66794]	catecholamine biosynthesis	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.: #2827]	Sample type/isolated from	sewage sludge
[Ref.: #2827]	Country	USA
[Ref.: #2827]	Country ISO 3 Code	USA
[Ref.: #2827]	Continent	North America
* marker position based on {}

Isolation sources categories

#Engineered

#Waste

#Sewage sludge

What are isolation sources categories?

[Ref.: #69479]

Global distribution of 16S sequence AM086646 (>99% sequence identity) for Desulfomonile tiedjei subclade from Microbeatlas

Aquatic Samples	3190
Soil Samples	1582
Animal Samples	211
Plant Samples	291
Total Samples	5274

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

[Ref.: #2827]

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]	Desulfomonile tiedjei partial 16S rRNA gene, strain DSM 6799	AM086646	1345	ENA	706587 tax ID	*

Genome sequence information:

	Sequence accession description	Seq. accession number	Assembly level	Sequence database	Associated NCBI tax ID
[Ref.: #66792]	Desulfomonile tiedjei DSM 6799	GCA_000266945	complete	GenBank	706587 tax ID	*
[Ref.: #66792]	Desulfomonile tiedjei DSM 6799	706587.9	plasmid	PATRIC	706587 tax ID	*
[Ref.: #66792]	Desulfomonile tiedjei DSM 6799	706587.4	complete	PATRIC	706587 tax ID	*
[Ref.: #66792]	Desulfomonile tiedjei DCB-1, DSM 6799	2509601019	complete	JGI IMG/M	706587 tax ID	*

[Ref.: #2827]

GC-content

49.0 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: Desulfomonile tiedjei DSM 6799 DSM 6799 NCBI: GCA_000266945.1
[Ref.: #69481]	spore-forming	no	99	no

	Trait	Prediction	Confidence in %	In training data
	Predictions from Diaspora project based on: Desulfomonile tiedjei DSM 6799 DSM 6799 NCBI: GCA_000266945.1
[Ref.: #69480]	motile	no	80.668	no
[Ref.: #69480]	flagellated	no	98.106	no
[Ref.: #69480]	gram-positive	no	98.497	no
[Ref.: #69480]	anaerobic	yes	96.745	yes
[Ref.: #69480]	aerobic	no	96.85	yes
[Ref.: #69480]	halophile	no	94.694	no
[Ref.: #69480]	spore-forming	no	85.379	no
[Ref.: #69480]	thermophile	no	79.401	yes
[Ref.: #69480]	glucose-util	yes	54.153	no
[Ref.: #69480]	glucose-ferment	no	89.557	no

Availability in culture collections External links

[Ref.: #2827]

Culture collection no.

DSM 6799, ATCC 49306

[Ref.: #85687]

SI-ID 42414

Literature:

Only first 10 entries are displayed. Click here to see all.

Topic	Title	Authors	Journal	DOI	Year
Metabolism	Long-Chain Fatty Acids Degradation by Desulfomonile Species and Proposal of "Candidatus Desulfomonile Palmitatoxidans".	Alves JI, Salvador AF, Castro AR, Zheng Y, Nijsse B, Atashgahi S, Sousa DZ, Stams AJM, Alves MM, Cavaleiro AJ	Front Microbiol	10.3389/fmicb.2020.539604	2020	*
Metabolism	snr-1 gene is required for nitrate reduction in Pseudomonas aeruginosa PAO1.	Kerschen EJ, Irani VR, Hassett DJ, Rowe JJ	J Bacteriol	10.1128/JB.183.6.2125-2131.2001	2001	*
Phylogeny	Desulfomonile limimaris sp. nov., an anaerobic dehalogenating bacterium from marine sediments.	Sun B, Cole JR, Tiedje JM	Int J Syst Evol Microbiol	10.1099/00207713-51-2-365	2001	*
Metabolism	Evidence for a chemiosmotic model of dehalorespiration in Desulfomonile tiedjei DCB-1.	Louie TM, Mohn WW	J Bacteriol	10.1128/JB.181.1.40-46.1999	1999	*
Enzymology	Purification, characterization and gene sequence analysis of a novel cytochrome c co-induced with reductive dechlorination activity in Desulfomonile tiedjei DCB-1.	Louie TM, Ni S, Xun L, Mohn WW	Arch Microbiol	10.1007/s002030050530	1997	*
Enzymology	Purification and characterization of a novel 3-chlorobenzoate-reductive dehalogenase from the cytoplasmic membrane of Desulfomonile tiedjei DCB-1.	Ni S, Fredrickson JK, Xun L	J Bacteriol	10.1128/jb.177.17.5135-5139.1995	1995	*
Enzymology	Tetrachloroethene and 3-chlorobenzoate dechlorination activities are co-induced in Desulfomonile tiedjei DCB-1.	Cole JR, Fathepure BZ, Tiedje JM	Biodegradation	10.1007/BF00695347	1995	*
Biotechnology	Bacterial dehalogenases: biochemistry, genetics, and biotechnological applications.	Fetzner S, Lingens F	Microbiol Rev	10.1128/mr.58.4.641-685.1994	1994	*
Metabolism	Microbial reductive dehalogenation.	Mohn WW, Tiedje JM	Microbiol Rev	10.1128/mr.56.3.482-507.1992	1992	*
Metabolism	Reductive dehalogenation of chlorophenols by Desulfomonile tiedjei DCB-1.	Mohn WW, Kennedy KJ	Appl Environ Microbiol	10.1128/aem.58.4.1367-1370.1992	1992	*
Metabolism	Specific deuteration of dichlorobenzoate during reductive dehalogenation by Desulfomonile tiedjei in D2O.	Griffith GD, Cole JR, Quensen JF 3rd, Tiedje JM	Appl Environ Microbiol	10.1128/aem.58.1.409-411.1992	1992	*
	Influence of substituents on reductive dehalogenation of 3-chlorobenzoate analogs.	Dolfing J, Tiedje JM	Appl Environ Microbiol	10.1128/aem.57.3.820-824.1991	1991	*

References

#2827

Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 6799

#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) .

#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 )

#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 )

#85687

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-ID42414.1 )

* These data were automatically processed and therefore are not curated

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Desulfomonile tiedjei DSM 6799 DSM 6799

Desulfomonile tiedjei DSM 6799 DSM 6799

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