Name: Desulfovibrio piger DSM 749
Creator: BacDive
License: http://creativecommons.org/licenses/by-nc/4.0/

Strain identifier

BacDive ID: 4070

Type strain:

Species: Desulfovibrio piger

Culture col. no.: DSM 749, ATCC 29098, JCM 12224, VPI 11112, VPI C3-23

Strain history: <- N. Pfennig, Gesellschaft für Strahlen- und Umweltforschung mbH München in Göttingen, Germany; VPI 11112 <- W. E. C. Moore, Virginia Polytechnical Institute and State University, Blacksburg, V., USA

NCBI tax ID(s): 411464 (strain), 901 (species)

SI-ID 39351

ATCC 29098, DSM 749, JCM 12224

Other strains from Desulfovibrio piger

D. piger PG-251-APC-1, DSM 106036

Section

Desulfovibrio piger DSM 749 is an anaerobe, mesophilic bacterium that was isolated from human faeces.

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	*Desulfovibrionales*
	Family	*Desulfovibrionaceae*
	Genus	*Desulfovibrio*
	Species	**Desulfovibrio piger**
	Full Scientific Name (LPSN)	Desulfovibrio piger (Moore et al. 1976) Loubinoux et al. 2002

Synonym

Desulfomonas pigra

Information on culture and growth conditions Culture and growth conditions

[Ref.: #422]

Culture medium

DESULFOVIBRIO (MV) MEDIUM (DSMZ Medium 641)

[Ref.: #422]

Culture medium growth

[Ref.: #422]

Culture medium link

Medium recipe at MediaDive

[Ref.: #422]

Culture medium composition

expand / minimize

	Temperatures	Kind of temperature		Temperature
[Ref.: #422]			growth	37 °C

[Ref.: #422]

Temperature range

mesophilic

Information on physiology and metabolism Physiology and metabolism

[Ref.: #422]

Oxygen tolerance

anaerobe

	Pathway	Enzyme coverage	Annotated reactions
	Pathway annotation	Computationally determined by
[Ref.: #66794]	reductive acetyl coenzyme A pathway	100	7 of 7
[Ref.: #66794]	1,4-dihydroxy-6-naphthoate biosynthesis	100	6 of 6
[Ref.: #66794]	methylglyoxal degradation	100	5 of 5
[Ref.: #66794]	ppGpp biosynthesis	100	4 of 4
[Ref.: #66794]	cis-vaccenate biosynthesis	100	2 of 2
[Ref.: #66794]	palmitate biosynthesis	100	22 of 22
[Ref.: #66794]	biotin biosynthesis	100	4 of 4
[Ref.: #66794]	L-lactaldehyde degradation	100	3 of 3
[Ref.: #66794]	aspartate and asparagine metabolism	100	9 of 9
[Ref.: #66794]	chorismate metabolism	100	9 of 9
[Ref.: #66794]	folate polyglutamylation	100	1 of 1
[Ref.: #66794]	formaldehyde oxidation	100	3 of 3
[Ref.: #66794]	coenzyme A metabolism	100	4 of 4
[Ref.: #66794]	CDP-diacylglycerol biosynthesis	100	2 of 2
[Ref.: #66794]	anapleurotic synthesis of oxalacetate	100	1 of 1
[Ref.: #66794]	UDP-GlcNAc biosynthesis	100	3 of 3
[Ref.: #66794]	molybdenum cofactor biosynthesis	88.89	8 of 9
[Ref.: #66794]	valine metabolism	88.89	8 of 9
[Ref.: #66794]	photosynthesis	85.71	12 of 14
[Ref.: #66794]	ubiquinone biosynthesis	85.71	6 of 7
[Ref.: #66794]	vitamin B12 metabolism	82.35	28 of 34
[Ref.: #66794]	purine metabolism	80.85	76 of 94
[Ref.: #66794]	lipoate biosynthesis	80	4 of 5
[Ref.: #66794]	threonine metabolism	80	8 of 10
[Ref.: #66794]	hydrogen production	80	4 of 5
[Ref.: #66794]	peptidoglycan biosynthesis	80	12 of 15
[Ref.: #66794]	tetrahydrofolate metabolism	78.57	11 of 14
[Ref.: #66794]	serine metabolism	77.78	7 of 9
[Ref.: #66794]	vitamin B1 metabolism	76.92	10 of 13
[Ref.: #66794]	CMP-KDO biosynthesis	75	3 of 4
[Ref.: #66794]	6-hydroxymethyl-dihydropterin diphosphate biosynthesis	75	6 of 8
[Ref.: #66794]	butanoate fermentation	75	3 of 4
[Ref.: #66794]	acetate fermentation	75	3 of 4
[Ref.: #66794]	glycogen biosynthesis	75	3 of 4
[Ref.: #66794]	cardiolipin biosynthesis	71.43	5 of 7
[Ref.: #66794]	polyamine pathway	69.57	16 of 23
[Ref.: #66794]	phenylalanine metabolism	69.23	9 of 13
[Ref.: #66794]	methionine metabolism	69.23	18 of 26
[Ref.: #66794]	alanine metabolism	68.97	20 of 29
[Ref.: #66794]	glutamate and glutamine metabolism	67.86	19 of 28
[Ref.: #66794]	acetoin degradation	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]	flavin biosynthesis	66.67	10 of 15
[Ref.: #66794]	cysteine metabolism	66.67	12 of 18
[Ref.: #66794]	pyrimidine metabolism	66.67	30 of 45
[Ref.: #66794]	CO2 fixation in Crenarchaeota	66.67	6 of 9
[Ref.: #66794]	selenocysteine biosynthesis	66.67	4 of 6
[Ref.: #66794]	glycolysis	64.71	11 of 17
[Ref.: #66794]	heme metabolism	64.29	9 of 14
[Ref.: #66794]	C4 and CAM-carbon fixation	62.5	5 of 8
[Ref.: #66794]	isoleucine metabolism	62.5	5 of 8
[Ref.: #66794]	arginine metabolism	62.5	15 of 24
[Ref.: #66794]	glycogen metabolism	60	3 of 5
[Ref.: #66794]	glycine betaine biosynthesis	60	3 of 5
[Ref.: #66794]	starch degradation	60	6 of 10
[Ref.: #66794]	oxidative phosphorylation	58.24	53 of 91
[Ref.: #66794]	propanol degradation	57.14	4 of 7
[Ref.: #66794]	citric acid cycle	57.14	8 of 14
[Ref.: #66794]	d-mannose degradation	55.56	5 of 9
[Ref.: #66794]	nitrate assimilation	55.56	5 of 9
[Ref.: #66794]	proline metabolism	54.55	6 of 11
[Ref.: #66794]	isoprenoid biosynthesis	53.85	14 of 26
[Ref.: #66794]	non-pathway related	52.63	20 of 38
[Ref.: #66794]	histidine metabolism	51.72	15 of 29
[Ref.: #66794]	sulfopterin metabolism	50	2 of 4
[Ref.: #66794]	ethanol fermentation	50	1 of 2
[Ref.: #66794]	ketogluconate metabolism	50	4 of 8
[Ref.: #66794]	glycolate and glyoxylate degradation	50	3 of 6
[Ref.: #66794]	aminopropanol phosphate biosynthesis	50	1 of 2
[Ref.: #66794]	dTDPLrhamnose biosynthesis	50	4 of 8
[Ref.: #66794]	suberin monomers biosynthesis	50	1 of 2
[Ref.: #66794]	gluconeogenesis	50	4 of 8
[Ref.: #66794]	phenylmercury acetate degradation	50	1 of 2
[Ref.: #66794]	glycine metabolism	50	5 of 10
[Ref.: #66794]	toluene degradation	50	2 of 4
[Ref.: #66794]	lactate fermentation	50	2 of 4
[Ref.: #66794]	lipid metabolism	48.39	15 of 31
[Ref.: #66794]	lysine metabolism	47.62	20 of 42
[Ref.: #66794]	tryptophan metabolism	47.37	18 of 38
[Ref.: #66794]	urea cycle	46.15	6 of 13
[Ref.: #66794]	sulfate reduction	46.15	6 of 13
[Ref.: #66794]	leucine metabolism	46.15	6 of 13
[Ref.: #66794]	pentose phosphate pathway	45.45	5 of 11
[Ref.: #66794]	vitamin B6 metabolism	45.45	5 of 11
[Ref.: #66794]	lipid A biosynthesis	44.44	4 of 9
[Ref.: #66794]	degradation of hexoses	44.44	8 of 18
[Ref.: #66794]	tyrosine metabolism	42.86	6 of 14
[Ref.: #66794]	glutathione metabolism	42.86	6 of 14
[Ref.: #66794]	degradation of aromatic, nitrogen containing compounds	41.67	5 of 12
[Ref.: #66794]	factor 420 biosynthesis	40	2 of 5
[Ref.: #66794]	coenzyme M biosynthesis	40	4 of 10
[Ref.: #66794]	propionate fermentation	40	4 of 10
[Ref.: #66794]	arachidonate biosynthesis	40	2 of 5
[Ref.: #66794]	phosphatidylethanolamine bioynthesis	38.46	5 of 13
[Ref.: #66794]	degradation of sugar acids	36	9 of 25
[Ref.: #66794]	phenol degradation	35	7 of 20
[Ref.: #66794]	methane metabolism	33.33	1 of 3
[Ref.: #66794]	cyanate degradation	33.33	1 of 3
[Ref.: #66794]	IAA biosynthesis	33.33	1 of 3
[Ref.: #66794]	pantothenate biosynthesis	33.33	2 of 6
[Ref.: #66794]	acetyl CoA biosynthesis	33.33	1 of 3
[Ref.: #66794]	androgen and estrogen metabolism	31.25	5 of 16
[Ref.: #66794]	4-hydroxyphenylacetate degradation	30	3 of 10
[Ref.: #66794]	degradation of pentoses	28.57	8 of 28
[Ref.: #66794]	cyclohexanol degradation	25	1 of 4
[Ref.: #66794]	alginate biosynthesis	25	1 of 4
[Ref.: #66794]	degradation of sugar alcohols	25	4 of 16
[Ref.: #66794]	vitamin E metabolism	25	1 of 4
[Ref.: #66794]	ascorbate metabolism	22.73	5 of 22
		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.: #422]	Sample type/isolated from	human faeces
* marker position based on {}

Isolation sources categories

#Host	#Human	-
#Host Body Product	#Gastrointestinal tract	#Feces (Stool)

What are isolation sources categories?

[Ref.: #69479]

Global distribution of 16S sequence AF192152 (>99% sequence identity) for Desulfovibrio piger subclade from Microbeatlas

Aquatic Samples	4606
Soil Samples	1726
Animal Samples	113854
Plant Samples	581
Total Samples	120767

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

[Ref.: #422]

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.: #422]	Desulfomonas pigra 16S ribosomal RNA gene, complete sequence	AF192152	1542	ENA	411464 tax ID
[Ref.: #20218]	D.pigra 16S ribosomal rRNA	M34404	1378	ENA	901 tax ID	*

Genome sequence information:

	Sequence accession description	Seq. accession number	Assembly level	Sequence database	Associated NCBI tax ID
[Ref.: #66792]	Desulfovibrio piger ATCC 29098	GCA_000156375	scaffold	GenBank	411464 tax ID	*
[Ref.: #66792]	Desulfovibrio piger ATCC 29098	411464.8	wgs	PATRIC	411464 tax ID	*
[Ref.: #66792]	Desulfovibrio piger ATCC 29098	642979316	draft	JGI IMG/M	411464 tax ID	*

[Ref.: #422]

GC-content

67.0 mol%

Data predicted using genome information as a basis Genome-based predictions

	Trait	Prediction	Confidence in %	In training data
	Predictions from Diaspora project based on: Desulfovibrio piger ATCC 29098 ATCC 29098 NCBI: GCA_000156375.1
[Ref.: #69480]	motile	yes	54.564	no
[Ref.: #69480]	flagellated	no	87.328	no
[Ref.: #69480]	gram-positive	no	97.535	no
[Ref.: #69480]	anaerobic	yes	99.5	yes
[Ref.: #69480]	aerobic	no	97.428	yes
[Ref.: #69480]	halophile	no	82.884	no
[Ref.: #69480]	spore-forming	no	95.185	no
[Ref.: #69480]	thermophile	no	89.58	yes
[Ref.: #69480]	glucose-util	no	64.981	no
[Ref.: #69480]	glucose-ferment	no	74.706	no

Availability in culture collections External links

[Ref.: #422]

Culture collection no.

DSM 749, ATCC 29098, JCM 12224, VPI 11112, VPI C3-23

[Ref.: #73573]

SI-ID 39351

Literature:

Topic	Title	Authors	Journal	DOI	Year
Genetics	Shotgun metagenomic sequencing revealed the prebiotic potential of a grain-based diet in mice.	Jangid A, Fukuda S, Suzuki Y, Taylor TD, Ohno H, Prakash T	Sci Rep	10.1038/s41598-022-10762-3	2022	*
Metabolism	Lactate has the potential to promote hydrogen sulphide formation in the human colon.	Marquet P, Duncan SH, Chassard C, Bernalier-Donadille A, Flint HJ	FEMS Microbiol Lett	10.1111/j.1574-6968.2009.01750.x	2009	*
Phylogeny	Reclassification of the only species of the genus Desulfomonas, Desulfomonas pigra, as Desulfovibrio piger comb. nov.	Loubinoux J, Valente FM, Pereira IA, Costa A, Grimont PA, Le Faou AE	Int J Syst Evol Microbiol	10.1099/00207713-52-4-1305	2002	*
Cultivation	[Rapid identification of Bilophila wadsworthia].	Sawamura H, Kato N, Sawa K, Watanabe K, Ueno K	Kansenshogaku Zasshi	10.11150/kansenshogakuzasshi1970.71.614	1997	*

References

#422	Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 749

#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) .

#73573

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-ID39351.1 )

* These data were automatically processed and therefore are not curated

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Desulfovibrio piger ATCC 29098 ATCC 29098

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