Name: Parasporobacterium paucivorans DSM 15970
Creator: BacDive
License: http://creativecommons.org/licenses/by-nc/4.0/

Strain identifier

BacDive ID: 6361

Type strain:

Species: Parasporobacterium paucivorans

Culture col. no.: DSM 15970, SYR 1

Strain history: <- B. P. Lomans, University of Nijmegen, Department of Microbiology and Evolutionary Biology, Nijmegen, Netherlands; SYR1 <- B. P. Lomans {1994}

NCBI tax ID(s): 1122934 (strain), 115544 (species)

SI-ID 131431

DSM 15970, NCCB 100052

Section

Parasporobacterium paucivorans DSM 15970 is an anaerobe, mesophilic, Gram-positive bacterium that was isolated from anaerobic sediment of eutrophic freshwater pond.

Gram-positive
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	*Bacillota*
	Class	*Clostridia*
	Order	*Eubacteriales*
	Family	*Lachnospiraceae*
	Genus	*Parasporobacterium*
	Species	**Parasporobacterium paucivorans**
	Full Scientific Name (LPSN)	Parasporobacterium paucivorans Lomans et al. 2004

Information on morphological and physiological properties Morphology

[Ref.: #69480]	Gram stain	positive Confidence in %99.719

Information on culture and growth conditions Culture and growth conditions

[Ref.: #6210]

Culture medium

ANAEROBIC FRESHWATER (FWM) MEDIUM (DSMZ Medium 503)

[Ref.: #6210]

Culture medium growth

[Ref.: #6210]

Culture medium link

Medium recipe at MediaDive

[Ref.: #6210]

Culture medium composition

expand / minimize

	Temperatures	Kind of temperature		Temperature
[Ref.: #6210]			growth	35 °C

[Ref.: #6210]

Temperature range

mesophilic

Information on physiology and metabolism Physiology and metabolism

[Ref.: #6210]	Oxygen tolerance	anaerobe
[Ref.: #69480]	Oxygen tolerance	anaerobe Confidence in %99.999

[Ref.: #69480]

Ability of spore formation

no Confidence in %99.964

	Pathway	Enzyme coverage	Annotated reactions
	Pathway annotation	Computationally determined by
[Ref.: #66794]	adipate degradation	100	2 of 2
[Ref.: #66794]	cardiolipin biosynthesis	100	7 of 7
[Ref.: #66794]	coenzyme A metabolism	100	4 of 4
[Ref.: #66794]	CDP-diacylglycerol biosynthesis	100	2 of 2
[Ref.: #66794]	UDP-GlcNAc biosynthesis	100	3 of 3
[Ref.: #66794]	reductive acetyl coenzyme A pathway	100	7 of 7
[Ref.: #66794]	suberin monomers biosynthesis	100	2 of 2
[Ref.: #66794]	anapleurotic synthesis of oxalacetate	100	1 of 1
[Ref.: #66794]	folate polyglutamylation	100	1 of 1
[Ref.: #66794]	ppGpp biosynthesis	100	4 of 4
[Ref.: #66794]	palmitate biosynthesis	95.45	21 of 22
[Ref.: #66794]	aspartate and asparagine metabolism	88.89	8 of 9
[Ref.: #66794]	chorismate metabolism	88.89	8 of 9
[Ref.: #66794]	molybdenum cofactor biosynthesis	88.89	8 of 9
[Ref.: #66794]	peptidoglycan biosynthesis	80	12 of 15
[Ref.: #66794]	cellulose degradation	80	4 of 5
[Ref.: #66794]	threonine metabolism	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]	valine metabolism	77.78	7 of 9
[Ref.: #66794]	CO2 fixation in Crenarchaeota	77.78	7 of 9
[Ref.: #66794]	vitamin B1 metabolism	76.92	10 of 13
[Ref.: #66794]	vitamin B12 metabolism	76.47	26 of 34
[Ref.: #66794]	acetate fermentation	75	3 of 4
[Ref.: #66794]	glycogen biosynthesis	75	3 of 4
[Ref.: #66794]	C4 and CAM-carbon fixation	75	6 of 8
[Ref.: #66794]	sulfopterin metabolism	75	3 of 4
[Ref.: #66794]	butanoate fermentation	75	3 of 4
[Ref.: #66794]	pentose phosphate pathway	72.73	8 of 11
[Ref.: #66794]	NAD metabolism	72.22	13 of 18
[Ref.: #66794]	heme metabolism	71.43	10 of 14
[Ref.: #66794]	tetrahydrofolate metabolism	71.43	10 of 14
[Ref.: #66794]	propanol degradation	71.43	5 of 7
[Ref.: #66794]	ubiquinone biosynthesis	71.43	5 of 7
[Ref.: #66794]	glycolysis	70.59	12 of 17
[Ref.: #66794]	urea cycle	69.23	9 of 13
[Ref.: #66794]	purine metabolism	68.09	64 of 94
[Ref.: #66794]	serine metabolism	66.67	6 of 9
[Ref.: #66794]	acetoin degradation	66.67	2 of 3
[Ref.: #66794]	pyrimidine metabolism	66.67	30 of 45
[Ref.: #66794]	enterobactin biosynthesis	66.67	2 of 3
[Ref.: #66794]	octane oxidation	66.67	2 of 3
[Ref.: #66794]	methane metabolism	66.67	2 of 3
[Ref.: #66794]	flavin biosynthesis	66.67	10 of 15
[Ref.: #66794]	L-lactaldehyde degradation	66.67	2 of 3
[Ref.: #66794]	d-mannose degradation	66.67	6 of 9
[Ref.: #66794]	formaldehyde oxidation	66.67	2 of 3
[Ref.: #66794]	alanine metabolism	65.52	19 of 29
[Ref.: #66794]	citric acid cycle	64.29	9 of 14
[Ref.: #66794]	glutamate and glutamine metabolism	64.29	18 of 28
[Ref.: #66794]	6-hydroxymethyl-dihydropterin diphosphate biosynthesis	62.5	5 of 8
[Ref.: #66794]	isoleucine metabolism	62.5	5 of 8
[Ref.: #66794]	ketogluconate metabolism	62.5	5 of 8
[Ref.: #66794]	methionine metabolism	61.54	16 of 26
[Ref.: #66794]	isoprenoid biosynthesis	61.54	16 of 26
[Ref.: #66794]	phenylalanine metabolism	61.54	8 of 13
[Ref.: #66794]	glycine betaine biosynthesis	60	3 of 5
[Ref.: #66794]	glycogen metabolism	60	3 of 5
[Ref.: #66794]	methylglyoxal degradation	60	3 of 5
[Ref.: #66794]	oxidative phosphorylation	57.14	52 of 91
[Ref.: #66794]	cysteine metabolism	55.56	10 of 18
[Ref.: #66794]	histidine metabolism	55.17	16 of 29
[Ref.: #66794]	sulfate reduction	53.85	7 of 13
[Ref.: #66794]	tryptophan metabolism	52.63	20 of 38
[Ref.: #66794]	polyamine pathway	52.17	12 of 23
[Ref.: #66794]	biotin biosynthesis	50	2 of 4
[Ref.: #66794]	ethanol fermentation	50	1 of 2
[Ref.: #66794]	aminopropanol phosphate biosynthesis	50	1 of 2
[Ref.: #66794]	dTDPLrhamnose biosynthesis	50	4 of 8
[Ref.: #66794]	cis-vaccenate biosynthesis	50	1 of 2
[Ref.: #66794]	lysine metabolism	50	21 of 42
[Ref.: #66794]	selenocysteine biosynthesis	50	3 of 6
[Ref.: #66794]	gluconeogenesis	50	4 of 8
[Ref.: #66794]	pantothenate biosynthesis	50	3 of 6
[Ref.: #66794]	vitamin E metabolism	50	2 of 4
[Ref.: #66794]	propionate fermentation	50	5 of 10
[Ref.: #66794]	arginine metabolism	50	12 of 24
[Ref.: #66794]	lipid metabolism	48.39	15 of 31
[Ref.: #66794]	leucine metabolism	46.15	6 of 13
[Ref.: #66794]	d-xylose degradation	45.45	5 of 11
[Ref.: #66794]	vitamin B6 metabolism	45.45	5 of 11
[Ref.: #66794]	non-pathway related	44.74	17 of 38
[Ref.: #66794]	nitrate assimilation	44.44	4 of 9
[Ref.: #66794]	ascorbate metabolism	40.91	9 of 22
[Ref.: #66794]	Entner Doudoroff pathway	40	4 of 10
[Ref.: #66794]	degradation of hexoses	38.89	7 of 18
[Ref.: #66794]	proline metabolism	36.36	4 of 11
[Ref.: #66794]	tyrosine metabolism	35.71	5 of 14
[Ref.: #66794]	degradation of aromatic, nitrogen containing compounds	33.33	4 of 12
[Ref.: #66794]	IAA biosynthesis	33.33	1 of 3
[Ref.: #66794]	lipid A biosynthesis	33.33	3 of 9
[Ref.: #66794]	4-hydroxymandelate degradation	33.33	3 of 9
[Ref.: #66794]	glycolate and glyoxylate degradation	33.33	2 of 6
[Ref.: #66794]	cyanate degradation	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]	coenzyme M biosynthesis	30	3 of 10
[Ref.: #66794]	glycine metabolism	30	3 of 10
[Ref.: #66794]	myo-inositol biosynthesis	30	3 of 10
[Ref.: #66794]	phenol degradation	30	6 of 20
[Ref.: #66794]	benzoyl-CoA degradation	28.57	2 of 7
[Ref.: #66794]	dolichyl-diphosphooligosaccharide biosynthesis	27.27	3 of 11
[Ref.: #66794]	metabolism of disaccharids	27.27	3 of 11
[Ref.: #66794]	cyclohexanol degradation	25	1 of 4
[Ref.: #66794]	lactate fermentation	25	1 of 4
[Ref.: #66794]	CMP-KDO biosynthesis	25	1 of 4
[Ref.: #66794]	degradation of sugar alcohols	25	4 of 16
[Ref.: #66794]	toluene degradation	25	1 of 4
[Ref.: #66794]	degradation of pentoses	21.43	6 of 28
[Ref.: #66794]	glutathione metabolism	21.43	3 of 14
		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.: #6210]	Sample type/isolated from	anaerobic sediment of eutrophic freshwater pond
[Ref.: #6210]	Geographic location (country and/or sea, region)	Nijmegen, Dekkerswald
[Ref.: #6210]	Country	Netherlands
[Ref.: #6210]	Country ISO 3 Code	NLD
[Ref.: #6210]	Continent	Europe
* marker position based on {}

Isolation sources categories

#Environmental	#Aquatic	#Freshwater
#Environmental	#Aquatic	#Pond (small)
#Environmental	#Aquatic	#Sediment
#Condition	#Anoxic (anaerobic)	-

What are isolation sources categories?

[Ref.: #69479]

Global distribution of 16S sequence AJ272036 (>99% sequence identity) for Parasporobacterium paucivorans subclade from Microbeatlas

Aquatic Samples	516
Soil Samples	76
Animal Samples	584
Plant Samples	56
Total Samples	1232

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

[Ref.: #6210]

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.: #6210]	Parasporobacterium paucivorans partial 16S rRNA gene, strain SYR1	AJ272036	1487	ENA	115544 tax ID

Genome sequence information:

	Sequence accession description	Seq. accession number	Assembly level	Sequence database	Associated NCBI tax ID
[Ref.: #66792]	Parasporobacterium paucivorans DSM 15970	GCA_900141895	contig	GenBank	1122934 tax ID	*
[Ref.: #66792]	Parasporobacterium paucivorans DSM 15970	1122934.3	wgs	PATRIC	1122934 tax ID	*
[Ref.: #66792]	Parasporobacterium paucivorans DSM 15970	2585427596	draft	JGI IMG/M	1122934 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: Parasporobacterium paucivorans DSM 15970 PATRIC: 1122934.3
[Ref.: #69481]	spore-forming	yes	69	no

	Trait	Prediction	Confidence in %	In training data
	Predictions from Diaspora project based on: Parasporobacterium paucivorans DSM 15970 PATRIC: 1122934.3
[Ref.: #69480]	motile	yes	72.533	no
[Ref.: #69480]	flagellated	no	70.463	no
[Ref.: #69480]	gram-positive	yes	54.396	no
[Ref.: #69480]	anaerobic	yes	99.7	no
[Ref.: #69480]	aerobic	no	98.81	no
[Ref.: #69480]	halophile	no	97.007	no
[Ref.: #69480]	spore-forming	yes	60.896	no
[Ref.: #69480]	glucose-util	yes	60.186	no
[Ref.: #69480]	thermophile	no	91.415	no
[Ref.: #69480]	glucose-ferment	no	52.062	no

Availability in culture collections External links

[Ref.: #6210]

Culture collection no.

DSM 15970, SYR 1

[Ref.: #75834]

SI-ID 131431

References

#6210

Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 15970

#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) .

#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 )

#75834

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-ID131431.1 )

* These data were automatically processed and therefore are not curated

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