Parasporobacterium paucivorans (DSM 15970, SYR 1)

Name: Parasporobacterium paucivorans (DSM 15970, SYR 1)
Creator: BacDive
License: http://creativecommons.org/licenses/by/4.0/

BacDive ID 6361

Type strain

Culture col. no. DSM 15970 SYR 1

NCBI tax ID(s) 1122934 115544

Special Collections DSMZ

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

Links

Parasporobacterium paucivorans DSM 15970 is an anaerobe bacterium that was isolated from anaerobic sediment of eutrophic freshwater pond.

anaerobe genome sequence 16S sequence Bacteria

Name and taxonomic classification

SI-ID 131431

DSM 15970,NCCB 100052

@ref 20215

Last LPSN update 2026-02-09 11:19:11

Domain Bacteria

Phylum Bacillota

Class Clostridia

Order Eubacteriales

Family Lachnospiraceae

Genus Parasporobacterium

Species Parasporobacterium paucivorans

Full scientific name Parasporobacterium paucivorans Lomans et al. 2004

Morphology

Culture and growth conditions

Culture medium

@ref	Name	Growth	Medium link	Composition
6210	ANAEROBIC FRESHWATER (FWM) MEDIUM (DSMZ Medium 503)		Medium recipe at MediaDive	Name: ANAEROBIC FRESHWATER (FWM) MEDIUM (DSMZ Medium 503) Composition: D-Glucose 4.98504 g/l Na2CO3 1.49551 g/l NaCl 0.997008 g/l KCl 0.498505 g/l MgCl2 x 6 H2O 0.398803 g/l Na2S x 9 H2O 0.299103 g/l NH4Cl 0.249252 g/l KH2PO4 0.199402 g/l CaCl2 x 2 H2O 0.149552 g/l HCl 0.00249252 g/l FeCl2 x 4 H2O 0.00149551 g/l Sodium resazurin 0.000498505 g/l NaOH 0.000498504 g/l Pyridoxine hydrochloride 0.000299103 g/l Nicotinic acid 0.000199402 g/l Thiamine-HCl x 2 H2O 0.000199402 g/l CoCl2 x 6 H2O 0.000189432 g/l Calcium pantothenate 9.97009e-05 g/l MnCl2 x 4 H2O 9.97009e-05 g/l Vitamin B12 9.97009e-05 g/l p-Aminobenzoic acid 7.97607e-05 g/l ZnCl2 6.97906e-05 g/l Na2MoO4 x 2 H2O 3.58923e-05 g/l NiCl2 x 6 H2O 2.39282e-05 g/l D-(+)-biotin 1.99402e-05 g/l H3BO3 5.98205e-06 g/l Na2WO4 x 2 H2O 3.98804e-06 g/l Na2SeO3 x 5 H2O 2.99103e-06 g/l CuCl2 x 2 H2O 1.99402e-06 g/l Distilled water

Culture temp

@ref	Growth	Type	Temperature (°C)
6210	positive	growth	35

Physiology and metabolism

Oxygen tolerance

@ref	Oxygen tolerance	Confidence
6210	anaerobe
125438	anaerobe	93.197
125439	anaerobe	99.9

Pathway annotation

Computationally determined by

@ref	pathway	enzyme coverage	annotated reactions
66794	adipate degradation	100	2 of 2
66794	cardiolipin biosynthesis	100	7 of 7
66794	coenzyme A metabolism	100	4 of 4
66794	CDP-diacylglycerol biosynthesis	100	2 of 2
66794	UDP-GlcNAc biosynthesis	100	3 of 3
66794	reductive acetyl coenzyme A pathway	100	7 of 7
66794	suberin monomers biosynthesis	100	2 of 2
66794	anapleurotic synthesis of oxalacetate	100	1 of 1
66794	folate polyglutamylation	100	1 of 1
66794	ppGpp biosynthesis	100	4 of 4
66794	palmitate biosynthesis	95.45	21 of 22
66794	aspartate and asparagine metabolism	88.89	8 of 9
66794	chorismate metabolism	88.89	8 of 9
66794	molybdenum cofactor biosynthesis	88.89	8 of 9
66794	peptidoglycan biosynthesis	80	12 of 15
66794	cellulose degradation	80	4 of 5
66794	threonine metabolism	80	8 of 10
66794	starch degradation	80	8 of 10
66794	hydrogen production	80	4 of 5
66794	photosynthesis	78.57	11 of 14
66794	valine metabolism	77.78	7 of 9
66794	CO2 fixation in Crenarchaeota	77.78	7 of 9
66794	vitamin B1 metabolism	76.92	10 of 13
66794	vitamin B12 metabolism	76.47	26 of 34
66794	acetate fermentation	75	3 of 4
66794	glycogen biosynthesis	75	3 of 4
66794	C4 and CAM-carbon fixation	75	6 of 8
66794	sulfopterin metabolism	75	3 of 4
66794	butanoate fermentation	75	3 of 4
66794	pentose phosphate pathway	72.73	8 of 11
66794	NAD metabolism	72.22	13 of 18
66794	heme metabolism	71.43	10 of 14
66794	tetrahydrofolate metabolism	71.43	10 of 14
66794	propanol degradation	71.43	5 of 7
66794	ubiquinone biosynthesis	71.43	5 of 7
66794	glycolysis	70.59	12 of 17
66794	urea cycle	69.23	9 of 13
66794	purine metabolism	68.09	64 of 94
66794	serine metabolism	66.67	6 of 9
66794	acetoin degradation	66.67	2 of 3
66794	pyrimidine metabolism	66.67	30 of 45
66794	enterobactin biosynthesis	66.67	2 of 3
66794	octane oxidation	66.67	2 of 3
66794	methane metabolism	66.67	2 of 3
66794	flavin biosynthesis	66.67	10 of 15
66794	L-lactaldehyde degradation	66.67	2 of 3
66794	d-mannose degradation	66.67	6 of 9
66794	formaldehyde oxidation	66.67	2 of 3
66794	alanine metabolism	65.52	19 of 29
66794	citric acid cycle	64.29	9 of 14
66794	glutamate and glutamine metabolism	64.29	18 of 28
66794	6-hydroxymethyl-dihydropterin diphosphate biosynthesis	62.5	5 of 8
66794	isoleucine metabolism	62.5	5 of 8
66794	ketogluconate metabolism	62.5	5 of 8
66794	methionine metabolism	61.54	16 of 26
66794	isoprenoid biosynthesis	61.54	16 of 26
66794	phenylalanine metabolism	61.54	8 of 13
66794	glycine betaine biosynthesis	60	3 of 5
66794	glycogen metabolism	60	3 of 5
66794	methylglyoxal degradation	60	3 of 5
66794	oxidative phosphorylation	57.14	52 of 91
66794	cysteine metabolism	55.56	10 of 18
66794	histidine metabolism	55.17	16 of 29
66794	sulfate reduction	53.85	7 of 13
66794	tryptophan metabolism	52.63	20 of 38
66794	polyamine pathway	52.17	12 of 23
66794	biotin biosynthesis	50	2 of 4
66794	ethanol fermentation	50	1 of 2
66794	aminopropanol phosphate biosynthesis	50	1 of 2
66794	dTDPLrhamnose biosynthesis	50	4 of 8
66794	cis-vaccenate biosynthesis	50	1 of 2
66794	lysine metabolism	50	21 of 42
66794	selenocysteine biosynthesis	50	3 of 6
66794	gluconeogenesis	50	4 of 8
66794	pantothenate biosynthesis	50	3 of 6
66794	vitamin E metabolism	50	2 of 4
66794	propionate fermentation	50	5 of 10
66794	arginine metabolism	50	12 of 24
66794	lipid metabolism	48.39	15 of 31
66794	leucine metabolism	46.15	6 of 13
66794	d-xylose degradation	45.45	5 of 11
66794	vitamin B6 metabolism	45.45	5 of 11
66794	non-pathway related	44.74	17 of 38
66794	nitrate assimilation	44.44	4 of 9
66794	ascorbate metabolism	40.91	9 of 22
66794	Entner Doudoroff pathway	40	4 of 10
66794	degradation of hexoses	38.89	7 of 18
66794	proline metabolism	36.36	4 of 11
66794	tyrosine metabolism	35.71	5 of 14
66794	degradation of aromatic, nitrogen containing compounds	33.33	4 of 12
66794	IAA biosynthesis	33.33	1 of 3
66794	lipid A biosynthesis	33.33	3 of 9
66794	4-hydroxymandelate degradation	33.33	3 of 9
66794	glycolate and glyoxylate degradation	33.33	2 of 6
66794	cyanate degradation	33.33	1 of 3
66794	androgen and estrogen metabolism	31.25	5 of 16
66794	phenylpropanoid biosynthesis	30.77	4 of 13
66794	coenzyme M biosynthesis	30	3 of 10
66794	glycine metabolism	30	3 of 10
66794	myo-inositol biosynthesis	30	3 of 10
66794	phenol degradation	30	6 of 20
66794	benzoyl-CoA degradation	28.57	2 of 7
66794	dolichyl-diphosphooligosaccharide biosynthesis	27.27	3 of 11
66794	metabolism of disaccharids	27.27	3 of 11
66794	cyclohexanol degradation	25	1 of 4
66794	lactate fermentation	25	1 of 4
66794	CMP-KDO biosynthesis	25	1 of 4
66794	degradation of sugar alcohols	25	4 of 16
66794	toluene degradation	25	1 of 4
66794	degradation of pentoses	21.43	6 of 28
66794	glutathione metabolism	21.43	3 of 14

Isolation, sampling and environmental information

Isolation source categories

Cat1	Cat2	Cat3
#Environmental	#Aquatic	#Freshwater
#Environmental	#Aquatic	#Pond (small)
#Environmental	#Aquatic	#Sediment
#Condition	#Anoxic (anaerobic)	-

Isolation

@ref	Sample type	Geographic location	Country	Country ISO 3 Code	Continent
6210	anaerobic sediment of eutrophic freshwater pond	Nijmegen, Dekkerswald	Netherlands	NLD	Europe

Taxonmaps

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

Interaction and safety

Risk assessment

@ref	Biosafety level	Biosafety level comment
6210	1	Risk group (German classification) According to TRBA 466

Sequence information

Genome sequences

@ref	Description	Assembly level	INSDC accession	BV-BRC accession	IMG accession	NCBI tax ID	Score
66792	IMG-taxon 2585427596 annotated assembly for Parasporobacterium paucivorans DSM 15970	contig	GCA_900141895	1122934.3	2585427596	1122934	66.54

16S sequences

@ref	Description	Accession	Length	Database	NCBI tax ID
6210	Parasporobacterium paucivorans partial 16S rRNA gene, strain SYR1	AJ272036	1487		115544

Genome-based predictions

Predictions

Predictions from Deep Learning for Genome Sequence Data. R package version 0.3.1 based on: Parasporobacterium paucivorans DSM 15970
NCBI: GCA_900141895

@ref	Trait	Model	Prediction	Confidence in %	In training data
125439	oxygen_tolerance	BacteriaNetⓘ	anaerobe	99.90	no
125439	gram_stain	BacteriaNetⓘ	variable	81.10	no
125439	motility	BacteriaNetⓘ	yes	68.10	no
125439	spore_formation	BacteriaNetⓘ	yes	58.00	no

Predictions from bacterial phenotypic traits through improved machine learning using high-quality, curated datasets based on: Parasporobacterium paucivorans DSM 15970
PATRIC: 1122934.3

@ref	Trait	Model	Prediction	Confidence in %	In training data
125438	gram-positive	gram-positiveⓘ	yes	62.42	no
125438	anaerobic	anaerobicⓘ	yes	93.20	yes
125438	spore-forming	spore-formingⓘ	no	52.11	no
125438	aerobic	aerobicⓘ	no	94.42	yes
125438	thermophilic	thermophileⓘ	no	84.92	yes
125438	flagellated	motile2+ⓘ	yes	74.46	no

Literature

Topic	Title	Authors	Journal	DOI	Year
Phylogeny	Deinococcus aerolatus sp. nov. and Deinococcus aerophilus sp. nov., isolated from air samples.	Yoo SH, Weon HY, Kim SJ, Kim YS, Kim BY, Kwon SW.	Int J Syst Evol Microbiol	10.1099/ijs.0.016030-0	2010

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 .
#125438	Julia Koblitz, Lorenz Christian Reimer, Rüdiger Pukall, Jörg Overmann: Predicting bacterial phenotypic traits through improved machine learning using high-quality, curated datasets. 2024 ( DOI 10.1101/2024.08.12.607695 )
#125439	Philipp Münch, René Mreches, Martin Binder, Hüseyin Anil Gündüz, Xiao-Yin To, Alice McHardy: deepG: Deep Learning for Genome Sequence Data. R package version 0.3.1 .
#126262	A. Lissin, I. Schober, J. F. Witte, H. Lüken, A. Podstawka, J. Koblitz, B. Bunk, P. Dawyndt, P. Vandamme, P. de Vos, J. Overmann, L. C. Reimer: StrainInfo—the central database for linked microbial strain identifiers. ( DOI 10.1093/database/baaf059 )

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Parasporobacterium paucivorans (DSM 15970, SYR 1)

Name and taxonomic classification

Morphology

Culture and growth conditions

Culture medium

Culture temp

Physiology and metabolism

Oxygen tolerance

Pathway annotation

Isolation, sampling and environmental information

Isolation source categories

Isolation

Taxonmaps

Interaction and safety

Risk assessment

Sequence information

Genome sequences

Genome browser: GCA_900141895

16S sequences

Genome-based predictions

Predictions

Literature

Literature

References

BacDive

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