Name: Propionicimonas paludicola Wd
Creator: BacDive
License: http://creativecommons.org/licenses/by-nc/4.0/

Strain identifier

BacDive ID: 12660

Type strain:

Species: Propionicimonas paludicola

Strain Designation: Wd

Culture col. no.: DSM 15597, JCM 11933, CCUG 53880

Strain history: A. Ueki strain Wd.

NCBI tax ID(s): 185243 (species)

SI-ID 128008

DSM 15597, JCM 11933, CCUG 53880

Other strains from Propionicimonas paludicola

P. paludicola WF, DSM 15598
P. paludicola JCM 11934

Section

Propionicimonas paludicola Wd is a microaerophile, mesophilic bacterium that was isolated from plant residue in irrigated rice field soil.

mesophilic
microaerophile
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	*Actinomycetota*
	Class	*Actinomycetes*
	Order	*Propionibacteriales*
	Family	*Propionibacteriaceae*
	Genus	*Propionicimonas*
	Species	**Propionicimonas paludicola**
	Full Scientific Name (LPSN)	Propionicimonas paludicola Akasaka et al. 2003

Information on culture and growth conditions Culture and growth conditions

[Ref.: #5898]

Culture medium

PYG MEDIUM (MODIFIED) (DSMZ Medium 104)

[Ref.: #5898]

Culture medium growth

[Ref.: #5898]

Culture medium link

Medium recipe at MediaDive

[Ref.: #5898]

Culture medium composition

expand / minimize

	Temperatures	Kind of temperature		Temperature
[Ref.: #5898]			growth	30 °C
[Ref.: #67770]			growth	30 °C

[Ref.: #5898]	Temperature range	mesophilic
[Ref.: #67770]	Temperature range	mesophilic

Information on physiology and metabolism Physiology and metabolism

[Ref.: #5898]

Oxygen tolerance

microaerophile

[Ref.: #67770]

Observation

quinones: MK-9(H₄), MK-10(H₄)

	Metabolite production	Metabolite	Production
[Ref.: #67770]		propionate ChEBI	yes

	Pathway	Enzyme coverage	Annotated reactions
	Pathway annotation	Computationally determined by
[Ref.: #66794]	cellulose degradation	100	5 of 5
[Ref.: #66794]	acetate fermentation	100	4 of 4
[Ref.: #66794]	palmitate biosynthesis	100	22 of 22
[Ref.: #66794]	cis-vaccenate biosynthesis	100	2 of 2
[Ref.: #66794]	starch degradation	100	10 of 10
[Ref.: #66794]	formaldehyde oxidation	100	3 of 3
[Ref.: #66794]	methylglyoxal degradation	100	5 of 5
[Ref.: #66794]	CDP-diacylglycerol biosynthesis	100	2 of 2
[Ref.: #66794]	UDP-GlcNAc biosynthesis	100	3 of 3
[Ref.: #66794]	lipoate biosynthesis	100	5 of 5
[Ref.: #66794]	folate polyglutamylation	100	1 of 1
[Ref.: #66794]	suberin monomers biosynthesis	100	2 of 2
[Ref.: #66794]	teichoic acid biosynthesis	100	1 of 1
[Ref.: #66794]	anapleurotic synthesis of oxalacetate	100	1 of 1
[Ref.: #66794]	photosynthesis	92.86	13 of 14
[Ref.: #66794]	serine metabolism	88.89	8 of 9
[Ref.: #66794]	CO2 fixation in Crenarchaeota	88.89	8 of 9
[Ref.: #66794]	propanol degradation	85.71	6 of 7
[Ref.: #66794]	NAD metabolism	83.33	15 of 18
[Ref.: #66794]	threonine metabolism	80	8 of 10
[Ref.: #66794]	glycogen metabolism	80	4 of 5
[Ref.: #66794]	peptidoglycan biosynthesis	80	12 of 15
[Ref.: #66794]	vitamin K metabolism	80	4 of 5
[Ref.: #66794]	alanine metabolism	79.31	23 of 29
[Ref.: #66794]	aspartate and asparagine metabolism	77.78	7 of 9
[Ref.: #66794]	valine metabolism	77.78	7 of 9
[Ref.: #66794]	chorismate metabolism	77.78	7 of 9
[Ref.: #66794]	pyrimidine metabolism	77.78	35 of 45
[Ref.: #66794]	vitamin B12 metabolism	76.47	26 of 34
[Ref.: #66794]	biotin biosynthesis	75	3 of 4
[Ref.: #66794]	glycogen biosynthesis	75	3 of 4
[Ref.: #66794]	gluconeogenesis	75	6 of 8
[Ref.: #66794]	C4 and CAM-carbon fixation	75	6 of 8
[Ref.: #66794]	glutamate and glutamine metabolism	75	21 of 28
[Ref.: #66794]	6-hydroxymethyl-dihydropterin diphosphate biosynthesis	75	6 of 8
[Ref.: #66794]	ppGpp biosynthesis	75	3 of 4
[Ref.: #66794]	sulfopterin metabolism	75	3 of 4
[Ref.: #66794]	proline metabolism	72.73	8 of 11
[Ref.: #66794]	pentose phosphate pathway	72.73	8 of 11
[Ref.: #66794]	metabolism of disaccharids	72.73	8 of 11
[Ref.: #66794]	ubiquinone biosynthesis	71.43	5 of 7
[Ref.: #66794]	citric acid cycle	71.43	10 of 14
[Ref.: #66794]	tetrahydrofolate metabolism	71.43	10 of 14
[Ref.: #66794]	cardiolipin biosynthesis	71.43	5 of 7
[Ref.: #66794]	heme metabolism	71.43	10 of 14
[Ref.: #66794]	glycolysis	70.59	12 of 17
[Ref.: #66794]	phenylalanine metabolism	69.23	9 of 13
[Ref.: #66794]	purine metabolism	68.09	64 of 94
[Ref.: #66794]	cyanate degradation	66.67	2 of 3
[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]	acetoin degradation	66.67	2 of 3
[Ref.: #66794]	L-lactaldehyde degradation	66.67	2 of 3
[Ref.: #66794]	non-pathway related	65.79	25 of 38
[Ref.: #66794]	oxidative phosphorylation	63.74	58 of 91
[Ref.: #66794]	d-xylose degradation	63.64	7 of 11
[Ref.: #66794]	degradation of sugar alcohols	62.5	10 of 16
[Ref.: #66794]	isoleucine metabolism	62.5	5 of 8
[Ref.: #66794]	histidine metabolism	62.07	18 of 29
[Ref.: #66794]	leucine metabolism	61.54	8 of 13
[Ref.: #66794]	isoprenoid biosynthesis	61.54	16 of 26
[Ref.: #66794]	lipid metabolism	61.29	19 of 31
[Ref.: #66794]	propionate fermentation	60	6 of 10
[Ref.: #66794]	Entner Doudoroff pathway	60	6 of 10
[Ref.: #66794]	metabolism of amino sugars and derivatives	60	3 of 5
[Ref.: #66794]	flavin biosynthesis	60	9 of 15
[Ref.: #66794]	glycine betaine biosynthesis	60	3 of 5
[Ref.: #66794]	degradation of aromatic, nitrogen containing compounds	58.33	7 of 12
[Ref.: #66794]	arginine metabolism	58.33	14 of 24
[Ref.: #66794]	methionine metabolism	57.69	15 of 26
[Ref.: #66794]	degradation of pentoses	57.14	16 of 28
[Ref.: #66794]	d-mannose degradation	55.56	5 of 9
[Ref.: #66794]	cysteine metabolism	55.56	10 of 18
[Ref.: #66794]	tryptophan metabolism	55.26	21 of 38
[Ref.: #66794]	vitamin B1 metabolism	53.85	7 of 13
[Ref.: #66794]	dTDPLrhamnose biosynthesis	50	4 of 8
[Ref.: #66794]	ethanol fermentation	50	1 of 2
[Ref.: #66794]	ketogluconate metabolism	50	4 of 8
[Ref.: #66794]	pantothenate biosynthesis	50	3 of 6
[Ref.: #66794]	degradation of hexoses	50	9 of 18
[Ref.: #66794]	adipate degradation	50	1 of 2
[Ref.: #66794]	lysine metabolism	50	21 of 42
[Ref.: #66794]	glycolate and glyoxylate degradation	50	3 of 6
[Ref.: #66794]	glycine metabolism	50	5 of 10
[Ref.: #66794]	phenylmercury acetate degradation	50	1 of 2
[Ref.: #66794]	coenzyme A metabolism	50	2 of 4
[Ref.: #66794]	butanoate fermentation	50	2 of 4
[Ref.: #66794]	vitamin E metabolism	50	2 of 4
[Ref.: #66794]	ribulose monophosphate pathway	50	1 of 2
[Ref.: #66794]	CMP-KDO biosynthesis	50	2 of 4
[Ref.: #66794]	aminopropanol phosphate biosynthesis	50	1 of 2
[Ref.: #66794]	phosphatidylethanolamine bioynthesis	46.15	6 of 13
[Ref.: #66794]	carotenoid biosynthesis	45.45	10 of 22
[Ref.: #66794]	vitamin B6 metabolism	45.45	5 of 11
[Ref.: #66794]	lipid A biosynthesis	44.44	4 of 9
[Ref.: #66794]	molybdenum cofactor biosynthesis	44.44	4 of 9
[Ref.: #66794]	tyrosine metabolism	42.86	6 of 14
[Ref.: #66794]	reductive acetyl coenzyme A pathway	42.86	3 of 7
[Ref.: #66794]	ethylmalonyl-CoA pathway	40	2 of 5
[Ref.: #66794]	arachidonate biosynthesis	40	2 of 5
[Ref.: #66794]	3-chlorocatechol degradation	40	2 of 5
[Ref.: #66794]	myo-inositol biosynthesis	40	4 of 10
[Ref.: #66794]	urea cycle	38.46	5 of 13
[Ref.: #66794]	androgen and estrogen metabolism	37.5	6 of 16
[Ref.: #66794]	carnitine metabolism	37.5	3 of 8
[Ref.: #66794]	glutathione metabolism	35.71	5 of 14
[Ref.: #66794]	acetyl CoA biosynthesis	33.33	1 of 3
[Ref.: #66794]	selenocysteine biosynthesis	33.33	2 of 6
[Ref.: #66794]	sulfoquinovose degradation	33.33	1 of 3
[Ref.: #66794]	IAA biosynthesis	33.33	1 of 3
[Ref.: #66794]	sphingosine metabolism	33.33	2 of 6
[Ref.: #66794]	(5R)-carbapenem carboxylate biosynthesis	33.33	1 of 3
[Ref.: #66794]	ascorbate metabolism	31.82	7 of 22
[Ref.: #66794]	coenzyme M biosynthesis	30	3 of 10
[Ref.: #66794]	phenol degradation	30	6 of 20
[Ref.: #66794]	bile acid biosynthesis, neutral pathway	29.41	5 of 17
[Ref.: #66794]	aclacinomycin biosynthesis	28.57	2 of 7
[Ref.: #66794]	benzoyl-CoA degradation	28.57	2 of 7
[Ref.: #66794]	mevalonate metabolism	28.57	2 of 7
[Ref.: #66794]	toluene degradation	25	1 of 4
[Ref.: #66794]	cyclohexanol degradation	25	1 of 4
[Ref.: #66794]	lactate fermentation	25	1 of 4
[Ref.: #66794]	allantoin degradation	22.22	2 of 9
[Ref.: #66794]	4-hydroxymandelate degradation	22.22	2 of 9
[Ref.: #66794]	arachidonic acid metabolism	22.22	4 of 18
[Ref.: #66794]	nitrate assimilation	22.22	2 of 9
		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.: #5898]	Sample type/isolated from	plant residue in irrigated rice field soil
[Ref.: #5898]	Geographic location (country and/or sea, region)	Yamagata
[Ref.: #5898]	Country	Japan
[Ref.: #5898]	Country ISO 3 Code	JPN
[Ref.: #5898]	Continent	Asia

[Ref.: #60050]	Sample type/isolated from	Plant residue in irrigated rice-field
[Ref.: #60050]	Geographic location (country and/or sea, region)	Yamagata Pref.
[Ref.: #60050]	Country	Japan
[Ref.: #60050]	Country ISO 3 Code	JPN
[Ref.: #60050]	Continent	Asia

[Ref.: #67770]	Sample type/isolated from	Plant residue in irrigated rice-field
[Ref.: #67770]	Geographic location (country and/or sea, region)	Yamagata Pref.
[Ref.: #67770]	Country	Japan
[Ref.: #67770]	Country ISO 3 Code	JPN
[Ref.: #67770]	Continent	Asia
* marker position based on {}

Isolation sources categories

#Engineered	#Agriculture	#Field
#Environmental	#Terrestrial	#Soil
#Host	#Plants	#Herbaceous plants (Grass,Crops)

What are isolation sources categories?

[Ref.: #69479]

Global distribution of 16S sequence FR733712 (>99% sequence identity) for Propionicimonas paludicola subclade from Microbeatlas

Aquatic Samples	717
Soil Samples	48
Animal Samples	41
Plant Samples	22
Total Samples	828

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

[Ref.: #5898]

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:

Only first 5 entries are displayed. Click here to see all.

	Sequence accession description	Seq. accession number	Sequence length (bp)	Sequence database	Associated NCBI tax ID
[Ref.: #5898]	Propionicimonas paludicola gene for 16S ribosomal RNA, partial sequence, strain:Wd	AB078858	1437	ENA	185243 tax ID
[Ref.: #20218]	Propionicimonas paludicola strain DSM 15597 16S ribosomal RNA gene, partial sequence	JQ899218	643	ENA	185243 tax ID	*
[Ref.: #20218]	Propionicimonas paludicola strain DSM 15597 16S ribosomal RNA gene, partial sequence	JQ899219	644	ENA	185243 tax ID	*
[Ref.: #20218]	Propionicimonas paludicola strain DSM 15597 16S ribosomal RNA gene, partial sequence	JQ899222	675	ENA	185243 tax ID	*
[Ref.: #20218]	Propionicimonas paludicola strain DSM 15597 16S ribosomal RNA gene, partial sequence	JQ899223	679	ENA	185243 tax ID	*
[Ref.: #20218]	Propionicimonas paludicola strain DSM 15597 16S ribosomal RNA gene, partial sequence	JQ899227	643	ENA	185243 tax ID	*
[Ref.: #20218]	Propionicimonas paludicola partial 16S rRNA gene, type strain DSM15597T	FR733712	1504	ENA	185243 tax ID	*

Genome sequence information:

	Sequence accession description	Seq. accession number	Assembly level	Sequence database	Associated NCBI tax ID
[Ref.: #67770]	Propionicimonas paludicola DSM 15597	GCA_002563675	contig	GenBank	185243 tax ID
[Ref.: #66792]	Propionicimonas paludicola strain DSM 15597	185243.3	wgs	PATRIC	185243 tax ID	*
[Ref.: #66792]	Propionicimonas paludicola DSM 15597	2627853595	draft	JGI IMG/M	185243 tax ID	*

[Ref.: #5898]	GC-content	68.7 mol%
[Ref.: #67770]	GC-content	68.7 mol%	high performance liquid chromatography (HPLC)

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

	Trait	Prediction	Confidence in %	In training data
	Predictions from Diaspora project based on: Propionicimonas paludicola strain DSM 15597 PATRIC: 185243.3
[Ref.: #69480]	motile	no	92.293	no
[Ref.: #69480]	gram-positive	yes	84.572	no
[Ref.: #69480]	anaerobic	no	89.754	yes
[Ref.: #69480]	aerobic	no	79.405	no
[Ref.: #69480]	halophile	no	96.443	no
[Ref.: #69480]	spore-forming	no	89.673	no
[Ref.: #69480]	glucose-util	yes	86.708	no
[Ref.: #69480]	flagellated	no	97.14	no
[Ref.: #69480]	thermophile	no	96.731	yes
[Ref.: #69480]	glucose-ferment	no	55.216	no

Availability in culture collections External links

[Ref.: #5898]

Culture collection no.

DSM 15597, JCM 11933, CCUG 53880

[Ref.: #81872]

SI-ID 128008

Literature:

Topic	Title	Authors	Journal	DOI	Year
Phylogeny	Propionicimonas ferrireducens sp. nov., isolated from dissimilatory iron(III)-reducing microbial enrichment obtained from paddy soil.	Zhou GW, Yang XR, Wadaan MAM, Hozzein WN, Zheng BX, Su JQ, Zhu YG	Int J Syst Evol Microbiol	10.1099/ijsem.0.002766	2018	*
Phylogeny	Propionicimonas paludicola gen. nov., sp. nov., a novel facultatively anaerobic, Gram-positive, propionate-producing bacterium isolated from plant residue in irrigated rice-field soil.	Akasaka H, Ueki A, Hanada S, Kamagata Y, Ueki K	Int J Syst Evol Microbiol	10.1099/ijs.0.02764-0	2003	*

References

#5898

Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 15597

#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 )

#60050 Culture Collection University of Gothenburg (CCUG) ; Curators of the CCUG; CCUG 53880

#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 )

#67770 Japan Collection of Microorganism (JCM) ; Curators of the JCM;

#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) .

#81872

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-ID128008.1 )

* These data were automatically processed and therefore are not curated

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Propionicimonas paludicola strain DSM 15597

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