Name: Planctomicrobium piriforme P3
Creator: BacDive
License: https://creativecommons.org/licenses/by/4.0/

Strain identifier

BacDive ID: 131336

Type strain:

Species: Planctomicrobium piriforme

Strain Designation: P3

Culture col. no.: DSM 26348, VKM B-2887

Strain history: <- S. N. Dedysh, Winogradsky Inst. Microbiol., RAS, Moscow, Russia; P3 <- I. S. Kulichevskaya

NCBI tax ID(s): 1576369 (species)

SI-ID 406861

DSM 26348

Special Collections

DSMZ

Section

When using BacDive for research please cite our paper

Planctomicrobium piriforme P3 is a mesophilic bacterium that was isolated from littoral sediment of a boreal lake.

mesophilic
16S sequence
Bacteria
genome sequence

Information on the name and the taxonomic classification. Name and taxonomic classification

	Last LPSN update	09-12-2024 (DD-MM-YYYY)
	Domain	*Bacteria*
	Phylum	*Planctomycetota*
	Class	*Planctomycetia*
	Order	*Planctomycetales*
	Family	*Planctomycetaceae*
	Genus	*Planctomicrobium*
	Species	**Planctomicrobium piriforme**
	Full Scientific Name (LPSN)	Planctomicrobium piriforme Kulichevskaya et al. 2015

Information on morphological and physiological properties Morphology

[Ref.: #125438]	Gram stain	negative Confidence in %93.483

Information on culture and growth conditions Culture and growth conditions

[Ref.: #22563]

Culture medium

PLANCTOMYCES PYREFORMIS MEDIUM (DSMZ Medium 1531)

[Ref.: #22563]

Culture medium growth

[Ref.: #22563]

Culture medium link

Medium recipe at MediaDive

[Ref.: #22563]

Culture medium composition

expand / minimize

	Temperatures	Kind of temperature		Temperature
[Ref.: #22563]			growth	28 °C

Information on physiology and metabolism Physiology and metabolism

[Ref.: #125439]

Oxygen tolerance

obligate aerobe Confidence in %98.9

[Ref.: #125439]

Ability of spore formation

no Confidence in %93.1

	Pathway	Enzyme coverage	Annotated reactions
	Pathway annotation	Computationally determined by
[Ref.: #66794]	L-lactaldehyde degradation	100	3 of 3
[Ref.: #66794]	C4 and CAM-carbon fixation	100	8 of 8
[Ref.: #66794]	acetoin degradation	100	3 of 3
[Ref.: #66794]	CDP-diacylglycerol biosynthesis	100	2 of 2
[Ref.: #66794]	coenzyme A metabolism	100	4 of 4
[Ref.: #66794]	aspartate and asparagine metabolism	100	9 of 9
[Ref.: #66794]	formaldehyde oxidation	100	3 of 3
[Ref.: #66794]	ethanol fermentation	100	2 of 2
[Ref.: #66794]	biotin biosynthesis	100	4 of 4
[Ref.: #66794]	methanofuran biosynthesis	100	5 of 5
[Ref.: #66794]	cis-vaccenate biosynthesis	100	2 of 2
[Ref.: #66794]	kanosamine biosynthesis II	100	2 of 2
[Ref.: #66794]	starch degradation	100	10 of 10
[Ref.: #66794]	gluconeogenesis	100	8 of 8
[Ref.: #66794]	palmitate biosynthesis	100	22 of 22
[Ref.: #66794]	adipate degradation	100	2 of 2
[Ref.: #66794]	ppGpp biosynthesis	100	4 of 4
[Ref.: #66794]	folate polyglutamylation	100	1 of 1
[Ref.: #66794]	anapleurotic synthesis of oxalacetate	100	1 of 1
[Ref.: #66794]	suberin monomers biosynthesis	100	2 of 2
[Ref.: #66794]	methylglyoxal degradation	100	5 of 5
[Ref.: #66794]	Entner Doudoroff pathway	90	9 of 10
[Ref.: #66794]	threonine metabolism	90	9 of 10
[Ref.: #66794]	chorismate metabolism	88.89	8 of 9
[Ref.: #66794]	valine metabolism	88.89	8 of 9
[Ref.: #66794]	serine metabolism	88.89	8 of 9
[Ref.: #66794]	heme metabolism	85.71	12 of 14
[Ref.: #66794]	ubiquinone biosynthesis	85.71	6 of 7
[Ref.: #66794]	phenylalanine metabolism	84.62	11 of 13
[Ref.: #66794]	NAD metabolism	83.33	15 of 18
[Ref.: #66794]	pentose phosphate pathway	81.82	9 of 11
[Ref.: #66794]	degradation of sugar alcohols	81.25	13 of 16
[Ref.: #66794]	3-chlorocatechol degradation	80	4 of 5
[Ref.: #66794]	glycine betaine biosynthesis	80	4 of 5
[Ref.: #66794]	lipid A biosynthesis	77.78	7 of 9
[Ref.: #66794]	molybdenum cofactor biosynthesis	77.78	7 of 9
[Ref.: #66794]	glycolysis	76.47	13 of 17
[Ref.: #66794]	isoleucine metabolism	75	6 of 8
[Ref.: #66794]	6-hydroxymethyl-dihydropterin diphosphate biosynthesis	75	6 of 8
[Ref.: #66794]	acetate fermentation	75	3 of 4
[Ref.: #66794]	CMP-KDO biosynthesis	75	3 of 4
[Ref.: #66794]	butanoate fermentation	75	3 of 4
[Ref.: #66794]	sulfopterin metabolism	75	3 of 4
[Ref.: #66794]	flavin biosynthesis	73.33	11 of 15
[Ref.: #66794]	methionine metabolism	73.08	19 of 26
[Ref.: #66794]	proline metabolism	72.73	8 of 11
[Ref.: #66794]	cardiolipin biosynthesis	71.43	5 of 7
[Ref.: #66794]	reductive acetyl coenzyme A pathway	71.43	5 of 7
[Ref.: #66794]	photosynthesis	71.43	10 of 14
[Ref.: #66794]	tetrahydrofolate metabolism	71.43	10 of 14
[Ref.: #66794]	purine metabolism	71.28	67 of 94
[Ref.: #66794]	propionate fermentation	70	7 of 10
[Ref.: #66794]	pyrimidine metabolism	68.89	31 of 45
[Ref.: #66794]	degradation of pentoses	67.86	19 of 28
[Ref.: #66794]	glutamate and glutamine metabolism	67.86	19 of 28
[Ref.: #66794]	lipid metabolism	67.74	21 of 31
[Ref.: #66794]	UDP-GlcNAc biosynthesis	66.67	2 of 3
[Ref.: #66794]	CO2 fixation in Crenarchaeota	66.67	6 of 9
[Ref.: #66794]	enterobactin biosynthesis	66.67	2 of 3
[Ref.: #66794]	d-mannose degradation	66.67	6 of 9
[Ref.: #66794]	cyanate degradation	66.67	2 of 3
[Ref.: #66794]	peptidoglycan biosynthesis	66.67	10 of 15
[Ref.: #66794]	glycolate and glyoxylate degradation	66.67	4 of 6
[Ref.: #66794]	tryptophan metabolism	65.79	25 of 38
[Ref.: #66794]	alanine metabolism	65.52	19 of 29
[Ref.: #66794]	isoprenoid biosynthesis	65.38	17 of 26
[Ref.: #66794]	lysine metabolism	64.29	27 of 42
[Ref.: #66794]	metabolism of disaccharids	63.64	7 of 11
[Ref.: #66794]	d-xylose degradation	63.64	7 of 11
[Ref.: #66794]	dTDPLrhamnose biosynthesis	62.5	5 of 8
[Ref.: #66794]	vitamin B1 metabolism	61.54	8 of 13
[Ref.: #66794]	leucine metabolism	61.54	8 of 13
[Ref.: #66794]	polyamine pathway	60.87	14 of 23
[Ref.: #66794]	non-pathway related	60.53	23 of 38
[Ref.: #66794]	cellulose degradation	60	3 of 5
[Ref.: #66794]	metabolism of amino sugars and derivatives	60	3 of 5
[Ref.: #66794]	gallate degradation	60	3 of 5
[Ref.: #66794]	glycogen metabolism	60	3 of 5
[Ref.: #66794]	lipoate biosynthesis	60	3 of 5
[Ref.: #66794]	histidine metabolism	58.62	17 of 29
[Ref.: #66794]	arginine metabolism	58.33	14 of 24
[Ref.: #66794]	citric acid cycle	57.14	8 of 14
[Ref.: #66794]	tyrosine metabolism	57.14	8 of 14
[Ref.: #66794]	propanol degradation	57.14	4 of 7
[Ref.: #66794]	nitrate assimilation	55.56	5 of 9
[Ref.: #66794]	oxidative phosphorylation	53.85	49 of 91
[Ref.: #66794]	degradation of sugar acids	52	13 of 25
[Ref.: #66794]	ascorbate metabolism	50	11 of 22
[Ref.: #66794]	phenylmercury acetate degradation	50	1 of 2
[Ref.: #66794]	coenzyme M biosynthesis	50	5 of 10
[Ref.: #66794]	1,4-dihydroxy-6-naphthoate biosynthesis	50	3 of 6
[Ref.: #66794]	carnitine metabolism	50	4 of 8
[Ref.: #66794]	cysteine metabolism	50	9 of 18
[Ref.: #66794]	ribulose monophosphate pathway	50	1 of 2
[Ref.: #66794]	glycine metabolism	50	5 of 10
[Ref.: #66794]	sphingosine metabolism	50	3 of 6
[Ref.: #66794]	quinate degradation	50	1 of 2
[Ref.: #66794]	glutathione metabolism	50	7 of 14
[Ref.: #66794]	lactate fermentation	50	2 of 4
[Ref.: #66794]	resorcinol degradation	50	1 of 2
[Ref.: #66794]	ketogluconate metabolism	50	4 of 8
[Ref.: #66794]	mannosylglycerate biosynthesis	50	1 of 2
[Ref.: #66794]	cyclohexanol degradation	50	2 of 4
[Ref.: #66794]	glycogen biosynthesis	50	2 of 4
[Ref.: #66794]	sulfate reduction	46.15	6 of 13
[Ref.: #66794]	phenylpropanoid biosynthesis	46.15	6 of 13
[Ref.: #66794]	vitamin B6 metabolism	45.45	5 of 11
[Ref.: #66794]	phenol degradation	45	9 of 20
[Ref.: #66794]	degradation of hexoses	44.44	8 of 18
[Ref.: #66794]	androgen and estrogen metabolism	43.75	7 of 16
[Ref.: #66794]	methanogenesis from CO2	41.67	5 of 12
[Ref.: #66794]	degradation of aromatic, nitrogen containing compounds	41.67	5 of 12
[Ref.: #66794]	vitamin K metabolism	40	2 of 5
[Ref.: #66794]	3-phenylpropionate degradation	40	6 of 15
[Ref.: #66794]	myo-inositol biosynthesis	40	4 of 10
[Ref.: #66794]	arachidonate biosynthesis	40	2 of 5
[Ref.: #66794]	urea cycle	38.46	5 of 13
[Ref.: #66794]	dolichyl-diphosphooligosaccharide biosynthesis	36.36	4 of 11
[Ref.: #66794]	acetyl CoA biosynthesis	33.33	1 of 3
[Ref.: #66794]	octane oxidation	33.33	1 of 3
[Ref.: #66794]	(5R)-carbapenem carboxylate biosynthesis	33.33	1 of 3
[Ref.: #66794]	IAA biosynthesis	33.33	1 of 3
[Ref.: #66794]	4-hydroxymandelate degradation	33.33	3 of 9
[Ref.: #66794]	selenocysteine biosynthesis	33.33	2 of 6
[Ref.: #66794]	arachidonic acid metabolism	33.33	6 of 18
[Ref.: #66794]	pantothenate biosynthesis	33.33	2 of 6
[Ref.: #66794]	carotenoid biosynthesis	31.82	7 of 22
[Ref.: #66794]	4-hydroxyphenylacetate degradation	30	3 of 10
[Ref.: #66794]	benzoyl-CoA degradation	28.57	2 of 7
[Ref.: #66794]	aclacinomycin biosynthesis	28.57	2 of 7
[Ref.: #66794]	cholesterol biosynthesis	27.27	3 of 11
[Ref.: #66794]	toluene degradation	25	1 of 4
[Ref.: #66794]	catecholamine biosynthesis	25	1 of 4
[Ref.: #66794]	alginate biosynthesis	25	1 of 4
[Ref.: #66794]	chlorophyll metabolism	22.22	4 of 18
		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.: #22563]	Sample type/isolated from	littoral sediment of a boreal lake
[Ref.: #22563]	Geographic location (country and/or sea, region)	Republic of Karelia, Valaam Island (61° 22' N 30° 56' E)
[Ref.: #22563]	Country	Russia
[Ref.: #22563]	Country ISO 3 Code	RUS
[Ref.: #22563]	Continent	Europe
[Ref.: #22563]	Geographic location	61.3667°/30.9333°
* marker position based on {}

Isolation sources categories

#Environmental	#Aquatic	#Lake (large)
#Environmental	#Aquatic	#Sediment
#Climate	#Temperate	#Boreal

What are isolation sources categories?

[Ref.: #69479]

Global distribution of 16S sequence KP161655 (>99% sequence identity) for Planctomicrobium piriforme subclade from Microbeatlas

Aquatic Samples	90
Soil Samples	164
Animal Samples	53
Plant Samples	8
Total Samples	315

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

[Ref.: #22563]

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.: #22563]	Planctomicrobium piriforme strain P3 16S ribosomal RNA gene, partial sequence	KP161655	1426	GenBank ENA	1576369 tax ID

Genome sequence information:

	Sequence accession description	Seq. accession number	Assembly level	Sequence database	Associated NCBI tax ID
[Ref.: #66792]	Planctomicrobium piriforme DSM 26348	GCA_900113665	contig	GenBank ENA	1576369 tax ID	*
[Ref.: #66792]	Planctomicrobium piriforme strain DSM 26348	1576369.4	wgs	PATRIC	1576369 tax ID	*
[Ref.: #66792]	Planctomicrobium piriforme DSM 26348	2675903691	draft	JGI IMG/M	1576369 tax ID	*

[Ref.: #22563]

GC-content

59.0 mol%

thermal denaturation, midpoint method (Tm)

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

	Model	Trait	Prediction	Confidence in %	In training data
	Predictions from bacterial phenotypic traits through improved machine learning using high-quality, curated datasets based on: Planctomicrobium piriforme strain DSM 26348 PATRIC: 1576369.4
[Ref.: #125438]	gram-positive	gram-positiveⓘ	no	93.483	no
[Ref.: #125438]	anaerobic	anaerobicⓘ	no	91.321	no
[Ref.: #125438]	spore-forming	spore-formingⓘ	no	75.151	no
[Ref.: #125438]	aerobic	aerobicⓘ	yes	80.36	no
[Ref.: #125438]	thermophile	thermophilicⓘ	no	91.886	yes
[Ref.: #125438]	motile2+	flagellatedⓘ	no	56.354	no

	Model	Trait	Prediction	Confidence in %
	Predictions from Deep Learning for Genome Sequence Data. R package version 0.3.1 based on: Planctomicrobium piriforme DSM 26348 NCBI: GCA_900113665
[Ref.: #125439]	BacteriaNet	spore_formationⓘ	no	93.1
[Ref.: #125439]	BacteriaNet	motilityⓘ	yes	62.5
[Ref.: #125439]	BacteriaNet	gram_stainⓘ	negative	85.6
[Ref.: #125439]	BacteriaNet	oxygen_toleranceⓘ	obligate aerobe	98.9

Availability in culture collections External links

[Ref.: #22563]

Culture collection no.

DSM 26348, VKM B-2887

[Ref.: #89777]

SI-ID 406861

Literature:

Topic	Title	Authors	Journal	DOI	Year
Phylogeny	Planctomicrobium piriforme gen. nov., sp. nov., a stalked planctomycete from a littoral wetland of a boreal lake.	Kulichevskaya IS, Ivanova AA, Detkova EN, Rijpstra WIC, Sinninghe Damste JS, Dedysh SN	Int J Syst Evol Microbiol	10.1099/ijs.0.000154	2015	*
Phylogeny	Alienimonas californiensis gen. nov. sp. nov., a novel Planctomycete isolated from the kelp forest in Monterey Bay.	Boersma AS, Kallscheuer N, Wiegand S, Rast P, Peeters SH, Mesman RJ, Heuer A, Boedeker C, Jetten MSM, Rohde M, Jogler M, Jogler C	Antonie Van Leeuwenhoek	10.1007/s10482-019-01367-4	2019	*

References

#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 )

#22563

Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 26348

#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 .

#89777

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-ID406861.1 )

#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 .

* These data were automatically processed and therefore are not curated

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Planctomicrobium piriforme strain DSM 26348

Planctomicrobium piriforme DSM 26348

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