Name: Paludibaculum fermentans P105
Creator: BacDive
License: https://creativecommons.org/licenses/by/4.0/

Strain identifier

BacDive ID: 24778

Type strain:

Species: Paludibaculum fermentans

Strain Designation: P105

Culture col. no.: DSM 26340, VKM B-2878

Strain history: <- S. N. Dedysh, Winogradsky Inst. Microbiol., RAS, Moscow, Russia; P105 <- I. S. Kulichevskaya

NCBI tax ID(s): 1473598 (species)

SI-ID 404464

DSM 26340

Special Collections

DSMZ

Section

Paludibaculum fermentans P105 is a microaerophile, Gram-negative bacterium that was isolated from anoxic peat layer of littoral wetland.

Gram-negative
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	*Acidobacteriota*
	Class	*Terriglobia*
	Order	*Bryobacterales*
	Family	*Bryobacteraceae*
	Genus	*Paludibaculum*
	Species	**Paludibaculum fermentans**
	Full Scientific Name (LPSN)	Paludibaculum fermentans Kulichevskaya et al. 2014

Information on morphological and physiological properties Morphology

[Ref.: #21349]

Incubation period

3-7 days

Information on culture and growth conditions Culture and growth conditions

[Ref.: #21349]

Culture medium

PLANCTOMYCES PYREFORMIS MEDIUM (DSMZ Medium 1531)

[Ref.: #21349]

Culture medium growth

[Ref.: #21349]

Culture medium link

Medium recipe at MediaDive

[Ref.: #21349]

Culture medium composition

expand / minimize

	Temperatures	Kind of temperature		Temperature
[Ref.: #21349]			growth	25 °C

Information on physiology and metabolism Physiology and metabolism

[Ref.: #21349]

Oxygen tolerance

microaerophile

	Metabolite	Utilization activity	Kind of utilization tested
[Ref.: #68369]	adipate ChEBI	-	assimilation	* from API 20NE
[Ref.: #68369]	arginine ChEBI	-	hydrolysis	* from API 20NE
[Ref.: #68369]	D-glucose ChEBI	-	assimilation	* from API 20NE
[Ref.: #68369]	D-glucose ChEBI	-	fermentation	* from API 20NE
[Ref.: #68369]	D-mannitol ChEBI	-	assimilation	* from API 20NE
[Ref.: #68369]	D-mannose ChEBI	-	assimilation	* from API 20NE
[Ref.: #68369]	decanoate ChEBI	-	assimilation	* from API 20NE
[Ref.: #68369]	esculin ChEBI	+	hydrolysis	* from API 20NE
[Ref.: #68369]	gelatin ChEBI	-	hydrolysis	* from API 20NE
[Ref.: #68369]	gluconate ChEBI	-	assimilation	* from API 20NE
[Ref.: #68369]	L-arabinose ChEBI	-	assimilation	* from API 20NE
[Ref.: #68369]	malate ChEBI	-	assimilation	* from API 20NE
[Ref.: #68369]	maltose ChEBI	-	assimilation	* from API 20NE
[Ref.: #68369]	N-acetylglucosamine ChEBI	-	assimilation	* from API 20NE
[Ref.: #68369]	tryptophan ChEBI	-	energy source	* from API 20NE
[Ref.: #68369]	urea ChEBI	-	hydrolysis	* from API 20NE
	Only first 10 entries are displayed. Click here to see all.

	Metabolite production	Metabolite	Production
[Ref.: #68369]		indole ChEBI	no	* from API 20NE

	Physiological tests	Metabolite	Indole test
[Ref.: #68369]		indole ChEBI	-	* from API 20NE

	Enzyme	Enzyme activity	EC number
[Ref.: #68382]	alkaline phosphatase	+	3.1.3.1	* from API zym
[Ref.: #68382]	alpha-chymotrypsin	-	3.4.21.1	* from API zym
[Ref.: #68382]	alpha-fucosidase	-	3.2.1.51	* from API zym
[Ref.: #68382]	alpha-galactosidase	-	3.2.1.22	* from API zym
[Ref.: #68382]	alpha-glucosidase	-	3.2.1.20	* from API zym
[Ref.: #68382]	alpha-mannosidase	-	3.2.1.24	* from API zym
[Ref.: #68369]	arginine dihydrolase	-	3.5.3.6	* from API 20NE
[Ref.: #68369]	beta-glucosidase	+	3.2.1.21	* from API 20NE
[Ref.: #68382]	beta-glucosidase	-	3.2.1.21	* from API zym
[Ref.: #68382]	beta-glucuronidase	-	3.2.1.31	* from API zym
[Ref.: #68382]	cystine arylamidase	-	3.4.11.3	* from API zym
[Ref.: #68382]	esterase lipase (C 8)	-		* from API zym
[Ref.: #68369]	gelatinase	-		* from API 20NE
[Ref.: #68382]	leucine arylamidase	+	3.4.11.1	* from API zym
[Ref.: #68382]	lipase (C 14)	-		* from API zym
[Ref.: #68382]	N-acetyl-beta-glucosaminidase	-	3.2.1.52	* from API zym
[Ref.: #68382]	trypsin	-	3.4.21.4	* from API zym
[Ref.: #68369]	urease	-	3.5.1.5	* from API 20NE
[Ref.: #68382]	valine arylamidase	+		* from API zym
	Only first 10 entries are displayed. Click here to see all.

API® 20NE:

Note that the displayed test results represent raw data and therefore may deviate!

	API ID	Reduction of nitratesNO3	Indole productionTRP	Fermentation of D-glucoseGLU_ Ferm	Arginine dihydrolaseADH (Arg)	Urease/urea hydrolysisURE	Esculin hydrolysis/beta-GlucosidaseESC	Gelatinase/gelatin hydrolysisGEL	beta-GalactosidasePNPG	Assimilation of D-glucoseGLU_ Assim	Assimilation of L-arabinoseARA	Assimilation of D-mannoseMNE	Assimilation of D-mannitolMAN	Assimilation of N-acetyl-glucosamineNAG	Assimilation of maltoseMAL	Assimilation of gluconateGNT	Assimilation of capric acidCAP	Assimilation adipic acidADI	Assimilation of malic acidMLT	Assimilation of citric acidCIT	Assimilation of phenyl-acetic acidPAC	Cytochrome oxidaseOX
[Ref.: #21349]	23928	+	-	-	-	-	+	-	+	-	-	-	-	-	-	-	-	-	-	-	-	not determinedn.d.
[Ref.: #21349]	25332	-	-	-	-	-	+	-	+/-	-	-	-	-	-	-	-	-	-	-	-	-	not determinedn.d.

API® zym:

Note that the displayed test results represent raw data and therefore may deviate!

	API ID	Control	2-naphthyl phosphateAlkaline phosphatase	2-naphthyl butyrateEsterase (C 4)	2-naphtyl caprylateEsterase Lipase (C 8)	2-naphthyl myristateLipase (C 14)	L-leucyl-2-naphthylamideLeucine arylamidase	L-valyl-2-naphthylamideValine arylamidase	L-cystyl-2-naphthylamideCystine arylamidase	N-benzoyl-DL-arginine-2-naphthylamideTrypsin	N-glutaryl-phenylalanine-2-naphthylamidealpha- Chymotrypsin	2-naphthyl phosphateAcid phosphatase	Naphthol-AS-BI-phosphateNaphthol-AS-BI-phosphohydrolase	6-Br-2-naphthyl-alphaD-galactpyranosidealpha- Galactosidase	2-naphthyl-betaD-galactpyranosidebeta- Galactosidase	Naphthol-AS-BI-betaD-glucuronidebeta- Glucuronidase	2-naphthyl-alphaD-glucopyranosidealpha- Glucosidase	6-Br-2-naphthyl-betaD-glucopyranosidebeta- Glucosidase	1-naphthyl-N-acetyl-betaD-glucosaminideN-acetyl-beta- glucosaminidase	6-Br-2-naphthyl-alphaD-mannopyranosidealpha- Mannosidase	2-naphthyl-alphaL-fucopyranosidealpha- Fucosidase
[Ref.: #21349]	14335	-	+	+/-	-	-	+	+	-	-	-	+/-	+/-	-	+/-	-	-	-	-	-	-

Information on isolation source, the sampling and environmental conditions Isolation, sampling and environmental information

[Ref.: #21349]	Sample type/isolated from	anoxic peat layer of littoral wetland
[Ref.: #21349]	Geographic location (country and/or sea, region)	Republic of Karelia, Valaam island in Lake Ladoga
[Ref.: #21349]	Country	Russia
[Ref.: #21349]	Country ISO 3 Code	RUS
[Ref.: #21349]	Continent	Europe
[Ref.: #21349]	Geographic location	61.3667°/30.9333°
* marker position based on {}

Isolation sources categories

#Environmental	#Terrestrial	#Wetland (Swamp)
#Host	#Plants	#Peat moss
#Condition	#Anoxic (anaerobic)	-

What are isolation sources categories?

[Ref.: #69479]

Global distribution of 16S sequence KJ461654 (>99% sequence identity) for Paludibaculum fermentans subclade from Microbeatlas

Aquatic Samples	136
Soil Samples	159
Animal Samples	25
Plant Samples	15
Total Samples	335

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

[Ref.: #21349]

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.: #21349]	Paludibaculum fermentans strain P105 16S ribosomal RNA gene, partial sequence	KJ461654	1413	GenBank ENA	1473598 tax ID

Genome sequence information:

	Sequence accession description	Seq. accession number	Assembly level	Sequence database	Associated NCBI tax ID
[Ref.: #66792]	Paludibaculum fermentans P105	GCA_015277775	complete	GenBank ENA	1473598 tax ID	*

[Ref.: #21349]

GC-content

60.5 mol%

thermal denaturation, midpoint method (Tm)

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

	Trait	Model	Prediction	Confidence in %	In training data
	Predictions from GenomeNet Sporulation v. 1 based on: Paludibaculum fermentans P105 NCBI: GCA_015277775.1
[Ref.: #69481]	spore-forming	spore-formingⓘ	no	81	no

	Trait	Model	Prediction	Confidence in %	In training data
	Predictions from Diaspora project based on: Paludibaculum fermentans P105 NCBI: GCA_015277775.1
[Ref.: #69480]	gram-positive	gram-positiveⓘ	no	85.409	no
[Ref.: #69480]	anaerobic	anaerobicⓘ	no	84.948	no
[Ref.: #69480]	aerobic	aerobicⓘ	yes	71.921	no
[Ref.: #69480]	spore-forming	spore-formingⓘ	no	70.091	no
[Ref.: #69480]	thermophilic	thermophileⓘ	no	94.339	yes
[Ref.: #69480]	flagellated	motile2+ⓘ	yes	52.723	no

Availability in culture collections External links

[Ref.: #21349]

Culture collection no.

DSM 26340, VKM B-2878

[Ref.: #88603]

SI-ID 404464

Literature:

Topic	Title	Authors	Journal	DOI	Year
Phylogeny	Paludibaculum fermentans gen. nov., sp. nov., a facultative anaerobe capable of dissimilatory iron reduction from subdivision 3 of the Acidobacteria.	Kulichevskaya IS, Suzina NE, Rijpstra WIC, Damste JSS, Dedysh SN	Int J Syst Evol Microbiol	10.1099/ijs.0.066175-0	2014	*

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 )

#21349

Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 26340

#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) .

#68369

Automatically annotated from API 20NE .

#68382

Automatically annotated from API zym .

#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 )

#88603

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-ID404464.1 )

* These data were automatically processed and therefore are not curated

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