Name: Pediococcus pentosaceus P. lin
Creator: BacDive
License: http://creativecommons.org/licenses/by-nc/4.0/

Strain identifier

BacDive ID: 6392

Type strain:

Species: Pediococcus pentosaceus

Strain Designation: P. lin

Culture col. no.: DSM 20333, ATCC 33314, IFO 3884, NBRC 3884, NCDO 1859, JCM 5885, BCRC 14053, CGMCC 1.2441, KCTC 3116, LMG 11385, NCIMB 12009, VKM B-2206, VTT E-88312, CIP 102261

Strain history: CIP <- 1986, NCFB, Pediococcus acidilactici <- 1965, IFO <- K. Kitahara, Pediococcus hennebergii

NCBI tax ID(s): 1255 (species)

SI-ID 14183

LMG 11385, ATCC 33314, DSM 20333, IFO 3884, NCFB 1859, NCIMB 12009, NCDO 1859, CIP 102261, JCM 5885, CCRC 14053, VKM B-2206, KCTC 3116, NBRC 3884, BCC 5373, BCRC 14053, CGMCC 1.2441, VTT E-88312

Other strains from Pediococcus pentosaceus

Section

Pediococcus pentosaceus P. lin is a mesophilic human pathogen that was isolated from sake mash.

human pathogen
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	*Bacilli*
	Order	*Lactobacillales*
	Family	*Lactobacillaceae*
	Genus	*Pediococcus*
	Species	**Pediococcus pentosaceus**
	Full Scientific Name (LPSN)	Pediococcus pentosaceus Mees 1934 (Approved Lists 1980)

Information on morphological and physiological properties Morphology

[Ref.: #69480]	Gram stain	positive Confidence in %100

[Ref.: #69480]	Motility	no Confidence in %92.821

Information on culture and growth conditions Culture and growth conditions

[Ref.: #8724]

Culture medium

MRS MEDIUM (DSMZ Medium 11)

[Ref.: #8724]

Culture medium growth

[Ref.: #8724]

Culture medium link

Medium recipe at MediaDive

[Ref.: #8724]

Culture medium composition

expand / minimize

[Ref.: #38895]

Culture medium

MEDIUM 41- for Lactobacillus, Leuconostoc, Weissella, Pediococcus, Sporolactobacillus inulinus

[Ref.: #38895]

Culture medium growth

[Ref.: #38895]

Culture medium composition

expand / minimize

[Ref.: #121663]

Culture medium

CIP Medium 41

[Ref.: #121663]

Culture medium growth

[Ref.: #121663]

Culture medium link

Medium recipe provided by DSMZ

		Temperature
[Ref.: #8724]	growth	30 °C
[Ref.: #38895]	growth	30 °C
[Ref.: #67770]	growth	37 °C

[Ref.: #8724]	Temperature range	mesophilic
[Ref.: #38895]	Temperature range	mesophilic
[Ref.: #67770]	Temperature range	mesophilic

Information on physiology and metabolism Physiology and metabolism

[Ref.: #69481]	Ability of spore formation	no Confidence in %98
[Ref.: #69480]	Ability of spore formation	no Confidence in %99.95

[Ref.: #8724]	Murein short key	A11.31
[Ref.: #8724]	Murein types	A4alpha L-Lys-D-Asp

	Metabolite	Utilization activity	Kind of utilization tested
[Ref.: #68371]	amygdalin ChEBI	+	builds acid from	* from API 50CH acid
[Ref.: #68371]	arbutin ChEBI	+	builds acid from	* from API 50CH acid
[Ref.: #68371]	cellobiose ChEBI	+	builds acid from	* from API 50CH acid
[Ref.: #68371]	D-arabinose ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #68371]	D-arabitol ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #68371]	D-fructose ChEBI	+	builds acid from	* from API 50CH acid
[Ref.: #68371]	D-fucose ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #68371]	D-galactose ChEBI	+	builds acid from	* from API 50CH acid
[Ref.: #68371]	D-glucose ChEBI	+	builds acid from	* from API 50CH acid
[Ref.: #68371]	D-lyxose ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #68371]	D-mannitol ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #68371]	D-mannose ChEBI	+	builds acid from	* from API 50CH acid
[Ref.: #68371]	D-ribose ChEBI	+	builds acid from	* from API 50CH acid
[Ref.: #68371]	D-sorbitol ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #68371]	D-tagatose ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #68371]	D-xylose ChEBI	+	builds acid from	* from API 50CH acid
[Ref.: #68371]	erythritol ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #68371]	esculin ChEBI	+	builds acid from	* from API 50CH acid
[Ref.: #68371]	galactitol ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #68371]	gentiobiose ChEBI	+	builds acid from	* from API 50CH acid
[Ref.: #68371]	gluconate ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #68371]	glycerol ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #68371]	glycogen ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #68371]	inulin ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #68371]	L-arabinose ChEBI	+	builds acid from	* from API 50CH acid
[Ref.: #68371]	L-arabitol ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #68371]	L-fucose ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #68371]	L-rhamnose ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #68371]	L-sorbose ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #68371]	L-xylose ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #68371]	lactose ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #68371]	maltose ChEBI	+	builds acid from	* from API 50CH acid
[Ref.: #68371]	melezitose ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #68371]	melibiose ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #68371]	methyl alpha-D-glucopyranoside ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #68371]	methyl alpha-D-mannoside ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #68371]	methyl beta-D-xylopyranoside ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #68371]	myo-inositol ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #68371]	N-acetylglucosamine ChEBI	+	builds acid from	* from API 50CH acid
[Ref.: #68371]	Potassium 2-ketogluconate ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #68371]	Potassium 5-ketogluconate ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #68371]	raffinose ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #68371]	ribitol ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #68371]	salicin ChEBI	+	builds acid from	* from API 50CH acid
[Ref.: #68371]	starch ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #68371]	sucrose ChEBI	+	builds acid from	* from API 50CH acid
[Ref.: #68371]	trehalose ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #68371]	turanose ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #68371]	xylitol ChEBI	-	builds acid from	* from API 50CH acid
	Only first 10 entries are displayed. Click here to see all.

API® 50CH acid:

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

	API ID	ControlQ	Acid from glycerolGLY	Acid from erythritolERY	Acid from D-arabinoseDARA	Acid from L-arabinoseLARA	Acid from D-riboseRIB	Acid from D-xyloseDXYL	Acid from L-xyloseLXYL	Acid from D-adonitolADO	Acid from methyl beta-D-xylopyranosideMDX	Acid from D-galactoseGAL	Acid from D-glucoseGLU	Acid from D-fructoseFRU	Acid from D-mannoseMNE	Acid from L-sorboseSBE	Acid from L-rhamnoseRHA	Acid from dulcitolDUL	Acid from inositolINO	Acid from D-mannitolMAN	Acid from D-sorbitolSOR	Acid from methyl alpha-D-mannopyranosideMDM	Acid from methyl alpha-D-glucopyranosideMDG	Acid from N-acetyl-glucosamineNAG	Acid from amygdalinAMY	Acid from arbutinARB	Acid from esculinESC	Acid from salicinSAL	Acid from cellobioseCEL	Acid from maltoseMAL	Acid from lactoseLAC	Acid from melibioseMEL	Acid from sucroseSAC	Acid from trehaloseTRE	Acid from inulinINU	Acid from melezitoseMLZ	Acid from raffinoseRAF	Acid from starchAMD	Acid from glycogenGLYG	Acid from xylitolXLT	Acid from gentiobioseGEN	Acid from turanoseTUR	Acid from D-lyxoseLYX	Acid from D-tagatoseTAG	Acid from D-fucoseDFUC	Acid from L-fucoseLFUC	Acid from D-arabitolDARL	Acid from L-arabitolLARL	Acid from gluconateGNT	Acid from 2-Ketogluconate2KG	Acid from 5-Ketogluconate5KG
[Ref.: #8724]	14625	-	-	-	-	+	+	+	-	-	-	+	+	+	+	-	-	-	-	-	-	-	-	+	+	+	+	+	+	+	-	-	+	-	-	-	-	-	-	-	+	-	-	-	-	-	-	-	-	-	-

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

[Ref.: #8724]	Sample type/isolated from	sake mash

[Ref.: #67770]	Sample type/isolated from	Sake mash

[Ref.: #121663]	Sample type/isolated from	Food, Sake mash
* marker position based on {}

Isolation sources categories

#Engineered	#Food production	#Fermented
#Engineered	#Food production	#Beverage

What are isolation sources categories?

[Ref.: #69479]

Global distribution of 16S sequence LC096205 (>99% sequence identity) for Pediococcus from Microbeatlas

Aquatic Samples	2228
Soil Samples	2103
Animal Samples	26184
Plant Samples	1535
Total Samples	32050

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

[Ref.: #8724]	Pathogenicity (human)	yes, in single cases
[Ref.: #8724]	Biosafety level	1	Risk group (German classification) According to TRBA 466
[Ref.: #121663]	Biosafety level	1	Risk group (French classification)

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.: #67770]	Pediococcus pentosaceus gene for 16S ribosomal RNA, partial sequence, strain: JCM 5885	LC096205	1486	ENA	1255 tax ID
[Ref.: #20218]	Pediococcus pentosaceus clone P24 16S ribosomal RNA gene, partial sequence	AF404733	516	ENA	1255 tax ID	*
[Ref.: #20218]	Pediococcus pentosaceus clone P24 16S ribosomal RNA gene, partial sequence; 16S-23S ribosomal RNA intergenic spacer, complete sequence; and 23S ribosomal RNA gene, partial sequence	AF405377	536	ENA	1255 tax ID	*

Genome sequence information:

	Sequence accession description	Seq. accession number	Assembly level	Sequence database	Associated NCBI tax ID
[Ref.: #66792]	Pediococcus pentosaceus DSM 20333	GCA_015613245	scaffold	GenBank	1255 tax ID	*
[Ref.: #66792]	Pediococcus pentosaceus strain DSM 20333	1255.182	wgs	PATRIC	1255 tax ID	*
[Ref.: #66792]	Pediococcus pentosaceus strain FDAARGOS_873	1255.193	complete	PATRIC	1255 tax ID	*

[Ref.: #8724]	GC-content	39.2 mol%
[Ref.: #67770]	GC-content	37.8 mol%

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: Pediococcus pentosaceus strain FDAARGOS_873 strain Not applicable PATRIC: 1255.193
[Ref.: #69481]	spore-forming	no	98	no

	Trait	Prediction	Confidence in %	In training data
	Predictions from Diaspora project based on: Pediococcus pentosaceus strain FDAARGOS_873 strain Not applicable PATRIC: 1255.193
[Ref.: #69480]	motile	no	94.311	no
[Ref.: #69480]	gram-positive	yes	96.886	no
[Ref.: #69480]	anaerobic	no	86.927	no
[Ref.: #69480]	aerobic	no	98.187	no
[Ref.: #69480]	halophile	yes	94.557	no
[Ref.: #69480]	spore-forming	no	94.878	no
[Ref.: #69480]	thermophile	no	99.701	no
[Ref.: #69480]	glucose-util	yes	91.824	no
[Ref.: #69480]	flagellated	no	98.363	no
[Ref.: #69480]	glucose-ferment	yes	90.677	no

Availability in culture collections External links

[Ref.: #8724]

Culture collection no.

DSM 20333, ATCC 33314, IFO 3884, NBRC 3884, NCDO 1859, JCM 5885, BCRC 14053, CGMCC 1.2441, KCTC 3116, LMG 11385, NCIMB 12009, VKM B-2206, VTT E-88312, CIP 102261

[Ref.: #75865]

SI-ID 14183

References

#8724

Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 20333

#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 )

#38895 ; Curators of the CIP;

#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) .

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

#68371

Automatically annotated from API 50CH acid .

#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 )

#75865

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-ID14183.1 )

#121663 Collection of Institut Pasteur ; Curators of the CIP; CIP 102261
* These data were automatically processed and therefore are not curated

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Pediococcus pentosaceus strain FDAARGOS_873 strain Not applicable

Pediococcus pentosaceus strain FDAARGOS_873 strain Not applicable

Change proposal

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