Pediococcus pentosaceus (DSM 20333, ATCC 33314, IFO 3884)

Name: Pediococcus pentosaceus (DSM 20333, ATCC 33314, IFO 3884)
Creator: BacDive
License: http://creativecommons.org/licenses/by/4.0/

BacDive ID 6392

Type strain

Strain Designation P. lin

Culture col. no. DSM 20333 ATCC 33314 IFO 3884 NBRC 3884 NCDO 1859 10 more

NCBI tax ID(s) 1255

Special Collections DSMZ JCM KCTC CIP

History <- NCDO (Pediococcus acidilactici) <- IFO <- K. Kitahara, P. lin ATCC 33314 <-- NCDO 1859 <-- IFO 3884 <-- K. Kitahara. CIP <- 1986, NCFB, Pediococcus acidilactici <- 1965, IFO <- K. Kitahara, Pediococcus hennebergii

Links

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

mesophilic genome sequence 16S sequence

Name and taxonomic classification

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

@ref 20215

Last LPSN update 2025-12-16 09:48:18

Domain Bacillati

Phylum Bacillota

Class Bacilli

Order Lactobacillales

Family Lactobacillaceae

Genus Pediococcus

Species Pediococcus pentosaceus

Full scientific name Pediococcus pentosaceus Mees 1934 (Approved Lists 1980)

BacDive ID	Other strains from **Pediococcus pentosaceus** (40)	Type strain
6393	P. pentosaceus DSM 20336, ATCC 33316, NCDO 990, WDCM 00158, ... (type strain)
6388	P. pentosaceus 32, DSM 20206, ATCC 8081, CCM 1578, NCDO ...
6389	P. pentosaceus 243d, DSM 20280
6390	P. pentosaceus 260a, DSM 20281
6391	P. pentosaceus 247c, DSM 20283
6394	P. pentosaceus Coster R 3, CCUG 28436, DSM 46292, CCM 822, ...
130992	P. pentosaceus JM-6755-f-WT, JM-80, DSM 28628
136079	P. pentosaceus CIP 102333
136495	P. pentosaceus CIP 54.91
136496	P. pentosaceus CIP 54.92, ATCC 10791, NCDO 814, NCTC 8066, ...
137006	P. pentosaceus 2001886, CIP 109663
137941	P. pentosaceus CIP 102244
143847	P. pentosaceus CCUG 21536, CCM 2483, ATCC 25745
145700	P. pentosaceus CCUG 29309
148603	P. pentosaceus CCUG 35694
149148	P. pentosaceus CCUG 36942
149342	P. pentosaceus CCUG 37545
149378	P. pentosaceus CCUG 37613
149422	P. pentosaceus CCUG 37701
149670	P. pentosaceus CCUG 38155
150415	P. pentosaceus CCUG 39851
150614	P. pentosaceus CCUG 41759
151859	P. pentosaceus CCUG 45064
152965	P. pentosaceus CCUG 48142
153377	P. pentosaceus CCUG 49383
162731	P. pentosaceus JCM 20076, IAM 1150
162816	P. pentosaceus JCM 2023, TISTR 414
162818	P. pentosaceus JCM 2024, TISTR 415
162831	P. pentosaceus JCM 2026
162843	P. pentosaceus JCM 2028
162847	P. pentosaceus JCM 2029
162855	P. pentosaceus JCM 2030
162865	P. pentosaceus JCM 2031
162869	P. pentosaceus JCM 20314, IAM 10073, IAM 12285
162932	P. pentosaceus JCM 20452, IAM 12293, IFO 3893, NBRC 3893, ...
162933	P. pentosaceus JCM 20453, IAM 12294
162936	P. pentosaceus JCM 20457, IAM 12298, NCDO 992
162937	P. pentosaceus JCM 20458, IAM 12299, NISL 7108
162938	P. pentosaceus JCM 20459, IAM 12300, IFO 3892, NBRC 3892, ...
173384	P. pentosaceus 7837, CRBIP24.170

Morphology

Cell morphology

@ref	Motility	Confidence	Gram stain
125438		93
125438		94.479	positive

Culture and growth conditions

Culture medium

@ref	Name	Medium link	Composition
8724	MRS MEDIUM (DSMZ Medium 11)	Medium recipe at MediaDive	Name: MRS MEDIUM (DSMZ Medium 11) Composition: Glucose 20.0 g/l Casein peptone 10.0 g/l Meat extract 10.0 g/l Na-acetate 5.0 g/l Yeast extract 5.0 g/l (NH4)3 citrate 2.0 g/l K2HPO4 2.0 g/l Tween 80 1.0 g/l MgSO4 x 7 H2O 0.2 g/l MnSO4 x H2O 0.05 g/l Distilled water
38895	MEDIUM 41- for Lactobacillus, Leuconostoc, Weissella, Pediococcus, Sporolactobacillus inulinus		Distilled water make up to (1000.000 ml);Man Rogosa Sharp broth (55.000 g)
121663	CIP Medium 41	Medium recipe at CIP

Culture temp

@ref	Growth	Type	Temperature (°C)	Range
8724	positive	growth	30	mesophilic
38895	positive	growth	30	mesophilic
67770	positive	growth	37	mesophilic

Physiology and metabolism

Oxygen tolerance

@ref	Oxygen tolerance	Confidence
125439	obligate aerobe	97.1

Spore formation

@ref	Spore formation	Confidence
125438		93.236

Murein

@ref	Murein short key	Type
8724	A11.31	A4alpha L-Lys-D-Asp

Metabolite utilization

@ref	Chebi-ID	Metabolite	Utilization activity	Kind of utilization tested
68371	27613 ChEBI	amygdalin	+	builds acid from	from API 50CH acid
68371	18305 ChEBI	arbutin	+	builds acid from	from API 50CH acid
68371	17057 ChEBI	cellobiose	+	builds acid from	from API 50CH acid
68371	17108 ChEBI	D-arabinose	-	builds acid from	from API 50CH acid
68371	18333 ChEBI	D-arabitol	-	builds acid from	from API 50CH acid
68371	15824 ChEBI	D-fructose	+	builds acid from	from API 50CH acid
68371	28847 ChEBI	D-fucose	-	builds acid from	from API 50CH acid
68371	12936 ChEBI	D-galactose	+	builds acid from	from API 50CH acid
68371	17634 ChEBI	D-glucose	+	builds acid from	from API 50CH acid
68371	62318 ChEBI	D-lyxose	-	builds acid from	from API 50CH acid
68371	16899 ChEBI	D-mannitol	-	builds acid from	from API 50CH acid
68371	16024 ChEBI	D-mannose	+	builds acid from	from API 50CH acid
68371	16988 ChEBI	D-ribose	+	builds acid from	from API 50CH acid
68371	17924 ChEBI	D-sorbitol	-	builds acid from	from API 50CH acid
68371	16443 ChEBI	D-tagatose	-	builds acid from	from API 50CH acid
68371	65327 ChEBI	D-xylose	+	builds acid from	from API 50CH acid
68371	17113 ChEBI	erythritol	-	builds acid from	from API 50CH acid
68371	4853 ChEBI	esculin	+	builds acid from	from API 50CH acid
68371	16813 ChEBI	galactitol	-	builds acid from	from API 50CH acid
68371	28066 ChEBI	gentiobiose	+	builds acid from	from API 50CH acid
68371	24265 ChEBI	gluconate	-	builds acid from	from API 50CH acid
68371	17754 ChEBI	glycerol	-	builds acid from	from API 50CH acid
68371	28087 ChEBI	glycogen	-	builds acid from	from API 50CH acid
68371	15443 ChEBI	inulin	-	builds acid from	from API 50CH acid
68371	30849 ChEBI	L-arabinose	+	builds acid from	from API 50CH acid
68371	18403 ChEBI	L-arabitol	-	builds acid from	from API 50CH acid
68371	18287 ChEBI	L-fucose	-	builds acid from	from API 50CH acid
68371	62345 ChEBI	L-rhamnose	-	builds acid from	from API 50CH acid
68371	17266 ChEBI	L-sorbose	-	builds acid from	from API 50CH acid
68371	65328 ChEBI	L-xylose	-	builds acid from	from API 50CH acid
68371	17716 ChEBI	lactose	-	builds acid from	from API 50CH acid
68371	17306 ChEBI	maltose	+	builds acid from	from API 50CH acid
68371	6731 ChEBI	melezitose	-	builds acid from	from API 50CH acid
68371	28053 ChEBI	melibiose	-	builds acid from	from API 50CH acid
68371	320061 ChEBI	methyl alpha-D-glucopyranoside	-	builds acid from	from API 50CH acid
68371	43943 ChEBI	methyl alpha-D-mannoside	-	builds acid from	from API 50CH acid
68371	74863 ChEBI	methyl beta-D-xylopyranoside	-	builds acid from	from API 50CH acid
68371	17268 ChEBI	myo-inositol	-	builds acid from	from API 50CH acid
68371	59640 ChEBI	N-acetylglucosamine	+	builds acid from	from API 50CH acid
68371		Potassium 2-ketogluconate	-	builds acid from	from API 50CH acid
68371		Potassium 5-ketogluconate	-	builds acid from	from API 50CH acid
68371	16634 ChEBI	raffinose	-	builds acid from	from API 50CH acid
68371	15963 ChEBI	ribitol	-	builds acid from	from API 50CH acid
68371	17814 ChEBI	salicin	+	builds acid from	from API 50CH acid
68371	28017 ChEBI	starch	-	builds acid from	from API 50CH acid
68371	17992 ChEBI	sucrose	+	builds acid from	from API 50CH acid
68371	27082 ChEBI	trehalose	-	builds acid from	from API 50CH acid
68371	32528 ChEBI	turanose	-	builds acid from	from API 50CH acid
68371	17151 ChEBI	xylitol	-	builds acid from	from API 50CH acid

API 50CHac

@ref	ControlQ	GLY	ERY	DARA	LARA	RIB	DXYL	LXYL	ADO	MDX	GAL	GLU	FRU	MNE	SBE	RHA	DUL	INO	MAN	SOR	MDM	MDG	NAG	AMY	ARB	ESC	SAL	CEL	MAL	LAC	MEL	SAC	TRE	INU	MLZ	RAF	AMD	GLYG	XLT	GEN	TUR	LYX	TAG	DFUC	LFUC	DARL	LARL	GNT	2KG	5KG
8724	-	-	-	-	+	+	+	-	-	-	+	+	+	+	-	-	-	-	-	-	-	-	+	+	+	+	+	+	+	-	-	+	-	-	-	-	-	-	-	+	-	-	-	-	-	-	-	-	-	-

Isolation, sampling and environmental information

Isolation source categories

Cat1	Cat2	Cat3
#Engineered	#Food production	#Fermented
#Engineered	#Food production	#Beverage

Isolation

@ref	Sample type
8724	sake mash
67770	Sake mash
121663	Food, Sake mash

Taxonmaps

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

Interaction and safety

Risk assessment

@ref	Pathogenicity human	Biosafety level	Biosafety level comment
8724	yes, in single cases	1	Risk group (German classification) According to TRBA 466
121663		1	Risk group (French classification) According to TRBA 466

Sequence information

Genome sequences

@ref	Description	Assembly level	INSDC accession	BV-BRC accession	NCBI tax ID	Score
124043	ASM1602869v1 assembly for Pediococcus pentosaceus FDAARGOS_873	complete	GCA_016028695	1255.193	1255	93.87
66792	ASM1561324v1 assembly for Pediococcus pentosaceus DSM 20333	scaffold	GCA_015613245	1255.182	1255	71.36

16S sequences

@ref	Description	Accession	Length	Database	NCBI tax ID
67770	Pediococcus pentosaceus gene for 16S ribosomal RNA, partial sequence, strain: JCM 5885	LC096205	1486		1255

GC content

@ref	GC-content (mol%)
8724	39.2
67770	37.8

Genome-based predictions

Predictions

Predictions from Deep Learning for Genome Sequence Data. R package version 0.3.1 based on: Pediococcus pentosaceus strain FDAARGOS_873
PATRIC: 1255.193

@ref	Trait	Model	Prediction	Confidence in %	In training data
125439	oxygen_tolerance	BacteriaNetⓘ	obligate aerobe	97.10	no
125439	gram_stain	BacteriaNetⓘ	variable	76.40	no
125439	motility	BacteriaNetⓘ	yes	79.20	no
125439	spore_formation	BacteriaNetⓘ	yes	83.90	no

Predictions from bacterial phenotypic traits through improved machine learning using high-quality, curated datasets based on: Pediococcus pentosaceus strain FDAARGOS_873 strain Not applicable
PATRIC: 1255.193

@ref	Trait	Model	Prediction	Confidence in %	In training data
125438	gram-positive	gram-positiveⓘ	yes	94.48	no
125438	anaerobic	anaerobicⓘ	no	84.72	no
125438	spore-forming	spore-formingⓘ	no	93.24	no
125438	aerobic	aerobicⓘ	no	96.23	no
125438	thermophilic	thermophileⓘ	no	97.50	no
125438	flagellated	motile2+ⓘ	no	93.00	no

Literature

Topic	Title	Authors	Journal	DOI	Year
	Valorization of Xylose-Rich Medium from Cynara cardunculus Stalks for Lactic Acid Production via Microbial Fermentation.	Russo G, Gelosia M, Fabbrizi G, Angrisano M, Policastro G, Cavalaglio G.	Polymers (Basel)	10.3390/polym16243577	2024
	Heme and menaquinone induced electron transport in lactic acid bacteria.	Brooijmans R, Smit B, Santos F, van Riel J, de Vos WM, Hugenholtz J.	Microb Cell Fact	10.1186/1475-2859-8-28	2009
	Changes in physicochemical and microbiological properties of isoflavone-treated dry-cured sausage from sulfur-fed pork during storage.	Kim JH, Pyun CW, Hong GE, Kim SK, Yang CY, Lee CH.	J Anim Sci Technol	10.1186/2055-0391-56-21	2014
Phylogeny	Phenotypic and genotypic characterization of Pediococcus strains isolated from human clinical sources.	Barros RR, Carvalho MG, Peralta JM, Facklam RR, Teixeira LM.	J Clin Microbiol	10.1128/jcm.39.4.1241-1246.2001	2001
Phylogeny	Isolation and characterization of bacteriophages from fermenting sauerkraut.	Yoon SS, Barrangou-Poueys R, Breidt F, Klaenhammer TR, Fleming HP.	Appl Environ Microbiol	10.1128/aem.68.2.973-976.2002	2002
	Clinical and microbiologic characteristics of pediococci.	Riebel WJ, Washington JA.	J Clin Microbiol	10.1128/jcm.28.6.1348-1355.1990	1990
Phylogeny	Identification to the species level of Lactobacillus isolated in probiotic prospecting studies of human, animal or food origin by 16S-23S rRNA restriction profiling.	Moreira JL, Mota RM, Horta MF, Teixeira SM, Neumann E, Nicoli JR, Nunes AC.	BMC Microbiol	10.1186/1471-2180-5-15	2005
Phylogeny	Identification of gram-positive coccal and coccobacillary vancomycin-resistant bacteria.	Facklam R, Hollis D, Collins MD.	J Clin Microbiol	10.1128/jcm.27.4.724-730.1989	1989
	Plasmid transfer in Pediococcus spp.: intergeneric and intrageneric transfer of pIP501.	Gonzalez CF, Kunka BS.	Appl Environ Microbiol	10.1128/aem.46.1.81-89.1983	1983
	Investigation of Bacteriocin Production Ability of Pediococcus acidilactici JM01 and Probiotic Properties Isolated From Tarak, a Conventional Korean Fermented Milk.	Ahn H, Lee HJ.	Food Sci Nutr	10.1002/fsn3.71003	2025
	Engineering increased stability in the antimicrobial peptide pediocin PA-1.	Johnsen L, Fimland G, Eijsink V, Nissen-Meyer J.	Appl Environ Microbiol	10.1128/aem.66.11.4798-4802.2000	2000
Metabolism	A C-terminal disulfide bridge in pediocin-like bacteriocins renders bacteriocin activity less temperature dependent and is a major determinant of the antimicrobial spectrum.	Fimland G, Johnsen L, Axelsson L, Brurberg MB, Nes IF, Eijsink VG, Nissen-Meyer J.	J Bacteriol	10.1128/jb.182.9.2643-2648.2000	2000
	Isolation, Characterization, and Comparative Genomics of the Novel Potential Probiotics from Canine Feces.	Foongsawat N, Sunthornthummas S, Nantavisai K, Surachat K, Rangsiruji A, Sarawaneeyaruk S, Insian K, Sukontasing S, Suwannasai N, Pringsulaka O.	Food Sci Anim Resour	10.5851/kosfa.2023.e28	2023
	Physicochemical and sensory characterization of functional synbiotic Labneh fortified with the bacteriocin-producing Lactiplantibacillus plantarum strain GA7 and nano-encapsulated Tirmania pinoyi extract.	Daba GM, Elkhateeb WA, Saleh SAA, Soliman TN, El-Dein AN.	Microb Cell Fact	10.1186/s12934-024-02631-7	2025
	A Novel C-Terminal Truncated Bacteriocin Found by Comparison between Leuconostoc mesenteroides 406 and 213M0 Isolated from Mongolian Traditional Fermented Milk, Airag.	Hasiqimuge, Hano C, Arakawa K, Yoshida S, Zhao J, Toh H, Morita H, Miyamoto T.	Microorganisms	10.3390/microorganisms12091781	2024
Metabolism	Lethal hydroxyl radical accumulation by a lactococcal bacteriocin, lacticin Q.	Li M, Yoneyama F, Toshimitsu N, Zendo T, Nakayama J, Sonomoto K.	Antimicrob Agents Chemother	10.1128/aac.00638-13	2013
Metabolism	Garvieacin Q, a novel class II bacteriocin from Lactococcus garvieae BCC 43578.	Tosukhowong A, Zendo T, Visessanguan W, Roytrakul S, Pumpuang L, Jaresitthikunchai J, Sonomoto K.	Appl Environ Microbiol	10.1128/aem.06891-11	2012
Metabolism	Cooperative transport between NukFEG and NukH in immunity against the lantibiotic nukacin ISK-1 produced by Staphylococcus warneri ISK-1.	Okuda K, Aso Y, Nakayama J, Sonomoto K.	J Bacteriol	10.1128/jb.01300-07	2008
Metabolism	Identification and characterization of leucocyclicin Q, a novel cyclic bacteriocin produced by Leuconostoc mesenteroides TK41401.	Masuda Y, Ono H, Kitagawa H, Ito H, Mu F, Sawa N, Zendo T, Sonomoto K.	Appl Environ Microbiol	10.1128/aem.06348-11	2011
Metabolism	Isolation and characterization of enterocin W, a novel two-peptide lantibiotic produced by Enterococcus faecalis NKR-4-1.	Sawa N, Wilaipun P, Kinoshita S, Zendo T, Leelawatcharamas V, Nakayama J, Sonomoto K.	Appl Environ Microbiol	10.1128/aem.06497-11	2012
Metabolism	Lysine-oriented charges trigger the membrane binding and activity of nukacin ISK-1.	Asaduzzaman SM, Nagao J, Aso Y, Nakayama J, Sonomoto K.	Appl Environ Microbiol	10.1128/aem.00678-06	2006
Metabolism	Lactococcin Q, a novel two-peptide bacteriocin produced by Lactococcus lactis QU 4.	Zendo T, Koga S, Shigeri Y, Nakayama J, Sonomoto K.	Appl Environ Microbiol	10.1128/aem.72.5.3383-3389.2006	2006
	The genus Weissella: taxonomy, ecology and biotechnological potential.	Fusco V, Quero GM, Cho GS, Kabisch J, Meske D, Neve H, Bockelmann W, Franz CM.	Front Microbiol	10.3389/fmicb.2015.00155	2015
Pathogenicity	Identification and characterization of lactocyclicin Q, a novel cyclic bacteriocin produced by Lactococcus sp. strain QU 12.	Sawa N, Zendo T, Kiyofuji J, Fujita K, Himeno K, Nakayama J, Sonomoto K.	Appl Environ Microbiol	10.1128/aem.02299-08	2009
Metabolism	Bioengineering of a Nisin A-producing Lactococcus lactis to create isogenic strains producing the natural variants Nisin F, Q and Z.	Piper C, Hill C, Cotter PD, Ross RP.	Microb Biotechnol	10.1111/j.1751-7915.2010.00207.x	2011
	Structural analysis and characterization of lacticin Q, a novel bacteriocin belonging to a new family of unmodified bacteriocins of gram-positive bacteria.	Fujita K, Ichimasa S, Zendo T, Koga S, Yoneyama F, Nakayama J, Sonomoto K.	Appl Environ Microbiol	10.1128/aem.02286-06	2007
Metabolism	Transcriptomic Analysis of Pediococcus pentosaceus Reveals Carbohydrate Metabolic Dynamics Under Lactic Acid Stress.	Han D, Yan Q, Liu J, Jiang Z, Yang S.	Front Microbiol	10.3389/fmicb.2021.736411	2021

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 )
#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 .
#121663	Collection of Institut Pasteur ; Curators of the CIP; CIP 102261
#124043	Isabel Schober, Julia Koblitz: Data extracted from sequence databases, automatically matched based on designation and taxonomy .
#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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Pediococcus pentosaceus (DSM 20333, ATCC 33314, IFO 3884)

Name and taxonomic classification

Morphology

Cell morphology

Culture and growth conditions

Culture medium

Culture temp

Physiology and metabolism

Oxygen tolerance

Spore formation

Murein

Metabolite utilization

API 50CHac

Isolation, sampling and environmental information

Isolation source categories

Isolation

Taxonmaps

Interaction and safety

Risk assessment

Sequence information

Genome sequences

Genome browser: GCA_016028695

16S sequences

GC content

Genome-based predictions

Predictions

Literature

Literature

References

BacDive

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