Name: Pediococcus damnosus Be1
Creator: BacDive
License: https://creativecommons.org/licenses/by/4.0/

Strain identifier

BacDive ID: 6384

Type strain:

Species: Pediococcus damnosus

Strain Designation: Be1, Be.1

Culture col. no.: DSM 20331, ATCC 29358, NCDO 1832, WDCM 00022, CCUG 32251, LMG 11484, NCIMB 12010, CIP 102264, CCM 3453, JCM 5886, BCRC 12840, CECT 793, CGMCC 1.2692, KCTC 3770, NBRC 107867, VKM B-1602, VTT E-91459, CCUG 21535

Strain history: CIP <- 1986, NCFB <- Queen Elizabeth College, London, UK <- D.H. Williamson, Brewing Res. Trust., UK: strain Be.1

NCBI tax ID(s): 51663 (species)

SI-ID 3818

LMG 11484, ATCC 29358, CCM 3453, CCUG 32251, CIP 102264, JCM 5886, NCFB 1832, NCIMB 12010, NCDO 1832, CCUG 21535, NCIB 12010, CCRC 12840, CECT793, VKM B-1602, VTT E-91459, KCTC 3770, BCRC 12840, CGMCC 1.2692, DSM 20331

Other strains from Pediococcus damnosus

P. damnosus 144a, DSM 20289
P. damnosus 38b, DSM 20291
P. damnosus CCUG 41974, ATCC 43013, LMG 16740

Section

Pediococcus damnosus Be1 is a microaerophile, Gram-positive bacterium that was isolated from lager beer yeast.

Gram-positive
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	*Bacillota*
	Class	*Bacilli*
	Order	*Lactobacillales*
	Family	*Lactobacillaceae*
	Genus	*Pediococcus*
	Species	**Pediococcus damnosus**
	Full Scientific Name (LPSN)	Pediococcus damnosus Claussen 1903 (Approved Lists 1980)

Information on morphological and physiological properties Morphology

[Ref.: #118851]	Gram stain	positive
[Ref.: #69480]	Gram stain	positive Confidence in %96.47

[Ref.: #118851]	Cell shape	coccus-shaped

[Ref.: #118851]	Motility	no
[Ref.: #69480]	Motility	no Confidence in %94.843

Information on culture and growth conditions Culture and growth conditions

[Ref.: #8722]

Culture medium

PEDIOCOCCUS DAMNOSUS MEDIUM (DSMZ Medium 231)

[Ref.: #8722]

Culture medium growth

[Ref.: #8722]

Culture medium link

Medium recipe at MediaDive

[Ref.: #8722]

Culture medium composition

expand / minimize

[Ref.: #41846]

Culture medium

MEDIUM 43 - for Lactobacillus hamsteri and Lactobacillus ruminis

[Ref.: #41846]

Culture medium growth

[Ref.: #41846]

Culture medium composition

expand / minimize

[Ref.: #118851]

Culture medium

CIP Medium 41

[Ref.: #118851]

Culture medium growth

[Ref.: #118851]

Culture medium link

Medium recipe provided by DSMZ

		Temperature
[Ref.: #8722]	growth	26 °C
[Ref.: #41846]	growth	25 °C
[Ref.: #50930]	growth	30 °C
[Ref.: #67770]	growth	26 °C

Information on physiology and metabolism Physiology and metabolism

[Ref.: #8722]	Oxygen tolerance	microaerophile
[Ref.: #50930]	Oxygen tolerance	anaerobe

[Ref.: #69480]

Ability of spore formation

no Confidence in %93.828

[Ref.: #8722]	Murein short key	A11.31
[Ref.: #8722]	Murein types	A4alpha L-Lys-D-Asp

	Metabolite	Utilization activity	Kind of utilization tested
[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.: #118851]	nitrate ChEBI	+	reduction
[Ref.: #118851]	nitrite ChEBI	-	reduction
[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]	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.

	Metabolite production	Metabolite	Production
[Ref.: #118851]		indole ChEBI	no

	Enzyme	Enzyme activity	EC number
[Ref.: #68382]	acid phosphatase	-	3.1.3.2	* from API zym
[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.: #68382]	beta-galactosidase	-	3.2.1.23	* from API zym
[Ref.: #68382]	beta-glucosidase	+	3.2.1.21	* from API zym
[Ref.: #68382]	beta-glucuronidase	-	3.2.1.31	* from API zym
[Ref.: #118851]	catalase	-	1.11.1.6
[Ref.: #68382]	cystine arylamidase	-	3.4.11.3	* from API zym
[Ref.: #68382]	esterase (C 4)	+		* from API zym
[Ref.: #68382]	esterase lipase (C 8)	-		* from API zym
[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]	naphthol-AS-BI-phosphohydrolase	+		* from API zym
[Ref.: #118851]	oxidase	-
[Ref.: #68382]	trypsin	-	3.4.21.4	* from API zym
[Ref.: #118851]	urease	-	3.5.1.5
[Ref.: #68382]	valine arylamidase	-		* from API zym
	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.: #8722]	14953	-	-	-	-	-	-	-	-	-	-	+	+	+	+	-	-	-	-	-	-	-	-	-	+	+	+	+	+	-	-	-	-	+	-	-	-	-	-	-	+	-	-	-	-	-	-	-	-	-	-
[Ref.: #8722]	14950	-	-	-	-	-	-	-	-	-	-	+	+	+	+	-	-	-	-	-	-	-	-	-	+	+	+	+	+	-	-	-	-	+	-	-	-	-	-	-	+	-	-	-	-	-	-	-	-	-	-
[Ref.: #8722]	14622	-	-	-	-	-	-	-	-	-	-	+	+	+	+	-	-	-	-	-	-	-	-	-	+	+	+	+	+	-	-	-	-	+	-	-	-	-	-	-	+	-	-	-	-	-	-	-	-	-	-
[Ref.: #8722]	14620	-	-	-	-	-	-	-	-	-	-	+	+	+	+	-	-	-	-	-	-	-	-	-	+	+	+	+	+	-	-	-	-	+	-	-	-	-	-	-	+	-	-	-	-	-	-	-	-	-	-
[Ref.: #8722]	14619	-	-	-	-	-	-	-	-	-	-	+	+	+	+	-	-	-	-	-	-	-	-	-	+/-	-	+	+	+	-	-	-	-	+/-	-	-	-	-	-	-	+	-	-	-	-	-	-	-	-	-	-
[Ref.: #8722]	14618	-	-	-	-	-	-	-	-	-	-	+	+	+	+	-	-	-	-	-	-	-	-	-	+	+	+	+	+	-	-	-	-	+	-	-	-	-	-	-	+	-	-	-	-	-	-	-	-	-	-

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.: #118851]	6980	-	+	+	-	-	-	-	-	-	-	-	+	-	-	-	+	+	-	-	-

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

[Ref.: #8722]	Sample type/isolated from	lager beer yeast

[Ref.: #50930]	Sample type/isolated from	Lager beer yeast

[Ref.: #67770]	Sample type/isolated from	Lager beer yeast

[Ref.: #118851]	Sample type/isolated from	Food, Lager beer yeast
* marker position based on {}

Isolation sources categories

#Host

#Yeast

What are isolation sources categories?

[Ref.: #69479]

Global distribution of 16S sequence AJ318414 (>99% sequence identity) for Pediococcus from Microbeatlas

Aquatic Samples	624
Soil Samples	421
Animal Samples	11554
Plant Samples	443
Total Samples	13042

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

[Ref.: #8722]	Biosafety level	1	Risk group (German classification) According to TRBA 466
[Ref.: #118851]	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.: #20218]	Pediococcus damnosus clone P11 16S ribosomal RNA gene, partial sequence	AF404721	517	GenBank ENA	51663 tax ID	*
[Ref.: #20218]	Pediococcus damnosus clone P11 16S ribosomal RNA gene, partial sequence; 16S-23S ribosomal RNA intergenic spacer, complete sequence; and 23S ribosomal RNA gene, partial sequence	AF405365	531	GenBank ENA	51663 tax ID	*
[Ref.: #20218]	Pediococcus damnosus 16S rRNA gene, strain DSM 20331	AJ318414	1561	GenBank ENA	51663 tax ID	*
[Ref.: #20218]	Pediococcus damnosus DNA for 16S rRNA, partial sequence	D87678	1497	GenBank ENA	51663 tax ID	*

Genome sequence information:

	Sequence accession description	Seq. accession number	Assembly level	Sequence database	Associated NCBI tax ID
[Ref.: #66792]	Pediococcus damnosus DSM 20331	GCA_001437255	contig	GenBank ENA	51663 tax ID	*
[Ref.: #66792]	Pediococcus damnosus strain DSM 20331	51663.50	wgs	PATRIC	51663 tax ID	*
[Ref.: #66792]	Pediococcus damnosus DSM 20331	2675903387	draft	JGI IMG/M	51663 tax ID	*

[Ref.: #8722]	GC-content	37.1 mol%
[Ref.: #67770]	GC-content	40 mol%	thermal denaturation, midpoint method (Tm)

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

	Trait	Prediction	Confidence in %	In training data
	Predictions from Diaspora project based on: Pediococcus damnosus strain DSM 20331 PATRIC: 51663.50
[Ref.: #69480]	gram-positive	yes	96.47	no
[Ref.: #69480]	anaerobic	no	93.909	no
[Ref.: #69480]	halophile	yes	89.182	no
[Ref.: #69480]	spore-forming	no	93.828	no
[Ref.: #69480]	glucose-util	yes	92.624	no
[Ref.: #69480]	aerobic	no	97.743	no
[Ref.: #69480]	thermophile	no	98.821	yes
[Ref.: #69480]	flagellated	no	98.631	no
[Ref.: #69480]	motile	no	94.843	no
[Ref.: #69480]	glucose-ferment	yes	88.943	no

Availability in culture collections External links

[Ref.: #8722]

Culture collection no.

DSM 20331, ATCC 29358, NCDO 1832, WDCM 00022, CCUG 32251, LMG 11484, NCIMB 12010, CIP 102264, CCM 3453, JCM 5886, BCRC 12840, CECT 793, CGMCC 1.2692, KCTC 3770, NBRC 107867, VKM B-1602, VTT E-91459, CCUG 21535

[Ref.: #75857]

SI-ID 3818

Literature:

Topic	Title	Authors	Journal	DOI	Year
Phylogeny	Pediococcus ethanolidurans sp. nov., isolated from the walls of a distilled-spirit-fermenting cellar.	Liu L, Zhang B, Tong H, Dong X	Int J Syst Evol Microbiol	10.1099/ijs.0.64407-0	2006	*
Phylogeny	Pediococcus cellicola sp. nov., a novel lactic acid coccus isolated from a distilled-spirit-fermenting cellar.	Zhang B, Tong H, Dong X	Int J Syst Evol Microbiol	10.1099/ijs.0.63778-0	2005	*
Enzymology	Inactivation kinetics of beer spoilage bacteria (Lactobacillus brevis, Lactobacillus casei, and Pediococcus damnosus) during acid washing of brewing yeast.	Munford ARG, Chaves RD, Sant'Ana AS	Food Microbiol	10.1016/j.fm.2020.103513	2020	*

References

#8722

Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 20331

#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 )

#41846 ; Curators of the CIP;
#50930 Culture Collection University of Gothenburg (CCUG) ; Curators of the CCUG; CCUG 32251

#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 .

#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) .

#75857

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-ID3818.1 )

#118851 Collection of Institut Pasteur ; Curators of the CIP; CIP 102264
* These data were automatically processed and therefore are not curated

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Pediococcus damnosus strain DSM 20331

Change proposal

Change proposal