Companilactobacillus alimentarius (DSM 20249, ATCC 29643, CCUG 30672)

Name: Companilactobacillus alimentarius (DSM 20249, ATCC 29643, CCUG 30672)
Creator: BacDive
License: http://creativecommons.org/licenses/by/4.0/

BacDive ID 6410

Type strain

Strain Designation R 13, R13

Culture col. no. DSM 20249 ATCC 29643 CCUG 30672 R 13 NRIC 1640 12 more

NCBI tax ID(s) 1423720 1602

Special Collections DSMZ CCUG JCM KCTC CIP

Links

Companilactobacillus alimentarius R 13 is an anaerobe, mesophilic, Gram-positive prokaryote that produces lactate and was isolated from marinated fish product.

lactate production Gram-positive rod-shaped anaerobe mesophilic genome sequence 16S sequence

Name and taxonomic classification

SI-ID 8644

LMG 9187,ATCC 29643,CCUG 30672,DSM 20249,JCM 1095,NCFB 2329,NCIMB 11994,NBRC-106464,BCRC:80242,CIP 102986,NCDO 2329,NCIB 11994,CCRC 12932,CECT 570,KCTC 3593,BCRC 12932,NBIMCC 3315

@ref 20215

Last LPSN update 2025-12-16 09:48:19

Domain Bacillati

Phylum Bacillota

Class Bacilli

Order Lactobacillales

Family Lactobacillaceae

Genus Companilactobacillus

Species Companilactobacillus alimentarius

Full scientific name Companilactobacillus alimentarius (Reuter 1983 ex Reuter 1970) Zheng et al. 2020

Synonyms (1)

Lactobacillus alimentarius

BacDive ID	Other strains from **Companilactobacillus alimentarius** (1)	Type strain
6409	C. alimentarius R 100d, DSM 20181, ATCC 29647, CIP 105163

Morphology

Cell morphology

@ref	Gram stain	Cell shape
116236	positive	rod-shaped
125438
125438	positive
125439	positive

Culture and growth conditions

Culture medium

@ref	Name	Medium link	Composition
8660	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
40496	MEDIUM 40- for Lactobacillus and Leuconostoc		Distilled water make up to (1000.000 ml);Man Rogosa Sharp agar (68.000 g)
116236	CIP Medium 40	Medium recipe at CIP

Culture temp

@ref	Growth	Type	Temperature (°C)	Range
8660	positive	growth	30	mesophilic
40496	positive	growth	30	mesophilic
50209	positive	growth	30	mesophilic
67770	positive	growth	30	mesophilic
116236	positive	growth	30-37	mesophilic
116236	negative	growth	10
116236	negative	growth	15
116236	negative	growth	22
116236	negative	growth	45

Physiology and metabolism

Oxygen tolerance

@ref	Oxygen tolerance
50209	anaerobe
125439	microaerophile

Compound production

8660

CompoundL(+) lactic acid

Murein

@ref	Murein short key	Type
8660	A11.31	A4alpha L-Lys-D-Asp

Metabolite utilization

@ref	Chebi-ID	Metabolite	Utilization activity	Kind of utilization tested
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	28847 ChEBI	D-fucose	-	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	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	16813 ChEBI	galactitol	-	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	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	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
116236	17632 ChEBI	nitrate	-	reduction
116236	17632 ChEBI	nitrate	+	respiration
116236	16301 ChEBI	nitrite	-	reduction
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	28017 ChEBI	starch	-	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

Metabolite tests

@ref	Chebi-ID	Metabolite	Voges-proskauer-test
116236	15688 ChEBI	acetoin	+

Enzymes

@ref	Value	Activity	Ec
68382	acid phosphatase	+	3.1.3.2	from API zym
116236	alcohol dehydrogenase	-	1.1.1.1
68382	alkaline phosphatase	-	3.1.3.1	from API zym
68382	alpha-chymotrypsin	-	3.4.21.1	from API zym
68382	alpha-fucosidase	-	3.2.1.51	from API zym
68382	alpha-galactosidase	-	3.2.1.22	from API zym
68382	alpha-glucosidase	-	3.2.1.20	from API zym
68382	alpha-mannosidase	-	3.2.1.24	from API zym
68382	beta-galactosidase	-	3.2.1.23	from API zym
68382	beta-glucosidase	+	3.2.1.21	from API zym
68382	beta-glucuronidase	-	3.2.1.31	from API zym
116236	catalase	-	1.11.1.6
68382	cystine arylamidase	-	3.4.11.3	from API zym
68382	esterase (C 4)	-		from API zym
68382	esterase lipase (C 8)	-		from API zym
68382	leucine arylamidase	-	3.4.11.1	from API zym
68382	lipase (C 14)	-		from API zym
116236	lysine decarboxylase	-	4.1.1.18
68382	N-acetyl-beta-glucosaminidase	-	3.2.1.52	from API zym
68382	naphthol-AS-BI-phosphohydrolase	+		from API zym
116236	ornithine decarboxylase	-	4.1.1.17
116236	oxidase	-
68382	trypsin	-	3.4.21.4	from API zym
68382	valine arylamidase	-		from API zym

API zym

@ref	Control	Alkaline phosphatase	Esterase (C 4)	2-naphtyl caprylateEsterase Lipase (C 8)	Lipase (C 14)	L-leucyl-2-naphthylamideLeucine arylamidase	L-valyl-2-naphthylamideValine arylamidase	L-cystyl-2-naphthylamideCystine arylamidase	Trypsin	alpha- Chymotrypsin	Acid phosphatase	Naphthol-AS-BI-phosphateNaphthol-AS-BI-phosphohydrolase	alpha- Galactosidase	beta- Galactosidase	beta- Glucuronidase	alpha- Glucosidase	beta- Glucosidase	N-acetyl-beta- glucosaminidase	alpha- Mannosidase	alpha- Fucosidase
116236	-	-	-	-	-	-	-	-	-	-	+	+	-	-	-	-	+	-	-	-

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
8660	-	-	-	-	+	-	-	-	-	-	-	+	+	+	-	-	-	-	-	-	-	-	+	+	+	+	+	+	-	-	-	+	+	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-
8660	-	-	-	-	+	+	-	-	-	-	+	+	+	+	-	-	-	-	-	-	-	-	+	+	+	+	+	+	+	-	-	+	+	-	-	-	-	-	-	+	-	-	-	-	-	-	-	+	+	-
116236	not determinedn.d.	-	-	-	+/-	+/-	-	-	-	-	-	+/-	+/-	+/-	-	-	-	-	-	-	-	-	+/-	+/-	-	+/-	+/-	+/-	-	-	-	+/-	+/-	-	-	-	-	-	-	+/-	-	-	-	-	-	-	-	+/-	-	-

API biotype100

@ref	ControlQ	D-glucose as carbon sourceGLU	D-fructose as carbon sourceFRU	D-galactose as carbon sourceGAL	D-trehalose as carbon sourceTRE	D-mannose as carbon sourceMNE	L-sorbose as carbon sourceSBE	D-melibiose as carbon sourceMEL	sucrose as carbon sourceSAC	D-raffinose as carbon sourceRAF	maltotriose as carbon sourceMTE	maltose as carbon sourceMAL	lactose as carbon sourceLAC	lactulose as carbon sourceLTE	1-O-methyl-beta-galactopyranoside as carbon sourceMbGa	1-O-methyl-alpha-galactopyranoside as carbon sourceMaGa	D-cellobiose as carbon sourceCEL	gentiobiose as carbon sourceGEN	1-O-methyl-beta-D-glucopyranoside as carbon sourceMbGu	esculin as carbon sourceESC	D-ribose as carbon sourceRIB	L-arabinose as carbon sourceARA	D-xylose as carbon sourceXYL	palatinose as carbon sourcePLE	L-rhamnose as carbon sourceRHA	L-fucose as carbon sourceFUC	D-melezitose as carbon sourceMLZ	D-arabitol as carbon sourceDARL	L-arabitol as carbon sourceLARL	xylitol as carbon sourceXLT	dulcitol as carbon sourceDUL	D-tagatose as carbon sourceTAG	glycerol as carbon sourceGLY	myo-inositol as carbon sourceINO	D-mannitol as carbon sourceMAN	maltitol as carbon sourceMTL	D-turanose as carbon sourceTUR	D-sorbitol as carbon sourceSOR	adonitol as carbon sourceADO	hydroxyquinoline-beta-glucuronide as carbon sourceHBG	D-lyxose as carbon sourceLYX	i-erythritol as carbon sourceERY	1-O-methyl-alpha-D-glucoside as carbon sourceMDG	3-O-methyl-D-glucose as carbon source3MDG	D-saccharate as carbon sourceSAT	mucate as carbon sourceMUC	L-tartrate as carbon sourceLTAT	D-tartrate as carbon sourceDTAT	meso-tartrate as carbon sourceMTAT	D-malate as carbon sourceDMLT	L-malate as carbon sourceLMLT	cis-aconitate as carbon sourceCATE	trans-aconitate as carbon sourceTATE	tricarballylate as carbon sourceTTE	citrate as carbon sourceCIT	D-glucuronate as carbon sourceGRT	D-galacturonate as carbon sourceGAT	2-ketogluconate as carbon source2KG	5-ketogluconate as carbon source5KG	tryptophan as carbon sourceTRY	N-acetyl-D-glucosamine as carbon sourceNAG	D-gluconate as carbon sourceGNT	phenylacetate as carbon sourcePAC	protocatechuate as carbon sourcePAT	4-hydroxybenzoate as carbon sourcepOBE	quinate as carbon sourceQAT	gentisate as carbon sourceGTE	3-hydroxybenzoate as carbon sourcemOBE	benzoate as carbon sourceBAT	3-phenylpropionate as carbon sourcePPAT	m-coumarate as carbon sourceCMT	trigonelline as carbon sourceTGE	betaine as carbon sourceBET	putrescine as carbon sourcePCE	4-aminobutyrate as carbon sourceABT	histamine as carbon sourceHIN	DL-lactate as carbon sourceLAT	caprate as carbon sourceCAP	caprylate as carbon sourceCYT	L-histidine as carbon sourceHIS	succinate as carbon sourceSUC	fumarate as carbon sourceFUM	glutarate as carbon sourceGRE	DL-glycerate as carbon sourceGYT	5-aminovalerate as carbon sourceAVT	ethanolamine as carbon sourceETN	tryptamine as carbon sourceTTN	D-glucosamine as carbon sourceGLN	itaconate as carbon sourceITA	3-hydroxybutyrate as carbon source3OBU	L-aspartate as carbon sourceAPT	L-glutamate as carbon sourceGTT	L-proline as carbon sourcePRO	D-alanine as carbon sourceDALA	L-alanine as carbon sourceLALA	L-serine as carbon sourceSER	malonate as carbon sourceMNT	propionate as carbon sourcePROP	L-tyrosine as carbon sourceTYR	2-ketoglutarate as carbon source2KT
116236	not determinedn.d.	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	+	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	+	-	-	+	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	+	-	-	-	-	-	-	-	-	-	-	-	-

Isolation, sampling and environmental information

Isolation source categories

Cat1	Cat2	Cat3
#Engineered	#Food production	#Food
#Host	#Fishes	-

Isolation

@ref	Sample type
8660	marinated fish product
50209	Marinated fish product
67770	Marinated fish product
116236	Food, Marinated fish product

Taxonmaps

69479

Global distribution of 16S sequence LC063166 (>99% sequence identity) for Companilactobacillus alimentarius from Microbeatlas

Aquatic Samples	47
Soil Samples	61
Animal Samples	461
Plant Samples	62
Total Samples	631

Interaction and safety

Risk assessment

@ref	Biosafety level	Biosafety level comment
8660	1	Risk group (German classification) According to TRBA 466
116236	1	Risk group (French classification) According to TRBA 466

Sequence information

Genome sequences

@ref	Description	Assembly level	INSDC accession	BV-BRC accession	IMG accession	NCBI tax ID	Score
66792	ASM284989v1 assembly for Companilactobacillus alimentarius DSM 20249	complete	GCA_002849895	1423720.4	2802429297	1423720	97.58
67770	ASM799179v1 assembly for Companilactobacillus alimentarius NBRC 106464	contig	GCA_007991795	1602.4		1602	70.76
67770	ASM143474v1 assembly for Companilactobacillus alimentarius DSM 20249	scaffold	GCA_001434745	1423720.3	2700989133	1423720	66.85

Genome browser: GCA_002849895

16S sequences

@ref	Description	Accession	Length	NCBI tax ID
20218	Lactobacillus alimentarius 16S-23S ribosomal RNA small intergenic spacer region, complete sequence	AF500492	230	1602
20218	Lactobacillus alimentarius 16S-23S ribosomal RNA large intergenic spacer region; and tRNA-Ile and tRNA-Ala genes, complete sequence	AF500493	425	1602
20218	Lactobacillus alimentarius strain DSM 20249 16S ribosomal RNA gene, partial sequence	M58804	1514	1602
20218	Lactobacillus alimentarius gene for 16S rRNA, partial sequence, strain: JCM 1095	AB289025	694	1602
20218	Lactobacillus alimentarius gene for 16S ribosomal RNA, partial sequence	D31677	187	1602
20218	Lactobacillus alimentarius partial 23S rRNA gene and 16S-23S IGS, strain LMG 9187	AJ616015	701	1602
67770	Lactobacillus alimentarius gene for 16S ribosomal RNA, partial sequence, strain: JCM 1095	LC063166	1528	1602
124043	Lactobacillus alimentarius gene for 16S rRNA, partial sequence, strain: NBRC 106464.	AB626058	1492	1602

GC content

@ref	GC-content (mol%)
8660	37.0
67770	35.4
67770	37

Genome-based predictions

Predictions

Predictions from Deep Learning for Genome Sequence Data. R package version 0.3.1 based on: Companilactobacillus alimentarius DSM 20249
NCBI: GCA_002849895

@ref	Trait	Model	Prediction	Confidence in %	In training data
125439	spore_formation	BacteriaNetⓘ	no	75.40	no
125439	motility	BacteriaNetⓘ	no	66.20	no
125439	gram_stain	BacteriaNetⓘ	positive	93.00	no
125439	oxygen_tolerance	BacteriaNetⓘ	microaerophile	95.50	no

Predictions from bacterial phenotypic traits through improved machine learning using high-quality, curated datasets based on: Companilactobacillus alimentarius DSM 20249 DSM 20249
NCBI: GCA_002849895.1

@ref	Trait	Model	Prediction	Confidence in %	In training data
125438	gram-positive	gram-positiveⓘ	yes	94.47	no
125438	anaerobic	anaerobicⓘ	no	74.81	yes
125438	aerobic	aerobicⓘ	no	93.76	yes
125438	spore-forming	spore-formingⓘ	no	88.33	no
125438	thermophilic	thermophileⓘ	no	97.00	yes
125438	flagellated	motile2+ⓘ	no	92.50	no

Literature

Topic	Title	Authors	Journal	DOI	Year
Genetics	Biochemical and Genomic Characterization of Two New Strains of Lacticaseibacillus paracasei Isolated from the Traditional Corn-Based Beverage of South Africa, Mahewu, and Their Comparison with Strains Isolated from Kefir Grains.	Moiseenko KV, Begunova AV, Savinova OS, Glazunova OA, Rozhkova IV, Fedorova TV.	Foods	10.3390/foods12010223	2023
Phylogeny	Denaturing gradient gel electrophoresis analysis of the 16S rRNA gene V1 region to monitor dynamic changes in the bacterial population during fermentation of Italian sausages.	Cocolin L, Manzano M, Cantoni C, Comi G.	Appl Environ Microbiol	10.1128/aem.67.11.5113-5121.2001	2001
Metabolism	Characterization and identification of Pediococcus species isolated from forage crops and their application for silage preparation.	Cai Y, Kumai S, Ogawa M, Benno Y, Nakase T.	Appl Environ Microbiol	10.1128/aem.65.7.2901-2906.1999	1999
Metabolism	Characterization and determination of origin of lactic acid bacteria from a sorghum-based fermented weaning food by analysis of soluble proteins and amplified fragment length polymorphism fingerprinting.	Kunene NF, Geornaras I, von Holy A, Hastings JW.	Appl Environ Microbiol	10.1128/aem.66.3.1084-1092.2000	2000
Phylogeny	Polyphasic characterization of two novel Lactobacillus spp. isolated from blown salami packages: Description of Lactobacillus halodurans sp. nov. and Lactobacillus salsicarnum sp. nov.	Schuster JA, Klingl A, Vogel RF, Ehrmann MA	Syst Appl Microbiol	10.1016/j.syapm.2019.126023	2019
Phylogeny	Lactobacillus versmoldensis sp. nov., isolated from raw fermented sausage.	Krockel L, Schillinger U, Franz CMAP, Bantleon A, Ludwig W	Int J Syst Evol Microbiol	10.1099/ijs.0.02387-0	2003
Phylogeny	Lactobacillus kimchii sp. nov., a new species from kimchi.	Yoon JH, Kang SS, Mheen TI, Ahn JS, Lee HJ, Kim TK, Park CS, Kho YH, Kang KH, Park YH	Int J Syst Evol Microbiol	10.1099/00207713-50-5-1789	2000
Phylogeny	Lactobacillus alimentarius sp. nov., nom rev. and Lactobacillus farciminis sp. nov., nom. rev.	Reuter G	Syst Appl Microbiol	10.1016/S0723-2020(83)80055-1	1983

References

#8660	Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 20249
#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 )
#40496	; Curators of the CIP;
#50209	Culture Collection University of Gothenburg (CCUG) ; Curators of the CCUG; CCUG 30672
#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 .
#116236	Collection of Institut Pasteur ; Curators of the CIP; CIP 102986
#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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Companilactobacillus alimentarius (DSM 20249, ATCC 29643, CCUG 30672)

Name and taxonomic classification

Morphology

Cell morphology

Culture and growth conditions

Culture medium

Culture temp

Physiology and metabolism

Oxygen tolerance

Compound production

Murein

Metabolite utilization

Metabolite tests

Enzymes

API zym

API 50CHac

API biotype100

Isolation, sampling and environmental information

Isolation source categories

Isolation

Taxonmaps

Interaction and safety

Risk assessment

Sequence information

Genome sequences

Genome browser: GCA_002849895

16S sequences

GC content

Genome-based predictions

Predictions

Literature

Literature

References

BacDive

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