Companilactobacillus farciminis (DSM 20184, ATCC 29644, NCIB 11717)

Name: Companilactobacillus farciminis (DSM 20184, ATCC 29644, NCIB 11717)
Creator: BacDive
License: http://creativecommons.org/licenses/by/4.0/

BacDive ID 6455

Type strain

Strain Designation Rv4 na, Rv4na

Culture col. no. DSM 20184 ATCC 29644 NCIB 11717 CCUG 30671 Rv4 na 14 more

NCBI tax ID(s) 1612

Special Collections DSMZ CCUG JCM KCTC CIP

History <- G. Reuter, Rv4 na T. Mitsuoka S8-22 <-- DSM 20184 <-- G. Reuter Rv4 na. CIP <- 1988, DSM <- G. Reuter: strain Rv4na

Links

Companilactobacillus farciminis Rv4 na is a facultative anaerobe, mesophilic, Gram-positive prokaryote that was isolated from sausage.

Gram-positive rod-shaped facultative anaerobe mesophilic genome sequence 16S sequence

Name and taxonomic classification

SI-ID 3284

LMG 9200,ATCC 29644,JCM 1097,NCFB 2330,NCIMB 11717,CCUG 30671,NCIB 11717,CIP 103136,NCDO 2330,IMET 11462,CCRC 14043,CECT 571,KCTC 3681,NRRL B-4566,BCRC 14043,VTT E-991267,DSM 20184

@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 farciminis

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

Synonyms (1)

Lactobacillus farciminis

BacDive ID	Other strains from **Companilactobacillus farciminis** (2)	Type strain
6456	C. farciminis Rv1mc, DSM 20180, ATCC 29645, JCM 1092
6528	C. farciminis DSM 20182, Lev II, CIP 102987, NCIMB 11954

Morphology

Cell morphology

@ref	Gram stain	Cell shape	Confidence
119281	positive	rod-shaped
125438			93
125438	positive		94.428

Colony morphology

Culture and growth conditions

Culture medium

@ref	Name	Medium link	Composition
8460	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
38122	MEDIUM 40- for Lactobacillus and Leuconostoc		Distilled water make up to (1000.000 ml);Man Rogosa Sharp agar (68.000 g)
119281	CIP Medium 41	Medium recipe at CIP
119281	CIP Medium 40	Medium recipe at CIP

Culture temp

@ref	Growth	Type	Temperature (°C)	Range
8460	positive	growth	30	mesophilic
38122	positive	growth	30	mesophilic
67770	positive	growth	30	mesophilic
119281	positive	growth	15-37
119281	negative	growth	10
119281	negative	growth	45

Physiology and metabolism

Oxygen tolerance

@ref	Oxygen tolerance	Confidence
119281	facultative anaerobe
125439	obligate aerobe	97.9

Murein

@ref	Murein short key	Type
8460	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	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	16813 ChEBI	galactitol	-	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	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
119281	17632 ChEBI	nitrate	-	reduction
119281	17632 ChEBI	nitrate	+	respiration
119281	16301 ChEBI	nitrite	-	reduction
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	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

Antibiotic resistance

@ref	Metabolite	Is sensitive	Is resistant
119281	0129 (2,4-Diamino-6,7-di-iso-propylpteridine phosphate)

Metabolite tests

@ref	Chebi-ID	Metabolite	Voges-proskauer-test
119281	15688 ChEBI	acetoin	-

Enzymes

@ref	Value	Activity	Ec
68382	acid phosphatase	+	3.1.3.2	from API zym
119281	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
119281	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
119281	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
119281	ornithine decarboxylase	-	4.1.1.17
119281	oxidase	-
68382	trypsin	-	3.4.21.4	from API zym
68382	valine arylamidase	+		from API zym

Pathway annotation

Computationally determined by

@ref	pathway	enzyme coverage	annotated reactions
66794	CDP-diacylglycerol biosynthesis	100	2 of 2
66794	coenzyme A metabolism	100	4 of 4
66794	cis-vaccenate biosynthesis	100	2 of 2
66794	acetate fermentation	100	4 of 4
66794	UDP-GlcNAc biosynthesis	100	3 of 3
66794	folate polyglutamylation	100	1 of 1
66794	ppGpp biosynthesis	100	4 of 4
66794	ceramide biosynthesis	100	1 of 1
66794	acetoin degradation	100	3 of 3
66794	formaldehyde oxidation	100	3 of 3
66794	aspartate and asparagine metabolism	88.89	8 of 9
66794	C4 and CAM-carbon fixation	87.5	7 of 8
66794	gluconeogenesis	87.5	7 of 8
66794	palmitate biosynthesis	81.82	18 of 22
66794	flavin biosynthesis	80	12 of 15
66794	peptidoglycan biosynthesis	80	12 of 15
66794	threonine metabolism	80	8 of 10
66794	sulfopterin metabolism	75	3 of 4
66794	photosynthesis	71.43	10 of 14
66794	starch degradation	70	7 of 10
66794	vitamin B1 metabolism	69.23	9 of 13
66794	phenylalanine metabolism	69.23	9 of 13
66794	purine metabolism	67.02	63 of 94
66794	L-lactaldehyde degradation	66.67	2 of 3
66794	valine metabolism	66.67	6 of 9
66794	serine metabolism	66.67	6 of 9
66794	cyanate degradation	66.67	2 of 3
66794	glycolysis	64.71	11 of 17
66794	pentose phosphate pathway	63.64	7 of 11
66794	alanine metabolism	62.07	18 of 29
66794	glutamate and glutamine metabolism	60.71	17 of 28
66794	glycogen metabolism	60	3 of 5
66794	cellulose degradation	60	3 of 5
66794	methylglyoxal degradation	60	3 of 5
66794	Entner Doudoroff pathway	60	6 of 10
66794	factor 420 biosynthesis	60	3 of 5
66794	metabolism of amino sugars and derivatives	60	3 of 5
66794	histidine metabolism	58.62	17 of 29
66794	oxidative phosphorylation	58.24	53 of 91
66794	methionine metabolism	57.69	15 of 26
66794	ubiquinone biosynthesis	57.14	4 of 7
66794	propanol degradation	57.14	4 of 7
66794	chorismate metabolism	55.56	5 of 9
66794	NAD metabolism	55.56	10 of 18
66794	non-pathway related	55.26	21 of 38
66794	metabolism of disaccharids	54.55	6 of 11
66794	arginine metabolism	54.17	13 of 24
66794	urea cycle	53.85	7 of 13
66794	cysteine metabolism	50	9 of 18
66794	glycolate and glyoxylate degradation	50	3 of 6
66794	ethanol fermentation	50	1 of 2
66794	6-hydroxymethyl-dihydropterin diphosphate biosynthesis	50	4 of 8
66794	suberin monomers biosynthesis	50	1 of 2
66794	glycogen biosynthesis	50	2 of 4
66794	butanoate fermentation	50	2 of 4
66794	selenocysteine biosynthesis	50	3 of 6
66794	isoleucine metabolism	50	4 of 8
66794	phenylmercury acetate degradation	50	1 of 2
66794	degradation of aromatic, nitrogen containing compounds	50	6 of 12
66794	adipate degradation	50	1 of 2
66794	tetrahydrofolate metabolism	50	7 of 14
66794	ketogluconate metabolism	50	4 of 8
66794	degradation of sugar alcohols	50	8 of 16
66794	quinate degradation	50	1 of 2
66794	pyrimidine metabolism	48.89	22 of 45
66794	proline metabolism	45.45	5 of 11
66794	d-xylose degradation	45.45	5 of 11
66794	lysine metabolism	45.24	19 of 42
66794	d-mannose degradation	44.44	4 of 9
66794	reductive acetyl coenzyme A pathway	42.86	3 of 7
66794	cardiolipin biosynthesis	42.86	3 of 7
66794	lipid metabolism	41.94	13 of 31
66794	glycine metabolism	40	4 of 10
66794	lipoate biosynthesis	40	2 of 5
66794	myo-inositol biosynthesis	40	4 of 10
66794	arachidonate biosynthesis	40	2 of 5
66794	isoprenoid biosynthesis	38.46	10 of 26
66794	degradation of pentoses	35.71	10 of 28
66794	acetyl CoA biosynthesis	33.33	1 of 3
66794	lipid A biosynthesis	33.33	3 of 9
66794	degradation of hexoses	33.33	6 of 18
66794	sphingosine metabolism	33.33	2 of 6
66794	IAA biosynthesis	33.33	1 of 3
66794	enterobactin biosynthesis	33.33	1 of 3
66794	octane oxidation	33.33	1 of 3
66794	androgen and estrogen metabolism	31.25	5 of 16
66794	leucine metabolism	30.77	4 of 13
66794	polyamine pathway	30.43	7 of 23
66794	mevalonate metabolism	28.57	2 of 7
66794	citric acid cycle	28.57	4 of 14
66794	vitamin B6 metabolism	27.27	3 of 11
66794	tryptophan metabolism	26.32	10 of 38
66794	carnitine metabolism	25	2 of 8
66794	cyclohexanol degradation	25	1 of 4
66794	lactate fermentation	25	1 of 4
66794	dTDPLrhamnose biosynthesis	25	2 of 8
66794	CMP-KDO biosynthesis	25	1 of 4
66794	toluene degradation	25	1 of 4
66794	degradation of sugar acids	24	6 of 25
66794	sulfate reduction	23.08	3 of 13
66794	ascorbate metabolism	22.73	5 of 22
66794	nitrate assimilation	22.22	2 of 9
66794	CO2 fixation in Crenarchaeota	22.22	2 of 9
66794	tyrosine metabolism	21.43	3 of 14
66794	glutathione metabolism	21.43	3 of 14
66794	heme metabolism	21.43	3 of 14

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
119281	-	+	-	-	-	+	+	-	-	-	+	+	-	-	-	+	+	-	-	-

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
8460	-	-	-	-	-	-	-	-	-	-	+	+	+	+	-	-	-	-	-	-	-	+	+	-	+	+	+	+	+	+	-	+	+	-	-	-	-	-	-	+	-	-	+	-	-	-	-	-	-	-
119281	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
119281	not determinedn.d.	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-

Isolation, sampling and environmental information

Isolation source categories

Cat1	Cat2	Cat3
#Engineered	#Food production	#Meat

Isolation

@ref	Sample type
8460	sausage
50208	Sausage
67770	Sausage
119281	Food, Sausage

Taxonmaps

69479

Global distribution of 16S sequence LC063168 (>99% sequence identity) for Lactobacillaceae from Microbeatlas

Aquatic Samples	342
Soil Samples	237
Animal Samples	2894
Plant Samples	234
Total Samples	3707

Interaction and safety

Risk assessment

@ref	Biosafety level	Biosafety level comment
8460	1	Risk group (German classification) According to TRBA 466
119281	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	ASM270674v1 assembly for Companilactobacillus farciminis KCTC 3681 = DSM 20184	complete	GCA_002706745	936140.8	2814123232	936140	96.99
67770	ASM435469v1 assembly for Companilactobacillus farciminis ATCC 29644	contig	GCA_004354695	1612.42		1612	71.91
67770	ASM18453v1 assembly for Companilactobacillus farciminis KCTC 3681 = DSM 20184	scaffold	GCA_000184535	936140.3	651324060	936140	70.07
67770	ASM143477v1 assembly for Companilactobacillus farciminis KCTC 3681 = DSM 20184	contig	GCA_001434775	936140.5	2667527616	936140	63.57

16S sequences

@ref	Description	Accession	Length	NCBI tax ID
20218	Lactobacillus farciminis strain ATCC 29644 16S ribosomal RNA gene, partial sequence	M58817	1515	1612
20218	Lactobacillus farciminis gene for 16S ribosomal RNA, partial sequence	AB840589	1515	1612
20218	Lactobacillus farciminis 16S-23S ribosomal RNA small intergenic spacer region, complete sequence	AF500490	194	936140
20218	Lactobacillus farciminis 16S-23S ribosomal RNA large intergenic spacer region; and tRNA-Ile and tRNA-Ala genes, complete sequence	AF500491	388	936140
20218	Lactobacillus farciminis partial 23S rRNA gene and 16S-23S IGS, strain DSM 20184	AJ616017	663	936140
20218	Lactobacillus farciminis gene for 16S rRNA, partial sequence, strain: JCM 1097	AB289103	682	936140
20218	Lactobacillus farciminis gene for 16S ribosomal RNA, partial sequence	D31688	177	936140
67770	Lactobacillus farciminis gene for 16S ribosomal RNA, partial sequence, strain: JCM 1097	LC063168	1528	936140
124043	Lactobacillus farciminis gene for 16S rRNA, partial sequence, strain: NBRC 107150.	AB626064	1492	1612

GC content

@ref	GC-content (mol%)	Method
8460	36.3
67770	36
67770	36.4	genome sequence analysis

Genome-based predictions

Predictions

Predictions from Deep Learning for Genome Sequence Data. R package version 0.3.1 based on: Companilactobacillus farciminis KCTC 3681 = DSM 20184
NCBI: GCA_002706745

@ref	Trait	Model	Prediction	Confidence in %	In training data
125439	spore_formation	BacteriaNetⓘ	no	74.50	no
125439	motility	BacteriaNetⓘ	no	66.60	no
125439	gram_stain	BacteriaNetⓘ	positive	88.10	no
125439	oxygen_tolerance	BacteriaNetⓘ	obligate aerobe	97.90	no

Predictions from bacterial phenotypic traits through improved machine learning using high-quality, curated datasets based on: Companilactobacillus farciminis KCTC 3681 = DSM 20184 DSM 20184
NCBI: GCA_002706745.1

@ref	Trait	Model	Prediction	Confidence in %	In training data
125438	gram-positive	gram-positiveⓘ	yes	94.43	no
125438	anaerobic	anaerobicⓘ	no	85.99	yes
125438	aerobic	aerobicⓘ	no	93.88	yes
125438	spore-forming	spore-formingⓘ	no	86.51	no
125438	thermophilic	thermophileⓘ	no	95.47	yes
125438	flagellated	motile2+ⓘ	no	93.00	no

Literature

Topic	Title	Authors	Journal	DOI	Year
	Insights into population adaptation and biodiversity of lactic acid bacteria in challenged date palm leaves silaging, using MALDI-TOF MS.	Jawaid MZ, Ashfaq MY, Al-Ghouti M, Zouari N.	Curr Res Microb Sci	10.1016/j.crmicr.2024.100235	2024
	Screening of lactobacilli strains isolated from artisanal Poro de Tabasco cheese for their ability to biosynthesise conjugated linoleic acid under simulated gastrointestinal conditions	Sosa-Castaneda J, Reyes-Diaz R, Heredia-Castro PY, Benitez-Romero L, Mendez-Romero JI, Hernandez-Mendoza A, Gonzalez-Cordova AF, Vallejo-Cordoba B.	International journal of food science and technology.		2023
	Efficacy of a feed additive consisting of Companilactobacillus farciminisCNCM I-3740 (Biacton®) for chickens and turkeys for fattening (ChemVet dk A/S).	EFSA Panel on Additives and Products or Substances used in Animal Feed (FEEDAP), Bampidis V, Azimonti G, Bastos ML, Christensen H, Dusemund B, Durjava M, Kouba M, Lopez-Alonso M, Lopez Puente S, Marcon F, Mayo B, Pechova A, Petkova M, Ramos F, Sanz Y, Villa RE, Woutersen R, Galobart J, Ortuno J, Brozzi R.	EFSA J	10.2903/j.efsa.2023.8049	2023
Pathogenicity	Exploring the impact of lactic acid bacteria on the biocontrol of toxigenic Fusarium spp. and their main mycotoxins.	Mateo EM, Tarazona A, Aznar R, Mateo F.	Int J Food Microbiol	10.1016/j.ijfoodmicro.2022.110054	2023
	Sourdough Breads Made with Selected Lactobacillus Strains and Spelt Flour Contain Peptides That Positively Impact Intestinal Barrier.	Cicchi C, Leri M, Bucciantini M, Galli V, Guerrini S, Jimenez-Ortas A, Ceacero-Heras D, Martinez-Augustin O, Pazzagli L, Luti S.	Foods	10.3390/foods14183184	2025
	Characterization of Lactic Acid Bacteria from Fermented Fish (pla-paeng-daeng) and Their Cholesterol-lowering and Immunomodulatory Effects.	Kingkaew E, Konno H, Hosaka Y, Phongsopitanun W, Tanasupawat S.	Microbes Environ	10.1264/jsme2.me22044	2023
	Reducing FODMAPs and improving bread quality using type II sourdough with selected starter cultures.	Menezes LAA, De Marco I, Neves Oliveira Dos Santos N, Costa Nunes C, Leite Cartabiano CE, Molognoni L, Pereira GVM, Daguer H, De Dea Lindner J.	Int J Food Sci Nutr	10.1080/09637486.2021.1892603	2021
	Efficacy of the feed additive containing Companilactobacillus farciminis (formerly Lactobacillus farciminis) CNCM I-3740 (Biacton^®) for chickens for fattening, turkeys for fattening and laying hens (ChemVet dk A/S).	EFSA Panel on Additives and Products or Substances used in Animal Feed (FEEDAP), Bampidis V, Azimonti G, Bastos ML, Christensen H, Dusemund B, Fasmon Durjava M, Kouba M, Lopez-Alonso M, Lopez Puente S, Marcon F, Mayo B, Pechova A, Petkova M, Ramos F, Ramos F, Sanz Y, Villa RE, Woutersen R, Dierick N, Martelli G, Anguita M, Brozzi R.	EFSA J	10.2903/j.efsa.2021.6627	2021
Cultivation	Practical media formulations for rapid growth of Lactobacillus iners and other vaginal bacteria.	Serrador D, Campbell JR, Getz LJ, Cheung D, Shefraw G, Kaul R, Navarre WW.	Appl Environ Microbiol	10.1128/aem.00183-25	2025
Metabolism	Enzyme systems involved in glucosinolate metabolism in Companilactobacillus farciminis KB1089.	Watanabe H, Usami R, Kishino S, Osada K, Aoki Y, Morisaka H, Takahashi M, Izumi Y, Bamba T, Aoki W, Suganuma H, Ogawa J.	Sci Rep	10.1038/s41598-021-03064-7	2021
	Safety and efficacy of a feed additive consisting of Lacticaseibacillus rhamnosus CNCM I-3698 and Companilactobacillus sp. CNCM I-3699 for weaned piglets (STI Biotechnologie).	EFSA Panel on Additives and Products or Substances used in Animal Feed (FEEDAP), Bampidis V, Azimonti G, Bastos ML, Christensen H, Dusemund B, Durjava M, Kouba M, Lopez-Alonso M, Lopez Puente S, Marcon F, Mayo B, Pechova A, Petkova M, Ramos F, Sanz Y, Villa RE, Woutersen R, Cocconcelli PS, Pettenati E, Anguita M, Brozzi R.	EFSA J	10.2903/j.efsa.2023.7858	2023
	Safety and efficacy of a feed additive consisting of Lacticaseibacillus rhamnosus CNCM I-3698 and Companilactobacillus sp. CNCM I-3699 for chickens for fattening (STI Biotechnologie).	EFSA Panel on Additives and Products or Substances used in Animal Feed (FEEDAP), Bampidis V, Azimonti G, Bastos ML, Christensen H, Dusemund B, Durjava M, Kouba M, Lopez-Alonso M, Lopez Puente S, Marcon F, Mayo B, Pechova A, Petkova M, Ramos F, Sanz Y, Villa RE, Woutersen R, Cocconcelli PS, Pettenati E, Anguita M, Brozzi R.	EFSA J	10.2903/j.efsa.2023.7857	2023
	Safety and efficacy of a feed additive consisting of Lacticaseibacillus rhamnosus CNCM I-3698 and Companilactobacillus sp. CNCM I-3699 for all animal species (STI Biotechnologie).	EFSA Panel on Additives and Products or Substances used in Animal Feed (FEEDAP), Bampidis V, Azimonti G, Bastos ML, Christensen H, Dusemund B, Durjava M, Kouba M, Lopez-Alonso M, Lopez Puente S, Marcon F, Mayo B, Pechova A, Petkova M, Ramos F, Sanz Y, Villa RE, Woutersen R, Cocconcelli PS, Pettenati E, Anguita M, Brozzi R.	EFSA J	10.2903/j.efsa.2023.7856	2023
	Oxazolidinone resistance genes in florfenicol-resistant enterococci from beef cattle and veal calves at slaughter.	Nuesch-Inderbinen M, Biggel M, Haussmann A, Treier A, Heyvaert L, Cernela N, Stephan R.	Front Microbiol	10.3389/fmicb.2023.1150070	2023
Genetics	16S-rRNA-Based Metagenomic Profiling of the Bacterial Communities in Traditional Bulgarian Sourdoughs.	Baev V, Apostolova E, Gotcheva V, Koprinarova M, Papageorgiou M, Rocha JM, Yahubyan G, Angelov A.	Microorganisms	10.3390/microorganisms11030803	2023
	Effect of Lactic Acid Bacteria Fermentation Agent on the Structure, Physicochemical Properties, and Digestive Characteristics of Corn, Oat, Barley, and Buckwheat Starch	You Z, Wang J, Teng W, Wang Y, Zhang Y, Cao J.	Foods		2025
	Lactiplantibacillus plantarum OLL2712 Induces Autophagy via MYD88 and Strengthens Tight Junction Integrity to Promote the Barrier Function in Intestinal Epithelial Cells.	Watanabe-Yasuoka Y, Gotou A, Shimizu S, Sashihara T.	Nutrients	10.3390/nu15122655	2023
	Characterization of microbiota of naturally fermented sauerkraut by high-throughput sequencing.	Zhang S, Zhang Y, Wu L, Zhang L, Wang S.	Food Sci Biotechnol	10.1007/s10068-022-01221-w	2023
	Compound lactic acid bacteria enhance the aerobic stability of Sesbania cannabina and corn mixed silage.	Tahir M, Wang T, Zhang J, Xia T, Deng X, Cao X, Zhong J.	BMC Microbiol	10.1186/s12866-025-03781-3	2025
Pathogenicity	Lactic Acid Bacteria as Potential Agents for Biocontrol of Aflatoxigenic and Ochratoxigenic Fungi.	Mateo EM, Tarazona A, Jimenez M, Mateo F.	Toxins (Basel)	10.3390/toxins14110807	2022
	Modulation of Fermentation Quality and Metabolome in Co-ensiling of Sesbania cannabina and Sweet Sorghum by Lactic Acid Bacterial Inoculants.	Xia T, Wang T, Sun J, Shi W, Liu Y, Huang F, Zhang J, Zhong J.	Front Microbiol	10.3389/fmicb.2022.851271	2022
	Lentilactobacillus buchneri domination during the fermentation of Japanese traditional fermented fish (funazushi).	Tanabe K, Monguchi M, Inoue R, Zamami R, Nakanishi R, Manabe A, Oe K, Komatsuzaki N, Shima J.	Food Sci Nutr	10.1002/fsn3.3002	2022
	Antimicrobial activity of the Lacticaseibacillus rhamnosus CRL 2244 and its impact on the phenotypic and transcriptional responses in carbapenem resistant Acinetobacter baumannii.	Rodriguez C, Ramlaoui D, Georgeos N, Gasca B, Leal C, Subils T, Tuttobene MR, Sieira R, Salzameda NT, Bonomo RA, Raya R, Ramirez MS.	Sci Rep	10.1038/s41598-023-41334-8	2023
	Microbial Control of Raw and Cold-Smoked Atlantic Salmon (Salmo salar) through a Microwave Plasma Treatment.	Weihe T, Wagner R, Schnabel U, Andrasch M, Su Y, Stachowiak J, Noll HJ, Ehlbeck J.	Foods	10.3390/foods11213356	2022
	Metabolic insights of lactic acid bacteria in reducing off-flavors and antinutrients in plant-based fermented dairy alternatives.	Molina GES, Ras G, da Silva DF, Duedahl-Olesen L, Hansen EB, Bang-Berthelsen CH.	Compr Rev Food Sci Food Saf	10.1111/1541-4337.70134	2025
	Screening of GABA-Producing Lactic Acid Bacteria from Thai Fermented Foods and Probiotic Potential of Levilactobacillus brevis F064A for GABA-Fermented Mulberry Juice Production.	Kanklai J, Somwong TC, Rungsirivanich P, Thongwai N.	Microorganisms	10.3390/microorganisms9010033	2020
	Reduction in Biogenic Amine Content in Baechu (Napa Cabbage) Kimchi by Biogenic Amine-Degrading Lactic Acid Bacteria.	Lee J, Jin YH, Pawluk AM, Mah JH.	Microorganisms	10.3390/microorganisms9122570	2021
	Acids produced by lactobacilli inhibit the growth of commensal Lachnospiraceae and S24-7 bacteria.	Brownlie EJE, Chaharlangi D, Wong EO, Kim D, Navarre WW.	Gut Microbes	10.1080/19490976.2022.2046452	2022
Pathogenicity	Supplementation with Combined Lactobacillus helveticus R0052 and Bifidobacterium longum R0175 Across Development Reveals Sex Differences in Physiological and Behavioural Effects of Western Diet in Long-Evans Rats.	Myles EM, O'Leary ME, Smith R, MacPherson CW, Oprea A, Melanson EH, Tompkins TA, Perrot TS.	Microorganisms	10.3390/microorganisms8101527	2020
Phylogeny	Classification of Latilactobacillus sakei subspecies based on MALDI-TOF MS protein profiles using machine learning models.	Kim E, Yang S-M, Lee S-Y, Jung D-H, Kim H-Y.	Microbiol Spectr	10.1128/spectrum.03668-23	2024
Pathogenicity	Structure and biological activities of a hexosamine-rich cell wall polysaccharide isolated from the probiotic Lactobacillus farciminis.	Maes E, Sadovskaya I, Leveque M, Elass-Rochard E, Payre B, Grard T, Theodorou V, Guerardel Y, Mercier-Bonin M	Glycoconj J	10.1007/s10719-018-09854-y	2019
Metabolism	A C69-family cysteine dipeptidase from Lactobacillus farciminis JCM1097 possesses strong Gly-Pro hydrolytic activity.	Sakamoto T, Otokawa T, Kono R, Shigeri Y, Watanabe K	J Biochem	10.1093/jb/mvt069	2013
Metabolism	In vitro characterization of aggregation and adhesion properties of viable and heat-killed forms of two probiotic Lactobacillus strains and interaction with foodborne zoonotic bacteria, especially Campylobacter jejuni.	Tareb R, Bernardeau M, Gueguen M, Vernoux JP	J Med Microbiol	10.1099/jmm.0.049965-0	2013
Genetics	Genome sequence of Lactobacillus farciminis KCTC 3681.	Nam SH, Choi SH, Kang A, Kim DW, Kim RN, Kim A, Kim DS, Park HS	J Bacteriol	10.1128/JB.00003-11	2011
Phylogeny	Companilactobacillus pabuli sp. nov., a lactic acid bacterium isolated from animal feed.	Jung JY, Kang HK, Jin HM, Han SS, Kwon YC, Eun JJ, Kim SC, Seo MJ, Ryu BG, Chung EJ	Int J Syst Evol Microbiol	10.1099/ijsem.0.004670	2021
Phylogeny	Lactobacillus zhachilii sp. nov., a lactic acid bacterium isolated from Zha-Chili.	Zhang Z, Hou Q, Wang Y, Li W, Zhao H, Sun Z, Guo Z	Int J Syst Evol Microbiol	10.1099/ijsem.0.003362	2019
Phylogeny	Lactobacillus formosensis sp. nov., a lactic acid bacterium isolated from fermented soybean meal.	Chang CH, Chen YS, Lee TT, Chang YC, Yu B	Int J Syst Evol Microbiol	10.1099/ijs.0.070938-0	2014
Phylogeny	Lactobacillus heilongjiangensis sp. nov., isolated from Chinese pickle.	Gu CT, Li CY, Yang LJ, Huo GC	Int J Syst Evol Microbiol	10.1099/ijs.0.053355-0	2013
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

#8460	Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 20184
#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 )
#38122	; Curators of the CIP;
#50208	Culture Collection University of Gothenburg (CCUG) ; Curators of the CCUG; CCUG 30671
#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) .
#66794	Antje Chang, Lisa Jeske, Sandra Ulbrich, Julia Hofmann, Julia Koblitz, Ida Schomburg, Meina Neumann-Schaal, Dieter Jahn, Dietmar Schomburg: BRENDA, the ELIXIR core data resource in 2021: new developments and updates. Nucleic Acids Res. 49: D498 - D508 2020 ( DOI 10.1093/nar/gkaa1025 , PubMed 33211880 )
#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 .
#119281	Collection of Institut Pasteur ; Curators of the CIP; CIP 103136
#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 farciminis (DSM 20184, ATCC 29644, NCIB 11717)

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