Name: Levilactobacillus zymae R-18615
Creator: BacDive
License: https://creativecommons.org/licenses/by/4.0/

Strain identifier

BacDive ID: 6660

Type strain:

Species: Levilactobacillus zymae

Strain Designation: R-18615

Culture col. no.: DSM 19395, CCM 7241, LMG 22198, CCUG 50163, JCM 15957, BCRC 80776, CIP 108703, NBRC 107157

Strain history: CIP <- 2005, CCM <- LMG <- P. Neyssen, IMDO, Vrije Univ., Brussels, Belgium: strain R-18615

NCBI tax ID(s): 1423817 (strain), 267363 (species)

SI-ID 280627

LMG 22198, CCM 7241, CCUG 50163, DSM 19395, JCM 15957, CIP 108703

Special Collections

Section

When using BacDive for research please cite our paper

Levilactobacillus zymae R-18615 is a microaerophile, mesophilic, Gram-positive bacterium that was isolated from artisanal wheat sourdough.

Gram-positive
rod-shaped
mesophilic
microaerophile
16S sequence
Bacteria
genome sequence

Information on the name and the taxonomic classification. Name and taxonomic classification

	Last LPSN update	09-12-2024 (DD-MM-YYYY)
	Domain	*Bacteria*
	Phylum	*Bacillota*
	Class	*Bacilli*
	Order	*Lactobacillales*
	Family	*Lactobacillaceae*
	Genus	*Levilactobacillus*
	Species	**Levilactobacillus zymae**
	Full Scientific Name (LPSN)	Levilactobacillus zymae (Vancanneyt et al. 2005) Zheng et al. 2020

Synonym

Lactobacillus zymae

Information on morphological and physiological properties Morphology

[Ref.: #31309]	Gram stain	positive
[Ref.: #124040]	Gram stain	positive
[Ref.: #125438]	Gram stain	positive Confidence in %93.214

[Ref.: #31309]	Cell length	11 µm

[Ref.: #31309]	Cell width	1 µm

[Ref.: #31309]	Cell shape	rod-shaped
[Ref.: #124040]	Cell shape	rod-shaped

[Ref.: #31309]	Motility	no
[Ref.: #124040]	Motility	no
[Ref.: #125438]	Motility	no Confidence in %90

[Ref.: #31309]

Pigment production

yes

Information on culture and growth conditions Culture and growth conditions

[Ref.: #8089]

Culture medium

PEDIOCOCCUS DAMNOSUS MEDIUM (DSMZ Medium 231)

[Ref.: #8089]

Culture medium growth

[Ref.: #8089]

Culture medium link

Medium recipe at MediaDive

[Ref.: #8089]

Culture medium composition

expand / minimize

[Ref.: #40644]

Culture medium

MEDIUM 40- for Lactobacillus and Leuconostoc

[Ref.: #40644]

Culture medium growth

[Ref.: #40644]

Culture medium composition

expand / minimize

[Ref.: #124040]

Culture medium

CIP Medium 40

[Ref.: #124040]

Culture medium growth

[Ref.: #124040]

Culture medium link

Medium recipe provided by DSMZ

	Kind of temperature		Temperature
[Ref.: #8089]		growth	30 °C
[Ref.: #31309]		optimum	7.5 °C
[Ref.: #40644]		growth	37 °C
[Ref.: #58766]		growth	37 °C
[Ref.: #67770]		growth	30 °C
[Ref.: #124040]		growth	10-37 °C
[Ref.: #124040]	no	growth	45 °C

Information on physiology and metabolism Physiology and metabolism

[Ref.: #8089]	Oxygen tolerance	microaerophile
[Ref.: #31309]	Oxygen tolerance	facultative anaerobe
[Ref.: #58766]	Oxygen tolerance	anaerobe
[Ref.: #124040]	Oxygen tolerance	facultative anaerobe
[Ref.: #125439]	Oxygen tolerance	anaerobe Confidence in %96.8

[Ref.: #31309]	Ability of spore formation	no
[Ref.: #125439]	Ability of spore formation	no Confidence in %94

	Halophily	Salt	Tested relation		Salt conc.
[Ref.: #31309]		NaCl		growth	<7	%
[Ref.: #31309]		NaCl		optimum	3.5	%

[Ref.: #31309]

Observation

aggregates in chains

	Metabolite	Utilization activity	Kind of utilization tested
[Ref.: #68371]	amygdalin ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #31309]	arabinose ChEBI	+	carbon source
[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-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.: #31309]	fructose ChEBI	+	carbon source
[Ref.: #68371]	galactitol ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #68371]	gentiobiose ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #31309]	gluconate ChEBI	+	carbon source
[Ref.: #68371]	gluconate ChEBI	+	builds acid from	* from API 50CH acid
[Ref.: #31309]	glucose ChEBI	+	carbon source
[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.: #31309]	L-arabitol ChEBI	+	carbon source
[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.: #31309]	maltose ChEBI	+	carbon source
[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.: #31309]	N-acetylglucosamine ChEBI	+	carbon source
[Ref.: #68371]	N-acetylglucosamine ChEBI	+	builds acid from	* from API 50CH acid
[Ref.: #124040]	nitrate ChEBI	-	reduction
[Ref.: #124040]	nitrate ChEBI	+	respiration
[Ref.: #124040]	nitrite ChEBI	-	reduction
[Ref.: #68371]	Potassium 2-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.: #31309]	ribose ChEBI	+	carbon source
[Ref.: #68371]	salicin ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #68371]	starch 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.

	Physiological tests	Metabolite	Voges-Proskauer-test
[Ref.: #124040]		acetoin ChEBI	-

	Enzyme	Enzyme activity	EC number
[Ref.: #124040]	alcohol dehydrogenase	-	1.1.1.1
[Ref.: #124040]	catalase	-	1.11.1.6
[Ref.: #124040]	lysine decarboxylase	-	4.1.1.18
[Ref.: #124040]	ornithine decarboxylase	-	4.1.1.17
[Ref.: #124040]	oxidase	-

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.: #8089]	15198	-	-	-	-	+	+	+	-	-	-	+	+	+	-	-	-	-	-	+/-	-	-	-	+	-	-	+	-	-	+	+	+	-	-	-	-	-	-	-	-	-	-	-	-	-	-	+	-	+	-	+
[Ref.: #8089]	15197	-	-	-	-	+	+	+	-	-	-	+	+	+	-	-	-	-	-	+	-	-	-	+	-	-	+	-	-	+	+	+	+	-	-	-	-	-	-	-	-	-	-	-	-	-	+	-	+	-	+/-

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

[Ref.: #8089]	Sample type/isolated from	artisanal wheat sourdough
[Ref.: #8089]	Country	Belgium
[Ref.: #8089]	Country ISO 3 Code	BEL
[Ref.: #8089]	Continent	Europe

[Ref.: #58766]	Sample type/isolated from	Wheat sourdough
[Ref.: #58766]	Country	Belgium
[Ref.: #58766]	Country ISO 3 Code	BEL
[Ref.: #58766]	Continent	Europe

[Ref.: #67770]	Sample type/isolated from	Wheat sourdough

[Ref.: #124040]	Sample type/isolated from	Food, Wheat sourdough
[Ref.: #124040]	Country	Belgium
[Ref.: #124040]	Country ISO 3 Code	BEL
[Ref.: #124040]	Continent	Europe
[Ref.: #124040]	Isolation date	2003
* marker position based on {}

Isolation sources categories

#Engineered

#Food production

#Food

What are isolation sources categories?

[Ref.: #69479]

Global distribution of 16S sequence LC480814 (>99% sequence identity) for Levilactobacillus from Microbeatlas

Aquatic Samples	158
Soil Samples	49
Animal Samples	2008
Plant Samples	170
Total Samples	2385

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

[Ref.: #8089]	Biosafety level	1	Risk group (German classification) According to TRBA 466
[Ref.: #124040]	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.: #8089]	Lactobacillus zymae 16S rRNA gene, type strain LMG 22198	AJ632157	1518	GenBank ENA	267363 tax ID
[Ref.: #67770]	Lactobacillus zymae JCM 15957 gene for 16S ribosomal RNA, partial sequence	LC480814	1505	GenBank ENA	267363 tax ID
[Ref.: #124043]	Lactobacillus zymae gene for 16S rRNA, partial sequence, strain: NBRC 107157.	AB626071	1491	GenBank ENA	267363 tax ID	*

Genome sequence information:

	Sequence accession description	Seq. accession number	Assembly level	Sequence database	Associated NCBI tax ID
[Ref.: #67770]	Levilactobacillus zymae DSM 19395	GCA_001434115	scaffold	GenBank ENA	1423817 tax ID
[Ref.: #66792]	Levilactobacillus zymae NBRC 107157	GCA_007991995	contig	GenBank ENA	267363 tax ID	*
[Ref.: #66792]	Lactobacillus zymae DSM 19395	1423817.3	wgs	PATRIC	1423817 tax ID	*
[Ref.: #66792]	Lactobacillus zymae strain NBRC 107157	267363.7	wgs	PATRIC	267363 tax ID	*
[Ref.: #66792]	Levilactobacillus zymae DSM 19395	2660238323	draft	JGI IMG/M	1423817 tax ID	*

[Ref.: #8089]	GC-content	53 mol%
[Ref.: #31309]	GC-content	54 mol%
[Ref.: #67770]	GC-content	53.6 mol%	genome sequence analysis
[Ref.: #67770]	GC-content	53-54 mol%	high performance liquid chromatography (HPLC)

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

	Model	Trait	Prediction	Confidence in %	In training data
	Predictions from bacterial phenotypic traits through improved machine learning using high-quality, curated datasets based on: Lactobacillus zymae DSM 19395 PATRIC: 1423817.3
[Ref.: #125438]	gram-positive	gram-positiveⓘ	yes	93.214	yes
[Ref.: #125438]	anaerobic	anaerobicⓘ	no	81.953	no
[Ref.: #125438]	spore-forming	spore-formingⓘ	no	79.525	no
[Ref.: #125438]	aerobic	aerobicⓘ	no	94.864	yes
[Ref.: #125438]	thermophile	thermophilicⓘ	no	95.577	yes
[Ref.: #125438]	motile2+	flagellatedⓘ	no	90	yes

	Model	Trait	Prediction	Confidence in %
	Predictions from Deep Learning for Genome Sequence Data. R package version 0.3.1 based on: Levilactobacillus zymae DSM 19395 NCBI: GCA_001434115
[Ref.: #125439]	BacteriaNet	spore_formationⓘ	no	94
[Ref.: #125439]	BacteriaNet	motilityⓘ	no	82.9
[Ref.: #125439]	BacteriaNet	gram_stainⓘ	positive	81.5
[Ref.: #125439]	BacteriaNet	oxygen_toleranceⓘ	anaerobe	96.8

Availability in culture collections External links

[Ref.: #8089]

Culture collection no.

DSM 19395, CCM 7241, LMG 22198, CCUG 50163, JCM 15957, BCRC 80776, CIP 108703, NBRC 107157

[Ref.: #76134]

SI-ID 280627

Literature:

Topic	Title	Authors	Journal	DOI	Year
Phylogeny	Lactobacillus acidifarinae sp. nov. and Lactobacillus zymae sp. nov., from wheat sourdoughs.	Vancanneyt M, Neysens P, De Wachter M, Engelbeen K, Snauwaert C, Cleenwerck I, Van der Meulen R, Hoste B, Tsakalidou E, De Vuyst L, Swings J	Int J Syst Evol Microbiol	10.1099/ijs.0.63274-0	2005	*

References

#8089

Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 19395

#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 )

#31309

Barberan A, Caceres Velazquez H, Jones S, Fierer N.: Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information. mSphere 2: 2017 ( DOI 10.1128/mSphere.00237-17 , PubMed 28776041 ) - originally annotated from #27624 (see below)

#40644 ; Curators of the CIP;
#58766 Culture Collection University of Gothenburg (CCUG) ; Curators of the CCUG; CCUG 50163

#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 .

#76134

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-ID280627.1 )

#124040 Collection of Institut Pasteur ; Curators of the CIP; CIP 108703

#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 .

#27624

IJSEM 615 2005 ( DOI 10.1099/ijs.0.63274-0 , PubMed 15774633 )

* These data were automatically processed and therefore are not curated

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Lactobacillus zymae DSM 19395

Levilactobacillus zymae DSM 19395

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Change proposal