Limosilactobacillus secaliphilus (DSM 17896, CCUG 53218, TMW 1.1309)

Name: Limosilactobacillus secaliphilus (DSM 17896, CCUG 53218, TMW 1.1309)
Creator: BacDive
License: http://creativecommons.org/licenses/by/4.0/

BacDive ID 6669

Type strain

Culture col. no. DSM 17896 CCUG 53218 TMW 1.1309 CIP 109557 JCM 15613

NCBI tax ID(s) 396268

Special Collections DSMZ CCUG JCM CIP Literature strains

History <- M.A. Ehrmann <- M. Brandt <- Ernst Böcker GmbH, strain WP/5 CCUG 53218 <-- M. Ehrmann TMW 1.1309. CIP <- 2007, CCUG <- 2006, M. Ehrmann, Munich Univ., Freising, Germany: strain TMW 1.1309

Links

Limosilactobacillus secaliphilus DSM 17896 is a microaerophile, Gram-positive, rod-shaped bacterium that was isolated from sour dough.

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

Name and taxonomic classification

SI-ID 302644

CCUG 53218,DSM 17896,LMG 24164,CIP 109557,JCM 15613

@ref 20215

Last LPSN update 2026-02-09 11:19:17

Domain Bacteria

Phylum Bacillota

Class Bacilli

Order Lactobacillales

Family Lactobacillaceae

Genus Limosilactobacillus

Species Limosilactobacillus secaliphilus

Full scientific name Limosilactobacillus secaliphilus (Ehrmann et al. 2007) Zheng et al. 2020

Synonyms (1)

Lactobacillus secaliphilus

Morphology

Cell morphology

@ref	Gram stain	Cell length	Cell width	Cell shape	Confidence
31950	positive	02-04 µm	0.5-1 µm	rod-shaped
122530	positive			rod-shaped
125438					91
125438	positive				94.102

Pigmentation

31950

Productionno

Culture and growth conditions

Culture medium

@ref	Name	Medium link	Composition
7230	LACTOBACILLUS MEDIUM III (DSMZ Medium 638)	Medium recipe at MediaDive	Name: LACTOBACILLUS MEDIUM III (DSMZ Medium 638) Composition: Tryptone 10.0 g/l Glucose 7.0 g/l Maltose 7.0 g/l Fructose 7.0 g/l Na-acetate x 3 H2O 5.0 g/l Yeast extract 5.0 g/l Meat extract 5.0 g/l K2HPO4 x 3 H2O 2.6 g/l (NH4)2 citrate 2.0 g/l Na-gluconate 2.0 g/l L-Cysteine HCl x H2O 0.5 g/l MgSO4 x 7 H2O 0.1 g/l MnSO4 x 4 H2O 0.05 g/l Tween 80 Distilled water
37765	MEDIUM 40- for Lactobacillus and Leuconostoc		Distilled water make up to (1000.000 ml);Man Rogosa Sharp agar (68.000 g)
122530	CIP Medium 40	Medium recipe at CIP

Culture temp

@ref	Growth	Type	Temperature (°C)
7230	positive	growth	37
31950	positive	growth	35-45
31950	positive	optimum	40
37765	positive	growth	37
59833	positive	growth	37
67770	positive	growth	37

Physiology and metabolism

Oxygen tolerance

@ref	Oxygen tolerance
7230	microaerophile
31950	facultative anaerobe
59833	microaerophile
122530	facultative anaerobe

Spore formation

@ref	Spore formation	Confidence
31950
125438		90.352

Halophily

@ref	Salt	Growth	Tested relation	Concentration
31950	NaCl	positive	optimum	3 %

Metabolite utilization

@ref	Chebi-ID	Metabolite	Utilization activity	Kind of utilization tested
122530	17632 ChEBI	nitrate	+	reduction
122530	16301 ChEBI	nitrite	-	reduction
31950	33942 ChEBI	ribose	+	carbon source
31950	17992 ChEBI	sucrose	+	carbon source

Metabolite production

@ref	Chebi-ID	Metabolite	Production
122530	35581 ChEBI	indole

Enzymes

@ref	Value	Activity	Ec
68382	acid phosphatase	-	3.1.3.2	from API zym
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
122530	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
68382	N-acetyl-beta-glucosaminidase	-	3.2.1.52	from API zym
68382	naphthol-AS-BI-phosphohydrolase	-		from API zym
122530	oxidase	-
68382	trypsin	+	3.4.21.4	from API zym
122530	urease	+	3.5.1.5
68382	valine arylamidase	-		from API zym

Pathway annotation

Computationally determined by

@ref	pathway	enzyme coverage	annotated reactions
66794	acetoin degradation	100	3 of 3
66794	ppGpp biosynthesis	100	4 of 4
66794	cis-vaccenate biosynthesis	100	2 of 2
66794	coenzyme A metabolism	100	4 of 4
66794	CDP-diacylglycerol biosynthesis	100	2 of 2
66794	UDP-GlcNAc biosynthesis	100	3 of 3
66794	folate polyglutamylation	100	1 of 1
66794	peptidoglycan biosynthesis	86.67	13 of 15
66794	palmitate biosynthesis	81.82	18 of 22
66794	aspartate and asparagine metabolism	77.78	7 of 9
66794	acetate fermentation	75	3 of 4
66794	pentose phosphate pathway	72.73	8 of 11
66794	photosynthesis	71.43	10 of 14
66794	cardiolipin biosynthesis	71.43	5 of 7
66794	valine metabolism	66.67	6 of 9
66794	formaldehyde oxidation	66.67	2 of 3
66794	d-xylose degradation	63.64	7 of 11
66794	ketogluconate metabolism	62.5	5 of 8
66794	gluconeogenesis	62.5	5 of 8
66794	C4 and CAM-carbon fixation	62.5	5 of 8
66794	phenylalanine metabolism	61.54	8 of 13
66794	NAD metabolism	61.11	11 of 18
66794	threonine metabolism	60	6 of 10
66794	glycogen metabolism	60	3 of 5
66794	Entner Doudoroff pathway	60	6 of 10
66794	degradation of pentoses	57.14	16 of 28
66794	propanol degradation	57.14	4 of 7
66794	degradation of sugar alcohols	56.25	9 of 16
66794	pyrimidine metabolism	53.33	24 of 45
66794	glycolysis	52.94	9 of 17
66794	glycogen biosynthesis	50	2 of 4
66794	glycolate and glyoxylate degradation	50	3 of 6
66794	ethanol fermentation	50	1 of 2
66794	ribulose monophosphate pathway	50	1 of 2
66794	butanoate fermentation	50	2 of 4
66794	sulfopterin metabolism	50	2 of 4
66794	mannosylglycerate biosynthesis	50	1 of 2
66794	suberin monomers biosynthesis	50	1 of 2
66794	adipate degradation	50	1 of 2
66794	purine metabolism	48.94	46 of 94
66794	degradation of sugar acids	48	12 of 25
66794	d-mannose degradation	44.44	4 of 9
66794	serine metabolism	44.44	4 of 9
66794	CO2 fixation in Crenarchaeota	44.44	4 of 9
66794	mevalonate metabolism	42.86	3 of 7
66794	glutathione metabolism	42.86	6 of 14
66794	glutamate and glutamine metabolism	42.86	12 of 28
66794	ubiquinone biosynthesis	42.86	3 of 7
66794	tetrahydrofolate metabolism	42.86	6 of 14
66794	non-pathway related	42.11	16 of 38
66794	lysine metabolism	40.48	17 of 42
66794	3-chlorocatechol degradation	40	2 of 5
66794	arachidonate biosynthesis	40	2 of 5
66794	methylglyoxal degradation	40	2 of 5
66794	lipoate biosynthesis	40	2 of 5
66794	oxidative phosphorylation	39.56	36 of 91
66794	degradation of hexoses	38.89	7 of 18
66794	lipid metabolism	38.71	12 of 31
66794	vitamin B1 metabolism	38.46	5 of 13
66794	alanine metabolism	37.93	11 of 29
66794	6-hydroxymethyl-dihydropterin diphosphate biosynthesis	37.5	3 of 8
66794	dTDPLrhamnose biosynthesis	37.5	3 of 8
66794	isoleucine metabolism	37.5	3 of 8
66794	proline metabolism	36.36	4 of 11
66794	ascorbate metabolism	36.36	8 of 22
66794	lipid A biosynthesis	33.33	3 of 9
66794	flavin biosynthesis	33.33	5 of 15
66794	octane oxidation	33.33	1 of 3
66794	acetyl CoA biosynthesis	33.33	1 of 3
66794	degradation of aromatic, nitrogen containing compounds	33.33	4 of 12
66794	sphingosine metabolism	33.33	2 of 6
66794	selenocysteine biosynthesis	33.33	2 of 6
66794	L-lactaldehyde degradation	33.33	1 of 3
66794	IAA biosynthesis	33.33	1 of 3
66794	tryptophan metabolism	31.58	12 of 38
66794	phenylpropanoid biosynthesis	30.77	4 of 13
66794	isoprenoid biosynthesis	30.77	8 of 26
66794	methionine metabolism	30.77	8 of 26
66794	starch degradation	30	3 of 10
66794	glycine metabolism	30	3 of 10
66794	reductive acetyl coenzyme A pathway	28.57	2 of 7
66794	histidine metabolism	27.59	8 of 29
66794	vitamin B6 metabolism	27.27	3 of 11
66794	metabolism of disaccharids	27.27	3 of 11
66794	lactate fermentation	25	1 of 4
66794	carnitine metabolism	25	2 of 8
66794	cyclohexanol degradation	25	1 of 4
66794	leucine metabolism	23.08	3 of 13
66794	sulfate reduction	23.08	3 of 13
66794	urea cycle	23.08	3 of 13
66794	cysteine metabolism	22.22	4 of 18
66794	nitrate assimilation	22.22	2 of 9
66794	chorismate metabolism	22.22	2 of 9
66794	tyrosine 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
122530	-	-	-	-	-	-	-	-	+	-	-	-	-	-	-	-	-	-	-	-

Isolation, sampling and environmental information

Isolation source categories

Cat1	Cat2	Cat3
#Engineered	#Food production	#Fermented

Isolation

@ref	Sample type	Geographic location	Country	Country ISO 3 Code	Continent
7230	sour dough		Germany	DEU	Europe
59833	Rye sourdough	Minden	Germany	DEU	Europe
67770	Type II sourdough fermentation
122530	Rye sourdough	Minden	Germany	DEU	Europe

Taxonmaps

69479

Global distribution of 16S sequence AM279150 (>99% sequence identity) for Limosilactobacillus secaliphilus subclade from Microbeatlas

Aquatic Samples	287
Soil Samples	217
Animal Samples	10646
Plant Samples	289
Total Samples	11439

Interaction and safety

Risk assessment

@ref	Biosafety level	Biosafety level comment
7230	1	Risk group (German classification) According to TRBA 466
122530	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
67770	ASM143705v1 assembly for Limosilactobacillus secaliphilus DSM 17896	scaffold	GCA_001437055	396268.3	2671180593	396268	69.2

16S sequences

@ref	Description	Accession	Length	Database	NCBI tax ID
7230	Lactobacillus secaliphilus 16S rRNA gene, type strain TMW 1.1309T	AM279150	1551		396268
67770	Lactobacillus secaliphilus JCM 15613 gene for 16S ribosomal RNA, partial sequence	LC480808	1514		396268

GC content

@ref	GC-content (mol%)
7230	48.0
31950	48
67770	47.7

Genome-based predictions

Predictions

Predictions from Deep Learning for Genome Sequence Data. R package version 0.3.1 based on: Limosilactobacillus secaliphilus DSM 17896
NCBI: GCA_001437055

@ref	Trait	Model	Prediction	Confidence in %	In training data
125439	spore_formation	BacteriaNetⓘ	yes	58.10	no
125439	motility	BacteriaNetⓘ	yes	56.00	no
125439	gram_stain	BacteriaNetⓘ	variable	69.40	no
125439	oxygen_tolerance	BacteriaNetⓘ	microaerophile	86.90	no

Predictions from bacterial phenotypic traits through improved machine learning using high-quality, curated datasets based on: Lactobacillus secaliphilus strain DSM 17896
PATRIC: 396268.3

@ref	Trait	Model	Prediction	Confidence in %	In training data
125438	gram-positive	gram-positiveⓘ	yes	94.10	no
125438	anaerobic	anaerobicⓘ	no	84.76	yes
125438	spore-forming	spore-formingⓘ	no	90.35	yes
125438	aerobic	aerobicⓘ	no	93.15	yes
125438	thermophilic	thermophileⓘ	no	95.50	yes
125438	flagellated	motile2+ⓘ	no	91.00	yes

Literature

Topic	Title	Authors	Journal	DOI	Year
Enzymology	Identification and Thermostability Modification of the Mesophilic L-asparaginase from Limosilactobacillus secaliphilus.	Zhang W, Dai Q, Huang Z, Xu W.	Appl Biochem Biotechnol	10.1007/s12010-023-04715-3	2024
Genetics	Metagenomics and Metagenome-Assembled Genomes: Analysis of Cupei from Sichuan Baoning Vinegar, One of the Four Traditional Renowned Vinegars in China.	Wu J, Zhao N, Li Q, Zhao K, Tu M, Li J, Hu K, Chen S, Liu S, Liu A.	Foods	10.3390/foods14030398	2025
Genetics	Genomic diversity of genus Limosilactobacillus.	Ksiezarek M, Grosso F, Ribeiro TG, Peixe L.	Microb Genom	10.1099/mgen.0.000847	2022
Metabolism	Co-Occurrence of Regulated and Emerging Mycotoxins in Corn Silage: Relationships with Fermentation Quality and Bacterial Communities.	Gallo A, Ghilardelli F, Atzori AS, Zara S, Novak B, Faas J, Fancello F.	Toxins (Basel)	10.3390/toxins13030232	2021
Phylogeny	Lactobacillus alvi sp. nov., isolated from the intestinal tract of chicken.	Kim HJ, Eom SJ, Park SJ, Cha CJ, Kim GB	FEMS Microbiol Lett	10.1111/j.1574-6968.2011.02361.x	2011
Phylogeny	Lactobacillus secaliphilus sp. nov., isolated from type II sourdough fermentation.	Ehrmann MA, Brandt M, Stolz P, Vogel RF, Korakli M	Int J Syst Evol Microbiol	10.1099/ijs.0.64700-0	2007

References

#7230	Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 17896
#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 )
#28206	IJSEM 745 2007 ( DOI 10.1099/ijs.0.64700-0 , PubMed 17392199 )
#31950	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 #28206
#37765	; Curators of the CIP;
#59833	Culture Collection University of Gothenburg (CCUG) ; Curators of the CCUG; CCUG 53218
#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;
#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 .
#122530	Collection of Institut Pasteur ; Curators of the CIP; CIP 109557
#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 )

Rate our new design

Content

About us

Limosilactobacillus secaliphilus (DSM 17896, CCUG 53218, TMW 1.1309)

Name and taxonomic classification

Morphology

Cell morphology

Pigmentation

Culture and growth conditions

Culture medium

Culture temp

Physiology and metabolism

Oxygen tolerance

Spore formation

Halophily

Metabolite utilization

Metabolite production

Enzymes

Pathway annotation

API zym

Isolation, sampling and environmental information

Isolation source categories

Isolation

Taxonmaps

Interaction and safety

Risk assessment

Sequence information

Genome sequences

Genome browser: GCA_001437055

16S sequences

GC content

Genome-based predictions

Predictions

Literature

Literature

References

BacDive

Help

Social Media