Name: Limosilactobacillus secaliphilus DSM 17896
Creator: BacDive
License: https://creativecommons.org/licenses/by/4.0/

Strain identifier

BacDive ID: 6669

Type strain:

Species: Limosilactobacillus secaliphilus

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

Strain history: CIP <- 2007, CCUG <- 2006, M. Ehrmann, Munich Univ., Freising, Germany: strain TMW 1.1309

NCBI tax ID(s): 396268 (species)

SI-ID 302644

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

Special Collections

Section

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

Gram-positive
rod-shaped
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	*Limosilactobacillus*
	Species	**Limosilactobacillus secaliphilus**
	Full Scientific Name (LPSN)	Limosilactobacillus secaliphilus (Ehrmann et al. 2007) Zheng et al. 2020

Synonym

Lactobacillus secaliphilus

Information on morphological and physiological properties Morphology

[Ref.: #31950]	Gram stain	positive
[Ref.: #122530]	Gram stain	positive
[Ref.: #69480]	Gram stain	positive Confidence in %94.102

[Ref.: #31950]	Cell length	02-04 µm

[Ref.: #31950]	Cell width	0.5-1 µm

[Ref.: #31950]	Cell shape	rod-shaped
[Ref.: #122530]	Cell shape	rod-shaped

[Ref.: #31950]	Motility	no
[Ref.: #122530]	Motility	no
[Ref.: #69480]	Motility	no Confidence in %91

[Ref.: #31950]

Pigment production

Information on culture and growth conditions Culture and growth conditions

[Ref.: #7230]

Culture medium

LACTOBACILLUS MEDIUM III (DSMZ Medium 638)

[Ref.: #7230]

Culture medium growth

[Ref.: #7230]

Culture medium link

Medium recipe at MediaDive

[Ref.: #7230]

Culture medium composition

expand / minimize

[Ref.: #37765]

Culture medium

MEDIUM 40- for Lactobacillus and Leuconostoc

[Ref.: #37765]

Culture medium growth

[Ref.: #37765]

Culture medium composition

expand / minimize

[Ref.: #122530]

Culture medium

CIP Medium 40

[Ref.: #122530]

Culture medium growth

[Ref.: #122530]

Culture medium link

Medium recipe provided by DSMZ

		Temperature
[Ref.: #7230]	growth	37 °C
[Ref.: #31950]	growth	35-45 °C
[Ref.: #31950]	optimum	40 °C
[Ref.: #37765]	growth	37 °C
[Ref.: #59833]	growth	37 °C
[Ref.: #67770]	growth	37 °C

Information on physiology and metabolism Physiology and metabolism

[Ref.: #7230]	Oxygen tolerance	microaerophile
[Ref.: #31950]	Oxygen tolerance	facultative anaerobe
[Ref.: #59833]	Oxygen tolerance	microaerophile
[Ref.: #122530]	Oxygen tolerance	facultative anaerobe

[Ref.: #31950]	Ability of spore formation	no
[Ref.: #69480]	Ability of spore formation	no Confidence in %90.352
[Ref.: #69481]	Ability of spore formation	no Confidence in %100

	Halophily	Salt	Tested relation		Salt conc.
[Ref.: #31950]		NaCl		optimum	3	%

	Metabolite	Utilization activity	Kind of utilization tested
[Ref.: #122530]	nitrate ChEBI	+	reduction
[Ref.: #122530]	nitrite ChEBI	-	reduction
[Ref.: #31950]	ribose ChEBI	+	carbon source
[Ref.: #31950]	sucrose ChEBI	+	carbon source

	Metabolite production	Metabolite	Production
[Ref.: #122530]		indole ChEBI	yes

	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.: #122530]	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.: #122530]	oxidase	-
[Ref.: #68382]	trypsin	+	3.4.21.4	* from API zym
[Ref.: #122530]	urease	+	3.5.1.5
[Ref.: #68382]	valine arylamidase	-		* from API zym
	Only first 10 entries are displayed. Click here to see all.

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.: #122530]	11952	-	-	-	-	-	-	-	-	+	-	-	-	-	-	-	-	-	-	-	-

	Pathway	Enzyme coverage	Annotated reactions
	Pathway annotation	Computationally determined by
[Ref.: #66794]	acetoin degradation	100	3 of 3
[Ref.: #66794]	ppGpp biosynthesis	100	4 of 4
[Ref.: #66794]	cis-vaccenate biosynthesis	100	2 of 2
[Ref.: #66794]	coenzyme A metabolism	100	4 of 4
[Ref.: #66794]	CDP-diacylglycerol biosynthesis	100	2 of 2
[Ref.: #66794]	UDP-GlcNAc biosynthesis	100	3 of 3
[Ref.: #66794]	folate polyglutamylation	100	1 of 1
[Ref.: #66794]	peptidoglycan biosynthesis	86.67	13 of 15
[Ref.: #66794]	palmitate biosynthesis	81.82	18 of 22
[Ref.: #66794]	aspartate and asparagine metabolism	77.78	7 of 9
[Ref.: #66794]	acetate fermentation	75	3 of 4
[Ref.: #66794]	pentose phosphate pathway	72.73	8 of 11
[Ref.: #66794]	photosynthesis	71.43	10 of 14
[Ref.: #66794]	cardiolipin biosynthesis	71.43	5 of 7
[Ref.: #66794]	valine metabolism	66.67	6 of 9
[Ref.: #66794]	formaldehyde oxidation	66.67	2 of 3
[Ref.: #66794]	d-xylose degradation	63.64	7 of 11
[Ref.: #66794]	ketogluconate metabolism	62.5	5 of 8
[Ref.: #66794]	gluconeogenesis	62.5	5 of 8
[Ref.: #66794]	C4 and CAM-carbon fixation	62.5	5 of 8
[Ref.: #66794]	phenylalanine metabolism	61.54	8 of 13
[Ref.: #66794]	NAD metabolism	61.11	11 of 18
[Ref.: #66794]	threonine metabolism	60	6 of 10
[Ref.: #66794]	glycogen metabolism	60	3 of 5
[Ref.: #66794]	Entner Doudoroff pathway	60	6 of 10
[Ref.: #66794]	degradation of pentoses	57.14	16 of 28
[Ref.: #66794]	propanol degradation	57.14	4 of 7
[Ref.: #66794]	degradation of sugar alcohols	56.25	9 of 16
[Ref.: #66794]	pyrimidine metabolism	53.33	24 of 45
[Ref.: #66794]	glycolysis	52.94	9 of 17
[Ref.: #66794]	glycogen biosynthesis	50	2 of 4
[Ref.: #66794]	glycolate and glyoxylate degradation	50	3 of 6
[Ref.: #66794]	ethanol fermentation	50	1 of 2
[Ref.: #66794]	ribulose monophosphate pathway	50	1 of 2
[Ref.: #66794]	butanoate fermentation	50	2 of 4
[Ref.: #66794]	sulfopterin metabolism	50	2 of 4
[Ref.: #66794]	mannosylglycerate biosynthesis	50	1 of 2
[Ref.: #66794]	suberin monomers biosynthesis	50	1 of 2
[Ref.: #66794]	adipate degradation	50	1 of 2
[Ref.: #66794]	purine metabolism	48.94	46 of 94
[Ref.: #66794]	degradation of sugar acids	48	12 of 25
[Ref.: #66794]	d-mannose degradation	44.44	4 of 9
[Ref.: #66794]	serine metabolism	44.44	4 of 9
[Ref.: #66794]	CO2 fixation in Crenarchaeota	44.44	4 of 9
[Ref.: #66794]	mevalonate metabolism	42.86	3 of 7
[Ref.: #66794]	glutathione metabolism	42.86	6 of 14
[Ref.: #66794]	glutamate and glutamine metabolism	42.86	12 of 28
[Ref.: #66794]	ubiquinone biosynthesis	42.86	3 of 7
[Ref.: #66794]	tetrahydrofolate metabolism	42.86	6 of 14
[Ref.: #66794]	non-pathway related	42.11	16 of 38
[Ref.: #66794]	lysine metabolism	40.48	17 of 42
[Ref.: #66794]	3-chlorocatechol degradation	40	2 of 5
[Ref.: #66794]	arachidonate biosynthesis	40	2 of 5
[Ref.: #66794]	methylglyoxal degradation	40	2 of 5
[Ref.: #66794]	lipoate biosynthesis	40	2 of 5
[Ref.: #66794]	oxidative phosphorylation	39.56	36 of 91
[Ref.: #66794]	degradation of hexoses	38.89	7 of 18
[Ref.: #66794]	lipid metabolism	38.71	12 of 31
[Ref.: #66794]	vitamin B1 metabolism	38.46	5 of 13
[Ref.: #66794]	alanine metabolism	37.93	11 of 29
[Ref.: #66794]	6-hydroxymethyl-dihydropterin diphosphate biosynthesis	37.5	3 of 8
[Ref.: #66794]	dTDPLrhamnose biosynthesis	37.5	3 of 8
[Ref.: #66794]	isoleucine metabolism	37.5	3 of 8
[Ref.: #66794]	proline metabolism	36.36	4 of 11
[Ref.: #66794]	ascorbate metabolism	36.36	8 of 22
[Ref.: #66794]	lipid A biosynthesis	33.33	3 of 9
[Ref.: #66794]	flavin biosynthesis	33.33	5 of 15
[Ref.: #66794]	octane oxidation	33.33	1 of 3
[Ref.: #66794]	acetyl CoA biosynthesis	33.33	1 of 3
[Ref.: #66794]	degradation of aromatic, nitrogen containing compounds	33.33	4 of 12
[Ref.: #66794]	sphingosine metabolism	33.33	2 of 6
[Ref.: #66794]	selenocysteine biosynthesis	33.33	2 of 6
[Ref.: #66794]	L-lactaldehyde degradation	33.33	1 of 3
[Ref.: #66794]	IAA biosynthesis	33.33	1 of 3
[Ref.: #66794]	tryptophan metabolism	31.58	12 of 38
[Ref.: #66794]	phenylpropanoid biosynthesis	30.77	4 of 13
[Ref.: #66794]	isoprenoid biosynthesis	30.77	8 of 26
[Ref.: #66794]	methionine metabolism	30.77	8 of 26
[Ref.: #66794]	starch degradation	30	3 of 10
[Ref.: #66794]	glycine metabolism	30	3 of 10
[Ref.: #66794]	reductive acetyl coenzyme A pathway	28.57	2 of 7
[Ref.: #66794]	histidine metabolism	27.59	8 of 29
[Ref.: #66794]	vitamin B6 metabolism	27.27	3 of 11
[Ref.: #66794]	metabolism of disaccharids	27.27	3 of 11
[Ref.: #66794]	lactate fermentation	25	1 of 4
[Ref.: #66794]	carnitine metabolism	25	2 of 8
[Ref.: #66794]	cyclohexanol degradation	25	1 of 4
[Ref.: #66794]	leucine metabolism	23.08	3 of 13
[Ref.: #66794]	sulfate reduction	23.08	3 of 13
[Ref.: #66794]	urea cycle	23.08	3 of 13
[Ref.: #66794]	cysteine metabolism	22.22	4 of 18
[Ref.: #66794]	nitrate assimilation	22.22	2 of 9
[Ref.: #66794]	chorismate metabolism	22.22	2 of 9
[Ref.: #66794]	tyrosine metabolism	21.43	3 of 14
		Only first 10 entries are displayed. Click here to see all.

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

[Ref.: #7230]	Sample type/isolated from	sour dough
[Ref.: #7230]	Country	Germany
[Ref.: #7230]	Country ISO 3 Code	DEU
[Ref.: #7230]	Continent	Europe

[Ref.: #59833]	Sample type/isolated from	Rye sourdough
[Ref.: #59833]	Geographic location (country and/or sea, region)	Minden
[Ref.: #59833]	Country	Germany
[Ref.: #59833]	Country ISO 3 Code	DEU
[Ref.: #59833]	Continent	Europe

[Ref.: #67770]	Sample type/isolated from	Type II sourdough fermentation

[Ref.: #122530]	Sample type/isolated from	Rye sourdough
[Ref.: #122530]	Geographic location (country and/or sea, region)	Minden
[Ref.: #122530]	Country	Germany
[Ref.: #122530]	Country ISO 3 Code	DEU
[Ref.: #122530]	Continent	Europe
* marker position based on {}

Isolation sources categories

#Engineered

#Food production

#Fermented

What are isolation sources categories?

[Ref.: #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

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

[Ref.: #7230]	Biosafety level	1	Risk group (German classification) According to TRBA 466
[Ref.: #122530]	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.: #7230]	Lactobacillus secaliphilus 16S rRNA gene, type strain TMW 1.1309T	AM279150	1551	GenBank ENA	396268 tax ID
[Ref.: #67770]	Lactobacillus secaliphilus JCM 15613 gene for 16S ribosomal RNA, partial sequence	LC480808	1514	GenBank ENA	396268 tax ID

Genome sequence information:

	Sequence accession description	Seq. accession number	Assembly level	Sequence database	Associated NCBI tax ID
[Ref.: #67770]	Limosilactobacillus secaliphilus DSM 17896	GCA_001437055	scaffold	GenBank ENA	396268 tax ID
[Ref.: #66792]	Lactobacillus secaliphilus strain DSM 17896	396268.3	wgs	PATRIC	396268 tax ID	*
[Ref.: #66792]	Limosilactobacillus secaliphilus DSM 17896	2671180593	draft	JGI IMG/M	396268 tax ID	*

[Ref.: #7230]	GC-content	48.0 mol%
[Ref.: #31950]	GC-content	48 mol%
[Ref.: #67770]	GC-content	47.7 mol%

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

	Trait	Model	Prediction	Confidence in %	In training data
	Predictions from GenomeNet Sporulation v. 1 based on: Limosilactobacillus secaliphilus DSM 17896 NCBI: GCA_001437055.1
[Ref.: #69481]	spore-forming	spore-formingⓘ	no	100	no

	Trait	Model	Prediction	Confidence in %	In training data
	Predictions from Diaspora project based on: Lactobacillus secaliphilus strain DSM 17896 PATRIC: 396268.3
[Ref.: #69480]	gram-positive	gram-positiveⓘ	yes	94.102	no
[Ref.: #69480]	anaerobic	anaerobicⓘ	no	84.755	yes
[Ref.: #69480]	spore-forming	spore-formingⓘ	no	90.352	yes
[Ref.: #69480]	aerobic	aerobicⓘ	no	93.151	yes
[Ref.: #69480]	thermophilic	thermophileⓘ	no	95.5	yes
[Ref.: #69480]	flagellated	motile2+ⓘ	no	91	yes

Availability in culture collections External links

[Ref.: #7230]

Culture collection no.

DSM 17896, CCUG 53218, TMW 1.1309, CIP 109557, JCM 15613

[Ref.: #76143]

SI-ID 302644

Literature:

Topic	Title	Authors	Journal	DOI	Year
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 )

#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 (see below)

#37765 ; Curators of the CIP;
#59833 Culture Collection University of Gothenburg (CCUG) ; Curators of the CCUG; CCUG 53218

#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;

#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) .

#69481

Xiao-Yin To, René Mreches, Martin Binder, Alice C. McHardy, Philipp C. Münch: Predictions based on the model GenomeNet Sporulation v. 1 . ( DOI 10.21203/rs.3.rs-2527258/v1 )

#76143

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-ID302644.1 )

#122530 Collection of Institut Pasteur ; Curators of the CIP; CIP 109557

#28206

IJSEM 745 2007 ( DOI 10.1099/ijs.0.64700-0 , PubMed 17392199 )

* These data were automatically processed and therefore are not curated

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Limosilactobacillus secaliphilus DSM 17896

Lactobacillus secaliphilus strain DSM 17896

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