Name: Lacrimispora sphenoides Thorlby
Creator: BacDive
License: http://creativecommons.org/licenses/by-nc/4.0/

Strain identifier

BacDive ID: 2704

Type strain:

Species: Lacrimispora sphenoides

Strain Designation: Thorlby, Tholby, 10086

Culture col. no.: DSM 632, ATCC 19403, NCIB 10627, NCTC 507, JCM 1415, BCRC 14515, CECT 796, CIP 104283, LMG 10390, NCIMB 10627

Strain history: CIP <- 1994, J.P. Carlier, Inst. Pasteur, Paris, France: strain 10086 <- NCTC <- M. Robertson, Lister Inst., UK: strain Tholby

NCBI tax ID(s): 29370 (species)

SI-ID 13622

LMG 10390, ATCC 19403, JCM 1415, NCIB 10627, NCTC 507, CIP 104283, CCRC 14515, NCIMB 10627, LMD 77.27, CECT 796, NCCB 77027, BCRC 14515, ACM 2787, KCTC 5653, DSM 632

Other strains from Lacrimispora sphenoides

L. sphenoides C2, DSM 614
L. sphenoides DSM 1225, UQM 780
L. sphenoides 50, DSM 4024, VKM B-1591
L. sphenoides H1_31, DSM 108199

Section

Lacrimispora sphenoides Thorlby is an anaerobe, spore-forming, mesophilic bacterium that was isolated from human gas gangrene.

Gram-positive
spore-forming
anaerobe
mesophilic
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	*Clostridia*
	Order	*Eubacteriales*
	Family	*Lachnospiraceae*
	Genus	*Lacrimispora*
	Species	**Lacrimispora sphenoides**
	Full Scientific Name (LPSN)	Lacrimispora sphenoides (Douglas et al. 1919) Haas and Blanchard 2020

	Synonym	"Bacillus* sphenoides"*
	Synonym	Clostridium sphenoides
	Synonym	Desulfotomaculum guttoideum

Information on morphological and physiological properties Morphology

[Ref.: #69480]	Gram stain	positive Confidence in %100

[Ref.: #123259]	Cell shape	rod-shaped

[Ref.: #123259]	Motility	yes

Information on culture and growth conditions Culture and growth conditions

[Ref.: #334]

Culture medium

CHOPPED MEAT MEDIUM WITH CARBOHYDRATES (DSMZ Medium 110)

[Ref.: #334]

Culture medium growth

[Ref.: #334]

Culture medium link

Medium recipe at MediaDive

[Ref.: #334]

Culture medium composition

expand / minimize

[Ref.: #41095]

Culture medium

MEDIUM 20 - for Anaerobic bacteria

[Ref.: #41095]

Culture medium growth

[Ref.: #41095]

Culture medium composition

expand / minimize

[Ref.: #123259]

Culture medium

CIP Medium 20

[Ref.: #123259]

Culture medium growth

[Ref.: #123259]

Culture medium link

Medium recipe provided by DSMZ

		Temperature
[Ref.: #334]	growth	37 °C
[Ref.: #41095]	growth	37 °C
[Ref.: #67770]	growth	37 °C
[Ref.: #123259]	growth	37 °C

[Ref.: #334]	Temperature range	mesophilic
[Ref.: #41095]	Temperature range	mesophilic
[Ref.: #67770]	Temperature range	mesophilic
[Ref.: #123259]	Temperature range	mesophilic

Information on physiology and metabolism Physiology and metabolism

[Ref.: #334]	Oxygen tolerance	anaerobe
[Ref.: #69480]	Oxygen tolerance	anaerobe Confidence in %98.597

[Ref.: #69481]	Ability of spore formation	yes Confidence in %100
[Ref.: #69480]	Ability of spore formation	yes Confidence in %99.461

	Metabolite utilization	Metabolite	Utilization activity	Kind of utilization tested
[Ref.: #123259]		esculin ChEBI	+	hydrolysis
[Ref.: #123259]		sodium thiosulfate ChEBI	-	builds gas from

	Antibiotica	Metabolite	Antibiotic sensitivity	Antibiotic resistance
[Ref.: #123259]		metronidazole ChEBI	yes	no

	Metabolite production	Metabolite	Production
[Ref.: #123259]		indole ChEBI	no

	Enzyme	Enzyme activity	EC number
[Ref.: #68382]	acid phosphatase	+	3.1.3.2	* from API zym
[Ref.: #123259]	alcohol dehydrogenase	-	1.1.1.1
[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.: #123259]	amylase	-
[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.: #123259]	caseinase	-	3.4.21.50
[Ref.: #123259]	catalase	-	1.11.1.6
[Ref.: #68382]	cystine arylamidase	-	3.4.11.3	* from API zym
[Ref.: #123259]	DNase	+
[Ref.: #68382]	esterase (C 4)	-		* from API zym
[Ref.: #68382]	esterase lipase (C 8)	-		* from API zym
[Ref.: #123259]	gelatinase	-
[Ref.: #68382]	leucine arylamidase	-	3.4.11.1	* from API zym
[Ref.: #68382]	lipase (C 14)	-		* from API zym
[Ref.: #123259]	lysine decarboxylase	-	4.1.1.18
[Ref.: #68382]	N-acetyl-beta-glucosaminidase	-	3.2.1.52	* from API zym
[Ref.: #68382]	naphthol-AS-BI-phosphohydrolase	-		* from API zym
[Ref.: #123259]	ornithine decarboxylase	-	4.1.1.17
[Ref.: #123259]	oxidase	-
[Ref.: #68382]	trypsin	-	3.4.21.4	* from API zym
[Ref.: #123259]	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.: #123259]	7874	-	+	-	-	-	-	-	-	-	-	+	-	+	+	-	+	+	-	-	-

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

[Ref.: #334]	Sample type/isolated from	human gas gangrene

[Ref.: #67770]	Sample type/isolated from	Human gas gangrene

[Ref.: #123259]	Sample type/isolated from	Human, Gas gangrene
[Ref.: #123259]	Country	United Kingdom
[Ref.: #123259]	Country ISO 3 Code	GBR
[Ref.: #123259]	Continent	Europe
[Ref.: #123259]	Isolation date	1920
* marker position based on {}

Isolation sources categories

#Infection	#Disease	-
#Host	#Human	-
#Host	#Microbial	#Bacteria

What are isolation sources categories?

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

[Ref.: #334]	Biosafety level	2	Risk group (German classification) According to TRBA 466
[Ref.: #123259]	Biosafety level	2	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.: #334]	Clostridium sphenoides gene for 16S rRNA, partial sequence, strain: ATCC 19403	AB075772	1504	ENA	1297793 tax ID
[Ref.: #67770]	[Clostridium] sphenoides gene for 16S ribosomal RNA, partial sequence, strain: JCM 1415	LC053840	1493	ENA	1297793 tax ID
[Ref.: #20218]	Clostridium sphenoides strain DSM 632 16S ribosomal RNA gene, partial sequence	HM245951	846	ENA	1297793 tax ID	*
[Ref.: #20218]	Clostridium sphenoides 16S rRNA gene, strain DSM 632	X73449	1522	ENA	1297793 tax ID	*

Genome sequence information:

Only first 5 entries are displayed. Click here to see all.

	Sequence accession description	Seq. accession number	Assembly level	Sequence database	Associated NCBI tax ID
[Ref.: #67770]	[Clostridium] sphenoides JCM 1415	GCA_001312385	contig	GenBank	1297793 tax ID
[Ref.: #67770]	Lacrimispora sphenoides NCTC507	GCA_900461315	contig	GenBank	29370 tax ID
[Ref.: #66792]	[Clostridium] sphenoides JCM 1415	1297793.6	complete	PATRIC	1297793 tax ID	*
[Ref.: #66792]	[Clostridium] sphenoides strain NCTC507	29370.3	wgs	PATRIC	29370 tax ID	*
[Ref.: #66792]	Lachnoclostridium sphenoides ATCC 19403	2675902961	draft	JGI IMG/M	1297793 tax ID	*
[Ref.: #66792]	Lachnoclostridium sphenoides JCM 1415	2728369722	draft	JGI IMG/M	1297793 tax ID	*

[Ref.: #334]	GC-content	41.0 mol%
[Ref.: #67770]	GC-content	41 mol%	thermal denaturation, midpoint method (Tm)

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

	Trait	Prediction	Confidence in %	In training data
	Predictions from GenomeNet Sporulation v. 1 based on: [Clostridium] sphenoides JCM 1415 PATRIC: 1297793.6
[Ref.: #69481]	spore-forming	yes	100	no

	Trait	Prediction	Confidence in %	In training data
	Predictions from Diaspora project based on: [Clostridium] sphenoides JCM 1415 PATRIC: 1297793.6
[Ref.: #69480]	motile	yes	79.214	no
[Ref.: #69480]	gram-positive	yes	56.818	no
[Ref.: #69480]	anaerobic	yes	98.422	no
[Ref.: #69480]	aerobic	no	98.78	yes
[Ref.: #69480]	halophile	no	93.46	no
[Ref.: #69480]	spore-forming	yes	88.741	no
[Ref.: #69480]	thermophile	no	98.803	yes
[Ref.: #69480]	glucose-util	yes	87.848	no
[Ref.: #69480]	flagellated	no	52.06	no
[Ref.: #69480]	glucose-ferment	yes	72.058	no

Availability in culture collections External links

[Ref.: #334]

Culture collection no.

DSM 632, ATCC 19403, NCIB 10627, NCTC 507, JCM 1415, BCRC 14515, CECT 796, CIP 104283, LMG 10390, NCIMB 10627

[Ref.: #72232]

SI-ID 13622

Literature:

Topic	Title	Authors	Journal	DOI	Year
Phylogeny	Clostridium geopurificans strain MJ1 sp. nov., a strictly anaerobic bacterium that grows via fermentation and reduces the cyclic nitramine explosive hexahydro-1,3,5-trinitro-1,3,5-triazine (RDX).	Kwon MJ, Wei N, Millerick K, Popovic J, Finneran K	Curr Microbiol	10.1007/s00284-014-0531-x	2014	*
Metabolism	Identification of the syntrophic partners in a coculture coupling anaerobic methanol oxidation to Fe(III) reduction.	Daniel R, Warnecke F, Potekhina JS, Gottschalk G	FEMS Microbiol Lett	10.1111/j.1574-6968.1999.tb08796.x	1999	*

References

#334	Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 632

#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 )

#41095 ; Curators of the CIP;

#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;

#68382

Automatically annotated from API zym .

#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 )

#72232

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-ID13622.1 )

#123259 Collection of Institut Pasteur ; Curators of the CIP; CIP 104283
* These data were automatically processed and therefore are not curated

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[Clostridium] sphenoides JCM 1415

[Clostridium] sphenoides JCM 1415

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