Lacrimispora sphenoides (DSM 632, ATCC 19403, NCIB 10627)

Name: Lacrimispora sphenoides (DSM 632, ATCC 19403, NCIB 10627)
Creator: BacDive
License: http://creativecommons.org/licenses/by/4.0/

BacDive ID 2704

Type strain

Strain Designation Thorlby, Tholby, 10086

Culture col. no. DSM 632 ATCC 19403 NCIB 10627 NCTC 507 Thorlby 8 more

NCBI tax ID(s) 1297793 29370

Special Collections DSMZ JCM CIP

Links

Lacrimispora sphenoides Thorlby is an anaerobe, mesophilic, motile prokaryote that was isolated from human gas gangrene.

motile rod-shaped anaerobe mesophilic genome sequence 16S sequence

Name and taxonomic classification

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

@ref 20215

Last LPSN update 2025-12-16 09:47:22

Domain Bacillati

Phylum Bacillota

Class Clostridia

Order Eubacteriales

Family Lachnospiraceae

Genus Lacrimispora

Species Lacrimispora sphenoides

Full scientific name Lacrimispora sphenoides (Douglas et al. 1919) Haas and Blanchard 2020

Synonyms (3)

Desulfotomaculum guttoideum
Clostridium sphenoides
"Bacillus sphenoides"

BacDive ID	Other strains from **Lacrimispora sphenoides** (4)	Type strain
2703	L. sphenoides C2, DSM 614
2705	L. sphenoides DSM 1225, UQM 780
11791	L. sphenoides 50, DSM 4024, VKM B-1591
158918	L. sphenoides H1_31, DSM 108199

Morphology

Cell morphology

@ref	Cell shape	Motility
123259	rod-shaped

Colony morphology

Culture and growth conditions

Culture medium

@ref	Name	Medium link	Composition
334	CHOPPED MEAT MEDIUM WITH CARBOHYDRATES (DSMZ Medium 110)	Medium recipe at MediaDive	Name: CHOPPED MEAT MEDIUM WITH CARBOHYDRATES (DSMZ Medium 110) Composition: Ground beef 500.0 g/l Casitone 30.0 g/l Agar 15.0 g/l K2HPO4 5.0 g/l Yeast extract 5.0 g/l D-Glucose 4.0 g/l Starch 1.0 g/l Maltose 1.0 g/l Cellobiose 1.0 g/l L-Cysteine HCl 0.5 g/l Ethanol 0.19 g/l Vitamin K3 0.05 g/l Hemin 0.005 g/l Sodium resazurin 0.0005 g/l Vitamin K1 NaOH Distilled water
41095	MEDIUM 20 - for Anaerobic bacteria		Agar (15.000 g);Glucose (5.000 g);Yeast extract (20.000 g);Tryptone (30.000 g);Cysteine hydrochloride (0.500 g);distilled water (1000.000 ml);Hemin solution -M00149 (25.000 ml)
123259	CIP Medium 20	Medium recipe at CIP

Culture temp

@ref	Growth	Type	Temperature (°C)	Range
334	positive	growth	37	mesophilic
41095	positive	growth	37	mesophilic
67770	positive	growth	37	mesophilic
123259	positive	growth	37	mesophilic

Physiology and metabolism

Oxygen tolerance

@ref	Oxygen tolerance	Confidence
334	anaerobe
125439	anaerobe	96.8

Spore formation

@ref	Spore formation	Confidence
125439		90.8

Metabolite utilization

@ref	Chebi-ID	Metabolite	Utilization activity	Kind of utilization tested
123259	4853 ChEBI	esculin	+	hydrolysis
123259	132112 ChEBI	sodium thiosulfate	-	builds gas from

Antibiotic resistance

@ref	ChEBI	Metabolite	Is sensitive	Is resistant
123259	6909	metronidazole

Metabolite production

@ref	Chebi-ID	Metabolite	Production
123259	35581 ChEBI	indole

Enzymes

@ref	Value	Activity	Ec
68382	acid phosphatase	+	3.1.3.2	from API zym
123259	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
123259	amylase	-
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
123259	caseinase	-	3.4.21.50
123259	catalase	-	1.11.1.6
68382	cystine arylamidase	-	3.4.11.3	from API zym
123259	DNase	+
68382	esterase (C 4)	-		from API zym
68382	esterase lipase (C 8)	-		from API zym
123259	gelatinase	-
68382	leucine arylamidase	-	3.4.11.1	from API zym
68382	lipase (C 14)	-		from API zym
123259	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
123259	ornithine decarboxylase	-	4.1.1.17
123259	oxidase	-
68382	trypsin	-	3.4.21.4	from API zym
123259	urease	-	3.5.1.5
68382	valine arylamidase	-		from API zym

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
123259	-	+	-	-	-	-	-	-	-	-	+	-	+	+	-	+	+	-	-	-

Isolation, sampling and environmental information

Isolation source categories

Cat1	Cat2	Cat3
#Infection	#Disease	-
#Host	#Human	-
#Host	#Microbial	#Bacteria

Isolation

@ref	Sample type	Country	Country ISO 3 Code	Continent	Isolation date
334	human gas gangrene
67770	Human gas gangrene
123259	Human, Gas gangrene	United Kingdom	GBR	Europe	1920

Interaction and safety

Risk assessment

@ref	Biosafety level	Biosafety level comment
334	2	Risk group (German classification) According to TRBA 466
123259	2	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	IMG-taxon 2675902961 annotated assembly for Lacrimispora sphenoides JCM 1415 ATCC 19403	chromosome	GCA_900105615	1297793.6	2675902961	1297793	87.72
67770	49699_G01 assembly for Lacrimispora sphenoides NCTC507	contig	GCA_900461315	29370.3	2808606748	29370	77.18
67770	ASM131238v1 assembly for Lacrimispora sphenoides JCM 1415	contig	GCA_001312385	1297793.5	2728369722	1297793	0.03

16S sequences

@ref	Description	Accession	Length	NCBI tax ID
20218	Clostridium sphenoides strain DSM 632 16S ribosomal RNA gene, partial sequence	HM245951	846	1297793
20218	Clostridium sphenoides 16S rRNA gene, strain DSM 632	X73449	1522	1297793
334	Clostridium sphenoides gene for 16S rRNA, partial sequence, strain: ATCC 19403	AB075772	1504	1297793
67770	[Clostridium] sphenoides gene for 16S ribosomal RNA, partial sequence, strain: JCM 1415	LC053840	1493	1297793
124043	Lacrimispora sphenoides DSM 632 gene for 16S rRNA, partial sequence.	LC752451	162	1297793

GC content

@ref	GC-content (mol%)	Method
334	41.0
67770	41	thermal denaturation, midpoint method (Tm)

Genome-based predictions

Predictions

Predictions from Deep Learning for Genome Sequence Data. R package version 0.3.1 based on: [Clostridium] sphenoides JCM 1415
PATRIC: 1297793.6

@ref	Trait	Model	Prediction	Confidence in %	In training data
125439	spore_formation	BacteriaNetⓘ	yes	90.80	no
125439	motility	BacteriaNetⓘ	yes	87.40	no
125439	gram_stain	BacteriaNetⓘ	variable	80.70	no
125439	oxygen_tolerance	BacteriaNetⓘ	anaerobe	96.80	no

Predictions from bacterial phenotypic traits through improved machine learning using high-quality, curated datasets based on: [Clostridium] sphenoides JCM 1415
PATRIC: 1297793.6

@ref	Trait	Model	Prediction	Confidence in %	In training data
125438	gram-positive	gram-positiveⓘ	yes	58.65	no
125438	anaerobic	anaerobicⓘ	yes	89.41	yes
125438	spore-forming	spore-formingⓘ	yes	71.93	no
125438	aerobic	aerobicⓘ	no	93.74	yes
125438	thermophilic	thermophileⓘ	no	95.21	yes
125438	flagellated	motile2+ⓘ	yes	75.72	no

Literature

Topic	Title	Authors	Journal	DOI	Year
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
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

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 .
#123259	Collection of Institut Pasteur ; Curators of the CIP; CIP 104283
#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 )

Rate our new design

Content

About us

Lacrimispora sphenoides (DSM 632, ATCC 19403, NCIB 10627)

Name and taxonomic classification

Morphology

Cell morphology

Colony morphology

Culture and growth conditions

Culture medium

Culture temp

Physiology and metabolism

Oxygen tolerance

Spore formation

Metabolite utilization

Antibiotic resistance

Metabolite production

Enzymes

API zym

Isolation, sampling and environmental information

Isolation source categories

Isolation

Interaction and safety

Risk assessment

Sequence information

Genome sequences

Genome browser: GCA_900105615

16S sequences

GC content

Genome-based predictions

Predictions

Literature

Literature

References

BacDive

Help

Social Media