Name: Thomasclavelia spiroformis DSM 1552
Creator: BacDive
License: https://creativecommons.org/licenses/by/4.0/

Strain identifier

BacDive ID: 2706

Type strain:

Species: Thomasclavelia spiroformis

Culture col. no.: DSM 1552, ATCC 29900, NCTC 11211, VPI C28-23-1A, JCM 1432, BCRC 14526, CCM 6168, CECT 4322, CIP 106966, AIP 10141

Strain history: CIP <- 2001, J.P. Carlier, Inst. Pasteur, France, Paris: strain AIP 10141 <- DSMZ <- C. Kaneuchi <- E.P. Cato: VPI C28-23-1A

NCBI tax ID(s): 29348 (species)

SI-ID 45881

ATCC 29900, NCTC 11211, CIP 106966, JCM 1432, CCM 6168, CCRC 14526, CECT 4322, CCUG 46384, CCUG 46510, BCRC 14526, DSM 1552

Special Collections

Section

Thomasclavelia spiroformis DSM 1552 is an anaerobe, Gram-positive, rod-shaped human pathogen that was isolated from human faeces.

Gram-positive
rod-shaped
anaerobe
human pathogen
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	*Erysipelotrichia*
	Order	*Erysipelotrichales*
	Family	*Coprobacillaceae*
	Genus	*Thomasclavelia*
	Species	**Thomasclavelia spiroformis**
	Full Scientific Name (LPSN)	Thomasclavelia spiroformis (Kaneuchi et al. 1979) Lawson et al. 2023

Synonym

Clostridium spiroforme

Information on morphological and physiological properties Morphology

[Ref.: #123267]	Gram stain	positive

[Ref.: #123267]	Cell shape	rod-shaped

[Ref.: #123267]	Motility	no

Information on culture and growth conditions Culture and growth conditions

[Ref.: #819]

Culture medium

CMC MEDIUM (N2/CO2) (DSMZ Medium 110a)

[Ref.: #819]

Culture medium growth

[Ref.: #819]

Culture medium link

Medium recipe at MediaDive

[Ref.: #819]

Culture medium composition

expand / minimize

[Ref.: #33027]

Culture medium

MEDIUM 20 - for Anaerobic bacteria

[Ref.: #33027]

Culture medium growth

[Ref.: #33027]

Culture medium composition

expand / minimize

[Ref.: #819]

Culture medium

PY + X MEDIUM (N2/CO2) (DSMZ Medium 104c)

[Ref.: #819]

Culture medium growth

[Ref.: #819]

Culture medium link

Medium recipe at MediaDive

[Ref.: #819]

Culture medium composition

expand / minimize

[Ref.: #123267]

Culture medium

CIP Medium 20

[Ref.: #123267]

Culture medium growth

[Ref.: #123267]

Culture medium link

Medium recipe provided by DSMZ

		Temperature
[Ref.: #819]	growth	37 °C
[Ref.: #33027]	growth	37 °C
[Ref.: #67770]	growth	37 °C
[Ref.: #123267]	growth	37 °C

Information on physiology and metabolism Physiology and metabolism

[Ref.: #819]	Oxygen tolerance	anaerobe
[Ref.: #123267]	Oxygen tolerance	anaerobe

	Metabolite	Utilization activity	Kind of utilization tested
[Ref.: #123267]	esculin ChEBI	-	hydrolysis
[Ref.: #123267]	nitrate ChEBI	-	reduction
[Ref.: #123267]	nitrate ChEBI	+	respiration
[Ref.: #123267]	nitrite ChEBI	-	reduction

	Metabolite production	Metabolite	Production
[Ref.: #123267]		indole ChEBI	no

	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.: #123267]	beta-galactosidase	+	3.2.1.23
[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.: #123267]	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.: #123267]	gelatinase	-
[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.: #123267]	oxidase	-
[Ref.: #68382]	trypsin	-	3.4.21.4	* from API zym
[Ref.: #123267]	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.: #123267]	9952	-	-	+	-	-	-	-	-	-	-	+	+	-	-	-	-	-	+	-	-

	Pathway	Enzyme coverage	Annotated reactions
	Pathway annotation	Computationally determined by
[Ref.: #66794]	adipate degradation	100	2 of 2
[Ref.: #66794]	cis-vaccenate biosynthesis	100	2 of 2
[Ref.: #66794]	coenzyme A metabolism	100	4 of 4
[Ref.: #66794]	L-lactaldehyde degradation	100	3 of 3
[Ref.: #66794]	teichoic acid biosynthesis	100	1 of 1
[Ref.: #66794]	CDP-diacylglycerol biosynthesis	100	2 of 2
[Ref.: #66794]	folate polyglutamylation	100	1 of 1
[Ref.: #66794]	UDP-GlcNAc biosynthesis	100	3 of 3
[Ref.: #66794]	anapleurotic synthesis of oxalacetate	100	1 of 1
[Ref.: #66794]	palmitate biosynthesis	90.91	20 of 22
[Ref.: #66794]	threonine metabolism	90	9 of 10
[Ref.: #66794]	valine metabolism	88.89	8 of 9
[Ref.: #66794]	aspartate and asparagine metabolism	88.89	8 of 9
[Ref.: #66794]	chorismate metabolism	88.89	8 of 9
[Ref.: #66794]	peptidoglycan biosynthesis	80	12 of 15
[Ref.: #66794]	glycogen metabolism	80	4 of 5
[Ref.: #66794]	NAD metabolism	77.78	14 of 18
[Ref.: #66794]	phenylalanine metabolism	76.92	10 of 13
[Ref.: #66794]	vitamin B1 metabolism	76.92	10 of 13
[Ref.: #66794]	dTDPLrhamnose biosynthesis	75	6 of 8
[Ref.: #66794]	ppGpp biosynthesis	75	3 of 4
[Ref.: #66794]	glycogen biosynthesis	75	3 of 4
[Ref.: #66794]	sulfopterin metabolism	75	3 of 4
[Ref.: #66794]	acetate fermentation	75	3 of 4
[Ref.: #66794]	C4 and CAM-carbon fixation	75	6 of 8
[Ref.: #66794]	purine metabolism	72.34	68 of 94
[Ref.: #66794]	cardiolipin biosynthesis	71.43	5 of 7
[Ref.: #66794]	photosynthesis	71.43	10 of 14
[Ref.: #66794]	glycolysis	70.59	12 of 17
[Ref.: #66794]	octane oxidation	66.67	2 of 3
[Ref.: #66794]	formaldehyde oxidation	66.67	2 of 3
[Ref.: #66794]	serine metabolism	66.67	6 of 9
[Ref.: #66794]	CO2 fixation in Crenarchaeota	66.67	6 of 9
[Ref.: #66794]	glycolate and glyoxylate degradation	66.67	4 of 6
[Ref.: #66794]	acetoin degradation	66.67	2 of 3
[Ref.: #66794]	pyrimidine metabolism	64.44	29 of 45
[Ref.: #66794]	glutamate and glutamine metabolism	64.29	18 of 28
[Ref.: #66794]	isoleucine metabolism	62.5	5 of 8
[Ref.: #66794]	methylglyoxal degradation	60	3 of 5
[Ref.: #66794]	glycine betaine biosynthesis	60	3 of 5
[Ref.: #66794]	metabolism of amino sugars and derivatives	60	3 of 5
[Ref.: #66794]	hydrogen production	60	3 of 5
[Ref.: #66794]	flavin biosynthesis	60	9 of 15
[Ref.: #66794]	alanine metabolism	58.62	17 of 29
[Ref.: #66794]	lipid metabolism	58.06	18 of 31
[Ref.: #66794]	tryptophan metabolism	57.89	22 of 38
[Ref.: #66794]	methionine metabolism	57.69	15 of 26
[Ref.: #66794]	propanol degradation	57.14	4 of 7
[Ref.: #66794]	polyamine pathway	56.52	13 of 23
[Ref.: #66794]	molybdenum cofactor biosynthesis	55.56	5 of 9
[Ref.: #66794]	lipid A biosynthesis	55.56	5 of 9
[Ref.: #66794]	non-pathway related	55.26	21 of 38
[Ref.: #66794]	histidine metabolism	55.17	16 of 29
[Ref.: #66794]	proline metabolism	54.55	6 of 11
[Ref.: #66794]	arginine metabolism	54.17	13 of 24
[Ref.: #66794]	leucine metabolism	53.85	7 of 13
[Ref.: #66794]	6-hydroxymethyl-dihydropterin diphosphate biosynthesis	50	4 of 8
[Ref.: #66794]	gluconeogenesis	50	4 of 8
[Ref.: #66794]	ethanol fermentation	50	1 of 2
[Ref.: #66794]	CMP-KDO biosynthesis	50	2 of 4
[Ref.: #66794]	Entner Doudoroff pathway	50	5 of 10
[Ref.: #66794]	selenocysteine biosynthesis	50	3 of 6
[Ref.: #66794]	biotin biosynthesis	50	2 of 4
[Ref.: #66794]	starch degradation	50	5 of 10
[Ref.: #66794]	mannosylglycerate biosynthesis	50	1 of 2
[Ref.: #66794]	phenylmercury acetate degradation	50	1 of 2
[Ref.: #66794]	ketogluconate metabolism	50	4 of 8
[Ref.: #66794]	butanoate fermentation	50	2 of 4
[Ref.: #66794]	suberin monomers biosynthesis	50	1 of 2
[Ref.: #66794]	tetrahydrofolate metabolism	50	7 of 14
[Ref.: #66794]	isoprenoid biosynthesis	46.15	12 of 26
[Ref.: #66794]	oxidative phosphorylation	46.15	42 of 91
[Ref.: #66794]	vitamin B6 metabolism	45.45	5 of 11
[Ref.: #66794]	lysine metabolism	45.24	19 of 42
[Ref.: #66794]	d-mannose degradation	44.44	4 of 9
[Ref.: #66794]	cysteine metabolism	44.44	8 of 18
[Ref.: #66794]	reductive acetyl coenzyme A pathway	42.86	3 of 7
[Ref.: #66794]	citric acid cycle	42.86	6 of 14
[Ref.: #66794]	ubiquinone biosynthesis	42.86	3 of 7
[Ref.: #66794]	factor 420 biosynthesis	40	2 of 5
[Ref.: #66794]	coenzyme M biosynthesis	40	4 of 10
[Ref.: #66794]	arachidonate biosynthesis	40	2 of 5
[Ref.: #66794]	urea cycle	38.46	5 of 13
[Ref.: #66794]	d-xylose degradation	36.36	4 of 11
[Ref.: #66794]	metabolism of disaccharids	36.36	4 of 11
[Ref.: #66794]	pentose phosphate pathway	36.36	4 of 11
[Ref.: #66794]	tyrosine metabolism	35.71	5 of 14
[Ref.: #66794]	sphingosine metabolism	33.33	2 of 6
[Ref.: #66794]	degradation of aromatic, nitrogen containing compounds	33.33	4 of 12
[Ref.: #66794]	degradation of hexoses	33.33	6 of 18
[Ref.: #66794]	IAA biosynthesis	33.33	1 of 3
[Ref.: #66794]	degradation of sugar alcohols	31.25	5 of 16
[Ref.: #66794]	sulfate reduction	30.77	4 of 13
[Ref.: #66794]	phenylpropanoid biosynthesis	30.77	4 of 13
[Ref.: #66794]	phosphatidylethanolamine bioynthesis	30.77	4 of 13
[Ref.: #66794]	propionate fermentation	30	3 of 10
[Ref.: #66794]	glycine metabolism	30	3 of 10
[Ref.: #66794]	degradation of pentoses	28.57	8 of 28
[Ref.: #66794]	benzoyl-CoA degradation	28.57	2 of 7
[Ref.: #66794]	dolichyl-diphosphooligosaccharide biosynthesis	27.27	3 of 11
[Ref.: #66794]	ascorbate metabolism	27.27	6 of 22
[Ref.: #66794]	toluene degradation	25	1 of 4
[Ref.: #66794]	cyclohexanol degradation	25	1 of 4
[Ref.: #66794]	lactate fermentation	25	1 of 4
[Ref.: #66794]	carnitine metabolism	25	2 of 8
[Ref.: #66794]	4-hydroxymandelate degradation	22.22	2 of 9
[Ref.: #66794]	glutathione 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.: #819]	Sample type/isolated from	human faeces
[Ref.: #819]	Country	USA
[Ref.: #819]	Country ISO 3 Code	USA
[Ref.: #819]	Continent	North America

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

[Ref.: #123267]	Sample type/isolated from	Human, Feces
* marker position based on {}

Isolation sources categories

#Host	#Human	-
#Host Body Product	#Gastrointestinal tract	#Feces (Stool)

What are isolation sources categories?

[Ref.: #69479]

Global distribution of 16S sequence X75908 (>99% sequence identity) for [Clostridium] spiroforme subclade from Microbeatlas

Aquatic Samples	1756
Soil Samples	558
Animal Samples	79526
Plant Samples	180
Total Samples	82020

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

[Ref.: #819]	Pathogenicity (human)	yes, in single cases
[Ref.: #819]	Biosafety level	1	Risk group (German classification) According to TRBA 466
[Ref.: #123267]	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.: #67770]	Clostridium spiroforme gene for 16S ribosomal RNA, partial sequence, strain: JCM 1432	AB818948	1486	GenBank ENA	29348 tax ID
[Ref.: #819]	Clostridium spiroforme 16S rRNA gene, strain DSM 1552	X73441	1519	GenBank ENA	428126 tax ID
[Ref.: #20218]	Clostridium spiroforme DSM 1552 16S ribosomal RNA gene, partial sequence	HM245952	821	GenBank ENA	428126 tax ID	*
[Ref.: #20218]	C.spiroforme 16S rRNA gene	X75908	1388	GenBank ENA	428126 tax ID	*

Genome sequence information:

	Sequence accession description	Seq. accession number	Assembly level	Sequence database	Associated NCBI tax ID
[Ref.: #67770]	Thomasclavelia spiroformis DSM 1552	GCA_000154805	scaffold	GenBank ENA	428126 tax ID
[Ref.: #66792]	Clostridium spiroforme DSM 1552	428126.7	wgs	PATRIC	428126 tax ID	*
[Ref.: #66792]	Erysipelatoclostridium spiroforme DSM 1552	641736169	draft	JGI IMG/M	428126 tax ID	*
[Ref.: #66792]	Thomasclavelia spiroformis DSM 1552	GCA_025149465	complete	GenBank ENA	428126 tax ID	*
[Ref.: #66792]	[Clostridium] spiroforme DSM 1552	428126.20	complete	PATRIC	428126 tax ID	*

[Ref.: #819]

GC-content

27.4 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: [Clostridium] spiroforme DSM 1552 DSM 1552 NCBI: GCA_000154805.1
[Ref.: #69481]	spore-forming	spore-formingⓘ	no	84	no

	Trait	Model	Prediction	Confidence in %	In training data
	Predictions from Diaspora project based on: [Clostridium] spiroforme DSM 1552 DSM 1552 NCBI: GCA_025149465.1
[Ref.: #69480]	gram-positive	gram-positiveⓘ	yes	79.498	no
[Ref.: #69480]	anaerobic	anaerobicⓘ	yes	85.226	yes
[Ref.: #69480]	aerobic	aerobicⓘ	no	98.921	no
[Ref.: #69480]	spore-forming	spore-formingⓘ	no	60.788	no
[Ref.: #69480]	thermophilic	thermophileⓘ	no	92.81	no
[Ref.: #69480]	flagellated	motile2+ⓘ	no	87.635	no

Availability in culture collections External links

[Ref.: #819]

Culture collection no.

DSM 1552, ATCC 29900, NCTC 11211, VPI C28-23-1A, JCM 1432, BCRC 14526, CCM 6168, CECT 4322, CIP 106966, AIP 10141

[Ref.: #72234]

SI-ID 45881

Literature:

Topic	Title	Authors	Journal	DOI	Year
Pathogenicity	Altered gut microbiota correlates with behavioral problems but not gastrointestinal symptoms in individuals with autism.	Chen YC, Lin HY, Chien Y, Tung YH, Ni YH, Gau SS	Brain Behav Immun	10.1016/j.bbi.2022.08.015	2022	*

References

#819	Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 1552

#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 )

#33027 ; 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) .

#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 )

#72234

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-ID45881.1 )

#123267 Collection of Institut Pasteur ; Curators of the CIP; CIP 106966
* These data were automatically processed and therefore are not curated

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[Clostridium] spiroforme DSM 1552 DSM 1552

[Clostridium] spiroforme DSM 1552 DSM 1552

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Change proposal