Name: Thomasclavelia cocleata I50
Creator: BacDive
License: http://creativecommons.org/licenses/by-nc/4.0/

Strain identifier

BacDive ID: 2575

Type strain:

Species: Thomasclavelia cocleata

Strain Designation: I50

Culture col. no.: CCUG 46310, CCUG 45854, DSM 1551, ATCC 29902, NCTC 11210, JCM 1397, BCRC 14465, CCM 6166

Strain history: C. Kaneuchi I 50 <-- K. Itoh 50.

NCBI tax ID(s): 1121304 (strain), 69824 (species)

SI-ID 39795

ATCC 29902, NCTC 11210, DSM 1551, JCM 1397, CCM 6166, CCRC 14465, CCUG45854, CCUG 46310, BCRC 14465

Section

Thomasclavelia cocleata I50 is an anaerobe, mesophilic, Gram-positive human pathogen that was isolated from caecal content; wildtype C57BL/6 mouse.

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

Synonym

Clostridium cocleatum

Information on morphological and physiological properties Morphology

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

[Ref.: #818]

Incubation period

1-2 days

Information on culture and growth conditions Culture and growth conditions

[Ref.: #818]

Culture medium

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

[Ref.: #818]

Culture medium growth

[Ref.: #818]

Culture medium link

Medium recipe at MediaDive

[Ref.: #818]

Culture medium composition

expand / minimize

		Temperature
[Ref.: #818]	growth	37 °C
[Ref.: #57145]	growth	37 °C
[Ref.: #67770]	growth	37 °C

[Ref.: #818]	Temperature range	mesophilic
[Ref.: #57145]	Temperature range	mesophilic
[Ref.: #67770]	Temperature range	mesophilic

Information on physiology and metabolism Physiology and metabolism

[Ref.: #818]	Oxygen tolerance	anaerobe
[Ref.: #57145]	Oxygen tolerance	anaerobe
[Ref.: #69480]	Oxygen tolerance	anaerobe Confidence in %99.999

[Ref.: #69480]

Ability of spore formation

no Confidence in %99.681

	Pathway	Enzyme coverage	Annotated reactions
	Pathway annotation	Computationally determined by
[Ref.: #66794]	cardiolipin biosynthesis	100	7 of 7
[Ref.: #66794]	teichoic acid biosynthesis	100	1 of 1
[Ref.: #66794]	CDP-diacylglycerol biosynthesis	100	2 of 2
[Ref.: #66794]	UDP-GlcNAc biosynthesis	100	3 of 3
[Ref.: #66794]	cis-vaccenate biosynthesis	100	2 of 2
[Ref.: #66794]	L-lactaldehyde degradation	100	3 of 3
[Ref.: #66794]	coenzyme A metabolism	100	4 of 4
[Ref.: #66794]	anapleurotic synthesis of oxalacetate	100	1 of 1
[Ref.: #66794]	folate polyglutamylation	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]	glycine betaine biosynthesis	80	4 of 5
[Ref.: #66794]	peptidoglycan biosynthesis	80	12 of 15
[Ref.: #66794]	hydrogen production	80	4 of 5
[Ref.: #66794]	NAD metabolism	77.78	14 of 18
[Ref.: #66794]	vitamin B1 metabolism	76.92	10 of 13
[Ref.: #66794]	acetate fermentation	75	3 of 4
[Ref.: #66794]	CMP-KDO biosynthesis	75	3 of 4
[Ref.: #66794]	glycogen biosynthesis	75	3 of 4
[Ref.: #66794]	ppGpp biosynthesis	75	3 of 4
[Ref.: #66794]	C4 and CAM-carbon fixation	75	6 of 8
[Ref.: #66794]	photosynthesis	71.43	10 of 14
[Ref.: #66794]	glycolysis	70.59	12 of 17
[Ref.: #66794]	phenylalanine metabolism	69.23	9 of 13
[Ref.: #66794]	pyrimidine metabolism	68.89	31 of 45
[Ref.: #66794]	serine metabolism	66.67	6 of 9
[Ref.: #66794]	flavin biosynthesis	66.67	10 of 15
[Ref.: #66794]	acetoin degradation	66.67	2 of 3
[Ref.: #66794]	d-mannose degradation	66.67	6 of 9
[Ref.: #66794]	formaldehyde oxidation	66.67	2 of 3
[Ref.: #66794]	octane oxidation	66.67	2 of 3
[Ref.: #66794]	purine metabolism	65.96	62 of 94
[Ref.: #66794]	tetrahydrofolate metabolism	64.29	9 of 14
[Ref.: #66794]	isoleucine metabolism	62.5	5 of 8
[Ref.: #66794]	methionine metabolism	61.54	16 of 26
[Ref.: #66794]	leucine metabolism	61.54	8 of 13
[Ref.: #66794]	methylglyoxal degradation	60	3 of 5
[Ref.: #66794]	starch degradation	60	6 of 10
[Ref.: #66794]	O-antigen biosynthesis	60	3 of 5
[Ref.: #66794]	glycogen metabolism	60	3 of 5
[Ref.: #66794]	alanine metabolism	58.62	17 of 29
[Ref.: #66794]	glutamate and glutamine metabolism	57.14	16 of 28
[Ref.: #66794]	propanol degradation	57.14	4 of 7
[Ref.: #66794]	polyamine pathway	56.52	13 of 23
[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]	suberin monomers biosynthesis	50	1 of 2
[Ref.: #66794]	dTDPLrhamnose biosynthesis	50	4 of 8
[Ref.: #66794]	Entner Doudoroff pathway	50	5 of 10
[Ref.: #66794]	cysteine metabolism	50	9 of 18
[Ref.: #66794]	glycolate and glyoxylate degradation	50	3 of 6
[Ref.: #66794]	sulfopterin metabolism	50	2 of 4
[Ref.: #66794]	dolichol and dolichyl phosphate biosynthesis	50	1 of 2
[Ref.: #66794]	ethanol fermentation	50	1 of 2
[Ref.: #66794]	butanoate fermentation	50	2 of 4
[Ref.: #66794]	biotin biosynthesis	50	2 of 4
[Ref.: #66794]	adipate degradation	50	1 of 2
[Ref.: #66794]	gluconeogenesis	50	4 of 8
[Ref.: #66794]	ketogluconate metabolism	50	4 of 8
[Ref.: #66794]	ribulose monophosphate pathway	50	1 of 2
[Ref.: #66794]	oxidative phosphorylation	49.45	45 of 91
[Ref.: #66794]	lysine metabolism	47.62	20 of 42
[Ref.: #66794]	tryptophan metabolism	47.37	18 of 38
[Ref.: #66794]	non-pathway related	47.37	18 of 38
[Ref.: #66794]	urea cycle	46.15	6 of 13
[Ref.: #66794]	pentose phosphate pathway	45.45	5 of 11
[Ref.: #66794]	lipid metabolism	45.16	14 of 31
[Ref.: #66794]	molybdenum cofactor biosynthesis	44.44	4 of 9
[Ref.: #66794]	CO2 fixation in Crenarchaeota	44.44	4 of 9
[Ref.: #66794]	ubiquinone biosynthesis	42.86	3 of 7
[Ref.: #66794]	citric acid cycle	42.86	6 of 14
[Ref.: #66794]	reductive acetyl coenzyme A pathway	42.86	3 of 7
[Ref.: #66794]	myo-inositol biosynthesis	40	4 of 10
[Ref.: #66794]	metabolism of amino sugars and derivatives	40	2 of 5
[Ref.: #66794]	factor 420 biosynthesis	40	2 of 5
[Ref.: #66794]	bacilysin biosynthesis	40	2 of 5
[Ref.: #66794]	arachidonate biosynthesis	40	2 of 5
[Ref.: #66794]	degradation of hexoses	38.89	7 of 18
[Ref.: #66794]	isoprenoid biosynthesis	38.46	10 of 26
[Ref.: #66794]	6-hydroxymethyl-dihydropterin diphosphate biosynthesis	37.5	3 of 8
[Ref.: #66794]	vitamin B6 metabolism	36.36	4 of 11
[Ref.: #66794]	d-xylose degradation	36.36	4 of 11
[Ref.: #66794]	metabolism of disaccharids	36.36	4 of 11
[Ref.: #66794]	lipid A biosynthesis	33.33	3 of 9
[Ref.: #66794]	cyanate degradation	33.33	1 of 3
[Ref.: #66794]	sphingosine metabolism	33.33	2 of 6
[Ref.: #66794]	IAA biosynthesis	33.33	1 of 3
[Ref.: #66794]	degradation of aromatic, nitrogen containing compounds	33.33	4 of 12
[Ref.: #66794]	enterobactin biosynthesis	33.33	1 of 3
[Ref.: #66794]	selenocysteine biosynthesis	33.33	2 of 6
[Ref.: #66794]	ascorbate metabolism	31.82	7 of 22
[Ref.: #66794]	phenylpropanoid biosynthesis	30.77	4 of 13
[Ref.: #66794]	propionate fermentation	30	3 of 10
[Ref.: #66794]	coenzyme M biosynthesis	30	3 of 10
[Ref.: #66794]	glycine metabolism	30	3 of 10
[Ref.: #66794]	tyrosine metabolism	28.57	4 of 14
[Ref.: #66794]	degradation of pentoses	28.57	8 of 28
[Ref.: #66794]	dolichyl-diphosphooligosaccharide biosynthesis	27.27	3 of 11
[Ref.: #66794]	carnitine metabolism	25	2 of 8
[Ref.: #66794]	lactate fermentation	25	1 of 4
[Ref.: #66794]	cyclohexanol degradation	25	1 of 4
[Ref.: #66794]	degradation of sugar alcohols	25	4 of 16
[Ref.: #66794]	vitamin E metabolism	25	1 of 4
[Ref.: #66794]	sulfate reduction	23.08	3 of 13
[Ref.: #66794]	phosphatidylethanolamine bioynthesis	23.08	3 of 13
[Ref.: #66794]	4-hydroxymandelate degradation	22.22	2 of 9
[Ref.: #66794]	nitrate assimilation	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.: #818]	Sample type/isolated from	caecal content; wildtype C57BL/6 mouse
[Ref.: #818]	Geographic location (country and/or sea, region)	Miyazaki
[Ref.: #818]	Country	Japan
[Ref.: #818]	Country ISO 3 Code	JPN
[Ref.: #818]	Continent	Asia

[Ref.: #57145]	Sample type/isolated from	Mouse cecum
[Ref.: #57145]	Country	Japan
[Ref.: #57145]	Country ISO 3 Code	JPN
[Ref.: #57145]	Continent	Asia

[Ref.: #67770]	Sample type/isolated from	Cecum of mouse
* marker position based on {}

Isolation sources categories

#Host	#Mammals	#Muridae (Mouse/Rat)
#Host Body-Site	#Gastrointestinal tract	#Large intestine
#Host Body Product	#Gastrointestinal tract	#Caecal content

What are isolation sources categories?

[Ref.: #69479]

Global distribution of 16S sequence Y18188 (>99% sequence identity) for [Clostridium] cocleatum subclade from Microbeatlas

Aquatic Samples	565
Soil Samples	695
Animal Samples	62316
Plant Samples	163
Total Samples	63739

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

[Ref.: #818]	Pathogenicity (human)	yes, in single cases
[Ref.: #818]	Biosafety level	1	Risk group (German classification) According to TRBA 466

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.: #818]	Clostridium cocleatum 16S rRNA gene, partial, strain DSM 1551	Y18188	1489	ENA	69824 tax ID
[Ref.: #20218]	[Clostridium] cocleatum gene for 16S ribosomal RNA, partial sequence	AB910744	1488	ENA	69824 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]	Thomasclavelia cocleata DSM 1551	GCA_900102365	scaffold	GenBank	69824 tax ID
[Ref.: #67770]	Thomasclavelia cocleata ATCC 29902	GCA_002803405	scaffold	GenBank	69824 tax ID
[Ref.: #66792]	[Clostridium] cocleatum strain ATCC 29902	69824.4	wgs	PATRIC	69824 tax ID	*
[Ref.: #66792]	[Clostridium] cocleatum strain DSM 1551	69824.3	wgs	PATRIC	69824 tax ID	*
[Ref.: #66792]	Erysipelatoclostridium cocleatum ATCC 29902	2574179769	draft	JGI IMG/M	69824 tax ID	*
[Ref.: #66792]	Clostridium cocleatum DSM 1551	2634166354	draft	JGI IMG/M	1121304 tax ID	*

[Ref.: #818]

GC-content

27.9 mol%

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] cocleatum DSM 1551 NCBI: GCA_900102365.1
[Ref.: #69481]	spore-forming	yes	56	no

Availability in culture collections External links

[Ref.: #818]

Culture collection no.

CCUG 46310, CCUG 45854, DSM 1551, ATCC 29902, NCTC 11210, JCM 1397, BCRC 14465, CCM 6166

[Ref.: #72108]

SI-ID 39795

References

#818	Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 1551

#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 )

#57145 Culture Collection University of Gothenburg (CCUG) ; Curators of the CCUG; CCUG 46310

#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;

#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 )

#72108

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-ID39795.1 )

* These data were automatically processed and therefore are not curated

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[Clostridium] cocleatum DSM 1551

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