Name: Thomasclavelia ramosa 113-I
Creator: BacDive
License: http://creativecommons.org/licenses/by-nc/4.0/

Strain identifier

BacDive ID: 2653

Type strain:

Species: Thomasclavelia ramosa

Strain Designation: 113-I

Culture col. no.: CCUG 24038, DSM 1402, ATCC 25582, NCIB 10673, VPI 0427, JCM 1298, BCRC 14518, KCTC 3323, NCIMB 10673, NCTC 11812

Strain history: ATCC 25582 <-- W. E. C. Moore VPI 0427 <-- A. R. Prévot 113-1 ("Ramibacterium ramosum").

NCBI tax ID(s): 445974 (strain), 1547 (species)

Section

Thomasclavelia ramosa 113-I is an anaerobe, mesophilic, Gram-positive bacterium of the family Coprobacillaceae.

Gram-positive
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	*Erysipelotrichia*
	Order	*Erysipelotrichales*
	Family	*Coprobacillaceae*
	Genus	*Thomasclavelia*
	Species	**Thomasclavelia ramosa**
	Full Scientific Name (LPSN)	Thomasclavelia ramosa (Veillon and Zuber 1898) Lawson et al. 2023

	Synonym	"Erysipelatoclostridium* ramosum"*
	Synonym	"Bacillus* ramosus"*
	Synonym	Clostridium ramosum

Information on morphological and physiological properties Morphology

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

Information on culture and growth conditions Culture and growth conditions

[Ref.: #489]

Culture medium

COLUMBIA BLOOD MEDIUM (DSMZ Medium 693)

[Ref.: #489]

Culture medium growth

[Ref.: #489]

Culture medium link

Medium recipe provided by DSMZ

[Ref.: #489]

Culture medium

FASTIDIOUS ANAEROBE BROTH (DSMZ Medium 1203a)

[Ref.: #489]

Culture medium growth

[Ref.: #489]

Culture medium link

Medium recipe provided by DSMZ

		Temperature
[Ref.: #489]	growth	37 °C
[Ref.: #47909]	growth	37 °C
[Ref.: #67770]	growth	37 °C

[Ref.: #489]	Temperature range	mesophilic
[Ref.: #47909]	Temperature range	mesophilic
[Ref.: #67770]	Temperature range	mesophilic

Information on physiology and metabolism Physiology and metabolism

[Ref.: #489]	Oxygen tolerance	anaerobe
[Ref.: #47909]	Oxygen tolerance	anaerobe
[Ref.: #69480]	Oxygen tolerance	anaerobe Confidence in %100

[Ref.: #69480]

Ability of spore formation

no Confidence in %99.289

	Metabolite	Utilization activity	Kind of utilization tested
[Ref.: #68367]	cellobiose ChEBI	+	builds acid from	* from API 20A
[Ref.: #68367]	D-glucose ChEBI	+	builds acid from	* from API 20A
[Ref.: #68367]	D-mannitol ChEBI	+	builds acid from	* from API 20A
[Ref.: #68367]	D-mannose ChEBI	+	builds acid from	* from API 20A
[Ref.: #68367]	D-xylose ChEBI	-	builds acid from	* from API 20A
[Ref.: #68367]	esculin ChEBI	+	hydrolysis	* from API 20A
[Ref.: #68367]	gelatin ChEBI	-	hydrolysis	* from API 20A
[Ref.: #68367]	glycerol ChEBI	-	builds acid from	* from API 20A
[Ref.: #68367]	L-arabinose ChEBI	-	builds acid from	* from API 20A
[Ref.: #68367]	L-rhamnose ChEBI	-	builds acid from	* from API 20A
[Ref.: #68367]	lactose ChEBI	+	builds acid from	* from API 20A
[Ref.: #68367]	maltose ChEBI	+	builds acid from	* from API 20A
[Ref.: #68367]	melezitose ChEBI	-	builds acid from	* from API 20A
[Ref.: #68367]	raffinose ChEBI	+	builds acid from	* from API 20A
[Ref.: #68367]	salicin ChEBI	+	builds acid from	* from API 20A
[Ref.: #68367]	sorbitol ChEBI	-	builds acid from	* from API 20A
[Ref.: #68367]	sucrose ChEBI	+	builds acid from	* from API 20A
[Ref.: #68367]	trehalose ChEBI	+	builds acid from	* from API 20A
[Ref.: #68367]	tryptophan ChEBI	-	energy source	* from API 20A
[Ref.: #68367]	urea ChEBI	-	hydrolysis	* from API 20A
	Only first 10 entries are displayed. Click here to see all.

	Metabolite production	Metabolite	Production
[Ref.: #68367]		indole ChEBI	no	* from API 20A

	Physiological tests	Metabolite	Indole test
[Ref.: #68367]		indole ChEBI	-	* from API 20A

	Enzyme	Enzyme activity	EC number
[Ref.: #68367]	beta-glucosidase	+	3.2.1.21	* from API 20A
[Ref.: #68367]	gelatinase	-		* from API 20A
[Ref.: #68367]	urease	-	3.5.1.5	* from API 20A

API® 20A:

Note that the displayed test results represent raw data and therefore may deviate!

	API ID	Indole productionIND	Urease/urea hydrolysisURE	Acid from D-glucoseGLU	Acid from D-mannitolMAN	Acid from lactoseLAC	Acid from sucroseSAC	Acid from maltoseMAL	Acid from salicinSAL	Acid from D-xyloseXYL	Acid from L-arabinoseARA	Gelatinase/gelatin hydrolysisGEL	Esculin hydrolysis/beta-glucosidaseESC	Acid from glycerolGLY	Acid from cellobioseCEL	Acid from D-mannoseMNE	Acid from melezitoseMLZ	Acid from raffinoseRAF	Acid from sorbitolSOR	Acid from L-rhamnoseRHA	Acid from trehaloseTRE	CatalaseCAT	Spores presentSPOR	GramGRAM	Morphology coccus="+" rod="-"COCC
[Ref.: #489]	2220	-	-	+	+	+	+	+	+	-	-	-	+	-	+	+	-	+	-	-	+	not determinedn.d.	not determinedn.d.	not determinedn.d.	not determinedn.d.

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

[Ref.: #69479]

Global distribution of 16S sequence AB595128 (>99% sequence identity) for Erysipelatoclostridium ramosum subclade from Microbeatlas

Aquatic Samples	2108
Soil Samples	626
Animal Samples	103847
Plant Samples	377
Total Samples	106958

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

[Ref.: #489]

Biosafety level

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.: #489]	Clostridium ramosum gene for 16S ribosomal RNA, partial sequence, strain: JCM 1298	AB595128	1488	ENA	1547 tax ID
[Ref.: #20218]	C.ramosum 16S ribosomal RNA small subunit	M23731	1530	ENA	1547 tax ID	*
[Ref.: #20218]	Clostridium ramosum DSM 1402 16S ribosomal RNA gene, partial sequence	HM245949	829	ENA	445974 tax ID	*
[Ref.: #20218]	Clostridium ramosum strain DSM 1402 16S ribosomal RNA gene, partial sequence	HQ012012	927	ENA	445974 tax ID	*
[Ref.: #20218]	Clostridium ramosum 16S rRNA gene, strain DSM 1402	X73440	1526	ENA	445974 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 ramosa DSM 1402	GCA_000154485	scaffold	GenBank	445974 tax ID
[Ref.: #66792]	Thomasclavelia ramosa DSM 1402	GCA_014131695	complete	GenBank	445974 tax ID	*
[Ref.: #66792]	Clostridium ramosum DSM 1402	445974.6	wgs	PATRIC	445974 tax ID	*
[Ref.: #66792]	Erysipelatoclostridium ramosum DSM 1402	445974.19	complete	PATRIC	445974 tax ID	*
[Ref.: #66792]	Erysipelatoclostridium ramosum strain FDAARGOS_906	1547.129	complete	PATRIC	1547 tax ID	*
[Ref.: #66792]	Erysipelatoclostridium ramosum DSM 1402	641736198	draft	JGI IMG/M	445974 tax ID	*

[Ref.: #489]	GC-content	31.4 mol%	sequence analysis
[Ref.: #67770]	GC-content	26 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: Erysipelatoclostridium ramosum DSM 1402 DSM 1402 NCBI: GCA_014131695.1
[Ref.: #69481]	spore-forming	no	58	no

	Trait	Prediction	Confidence in %	In training data
	Predictions from Diaspora project based on: Erysipelatoclostridium ramosum DSM 1402 DSM 1402 NCBI: GCA_014131695.1
[Ref.: #69480]	motile	no	90.161	no
[Ref.: #69480]	flagellated	no	91.849	no
[Ref.: #69480]	gram-positive	yes	95.359	no
[Ref.: #69480]	anaerobic	yes	97.739	no
[Ref.: #69480]	aerobic	no	98.507	no
[Ref.: #69480]	halophile	no	78.78	no
[Ref.: #69480]	spore-forming	no	66.639	no
[Ref.: #69480]	glucose-util	yes	85.881	no
[Ref.: #69480]	thermophile	no	97.928	yes
[Ref.: #69480]	glucose-ferment	yes	71.364	no

Availability in culture collections External links

[Ref.: #489]

Culture collection no.

CCUG 24038, DSM 1402, ATCC 25582, NCIB 10673, VPI 0427, JCM 1298, BCRC 14518, KCTC 3323, NCIMB 10673, NCTC 11812

Literature:

Topic	Title	Authors	Journal	DOI	Year
Phylogeny	Tannockella kyphosi gen. nov., sp. nov., a member of the family Erysipelotrichaceae, isolated from the hindgut of the marine herbivorous fish Kyphosus sydneyanus.	Pardesi B, Roberton AM, Wollmuth EM, Angert ER, Rosendale DI, White WL, Clements KD	Int J Syst Evol Microbiol	10.1099/ijsem.0.005374	2022	*
Phylogeny	Bacteriostatic effect of orally administered bovine lactoferrin on proliferation of Clostridium species in the gut of mice fed bovine milk.	Teraguchi S, Shin K, Ozawa K, Nakamura S, Fukuwatari Y, Tsuyuki S, Namihira H, Shimamura S	Appl Environ Microbiol	10.1128/aem.61.2.501-506.1995	1995	*

References

#489	Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 1402

#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 )

#47909 Culture Collection University of Gothenburg (CCUG) ; Curators of the CCUG; CCUG 24038

#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;

#68367

Automatically annotated from API 20A .

#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 )

* These data were automatically processed and therefore are not curated

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Erysipelatoclostridium ramosum DSM 1402 DSM 1402

Erysipelatoclostridium ramosum DSM 1402 DSM 1402

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