Name: Ruminiclostridium sufflavum CDT-1
Creator: BacDive
License: https://creativecommons.org/licenses/by/4.0/

Strain identifier

BacDive ID: 2848

Type strain:

Species: Ruminiclostridium sufflavum

Strain Designation: CDT-1

Culture col. no.: DSM 19573, JCM 14807

Strain history: A. Ueki CDT-1.

NCBI tax ID(s): 1121337 (strain), 396504 (species)

SI-ID 401866

DSM 19573

Special Collections

Section

Ruminiclostridium sufflavum CDT-1 is an anaerobe, spore-forming, Gram-negative bacterium that was isolated from rice-straw residue from a methanogenic reactor treating cattle waste.

Gram-negative
motile
rod-shaped
spore-forming
anaerobe
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	*Oscillospiraceae*
	Genus	*Ruminiclostridium*
	Species	**Ruminiclostridium sufflavum**
	Full Scientific Name (LPSN)	Ruminiclostridium sufflavum (Nishiyama et al. 2009) Zhang et al. 2018

Synonym

Clostridium sufflavum

Information on morphological and physiological properties Morphology

[Ref.: #28926]	Gram stain	negative

[Ref.: #28926]	Cell length	3.5 µm

[Ref.: #28926]	Cell width	0.55 µm

[Ref.: #28926]	Cell shape	rod-shaped

[Ref.: #28926]	Motility	yes

[Ref.: #28926]

Pigment production

yes

Information on culture and growth conditions Culture and growth conditions

[Ref.: #8187]

Culture medium

PY + X MEDIUM (DSMZ Medium 104b)

[Ref.: #8187]

Culture medium growth

[Ref.: #8187]

Culture medium link

Medium recipe at MediaDive

[Ref.: #8187]

Culture medium composition

expand / minimize

		Temperature
[Ref.: #8187]	growth	30 °C
[Ref.: #28926]	growth	20-33 °C
[Ref.: #28926]	optimum	33 °C
[Ref.: #67770]	growth	30 °C

	pH	Kind of pH		pH
[Ref.: #28926]			optimum	7.4
[Ref.: #28926]			growth	5.9-8.2

Information on physiology and metabolism Physiology and metabolism

[Ref.: #8187]	Oxygen tolerance	anaerobe
[Ref.: #28926]	Oxygen tolerance	anaerobe
[Ref.: #69480]	Oxygen tolerance	anaerobe Confidence in %90.141

[Ref.: #28926]	Ability of spore formation	yes
[Ref.: #69481]	Ability of spore formation	yes Confidence in %100

[Ref.: #28926]

Observation

aggregates in clumps

	Metabolite	Utilization activity	Kind of utilization tested
[Ref.: #28926]	acetate ChEBI	+	carbon source
[Ref.: #28926]	cellobiose ChEBI	+	carbon source
[Ref.: #28926]	ethanol ChEBI	+	carbon source
[Ref.: #28926]	fructose ChEBI	+	carbon source
[Ref.: #28926]	glucose ChEBI	+	carbon source
[Ref.: #28926]	ribose ChEBI	+	carbon source
[Ref.: #28926]	sorbitol ChEBI	+	carbon source
[Ref.: #28926]	xylose ChEBI	+	carbon source

	Metabolite production	Metabolite	Production
[Ref.: #28926]		methane ChEBI	yes

	Pathway	Enzyme coverage	Annotated reactions
	Pathway annotation	Computationally determined by
[Ref.: #66794]	glycogen metabolism	100	5 of 5
[Ref.: #66794]	ppGpp biosynthesis	100	4 of 4
[Ref.: #66794]	palmitate biosynthesis	100	22 of 22
[Ref.: #66794]	L-lactaldehyde degradation	100	3 of 3
[Ref.: #66794]	cis-vaccenate biosynthesis	100	2 of 2
[Ref.: #66794]	adipate degradation	100	2 of 2
[Ref.: #66794]	kanosamine biosynthesis II	100	2 of 2
[Ref.: #66794]	chorismate metabolism	100	9 of 9
[Ref.: #66794]	formaldehyde oxidation	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]	UDP-GlcNAc biosynthesis	100	3 of 3
[Ref.: #66794]	CDP-diacylglycerol biosynthesis	100	2 of 2
[Ref.: #66794]	threonine metabolism	90	9 of 10
[Ref.: #66794]	aspartate and asparagine metabolism	88.89	8 of 9
[Ref.: #66794]	vitamin B1 metabolism	84.62	11 of 13
[Ref.: #66794]	NAD metabolism	83.33	15 of 18
[Ref.: #66794]	metabolism of amino sugars and derivatives	80	4 of 5
[Ref.: #66794]	starch degradation	80	8 of 10
[Ref.: #66794]	hydrogen production	80	4 of 5
[Ref.: #66794]	cellulose degradation	80	4 of 5
[Ref.: #66794]	glycine betaine biosynthesis	80	4 of 5
[Ref.: #66794]	flavin biosynthesis	80	12 of 15
[Ref.: #66794]	Entner Doudoroff pathway	80	8 of 10
[Ref.: #66794]	peptidoglycan biosynthesis	80	12 of 15
[Ref.: #66794]	tetrahydrofolate metabolism	78.57	11 of 14
[Ref.: #66794]	valine metabolism	77.78	7 of 9
[Ref.: #66794]	d-mannose degradation	77.78	7 of 9
[Ref.: #66794]	phenylalanine metabolism	76.92	10 of 13
[Ref.: #66794]	glycolysis	76.47	13 of 17
[Ref.: #66794]	glycogen biosynthesis	75	3 of 4
[Ref.: #66794]	ketogluconate metabolism	75	6 of 8
[Ref.: #66794]	acetate fermentation	75	3 of 4
[Ref.: #66794]	C4 and CAM-carbon fixation	75	6 of 8
[Ref.: #66794]	gluconeogenesis	75	6 of 8
[Ref.: #66794]	methionine metabolism	73.08	19 of 26
[Ref.: #66794]	cardiolipin biosynthesis	71.43	5 of 7
[Ref.: #66794]	ubiquinone biosynthesis	71.43	5 of 7
[Ref.: #66794]	glutamate and glutamine metabolism	71.43	20 of 28
[Ref.: #66794]	photosynthesis	71.43	10 of 14
[Ref.: #66794]	alanine metabolism	68.97	20 of 29
[Ref.: #66794]	degradation of sugar alcohols	68.75	11 of 16
[Ref.: #66794]	purine metabolism	68.09	64 of 94
[Ref.: #66794]	enterobactin biosynthesis	66.67	2 of 3
[Ref.: #66794]	CO2 fixation in Crenarchaeota	66.67	6 of 9
[Ref.: #66794]	octane oxidation	66.67	2 of 3
[Ref.: #66794]	acetoin degradation	66.67	2 of 3
[Ref.: #66794]	serine metabolism	66.67	6 of 9
[Ref.: #66794]	methane metabolism	66.67	2 of 3
[Ref.: #66794]	glycolate and glyoxylate degradation	66.67	4 of 6
[Ref.: #66794]	cyanate degradation	66.67	2 of 3
[Ref.: #66794]	isoprenoid biosynthesis	65.38	17 of 26
[Ref.: #66794]	pyrimidine metabolism	64.44	29 of 45
[Ref.: #66794]	d-xylose degradation	63.64	7 of 11
[Ref.: #66794]	isoleucine metabolism	62.5	5 of 8
[Ref.: #66794]	dTDPLrhamnose biosynthesis	62.5	5 of 8
[Ref.: #66794]	6-hydroxymethyl-dihydropterin diphosphate biosynthesis	62.5	5 of 8
[Ref.: #66794]	leucine metabolism	61.54	8 of 13
[Ref.: #66794]	methylglyoxal degradation	60	3 of 5
[Ref.: #66794]	lipoate biosynthesis	60	3 of 5
[Ref.: #66794]	oxidative phosphorylation	59.34	54 of 91
[Ref.: #66794]	arginine metabolism	58.33	14 of 24
[Ref.: #66794]	lipid metabolism	58.06	18 of 31
[Ref.: #66794]	tryptophan metabolism	57.89	22 of 38
[Ref.: #66794]	reductive acetyl coenzyme A pathway	57.14	4 of 7
[Ref.: #66794]	degradation of pentoses	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]	lysine metabolism	54.76	23 of 42
[Ref.: #66794]	proline metabolism	54.55	6 of 11
[Ref.: #66794]	non-pathway related	52.63	20 of 38
[Ref.: #66794]	ethanol fermentation	50	1 of 2
[Ref.: #66794]	glycine metabolism	50	5 of 10
[Ref.: #66794]	sulfopterin metabolism	50	2 of 4
[Ref.: #66794]	CMP-KDO biosynthesis	50	2 of 4
[Ref.: #66794]	ribulose monophosphate pathway	50	1 of 2
[Ref.: #66794]	propionate fermentation	50	5 of 10
[Ref.: #66794]	selenocysteine biosynthesis	50	3 of 6
[Ref.: #66794]	degradation of hexoses	50	9 of 18
[Ref.: #66794]	myo-inositol biosynthesis	50	5 of 10
[Ref.: #66794]	dolichol and dolichyl phosphate biosynthesis	50	1 of 2
[Ref.: #66794]	suberin monomers biosynthesis	50	1 of 2
[Ref.: #66794]	mannosylglycerate biosynthesis	50	1 of 2
[Ref.: #66794]	cysteine metabolism	50	9 of 18
[Ref.: #66794]	citric acid cycle	50	7 of 14
[Ref.: #66794]	toluene degradation	50	2 of 4
[Ref.: #66794]	glutathione metabolism	50	7 of 14
[Ref.: #66794]	tyrosine metabolism	50	7 of 14
[Ref.: #66794]	butanoate fermentation	50	2 of 4
[Ref.: #66794]	urea cycle	46.15	6 of 13
[Ref.: #66794]	phenylpropanoid biosynthesis	46.15	6 of 13
[Ref.: #66794]	sulfate reduction	46.15	6 of 13
[Ref.: #66794]	pentose phosphate pathway	45.45	5 of 11
[Ref.: #66794]	lipid A biosynthesis	44.44	4 of 9
[Ref.: #66794]	nitrate assimilation	44.44	4 of 9
[Ref.: #66794]	degradation of sugar acids	44	11 of 25
[Ref.: #66794]	arachidonate biosynthesis	40	2 of 5
[Ref.: #66794]	ascorbate metabolism	36.36	8 of 22
[Ref.: #66794]	metabolism of disaccharids	36.36	4 of 11
[Ref.: #66794]	vitamin B6 metabolism	36.36	4 of 11
[Ref.: #66794]	acetyl CoA biosynthesis	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]	molybdenum cofactor biosynthesis	33.33	3 of 9
[Ref.: #66794]	pantothenate biosynthesis	33.33	2 of 6
[Ref.: #66794]	degradation of aromatic, nitrogen containing compounds	33.33	4 of 12
[Ref.: #66794]	benzoyl-CoA degradation	28.57	2 of 7
[Ref.: #66794]	arachidonic acid metabolism	27.78	5 of 18
[Ref.: #66794]	dolichyl-diphosphooligosaccharide biosynthesis	27.27	3 of 11
[Ref.: #66794]	alginate biosynthesis	25	1 of 4
[Ref.: #66794]	vitamin E metabolism	25	1 of 4
[Ref.: #66794]	lactate fermentation	25	1 of 4
[Ref.: #66794]	cyclohexanol degradation	25	1 of 4
[Ref.: #66794]	biotin biosynthesis	25	1 of 4
[Ref.: #66794]	carnitine metabolism	25	2 of 8
[Ref.: #66794]	androgen and estrogen metabolism	25	4 of 16
[Ref.: #66794]	vitamin B12 metabolism	23.53	8 of 34
[Ref.: #66794]	phosphatidylethanolamine bioynthesis	23.08	3 of 13
[Ref.: #66794]	4-hydroxymandelate degradation	22.22	2 of 9
[Ref.: #66794]	allantoin degradation	22.22	2 of 9
[Ref.: #66794]	heme 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.: #8187]	Sample type/isolated from	rice-straw residue from a methanogenic reactor treating cattle waste
[Ref.: #8187]	Geographic location (country and/or sea, region)	Hokkaido, Betsukai-machi
[Ref.: #8187]	Country	Japan
[Ref.: #8187]	Country ISO 3 Code	JPN
[Ref.: #8187]	Continent	Asia

[Ref.: #67770]	Sample type/isolated from	Methanogenic reactor treating cattle waste
* marker position based on {}

Isolation sources categories

#Engineered	#Bioreactor	-
#Engineered	#Waste	-
#Host	#Mammals	#Bovinae (Cow, Cattle)
#Host	#Plants	#Herbaceous plants (Grass,Crops)

What are isolation sources categories?

[Ref.: #69479]

Global distribution of 16S sequence AB267266 (>99% sequence identity) for Ruminiclostridium sufflavum from Microbeatlas

Aquatic Samples	321
Soil Samples	1497
Animal Samples	107
Plant Samples	94
Total Samples	2019

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

[Ref.: #8187]

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.: #8187]	[Clostridium] sufflavum gene for 16S ribosomal RNA, partial sequence	AB267266	1436	GenBank ENA	396504 tax ID

Genome sequence information:

	Sequence accession description	Seq. accession number	Assembly level	Sequence database	Associated NCBI tax ID
[Ref.: #66792]	Ruminiclostridium sufflavum DSM 19573	GCA_003208175	scaffold	GenBank ENA	1121337 tax ID	*
[Ref.: #66792]	[Clostridium] sufflavum DSM 19573	1121337.3	wgs	PATRIC	1121337 tax ID	*
[Ref.: #66792]	Ruminiclostridium sufflavum DSM 19573	2599185205	draft	JGI IMG/M	1121337 tax ID	*

[Ref.: #8187]	GC-content	40.7 mol%	high performance liquid chromatography (HPLC)
[Ref.: #28926]	GC-content	40.7 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: Ruminiclostridium sufflavum DSM 19573 DSM 19573 NCBI: GCA_003208175.1
[Ref.: #69481]	spore-forming	spore-formingⓘ	yes	100	no

	Trait	Model	Prediction	Confidence in %	In training data
	Predictions from Diaspora project based on: Ruminiclostridium sufflavum DSM 19573 DSM 19573 NCBI: GCA_003208175.1
[Ref.: #69480]	gram-positive	gram-positiveⓘ	no	56.397	yes
[Ref.: #69480]	anaerobic	anaerobicⓘ	yes	90.141	yes
[Ref.: #69480]	aerobic	aerobicⓘ	no	95.402	no
[Ref.: #69480]	spore-forming	spore-formingⓘ	yes	83.015	yes
[Ref.: #69480]	thermophilic	thermophileⓘ	no	70.884	yes
[Ref.: #69480]	flagellated	motile2+ⓘ	yes	78.387	no

Availability in culture collections External links

[Ref.: #8187]

Culture collection no.

DSM 19573, JCM 14807

[Ref.: #72372]

SI-ID 401866

Literature:

Topic	Title	Authors	Journal	DOI	Year
Phylogeny	Ruminiclostridium herbifermentans sp. nov., a mesophilic and moderately thermophilic cellulolytic and xylanolytic bacterium isolated from a lab-scale biogas fermenter fed with maize silage.	Rettenmaier R, Kowollik ML, Klingl A, Liebl W, Zverlov V	Int J Syst Evol Microbiol	10.1099/ijsem.0.004692	2021	*
Phylogeny	Clostridium sufflavum sp. nov., isolated from a methanogenic reactor treating cattle waste.	Nishiyama T, Ueki A, Kaku N, Ueki K	Int J Syst Evol Microbiol	10.1099/ijs.0.001719-0	2009	*

References

#8187

Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 19573

#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 )

#28926

Barberan A, Caceres Velazquez H, Jones S, Fierer N.: Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information. mSphere 2: 2017 ( DOI 10.1128/mSphere.00237-17 , PubMed 28776041 ) - originally annotated from #25365 (see below)

#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 )

#72372

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-ID401866.1 )

#25365

IJSEM 981 2009 ( DOI 10.1099/ijs.0.001719-0 , PubMed 19406778 )

* These data were automatically processed and therefore are not curated

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Ruminiclostridium sufflavum DSM 19573 DSM 19573

Ruminiclostridium sufflavum DSM 19573 DSM 19573

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