Name: Clostridium bornimense M2/40
Creator: BacDive
License: http://creativecommons.org/licenses/by-nc/4.0/

Strain identifier

BacDive ID: 23860

Type strain:

Species: Clostridium bornimense

Strain Designation: M2/40

Culture col. no.: DSM 25664, CECT 8097, KCTC 15508

Strain history: <- DSM <- S Hahnke, Institut fur Agrartechnik Bornim e.V., M2/40 <- J Striesow

NCBI tax ID(s): 1216932 (species)

SI-ID 404937

DSM 25664

Section

Clostridium bornimense M2/40 is an anaerobe, mesophilic, rod-shaped bacterium that was isolated from mesophilic biogas reactor fed with maize silage.

rod-shaped
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	*Clostridia*
	Order	*Eubacteriales*
	Family	*Clostridiaceae*
	Genus	*Clostridium*
	Species	**Clostridium bornimense**
	Full Scientific Name (LPSN)	Clostridium bornimense Hahnke et al. 2014

Information on morphological and physiological properties Morphology

[Ref.: #67771]	Gram stain	variable

[Ref.: #67771]	Cell shape	rod-shaped
[Ref.: #67771]	Cell shape	filament-shaped

Information on culture and growth conditions Culture and growth conditions

[Ref.: #20949]

Culture medium

PY + X MEDIUM (DSMZ Medium 104b)

[Ref.: #20949]

Culture medium growth

[Ref.: #20949]

Culture medium link

Medium recipe at MediaDive

[Ref.: #20949]

Culture medium composition

expand / minimize

	Temperatures	Kind of temperature		Temperature
[Ref.: #20949]			growth	35 °C
[Ref.: #67771]			growth	37 °C

[Ref.: #20949]	Temperature range	mesophilic
[Ref.: #67771]	Temperature range	mesophilic

Information on physiology and metabolism Physiology and metabolism

[Ref.: #20949]	Oxygen tolerance	anaerobe
[Ref.: #67771]	Oxygen tolerance	anaerobe

	Pathway	Enzyme coverage	Annotated reactions
	Pathway annotation	Computationally determined by
[Ref.: #66794]	C4 and CAM-carbon fixation	100	8 of 8
[Ref.: #66794]	cis-vaccenate biosynthesis	100	2 of 2
[Ref.: #66794]	coenzyme A metabolism	100	4 of 4
[Ref.: #66794]	sulfopterin metabolism	100	4 of 4
[Ref.: #66794]	adipate degradation	100	2 of 2
[Ref.: #66794]	cardiolipin biosynthesis	100	7 of 7
[Ref.: #66794]	CDP-diacylglycerol biosynthesis	100	2 of 2
[Ref.: #66794]	UDP-GlcNAc biosynthesis	100	3 of 3
[Ref.: #66794]	suberin monomers biosynthesis	100	2 of 2
[Ref.: #66794]	glycogen metabolism	100	5 of 5
[Ref.: #66794]	L-lactaldehyde degradation	100	3 of 3
[Ref.: #66794]	teichoic acid biosynthesis	100	1 of 1
[Ref.: #66794]	palmitate biosynthesis	100	22 of 22
[Ref.: #66794]	folate polyglutamylation	100	1 of 1
[Ref.: #66794]	anapleurotic synthesis of oxalacetate	100	1 of 1
[Ref.: #66794]	vitamin B1 metabolism	92.31	12 of 13
[Ref.: #66794]	starch degradation	90	9 of 10
[Ref.: #66794]	threonine metabolism	90	9 of 10
[Ref.: #66794]	chorismate metabolism	88.89	8 of 9
[Ref.: #66794]	aspartate and asparagine metabolism	88.89	8 of 9
[Ref.: #66794]	valine metabolism	88.89	8 of 9
[Ref.: #66794]	NAD metabolism	88.89	16 of 18
[Ref.: #66794]	gluconeogenesis	87.5	7 of 8
[Ref.: #66794]	reductive acetyl coenzyme A pathway	85.71	6 of 7
[Ref.: #66794]	phenylalanine metabolism	84.62	11 of 13
[Ref.: #66794]	vitamin B12 metabolism	82.35	28 of 34
[Ref.: #66794]	cellulose degradation	80	4 of 5
[Ref.: #66794]	glycine betaine biosynthesis	80	4 of 5
[Ref.: #66794]	peptidoglycan biosynthesis	80	12 of 15
[Ref.: #66794]	tetrahydrofolate metabolism	78.57	11 of 14
[Ref.: #66794]	glutamate and glutamine metabolism	78.57	22 of 28
[Ref.: #66794]	CO2 fixation in Crenarchaeota	77.78	7 of 9
[Ref.: #66794]	pyrimidine metabolism	77.78	35 of 45
[Ref.: #66794]	isoleucine metabolism	75	6 of 8
[Ref.: #66794]	CMP-KDO biosynthesis	75	3 of 4
[Ref.: #66794]	ppGpp biosynthesis	75	3 of 4
[Ref.: #66794]	6-hydroxymethyl-dihydropterin diphosphate biosynthesis	75	6 of 8
[Ref.: #66794]	acetate fermentation	75	3 of 4
[Ref.: #66794]	glycogen biosynthesis	75	3 of 4
[Ref.: #66794]	purine metabolism	73.4	69 of 94
[Ref.: #66794]	flavin biosynthesis	73.33	11 of 15
[Ref.: #66794]	alanine metabolism	72.41	21 of 29
[Ref.: #66794]	glutathione metabolism	71.43	10 of 14
[Ref.: #66794]	photosynthesis	71.43	10 of 14
[Ref.: #66794]	glycolysis	70.59	12 of 17
[Ref.: #66794]	non-pathway related	68.42	26 of 38
[Ref.: #66794]	serine metabolism	66.67	6 of 9
[Ref.: #66794]	formaldehyde oxidation	66.67	2 of 3
[Ref.: #66794]	glycolate and glyoxylate degradation	66.67	4 of 6
[Ref.: #66794]	octane oxidation	66.67	2 of 3
[Ref.: #66794]	acetoin degradation	66.67	2 of 3
[Ref.: #66794]	d-mannose degradation	66.67	6 of 9
[Ref.: #66794]	heme metabolism	64.29	9 of 14
[Ref.: #66794]	oxidative phosphorylation	63.74	58 of 91
[Ref.: #66794]	dTDPLrhamnose biosynthesis	62.5	5 of 8
[Ref.: #66794]	histidine metabolism	62.07	18 of 29
[Ref.: #66794]	methionine metabolism	61.54	16 of 26
[Ref.: #66794]	lipid metabolism	61.29	19 of 31
[Ref.: #66794]	methylglyoxal degradation	60	3 of 5
[Ref.: #66794]	lipoate biosynthesis	60	3 of 5
[Ref.: #66794]	hydrogen production	60	3 of 5
[Ref.: #66794]	degradation of aromatic, nitrogen containing compounds	58.33	7 of 12
[Ref.: #66794]	tryptophan metabolism	57.89	22 of 38
[Ref.: #66794]	lysine metabolism	57.14	24 of 42
[Ref.: #66794]	propanol degradation	57.14	4 of 7
[Ref.: #66794]	d-xylose degradation	54.55	6 of 11
[Ref.: #66794]	leucine metabolism	53.85	7 of 13
[Ref.: #66794]	urea cycle	53.85	7 of 13
[Ref.: #66794]	citric acid cycle	50	7 of 14
[Ref.: #66794]	ethanol fermentation	50	1 of 2
[Ref.: #66794]	butanoate fermentation	50	2 of 4
[Ref.: #66794]	ketogluconate metabolism	50	4 of 8
[Ref.: #66794]	biotin biosynthesis	50	2 of 4
[Ref.: #66794]	kanosamine biosynthesis II	50	1 of 2
[Ref.: #66794]	aminopropanol phosphate biosynthesis	50	1 of 2
[Ref.: #66794]	phenylmercury acetate degradation	50	1 of 2
[Ref.: #66794]	dolichol and dolichyl phosphate biosynthesis	50	1 of 2
[Ref.: #66794]	cysteine metabolism	50	9 of 18
[Ref.: #66794]	Entner Doudoroff pathway	50	5 of 10
[Ref.: #66794]	glycine metabolism	50	5 of 10
[Ref.: #66794]	isoprenoid biosynthesis	46.15	12 of 26
[Ref.: #66794]	sulfate reduction	46.15	6 of 13
[Ref.: #66794]	phosphatidylethanolamine bioynthesis	46.15	6 of 13
[Ref.: #66794]	arginine metabolism	45.83	11 of 24
[Ref.: #66794]	proline metabolism	45.45	5 of 11
[Ref.: #66794]	nitrate assimilation	44.44	4 of 9
[Ref.: #66794]	ubiquinone biosynthesis	42.86	3 of 7
[Ref.: #66794]	creatinine degradation	40	2 of 5
[Ref.: #66794]	propionate fermentation	40	4 of 10
[Ref.: #66794]	coenzyme M biosynthesis	40	4 of 10
[Ref.: #66794]	O-antigen biosynthesis	40	2 of 5
[Ref.: #66794]	metabolism of amino sugars and derivatives	40	2 of 5
[Ref.: #66794]	arachidonate biosynthesis	40	2 of 5
[Ref.: #66794]	phenylpropanoid biosynthesis	38.46	5 of 13
[Ref.: #66794]	vitamin B6 metabolism	36.36	4 of 11
[Ref.: #66794]	tyrosine metabolism	35.71	5 of 14
[Ref.: #66794]	polyamine pathway	34.78	8 of 23
[Ref.: #66794]	cyanate degradation	33.33	1 of 3
[Ref.: #66794]	acetyl CoA biosynthesis	33.33	1 of 3
[Ref.: #66794]	molybdenum cofactor biosynthesis	33.33	3 of 9
[Ref.: #66794]	degradation of hexoses	33.33	6 of 18
[Ref.: #66794]	lipid A biosynthesis	33.33	3 of 9
[Ref.: #66794]	selenocysteine biosynthesis	33.33	2 of 6
[Ref.: #66794]	enterobactin biosynthesis	33.33	1 of 3
[Ref.: #66794]	pantothenate biosynthesis	33.33	2 of 6
[Ref.: #66794]	IAA biosynthesis	33.33	1 of 3
[Ref.: #66794]	degradation of pentoses	32.14	9 of 28
[Ref.: #66794]	myo-inositol biosynthesis	30	3 of 10
[Ref.: #66794]	benzoyl-CoA degradation	28.57	2 of 7
[Ref.: #66794]	aclacinomycin biosynthesis	28.57	2 of 7
[Ref.: #66794]	pentose phosphate pathway	27.27	3 of 11
[Ref.: #66794]	metabolism of disaccharids	27.27	3 of 11
[Ref.: #66794]	dolichyl-diphosphooligosaccharide biosynthesis	27.27	3 of 11
[Ref.: #66794]	ascorbate metabolism	27.27	6 of 22
[Ref.: #66794]	cyclohexanol degradation	25	1 of 4
[Ref.: #66794]	toluene degradation	25	1 of 4
[Ref.: #66794]	degradation of sugar alcohols	25	4 of 16
[Ref.: #66794]	lactate fermentation	25	1 of 4
		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.: #20949]	Sample type/isolated from	mesophilic biogas reactor fed with maize silage
[Ref.: #20949]	Country	Germany
[Ref.: #20949]	Country ISO 3 Code	DEU
[Ref.: #20949]	Continent	Europe

[Ref.: #67771]	Sample type/isolated from	From mesophilic biogas reactor fed with maize silage
[Ref.: #67771]	Country	Germany
[Ref.: #67771]	Country ISO 3 Code	DEU
[Ref.: #67771]	Continent	Europe
* marker position based on {}

Isolation sources categories

#Engineered	#Bioreactor	-
#Host	#Plants	#Herbaceous plants (Grass,Crops)

What are isolation sources categories?

[Ref.: #69479]

Global distribution of 16S sequence JQ388596 (>99% sequence identity) for Clostridium bornimense subclade from Microbeatlas

Aquatic Samples	4683
Soil Samples	5821
Animal Samples	29158
Plant Samples	1308
Total Samples	40970

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

[Ref.: #20949]

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.: #20949]	Clostridium bornimense strain M2/40 16S ribosomal RNA gene, partial sequence	JQ388596	1363	ENA	1216932 tax ID

Genome sequence information:

	Sequence accession description	Seq. accession number	Assembly level	Sequence database	Associated NCBI tax ID
[Ref.: #66792]	Clostridium bornimense M2/40	2585427665	complete	JGI IMG/M	1216932 tax ID	*
[Ref.: #66792]	Clostridium bornimense M2/40	GCA_000577895	complete	GenBank	1216932 tax ID	*

[Ref.: #20949]	GC-content	29.6 mol%	high performance liquid chromatography (HPLC)
[Ref.: #67771]	GC-content	29.6 mol%

Availability in culture collections External links

[Ref.: #20949]

Culture collection no.

DSM 25664, CECT 8097, KCTC 15508

[Ref.: #87873]

SI-ID 404937

Literature:

Topic	Title	Authors	Journal	DOI	Year
Genetics	Genomics and prevalence of bacterial and archaeal isolates from biogas-producing microbiomes.	Maus I, Bremges A, Stolze Y, Hahnke S, Cibis KG, Koeck DE, Kim YS, Kreubel J, Hassa J, Wibberg D, Weimann A, Off S, Stantscheff R, Zverlov VV, Schwarz WH, Konig H, Liebl W, Scherer P, McHardy AC, Sczyrba A, Klocke M, Puhler A, Schluter A	Biotechnol Biofuels	10.1186/s13068-017-0947-1	2017	*
Phylogeny	Clostridium bornimense sp. nov., isolated from a mesophilic, two-phase, laboratory-scale biogas reactor.	Hahnke S, Striesow J, Elvert M, Mollar XP, Klocke M	Int J Syst Evol Microbiol	10.1099/ijs.0.059691-0	2014	*
Genetics	Complete genome analysis of Clostridium bornimense strain M2/40(T): A new acidogenic Clostridium species isolated from a mesophilic two-phase laboratory-scale biogas reactor.	Tomazetto G, Hahnke S, Koeck DE, Wibberg D, Maus I, Puhler A, Klocke M, Schluter A	J Biotechnol	10.1016/j.jbiotec.2015.08.001	2015	*
Genetics	Whole genome sequence of Clostridium bornimense strain M2/40 isolated from a lab-scale mesophilic two-phase biogas reactor digesting maize silage and wheat straw.	Hahnke S, Wibberg D, Tomazetto G, Puhler A, Klocke M, Schluter A	J Biotechnol	10.1016/j.jbiotec.2014.05.026	2014	*

References

#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 )

#20949

Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 25664

#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 )

#67771 Korean Collection for Type Cultures (KCTC) ; Curators of the KCTC;

#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 .

#87873

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-ID404937.1 )

* These data were automatically processed and therefore are not curated

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