Name: Clostridium sp. B6405
Creator: BacDive
License: http://creativecommons.org/licenses/by-nc/4.0/

Strain identifier

BacDive ID: 2686

Type strain:

Species: Clostridium sp.

Strain Designation: B6405

Culture col. no.: DSM 8431, ATCC 49440

Strain history: <- ATCC <- V. H. Varel; B6405 (Clostridium longisporum) {1987}

NCBI tax ID(s): 1761781 (species)

SI-ID 48479

DSM 8431

Other strains from Clostridium sp.

C. sp. London, DSM 3268
C. sp. Guariba, DSM 4685
C. sp. C1, DSM 12136
C. sp. AAM-1, DSM 10156
C. sp. KN-18, DSM 523, IFO 3353, NBRC ...
C. sp. M55, DSM 754, ATCC 13732
C. sp. DSM 1786, ATCC 25772, VPI 2461
C. sp. DSM 1975
C. sp. BAFF C3, S5, DSM 1985
C. sp. RB-9, DSM 2575, ATCC 39252
C. sp. DSM 2634, ATCC 13726
C. sp. KN245, DSM 5671
C. sp. 2b, DSM 5905, BKM B-1371, VKM B-1371
C. sp. 4, DSM 5906, BKM B-1364, VKM B-1364
C. sp. 1a, DSM 5907, BKM B-1360, VKM B-1360
C. sp. 11-2, 248 UNSW 047500, DSM 6646, ...
C. sp. 13-1, 248 UNSW 052700, DSM 6647, ...
C. sp. FS23, DSM 6876
C. sp. FS41, DSM 6877
C. sp. EV4, DSM 8245
C. sp. M5a3, DSM 10510
C. sp. KNNDS, DSM 10612
C. sp. DSM 10643, LIP 1
C. sp. 19gly4, DSM 11261
C. sp. A22b, DSM 11322, IAM 19228, JCM ...
C. sp. C8, DSM 11329, IAM 19232, JCM 7847
C. sp. 240-00, 296K/00, DSM 13576
C. sp. PXYL1, DSM 15427
C. sp. DSM 15346, ARC ArC5, ARC 5
C. sp. ID02-1354, TDO, DSM 15348
C. sp. ZIRB-1, DSM 15498
C. sp. EDB2, DSM 17592
C. sp. H1, DSM 46282, IMET 10868
C. sp. KO PS 7, DSM 30835
C. sp. DSM 7072, MCM B 501
C. sp. ZAQ-1, ZAQ-1A, DSM 15728
C. sp. 17cr1, DSM 16654
C. sp. BA-1, DSM 16988, MBIC 6483
C. sp. Mg50, DSM 17284
C. sp. RM-4, DSM 17699
C. sp. 14F, DSM 17811, VKM B-2368
C. sp. K311, DSM 19740
C. sp. Sanger 132, Sanger_132, DSM 102147
C. sp. U42, DSM 21318, NBRC 103937
C. sp. DSM 22005, USBA 49
C. sp. 6/1/45, DSM 24810, BEI HM-180
C. sp. 6/1/30, DSM 24813, BEI HM-173
C. sp. CCUG 7153
C. sp. CCUG 21842
C. sp. CCUG 21843
C. sp. CCUG 21844
C. sp. CCUG 31375
C. sp. CCUG 33682
C. sp. CCUG 33718
C. sp. CCUG 34451
C. sp. CCUG 34453
C. sp. CCUG 35213
C. sp. CCUG 39361
C. sp. CCUG 41374
C. sp. CCUG 42584
C. sp. CCUG 42741
C. sp. CCUG 42742
C. sp. CCUG 43338
C. sp. CCUG 43740
C. sp. CCUG 44367
C. sp. CCUG 47350
C. sp. CCUG 47909
C. sp. CCUG 47910
C. sp. CCUG 48774
C. sp. CCUG 49474
C. sp. CCUG 50469
C. sp. CCUG 50470
C. sp. CCUG 50471
C. sp. CCUG 53142
C. sp. CCUG 57327
C. sp. MASE-IM4, DSM 105631
C. sp. H6_19, DSM 108254
C. sp. HV4-5-A1G, DSM 104276
C. sp. SM-530-WT-3G, DSM 107452
C. sp. 1/7/47 FAA, DSM 24809
C. sp. 4/1/37 FAA, DSM 24811
C. sp. TG60-1, DSM 25153, NBRC 107100
C. sp. TG60-81, DSM 25154, NBRC 107101
C. sp. JCM 10513
C. sp. JCM 10514
C. sp. JCM 10515
C. sp. JCM 10516
C. sp. JCM 10517
C. sp. JCM 10518
C. sp. JCM 10519
C. sp. JCM 10522
C. sp. JCM 18678
C. sp. JCM 18679
C. sp. JCM 31251
C. sp. JCM 8022, IAM 19107

Section

Clostridium sp. B6405 is an anaerobe, spore-forming, mesophilic bacterium that was isolated from bison rumen.

Gram-positive
spore-forming
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*
	Full Scientific Name (LPSN)	Clostridium Prazmowski 1880 (Approved Lists 1980)

	Synonym	"Tyzzerella"
	Synonym	"Pseudoclostridium"
	Synonym	"Lachnoclostridium"
	Synonym	Anaerobacter
	Synonym	"Inflabilis"

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.: #3281]

Culture medium

RCM MEDIUM (N2/CO2) (DSMZ Medium 634c)

[Ref.: #3281]

Culture medium growth

[Ref.: #3281]

Culture medium link

Medium recipe at MediaDive

[Ref.: #3281]

Culture medium composition

expand / minimize

[Ref.: #3281]

Culture medium

CLOSTRIDIUM CHARTATABIDUM MEDIUM (DSMZ Medium 523)

[Ref.: #3281]

Culture medium growth

[Ref.: #3281]

Culture medium link

Medium recipe at MediaDive

[Ref.: #3281]

Culture medium composition

expand / minimize

	Temperatures	Kind of temperature		Temperature
[Ref.: #3281]			growth	37 °C

[Ref.: #3281]

Temperature range

mesophilic

Information on physiology and metabolism Physiology and metabolism

[Ref.: #3281]	Oxygen tolerance	anaerobe
[Ref.: #69480]	Oxygen tolerance	anaerobe Confidence in %99.726

[Ref.: #69481]	Ability of spore formation	yes Confidence in %98
[Ref.: #69480]	Ability of spore formation	yes Confidence in %99.998

	Pathway	Enzyme coverage	Annotated reactions
	Pathway annotation	Computationally determined by
[Ref.: #66794]	cellulose degradation	100	5 of 5
[Ref.: #66794]	adipate degradation	100	2 of 2
[Ref.: #66794]	L-lactaldehyde degradation	100	3 of 3
[Ref.: #66794]	C4 and CAM-carbon fixation	100	8 of 8
[Ref.: #66794]	gluconeogenesis	100	8 of 8
[Ref.: #66794]	biotin biosynthesis	100	4 of 4
[Ref.: #66794]	palmitate biosynthesis	100	22 of 22
[Ref.: #66794]	ppGpp biosynthesis	100	4 of 4
[Ref.: #66794]	threonine metabolism	100	10 of 10
[Ref.: #66794]	cis-vaccenate biosynthesis	100	2 of 2
[Ref.: #66794]	anapleurotic synthesis of oxalacetate	100	1 of 1
[Ref.: #66794]	UDP-GlcNAc biosynthesis	100	3 of 3
[Ref.: #66794]	CDP-diacylglycerol biosynthesis	100	2 of 2
[Ref.: #66794]	folate polyglutamylation	100	1 of 1
[Ref.: #66794]	coenzyme A metabolism	100	4 of 4
[Ref.: #66794]	formaldehyde oxidation	100	3 of 3
[Ref.: #66794]	reductive acetyl coenzyme A pathway	100	7 of 7
[Ref.: #66794]	glycogen metabolism	100	5 of 5
[Ref.: #66794]	starch degradation	90	9 of 10
[Ref.: #66794]	chorismate metabolism	88.89	8 of 9
[Ref.: #66794]	phenylalanine metabolism	84.62	11 of 13
[Ref.: #66794]	vitamin B1 metabolism	84.62	11 of 13
[Ref.: #66794]	NAD metabolism	83.33	15 of 18
[Ref.: #66794]	peptidoglycan biosynthesis	80	12 of 15
[Ref.: #66794]	Entner Doudoroff pathway	80	8 of 10
[Ref.: #66794]	vitamin B12 metabolism	79.41	27 of 34
[Ref.: #66794]	glutamate and glutamine metabolism	78.57	22 of 28
[Ref.: #66794]	photosynthesis	78.57	11 of 14
[Ref.: #66794]	CO2 fixation in Crenarchaeota	77.78	7 of 9
[Ref.: #66794]	valine metabolism	77.78	7 of 9
[Ref.: #66794]	aspartate and asparagine metabolism	77.78	7 of 9
[Ref.: #66794]	pyrimidine metabolism	77.78	35 of 45
[Ref.: #66794]	glycolysis	76.47	13 of 17
[Ref.: #66794]	alanine metabolism	75.86	22 of 29
[Ref.: #66794]	acetate fermentation	75	3 of 4
[Ref.: #66794]	glycogen biosynthesis	75	3 of 4
[Ref.: #66794]	isoleucine metabolism	75	6 of 8
[Ref.: #66794]	flavin biosynthesis	73.33	11 of 15
[Ref.: #66794]	purine metabolism	70.21	66 of 94
[Ref.: #66794]	d-mannose degradation	66.67	6 of 9
[Ref.: #66794]	molybdenum cofactor biosynthesis	66.67	6 of 9
[Ref.: #66794]	nitrate assimilation	66.67	6 of 9
[Ref.: #66794]	acetoin degradation	66.67	2 of 3
[Ref.: #66794]	octane oxidation	66.67	2 of 3
[Ref.: #66794]	heme metabolism	64.29	9 of 14
[Ref.: #66794]	d-xylose degradation	63.64	7 of 11
[Ref.: #66794]	proline metabolism	63.64	7 of 11
[Ref.: #66794]	oxidative phosphorylation	62.64	57 of 91
[Ref.: #66794]	arginine metabolism	62.5	15 of 24
[Ref.: #66794]	histidine metabolism	62.07	18 of 29
[Ref.: #66794]	methionine metabolism	61.54	16 of 26
[Ref.: #66794]	methylglyoxal degradation	60	3 of 5
[Ref.: #66794]	glycine betaine biosynthesis	60	3 of 5
[Ref.: #66794]	hydrogen production	60	3 of 5
[Ref.: #66794]	factor 420 biosynthesis	60	3 of 5
[Ref.: #66794]	lipid metabolism	58.06	18 of 31
[Ref.: #66794]	tryptophan metabolism	57.89	22 of 38
[Ref.: #66794]	isoprenoid biosynthesis	57.69	15 of 26
[Ref.: #66794]	tetrahydrofolate metabolism	57.14	8 of 14
[Ref.: #66794]	glutathione metabolism	57.14	8 of 14
[Ref.: #66794]	ubiquinone biosynthesis	57.14	4 of 7
[Ref.: #66794]	citric acid cycle	57.14	8 of 14
[Ref.: #66794]	serine metabolism	55.56	5 of 9
[Ref.: #66794]	metabolism of disaccharids	54.55	6 of 11
[Ref.: #66794]	pentose phosphate pathway	54.55	6 of 11
[Ref.: #66794]	leucine metabolism	53.85	7 of 13
[Ref.: #66794]	lysine metabolism	52.38	22 of 42
[Ref.: #66794]	suberin monomers biosynthesis	50	1 of 2
[Ref.: #66794]	dTDPLrhamnose biosynthesis	50	4 of 8
[Ref.: #66794]	butanoate fermentation	50	2 of 4
[Ref.: #66794]	glycolate and glyoxylate degradation	50	3 of 6
[Ref.: #66794]	aminopropanol phosphate biosynthesis	50	1 of 2
[Ref.: #66794]	sulfopterin metabolism	50	2 of 4
[Ref.: #66794]	CMP-KDO biosynthesis	50	2 of 4
[Ref.: #66794]	ethanol fermentation	50	1 of 2
[Ref.: #66794]	phenylmercury acetate degradation	50	1 of 2
[Ref.: #66794]	non-pathway related	50	19 of 38
[Ref.: #66794]	ketogluconate metabolism	50	4 of 8
[Ref.: #66794]	cysteine metabolism	50	9 of 18
[Ref.: #66794]	polyamine pathway	47.83	11 of 23
[Ref.: #66794]	sulfate reduction	46.15	6 of 13
[Ref.: #66794]	urea cycle	46.15	6 of 13
[Ref.: #66794]	degradation of sugar acids	44	11 of 25
[Ref.: #66794]	cardiolipin biosynthesis	42.86	3 of 7
[Ref.: #66794]	propanol degradation	42.86	3 of 7
[Ref.: #66794]	tyrosine metabolism	42.86	6 of 14
[Ref.: #66794]	degradation of aromatic, nitrogen containing compounds	41.67	5 of 12
[Ref.: #66794]	glycine metabolism	40	4 of 10
[Ref.: #66794]	myo-inositol biosynthesis	40	4 of 10
[Ref.: #66794]	arachidonate biosynthesis	40	2 of 5
[Ref.: #66794]	propionate fermentation	40	4 of 10
[Ref.: #66794]	bacilysin biosynthesis	40	2 of 5
[Ref.: #66794]	coenzyme M biosynthesis	40	4 of 10
[Ref.: #66794]	degradation of pentoses	39.29	11 of 28
[Ref.: #66794]	degradation of hexoses	38.89	7 of 18
[Ref.: #66794]	degradation of sugar alcohols	37.5	6 of 16
[Ref.: #66794]	6-hydroxymethyl-dihydropterin diphosphate biosynthesis	37.5	3 of 8
[Ref.: #66794]	vitamin B6 metabolism	36.36	4 of 11
[Ref.: #66794]	arachidonic acid metabolism	33.33	6 of 18
[Ref.: #66794]	cyanate degradation	33.33	1 of 3
[Ref.: #66794]	4-hydroxymandelate degradation	33.33	3 of 9
[Ref.: #66794]	lipid A biosynthesis	33.33	3 of 9
[Ref.: #66794]	pantothenate biosynthesis	33.33	2 of 6
[Ref.: #66794]	selenocysteine biosynthesis	33.33	2 of 6
[Ref.: #66794]	enterobactin biosynthesis	33.33	1 of 3
[Ref.: #66794]	IAA biosynthesis	33.33	1 of 3
[Ref.: #66794]	androgen and estrogen metabolism	31.25	5 of 16
[Ref.: #66794]	phenylpropanoid biosynthesis	30.77	4 of 13
[Ref.: #66794]	phosphatidylethanolamine bioynthesis	30.77	4 of 13
[Ref.: #66794]	benzoyl-CoA degradation	28.57	2 of 7
[Ref.: #66794]	dolichyl-diphosphooligosaccharide biosynthesis	27.27	3 of 11
[Ref.: #66794]	cyclohexanol degradation	25	1 of 4
[Ref.: #66794]	lactate fermentation	25	1 of 4
[Ref.: #66794]	carotenoid biosynthesis	22.73	5 of 22
[Ref.: #66794]	ascorbate metabolism	22.73	5 of 22
		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.: #3281]	Sample type/isolated from	bison rumen
[Ref.: #3281]	Country	USA
[Ref.: #3281]	Country ISO 3 Code	USA
[Ref.: #3281]	Continent	North America
* marker position based on {}

Isolation sources categories

#Host	#Mammals	#Bovinae (Cow, Cattle)
#Host Body-Site	#Gastrointestinal tract	#Stomach

What are isolation sources categories?

[Ref.: #69479]

Global distribution of 16S sequence X76164 (>99% sequence identity) for Clostridium from Microbeatlas

Aquatic Samples	90
Soil Samples	174
Animal Samples	2910
Plant Samples	69
Total Samples	3243

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.: #3281]	Clostridium longisporum 16S rRNA gene, strain DSM 8431	X76164	1464	ENA	1523 tax ID

Genome sequence information:

	Sequence accession description	Seq. accession number	Assembly level	Sequence database	Associated NCBI tax ID
[Ref.: #66792]	Clostridium sp. DSM 8431	GCA_900116755	scaffold	GenBank	1761781 tax ID	*
[Ref.: #66792]	Clostridium sp. DSM 8431	1761781.3	wgs	PATRIC	1761781 tax ID	*
[Ref.: #66792]	Clostridium sp. DSM 8431	2623621014	draft	JGI IMG/M	1761781 tax ID	*

[Ref.: #3281]

GC-content

33 mol%

Buoyant density centrifugation (BD)

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 sp. DSM 8431 DSM 8431 NCBI: GCA_900116755.1
[Ref.: #69481]	spore-forming	yes	98	no

	Trait	Prediction	Confidence in %	In training data
	Predictions from Diaspora project based on: Clostridium sp. DSM 8431 DSM 8431 NCBI: GCA_900116755.1
[Ref.: #69480]	motile	yes	81.29	no
[Ref.: #69480]	flagellated	yes	62.209	no
[Ref.: #69480]	gram-positive	yes	83.832	no
[Ref.: #69480]	anaerobic	yes	98.555	no
[Ref.: #69480]	aerobic	no	97.61	no
[Ref.: #69480]	halophile	no	90.584	no
[Ref.: #69480]	spore-forming	yes	93.568	no
[Ref.: #69480]	glucose-ferment	yes	74.234	no
[Ref.: #69480]	thermophile	no	90.732	yes
[Ref.: #69480]	glucose-util	yes	89.056	no

Availability in culture collections External links

[Ref.: #3281]

Culture collection no.

DSM 8431, ATCC 49440

[Ref.: #72214]

SI-ID 48479

Literature:

Topic	Title	Authors	Journal	DOI	Year
Enzymology	Cloning of an endo-(1-->4)-beta-glucanase gene, celA, from the rumen bacterium Clostridium sp. ('C. longisporum') and characterization of its product, CelA, in Escherichia coli.	Mittendorf V, Thomson JA	J Gen Microbiol	10.1099/00221287-139-12-3233	1993	*

References

#3281

Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 8431

#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 )

#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 )

#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 )

#72214

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-ID48479.1 )

* These data were automatically processed and therefore are not curated

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Clostridium sp. DSM 8431 DSM 8431

Clostridium sp. DSM 8431 DSM 8431

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