Name: Clostridium amylolyticum SW408
Creator: BacDive
License: https://creativecommons.org/licenses/by/4.0/

Strain identifier

BacDive ID: 2850

Type strain:

Species: Clostridium amylolyticum

Strain Designation: SW408

Culture col. no.: DSM 21864, AS 1.5069, CGMCC 1.5069, JCM 14823, KCTC 15216

Strain history: <- DSM <- JCM/RIKEN <- X Dong, Graduate School, CAS, Beijing, China, SW408

NCBI tax ID(s): 1121299 (strain), 1121298 (species)

SI-ID 402220

DSM 21864

Special Collections

Section

Clostridium amylolyticum SW408 is an anaerobe, spore-forming, Gram-positive bacterium that was isolated from H₂-producing upflow anaerobic sludge blanket reactor.

Gram-positive
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	*Clostridiaceae*
	Genus	*Clostridium*
	Species	**Clostridium amylolyticum**
	Full Scientific Name (LPSN)	Clostridium amylolyticum Song and Dong 2008

Information on morphological and physiological properties Morphology

[Ref.: #32527]	Gram stain	positive
[Ref.: #67771]	Gram stain	positive

[Ref.: #32527]	Cell length	2-7.5 µm

[Ref.: #32527]	Cell width	0.5-0.7 µm

[Ref.: #32527]	Cell shape	rod-shaped
[Ref.: #67771]	Cell shape	rod-shaped

[Ref.: #32527]	Motility	yes
[Ref.: #67771]	Motility	yes

[Ref.: #67771]	Flagellum arrangement	peritrichous

[Ref.: #32527]

Pigment production

yes

Information on culture and growth conditions Culture and growth conditions

[Ref.: #16000]

Culture medium

CHOPPED MEAT MEDIUM WITH CARBOHYDRATES (DSMZ Medium 110)

[Ref.: #16000]

Culture medium growth

[Ref.: #16000]

Culture medium link

Medium recipe at MediaDive

[Ref.: #16000]

Culture medium composition

expand / minimize

		Temperature
[Ref.: #16000]	growth	37 °C
[Ref.: #32527]	growth	25-45 °C
[Ref.: #32527]	optimum	37 °C
[Ref.: #67770]	growth	37 °C
[Ref.: #67771]	growth	37 °C

	pH	Kind of pH		pH
[Ref.: #32527]			optimum	7
[Ref.: #32527]			growth	04-09

Information on physiology and metabolism Physiology and metabolism

[Ref.: #16000]	Oxygen tolerance	anaerobe
[Ref.: #32527]	Oxygen tolerance	anaerobe
[Ref.: #67771]	Oxygen tolerance	anaerobe

[Ref.: #32527]	Ability of spore formation	yes
[Ref.: #69481]	Ability of spore formation	yes Confidence in %100

[Ref.: #32527]

Observation

aggregates in chains

	Metabolite	Utilization activity	Kind of utilization tested
[Ref.: #32527]	cellobiose ChEBI	+	carbon source
[Ref.: #32527]	esculin ChEBI	+	hydrolysis
[Ref.: #32527]	fructose ChEBI	+	carbon source
[Ref.: #32527]	galactose ChEBI	+	carbon source
[Ref.: #32527]	glucose ChEBI	+	carbon source
[Ref.: #32527]	lactose ChEBI	+	carbon source
[Ref.: #32527]	maltose ChEBI	+	carbon source
[Ref.: #32527]	mannitol ChEBI	+	carbon source
[Ref.: #32527]	mannose ChEBI	+	carbon source
[Ref.: #32527]	ribose ChEBI	+	carbon source
[Ref.: #32527]	sucrose ChEBI	+	carbon source
[Ref.: #32527]	trehalose ChEBI	+	carbon source
	Only first 10 entries are displayed. Click here to see all.

	Pathway	Enzyme coverage	Annotated reactions
	Pathway annotation	Computationally determined by
[Ref.: #66794]	cis-vaccenate biosynthesis	100	2 of 2
[Ref.: #66794]	metabolism of amino sugars and derivatives	100	5 of 5
[Ref.: #66794]	starch degradation	100	10 of 10
[Ref.: #66794]	gluconeogenesis	100	8 of 8
[Ref.: #66794]	C4 and CAM-carbon fixation	100	8 of 8
[Ref.: #66794]	ppGpp biosynthesis	100	4 of 4
[Ref.: #66794]	L-lactaldehyde degradation	100	3 of 3
[Ref.: #66794]	palmitate biosynthesis	100	22 of 22
[Ref.: #66794]	aspartate and asparagine metabolism	100	9 of 9
[Ref.: #66794]	methylglyoxal degradation	100	5 of 5
[Ref.: #66794]	formaldehyde oxidation	100	3 of 3
[Ref.: #66794]	anapleurotic synthesis of oxalacetate	100	1 of 1
[Ref.: #66794]	suberin monomers biosynthesis	100	2 of 2
[Ref.: #66794]	folate polyglutamylation	100	1 of 1
[Ref.: #66794]	adipate degradation	100	2 of 2
[Ref.: #66794]	UDP-GlcNAc biosynthesis	100	3 of 3
[Ref.: #66794]	CDP-diacylglycerol biosynthesis	100	2 of 2
[Ref.: #66794]	coenzyme A metabolism	100	4 of 4
[Ref.: #66794]	vitamin B1 metabolism	92.31	12 of 13
[Ref.: #66794]	chorismate metabolism	88.89	8 of 9
[Ref.: #66794]	propanol degradation	85.71	6 of 7
[Ref.: #66794]	NAD metabolism	83.33	15 of 18
[Ref.: #66794]	pyrimidine metabolism	82.22	37 of 45
[Ref.: #66794]	glutamate and glutamine metabolism	82.14	23 of 28
[Ref.: #66794]	glycogen metabolism	80	4 of 5
[Ref.: #66794]	threonine metabolism	80	8 of 10
[Ref.: #66794]	hydrogen production	80	4 of 5
[Ref.: #66794]	peptidoglycan biosynthesis	80	12 of 15
[Ref.: #66794]	glycine betaine biosynthesis	80	4 of 5
[Ref.: #66794]	cellulose degradation	80	4 of 5
[Ref.: #66794]	purine metabolism	78.72	74 of 94
[Ref.: #66794]	photosynthesis	78.57	11 of 14
[Ref.: #66794]	CO2 fixation in Crenarchaeota	77.78	7 of 9
[Ref.: #66794]	serine metabolism	77.78	7 of 9
[Ref.: #66794]	d-mannose degradation	77.78	7 of 9
[Ref.: #66794]	urea cycle	76.92	10 of 13
[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]	butanoate fermentation	75	3 of 4
[Ref.: #66794]	glycogen biosynthesis	75	3 of 4
[Ref.: #66794]	biotin biosynthesis	75	3 of 4
[Ref.: #66794]	pentose phosphate pathway	72.73	8 of 11
[Ref.: #66794]	cardiolipin biosynthesis	71.43	5 of 7
[Ref.: #66794]	ubiquinone biosynthesis	71.43	5 of 7
[Ref.: #66794]	Entner Doudoroff pathway	70	7 of 10
[Ref.: #66794]	phenylalanine metabolism	69.23	9 of 13
[Ref.: #66794]	degradation of sugar alcohols	68.75	11 of 16
[Ref.: #66794]	methane metabolism	66.67	2 of 3
[Ref.: #66794]	acetoin degradation	66.67	2 of 3
[Ref.: #66794]	cyanate degradation	66.67	2 of 3
[Ref.: #66794]	octane oxidation	66.67	2 of 3
[Ref.: #66794]	selenocysteine biosynthesis	66.67	4 of 6
[Ref.: #66794]	flavin biosynthesis	66.67	10 of 15
[Ref.: #66794]	degradation of hexoses	66.67	12 of 18
[Ref.: #66794]	oxidative phosphorylation	65.93	60 of 91
[Ref.: #66794]	isoprenoid biosynthesis	65.38	17 of 26
[Ref.: #66794]	degradation of pentoses	64.29	18 of 28
[Ref.: #66794]	glutathione metabolism	64.29	9 of 14
[Ref.: #66794]	vitamin B6 metabolism	63.64	7 of 11
[Ref.: #66794]	metabolism of disaccharids	63.64	7 of 11
[Ref.: #66794]	d-xylose degradation	63.64	7 of 11
[Ref.: #66794]	non-pathway related	63.16	24 of 38
[Ref.: #66794]	ketogluconate metabolism	62.5	5 of 8
[Ref.: #66794]	dTDPLrhamnose biosynthesis	62.5	5 of 8
[Ref.: #66794]	isoleucine metabolism	62.5	5 of 8
[Ref.: #66794]	methionine metabolism	61.54	16 of 26
[Ref.: #66794]	phenylacetate degradation (aerobic)	60	3 of 5
[Ref.: #66794]	myo-inositol biosynthesis	60	6 of 10
[Ref.: #66794]	factor 420 biosynthesis	60	3 of 5
[Ref.: #66794]	lipid metabolism	58.06	18 of 31
[Ref.: #66794]	citric acid cycle	57.14	8 of 14
[Ref.: #66794]	reductive acetyl coenzyme A pathway	57.14	4 of 7
[Ref.: #66794]	molybdenum cofactor biosynthesis	55.56	5 of 9
[Ref.: #66794]	lysine metabolism	54.76	23 of 42
[Ref.: #66794]	dolichol and dolichyl phosphate biosynthesis	50	1 of 2
[Ref.: #66794]	cysteine metabolism	50	9 of 18
[Ref.: #66794]	ethanol fermentation	50	1 of 2
[Ref.: #66794]	aminopropanol phosphate biosynthesis	50	1 of 2
[Ref.: #66794]	propionate fermentation	50	5 of 10
[Ref.: #66794]	vitamin E metabolism	50	2 of 4
[Ref.: #66794]	CMP-KDO biosynthesis	50	2 of 4
[Ref.: #66794]	arginine metabolism	50	12 of 24
[Ref.: #66794]	sulfopterin metabolism	50	2 of 4
[Ref.: #66794]	degradation of aromatic, nitrogen containing compounds	50	6 of 12
[Ref.: #66794]	ribulose monophosphate pathway	50	1 of 2
[Ref.: #66794]	glycine metabolism	50	5 of 10
[Ref.: #66794]	glycolate and glyoxylate degradation	50	3 of 6
[Ref.: #66794]	phosphatidylethanolamine bioynthesis	46.15	6 of 13
[Ref.: #66794]	histidine metabolism	44.83	13 of 29
[Ref.: #66794]	tryptophan metabolism	44.74	17 of 38
[Ref.: #66794]	polyamine pathway	43.48	10 of 23
[Ref.: #66794]	mevalonate metabolism	42.86	3 of 7
[Ref.: #66794]	tetrahydrofolate metabolism	42.86	6 of 14
[Ref.: #66794]	vitamin B12 metabolism	41.18	14 of 34
[Ref.: #66794]	ascorbate metabolism	40.91	9 of 22
[Ref.: #66794]	ethylmalonyl-CoA pathway	40	2 of 5
[Ref.: #66794]	3-chlorocatechol degradation	40	2 of 5
[Ref.: #66794]	coenzyme M biosynthesis	40	4 of 10
[Ref.: #66794]	lipoate biosynthesis	40	2 of 5
[Ref.: #66794]	vitamin K metabolism	40	2 of 5
[Ref.: #66794]	O-antigen biosynthesis	40	2 of 5
[Ref.: #66794]	bacilysin biosynthesis	40	2 of 5
[Ref.: #66794]	arachidonate biosynthesis	40	2 of 5
[Ref.: #66794]	arachidonic acid metabolism	38.89	7 of 18
[Ref.: #66794]	phenylpropanoid biosynthesis	38.46	5 of 13
[Ref.: #66794]	6-hydroxymethyl-dihydropterin diphosphate biosynthesis	37.5	3 of 8
[Ref.: #66794]	degradation of sugar acids	36	9 of 25
[Ref.: #66794]	3-phenylpropionate degradation	33.33	5 of 15
[Ref.: #66794]	valine metabolism	33.33	3 of 9
[Ref.: #66794]	lipid A biosynthesis	33.33	3 of 9
[Ref.: #66794]	nitrate assimilation	33.33	3 of 9
[Ref.: #66794]	IAA biosynthesis	33.33	1 of 3
[Ref.: #66794]	acetyl CoA biosynthesis	33.33	1 of 3
[Ref.: #66794]	enterobactin biosynthesis	33.33	1 of 3
[Ref.: #66794]	androgen and estrogen metabolism	31.25	5 of 16
[Ref.: #66794]	ginsenoside metabolism	31.25	5 of 16
[Ref.: #66794]	leucine metabolism	30.77	4 of 13
[Ref.: #66794]	sulfate reduction	30.77	4 of 13
[Ref.: #66794]	tyrosine metabolism	28.57	4 of 14
[Ref.: #66794]	benzoyl-CoA degradation	28.57	2 of 7
[Ref.: #66794]	dolichyl-diphosphooligosaccharide biosynthesis	27.27	3 of 11
[Ref.: #66794]	proline metabolism	27.27	3 of 11
[Ref.: #66794]	toluene degradation	25	1 of 4
[Ref.: #66794]	cyclohexanol degradation	25	1 of 4
[Ref.: #66794]	lactate fermentation	25	1 of 4
[Ref.: #66794]	methanogenesis from CO2	25	3 of 12
[Ref.: #66794]	4-hydroxymandelate degradation	22.22	2 of 9
		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.: #16000]	Sample type/isolated from	H₂-producing upflow anaerobic sludge blanket reactor
[Ref.: #16000]	Country	China
[Ref.: #16000]	Country ISO 3 Code	CHN
[Ref.: #16000]	Continent	Asia

[Ref.: #67770]	Sample type/isolated from	Laboratory-scale H₂-producing upflow anaerobic sludge blanket reactor

[Ref.: #67771]	Sample type/isolated from	From laboratory-scale H_2_-producing upflow anaerobic sludge blanket reactor
[Ref.: #67771]	Country	China
[Ref.: #67771]	Country ISO 3 Code	CHN
[Ref.: #67771]	Continent	Asia
* marker position based on {}

Isolation sources categories

#Engineered	#Bioreactor	-
#Environmental	#Terrestrial	#Mud (Sludge)
#Condition	#Anoxic (anaerobic)	-

What are isolation sources categories?

[Ref.: #69479]

Global distribution of 16S sequence NR_044386 (>99% sequence identity) for Clostridium amylolyticum subclade from Microbeatlas

Aquatic Samples	119
Soil Samples	141
Animal Samples	367
Plant Samples	21
Total Samples	648

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

[Ref.: #16000]

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.: #16000]	Clostridium amylolyticum strain SW408 16S ribosomal RNA gene, partial sequence	EU037903	1505	GenBank ENA	1121298 tax ID
[Ref.: #67771]	Clostridium amylolyticum strain SW408 16S ribosomal RNA, partial sequence	NR_044386	1505	GenBank ENA	1121298 tax ID

Genome sequence information:

	Sequence accession description	Seq. accession number	Assembly level	Sequence database	Associated NCBI tax ID
[Ref.: #67771]	Clostridium amylolyticum DSM 21864	GCA_900142075	scaffold	GenBank ENA	1121298 tax ID
[Ref.: #66792]	Clostridium amylolyticum strain DSM 21864	1121298.3	wgs	PATRIC	1121298 tax ID	*
[Ref.: #66792]	Clostridium amylolyticum DSM 21864	2703719061	draft	JGI IMG/M	1121298 tax ID	*

[Ref.: #16000]	GC-content	33.1 mol%	thermal denaturation, midpoint method (Tm)
[Ref.: #32527]	GC-content	33.1 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: Clostridium amylolyticum DSM 21864 NCBI: GCA_900142075.1
[Ref.: #69481]	spore-forming	spore-formingⓘ	yes	100	no

	Trait	Model	Prediction	Confidence in %	In training data
	Predictions from Diaspora project based on: Clostridium amylolyticum strain DSM 21864 PATRIC: 1121298.3
[Ref.: #69480]	gram-positive	gram-positiveⓘ	yes	62.69	no
[Ref.: #69480]	anaerobic	anaerobicⓘ	yes	82.428	yes
[Ref.: #69480]	spore-forming	spore-formingⓘ	yes	83.02	yes
[Ref.: #69480]	aerobic	aerobicⓘ	no	88.856	yes
[Ref.: #69480]	thermophilic	thermophileⓘ	no	88.349	no
[Ref.: #69480]	flagellated	motile2+ⓘ	yes	74.707	no

Availability in culture collections External links

[Ref.: #16000]

Culture collection no.

DSM 21864, AS 1.5069, CGMCC 1.5069, JCM 14823, KCTC 15216

[Ref.: #72374]

SI-ID 402220

Literature:

Topic	Title	Authors	Journal	DOI	Year
Phylogeny	Clostridium swellfunianum sp. nov., a novel anaerobic bacterium isolated from the pit mud of Chinese Luzhou-flavor liquor production.	Liu C, Huang D, Liu L, Zhang J, Deng Y, Chen L, Zhang W, Wu Z, Fan A, Lai D, Dai L	Antonie Van Leeuwenhoek	10.1007/s10482-014-0251-z	2014	*
Phylogeny	Clostridium amylolyticum sp. nov., isolated from H2-producing UASB granules.	Song L, Dong X	Int J Syst Evol Microbiol	10.1099/ijs.0.65635-0	2008	*

References

#16000

Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 21864

#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 )

#32527

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 #28745 (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;
#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 .

#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 )

#72374

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-ID402220.1 )

#28745

IJSEM 2132 2008 ( DOI 10.1099/ijs.0.65635-0 , PubMed 18768618 )

* These data were automatically processed and therefore are not curated

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Clostridium amylolyticum DSM 21864

Clostridium amylolyticum strain DSM 21864

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