Clostridium amylolyticum (DSM 21864, AS 1.5069, CGMCC 1.5069)

Name: Clostridium amylolyticum (DSM 21864, AS 1.5069, CGMCC 1.5069)
Creator: BacDive
License: http://creativecommons.org/licenses/by/4.0/

BacDive ID 2850

Type strain

Strain Designation SW408

Culture col. no. DSM 21864 AS 1.5069 CGMCC 1.5069 JCM 14823 KCTC 15216 1 more

NCBI tax ID(s) 1121299 1121298

Special Collections DSMZ JCM KCTC Literature strains

History DSMZ <- JCM/RIKEN <- X. Dong, Graduate School, CAS, Beijing, China; SW408 JCM <-- X. Dong SW408. KCTC <- DSM <- JCM/RIKEN <- X Dong, Graduate School, CAS, Beijing, China, SW408

Links

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

spore-forming Gram-positive motile rod-shaped anaerobe genome sequence 16S sequence Bacteria

Name and taxonomic classification

SI-ID 402220

KCTC 15216,JCM 14823,DSM 21864

@ref 20215

Last LPSN update 2026-05-29 08:25:34

Domain Bacteria

Phylum Bacillota

Class Clostridia

Order Eubacteriales

Family Clostridiaceae

Genus Clostridium

Species Clostridium amylolyticum

Full scientific name Clostridium amylolyticum Song and Dong 2008

Morphology

Cell morphology

@ref	Gram stain	Cell length	Cell width	Cell shape	Flagellum arrangement
32527	positive	2-7.5 µm	0.5-0.7 µm	rod-shaped
67771				rod-shaped	peritrichous
67771	positive

Pigmentation

32527

Productionyes

Culture and growth conditions

Culture medium

@ref	Name	Growth	Medium link	Composition
16000	CHOPPED MEAT MEDIUM WITH CARBOHYDRATES (DSMZ Medium 110)		Medium recipe at MediaDive	Name: CHOPPED MEAT MEDIUM WITH CARBOHYDRATES (DSMZ Medium 110) Composition: Ground beef 500.0 g/l Casitone 30.0 g/l Agar 15.0 g/l K2HPO4 5.0 g/l Yeast extract 5.0 g/l D-Glucose 4.0 g/l Starch 1.0 g/l Maltose 1.0 g/l Cellobiose 1.0 g/l L-Cysteine HCl 0.5 g/l Ethanol 0.19 g/l Vitamin K3 0.05 g/l Hemin 0.005 g/l Sodium resazurin 0.0005 g/l Vitamin K1 NaOH Distilled water

Culture temp

@ref	Growth	Type	Temperature (°C)
16000	positive	growth	37
32527	positive	growth	25-45
32527	positive	optimum	37
67770	positive	growth	37
67771	positive	growth	37

Culture pH

@ref	Ability	Type	PH	PH range
32527	positive	optimum	7
32527	positive	growth	04-09	alkaliphile

Physiology and metabolism

Oxygen tolerance

@ref	Oxygen tolerance	Confidence
16000	anaerobe
32527	anaerobe
67771	anaerobe
125439	facultative anaerobe	96.794

Spore formation

32527

Spore formationyes

Observation

32527

Observationaggregates in chains

Metabolite utilization

@ref	Chebi-ID	Metabolite	Utilization activity	Kind of utilization tested
32527	17057 ChEBI	cellobiose	+	carbon source
32527	4853 ChEBI	esculin	+	hydrolysis
32527	28757 ChEBI	fructose	+	carbon source
32527	28260 ChEBI	galactose	+	carbon source
32527	17234 ChEBI	glucose	+	carbon source
32527	17716 ChEBI	lactose	+	carbon source
32527	17306 ChEBI	maltose	+	carbon source
32527	29864 ChEBI	mannitol	+	carbon source
32527	37684 ChEBI	mannose	+	carbon source
32527	33942 ChEBI	ribose	+	carbon source
32527	17992 ChEBI	sucrose	+	carbon source
32527	27082 ChEBI	trehalose	+	carbon source

Pathway annotation

Computationally determined by

@ref	pathway	enzyme coverage	annotated reactions
66794	cis-vaccenate biosynthesis	100	2 of 2
66794	metabolism of amino sugars and derivatives	100	5 of 5
66794	starch degradation	100	10 of 10
66794	gluconeogenesis	100	8 of 8
66794	C4 and CAM-carbon fixation	100	8 of 8
66794	ppGpp biosynthesis	100	4 of 4
66794	L-lactaldehyde degradation	100	3 of 3
66794	palmitate biosynthesis	100	22 of 22
66794	aspartate and asparagine metabolism	100	9 of 9
66794	methylglyoxal degradation	100	5 of 5
66794	formaldehyde oxidation	100	3 of 3
66794	anapleurotic synthesis of oxalacetate	100	1 of 1
66794	suberin monomers biosynthesis	100	2 of 2
66794	folate polyglutamylation	100	1 of 1
66794	adipate degradation	100	2 of 2
66794	UDP-GlcNAc biosynthesis	100	3 of 3
66794	CDP-diacylglycerol biosynthesis	100	2 of 2
66794	coenzyme A metabolism	100	4 of 4
66794	vitamin B1 metabolism	92.31	12 of 13
66794	chorismate metabolism	88.89	8 of 9
66794	propanol degradation	85.71	6 of 7
66794	NAD metabolism	83.33	15 of 18
66794	pyrimidine metabolism	82.22	37 of 45
66794	glutamate and glutamine metabolism	82.14	23 of 28
66794	glycogen metabolism	80	4 of 5
66794	threonine metabolism	80	8 of 10
66794	hydrogen production	80	4 of 5
66794	peptidoglycan biosynthesis	80	12 of 15
66794	glycine betaine biosynthesis	80	4 of 5
66794	cellulose degradation	80	4 of 5
66794	purine metabolism	78.72	74 of 94
66794	photosynthesis	78.57	11 of 14
66794	CO2 fixation in Crenarchaeota	77.78	7 of 9
66794	serine metabolism	77.78	7 of 9
66794	d-mannose degradation	77.78	7 of 9
66794	urea cycle	76.92	10 of 13
66794	glycolysis	76.47	13 of 17
66794	alanine metabolism	75.86	22 of 29
66794	acetate fermentation	75	3 of 4
66794	butanoate fermentation	75	3 of 4
66794	glycogen biosynthesis	75	3 of 4
66794	biotin biosynthesis	75	3 of 4
66794	pentose phosphate pathway	72.73	8 of 11
66794	cardiolipin biosynthesis	71.43	5 of 7
66794	ubiquinone biosynthesis	71.43	5 of 7
66794	Entner Doudoroff pathway	70	7 of 10
66794	phenylalanine metabolism	69.23	9 of 13
66794	degradation of sugar alcohols	68.75	11 of 16
66794	methane metabolism	66.67	2 of 3
66794	acetoin degradation	66.67	2 of 3
66794	cyanate degradation	66.67	2 of 3
66794	octane oxidation	66.67	2 of 3
66794	selenocysteine biosynthesis	66.67	4 of 6
66794	flavin biosynthesis	66.67	10 of 15
66794	degradation of hexoses	66.67	12 of 18
66794	oxidative phosphorylation	65.93	60 of 91
66794	isoprenoid biosynthesis	65.38	17 of 26
66794	degradation of pentoses	64.29	18 of 28
66794	glutathione metabolism	64.29	9 of 14
66794	vitamin B6 metabolism	63.64	7 of 11
66794	metabolism of disaccharids	63.64	7 of 11
66794	d-xylose degradation	63.64	7 of 11
66794	non-pathway related	63.16	24 of 38
66794	ketogluconate metabolism	62.5	5 of 8
66794	dTDPLrhamnose biosynthesis	62.5	5 of 8
66794	isoleucine metabolism	62.5	5 of 8
66794	methionine metabolism	61.54	16 of 26
66794	phenylacetate degradation (aerobic)	60	3 of 5
66794	myo-inositol biosynthesis	60	6 of 10
66794	factor 420 biosynthesis	60	3 of 5
66794	lipid metabolism	58.06	18 of 31
66794	citric acid cycle	57.14	8 of 14
66794	reductive acetyl coenzyme A pathway	57.14	4 of 7
66794	molybdenum cofactor biosynthesis	55.56	5 of 9
66794	lysine metabolism	54.76	23 of 42
66794	dolichol and dolichyl phosphate biosynthesis	50	1 of 2
66794	cysteine metabolism	50	9 of 18
66794	ethanol fermentation	50	1 of 2
66794	aminopropanol phosphate biosynthesis	50	1 of 2
66794	propionate fermentation	50	5 of 10
66794	vitamin E metabolism	50	2 of 4
66794	CMP-KDO biosynthesis	50	2 of 4
66794	arginine metabolism	50	12 of 24
66794	sulfopterin metabolism	50	2 of 4
66794	degradation of aromatic, nitrogen containing compounds	50	6 of 12
66794	ribulose monophosphate pathway	50	1 of 2
66794	glycine metabolism	50	5 of 10
66794	glycolate and glyoxylate degradation	50	3 of 6
66794	phosphatidylethanolamine bioynthesis	46.15	6 of 13
66794	histidine metabolism	44.83	13 of 29
66794	tryptophan metabolism	44.74	17 of 38
66794	polyamine pathway	43.48	10 of 23
66794	mevalonate metabolism	42.86	3 of 7
66794	tetrahydrofolate metabolism	42.86	6 of 14
66794	vitamin B12 metabolism	41.18	14 of 34
66794	ascorbate metabolism	40.91	9 of 22
66794	ethylmalonyl-CoA pathway	40	2 of 5
66794	3-chlorocatechol degradation	40	2 of 5
66794	coenzyme M biosynthesis	40	4 of 10
66794	lipoate biosynthesis	40	2 of 5
66794	vitamin K metabolism	40	2 of 5
66794	O-antigen biosynthesis	40	2 of 5
66794	bacilysin biosynthesis	40	2 of 5
66794	arachidonate biosynthesis	40	2 of 5
66794	arachidonic acid metabolism	38.89	7 of 18
66794	phenylpropanoid biosynthesis	38.46	5 of 13
66794	6-hydroxymethyl-dihydropterin diphosphate biosynthesis	37.5	3 of 8
66794	degradation of sugar acids	36	9 of 25
66794	3-phenylpropionate degradation	33.33	5 of 15
66794	valine metabolism	33.33	3 of 9
66794	lipid A biosynthesis	33.33	3 of 9
66794	nitrate assimilation	33.33	3 of 9
66794	IAA biosynthesis	33.33	1 of 3
66794	acetyl CoA biosynthesis	33.33	1 of 3
66794	enterobactin biosynthesis	33.33	1 of 3
66794	androgen and estrogen metabolism	31.25	5 of 16
66794	ginsenoside metabolism	31.25	5 of 16
66794	leucine metabolism	30.77	4 of 13
66794	sulfate reduction	30.77	4 of 13
66794	tyrosine metabolism	28.57	4 of 14
66794	benzoyl-CoA degradation	28.57	2 of 7
66794	dolichyl-diphosphooligosaccharide biosynthesis	27.27	3 of 11
66794	proline metabolism	27.27	3 of 11
66794	toluene degradation	25	1 of 4
66794	cyclohexanol degradation	25	1 of 4
66794	lactate fermentation	25	1 of 4
66794	methanogenesis from CO2	25	3 of 12
66794	4-hydroxymandelate degradation	22.22	2 of 9

Isolation, sampling and environmental information

Isolation source categories

Cat1	Cat2	Cat3
#Engineered	#Bioreactor	-
#Environmental	#Terrestrial	#Mud (Sludge)
#Condition	#Anoxic (anaerobic)	-

Isolation

@ref	Sample type	Country	Country ISO 3 Code	Continent
16000	H₂-producing upflow anaerobic sludge blanket reactor	China	CHN	Asia
67770	Laboratory-scale H₂-producing upflow anaerobic sludge blanket reactor
67771	From laboratory-scale H_2_-producing upflow anaerobic sludge blanket reactor	China	CHN	Asia

Taxonmaps

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

Interaction and safety

Risk assessment

@ref	Biosafety level	Biosafety level comment
16000	1	Risk group (German classification) According to TRBA 466

Sequence information

Genome sequences

@ref	Description	Assembly level	INSDC accession	BV-BRC accession	IMG accession	NCBI tax ID	Score
67771	IMG-taxon 2703719061 annotated assembly for Clostridium amylolyticum DSM 21864	scaffold	GCA_900142075	1121298.3	2703719061	1121298	72.89

16S sequences

@ref	Description	Accession	Length	Database	NCBI tax ID
16000	Clostridium amylolyticum strain SW408 16S ribosomal RNA gene, partial sequence	EU037903	1505		1121298
67771	Clostridium amylolyticum strain SW408 16S ribosomal RNA, partial sequence	NR_044386	1505		1121298

GC content

@ref	GC-content (mol%)	Method
16000	33.1	thermal denaturation, midpoint method (Tm)
32527	33.1

Genome-based predictions

Predictions

Predictions from Deep Learning for Genome Sequence Data. R package version 0.3.1 based on: IMG-taxon 2703719061 annotated assembly for Clostridium amylolyticum DSM 21864
BV-BRC: 1121298.3

@ref	Trait	Model	Prediction	Confidence in %	In training data
125439	oxygen_tolerance	BacteriaNetⓘ	facultative anaerobe	96.79	no
125439	gram_stain	BacteriaNetⓘ	variable	52.21	no
125439	motility	BacteriaNetⓘ	yes	75.12	no
125439	spore_formation	BacteriaNetⓘ	yes	75.48	no

Predictions from bacterial phenotypic traits through improved machine learning using high-quality, curated datasets based on: Clostridium amylolyticum strain DSM 21864
PATRIC: 1121298.3

@ref	Trait	Model	Prediction	Confidence in %	In training data
125438	gram-positive	gram-positiveⓘ	yes	62.69	no
125438	anaerobic	anaerobicⓘ	yes	82.43	yes
125438	spore-forming	spore-formingⓘ	yes	83.02	yes
125438	aerobic	aerobicⓘ	no	88.86	yes
125438	thermophilic	thermophileⓘ	no	88.35	no
125438	flagellated	motile2+ⓘ	yes	74.71	no

Literature

Topic	Title	Authors	Journal	DOI	Year
Metabolism	Implementation of a biotechnological process for vat dyeing with woad.	Osimani A, Aquilanti L, Baldini G, Silvestri G, Butta A, Clementi F.	J Ind Microbiol Biotechnol	10.1007/s10295-012-1139-4	2012
	Heterologous 1,3-Propanediol Production Using Different Recombinant Clostridium beijerinckii DSM 6423 Strains.	Schoch T, Baur T, Kunz J, Stoferle S, Durre P.	Microorganisms	10.3390/microorganisms11030784	2023
Phylogeny	Characterization of bacterial communities in feces from healthy elderly volunteers and hospitalized elderly patients by using real-time PCR and effects of antibiotic treatment on the fecal microbiota.	Bartosch S, Fite A, Macfarlane GT, McMurdo ME.	Appl Environ Microbiol	10.1128/aem.70.6.3575-3581.2004	2004
Phylogeny	Clostridium lamae sp. nov., a novel bacterium isolated from the fresh feces of alpaca.	Li X, Li M, Shi W, Li X, Xiang Z, Su L.	Antonie Van Leeuwenhoek	10.1007/s10482-024-01931-7	2024
Phylogeny	Clostridium composti sp. nov., a new anaerobic bacteria isolated from compost.	Shin Y, Paek J, Son AY, Kim H, Kook JK, Paek WK, Chang YH.	Int J Syst Evol Microbiol	10.1099/ijsem.0.003074	2018
Phylogeny	Clostridium huakuii sp. nov., an anaerobic, acetogenic bacterium isolated from methanogenic consortia.	Ruan Z, Wang Y, Zhang C, Song J, Zhai Y, Zhuang Y, Wang H, Chen X, Li Y, Zhao B, Zhao B.	Int J Syst Evol Microbiol	10.1099/ijs.0.062711-0	2014
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 )
#28745	IJSEM 2132 2008 ( DOI 10.1099/ijs.0.65635-0 , PubMed 18768618 )
#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
#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 .
#125438	Julia Koblitz, Lorenz Christian Reimer, Rüdiger Pukall, Jörg Overmann: Predicting bacterial phenotypic traits through improved machine learning using high-quality, curated datasets. 2024 ( DOI 10.1101/2024.08.12.607695 )
#125439	Philipp Münch, René Mreches, Martin Binder, Hüseyin Anil Gündüz, Xiao-Yin To, Alice McHardy: deepG: Deep Learning for Genome Sequence Data. R package version 0.3.1 .
#126262	A. Lissin, I. Schober, J. F. Witte, H. Lüken, A. Podstawka, J. Koblitz, B. Bunk, P. Dawyndt, P. Vandamme, P. de Vos, J. Overmann, L. C. Reimer: StrainInfo—the central database for linked microbial strain identifiers. ( DOI 10.1093/database/baaf059 )

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Clostridium amylolyticum (DSM 21864, AS 1.5069, CGMCC 1.5069)

Name and taxonomic classification

Morphology

Cell morphology

Pigmentation

Culture and growth conditions

Culture medium

Culture temp

Culture pH

Physiology and metabolism

Oxygen tolerance

Spore formation

Observation

Metabolite utilization

Pathway annotation

Isolation, sampling and environmental information

Isolation source categories

Isolation

Taxonmaps

Interaction and safety

Risk assessment

Sequence information

Genome sequences

Genome browser: GCA_900142075

16S sequences

GC content

Genome-based predictions

Predictions

Literature

Literature

References

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