Clostridium homopropionicum (DSM 5847, ATCC 51426, LuHBu1)

Name: Clostridium homopropionicum (DSM 5847, ATCC 51426, LuHBu1)
Creator: BacDive
License: http://creativecommons.org/licenses/by/4.0/

BacDive ID 2753

Type strain

Strain Designation LuHBu1

Culture col. no. DSM 5847 ATCC 51426 LuHBu1

NCBI tax ID(s) 1121318 36844

Special Collections DSMZ

History <- C. Dörner, LuHBu1

Links

Clostridium homopropionicum LuHBu1 is an anaerobe bacterium that was isolated from anoxic sewage sludge.

anaerobe genome sequence 16S sequence Bacteria

Name and taxonomic classification

SI-ID 42977

ATCC 51426,DSM 5847

@ref 20215

Last LPSN update 2026-02-09 11:18:21

Domain Bacteria

Phylum Bacillota

Class Clostridia

Order Eubacteriales

Family Clostridiaceae

Genus Clostridium

Species Clostridium homopropionicum

Full scientific name Clostridium homopropionicum Dörner and Schink 1991

Morphology

Culture and growth conditions

Culture medium

@ref	Name	Growth	Medium link	Composition
2336	ANAEROBIC FRESHWATER (FWM) MEDIUM (DSMZ Medium 503)		Medium recipe at MediaDive	Name: ANAEROBIC FRESHWATER (FWM) MEDIUM (DSMZ Medium 503; with strain-specific modifications) Composition: Na-3-hydroxybutyrate 1.49551 g/l Na2CO3 1.49551 g/l NaCl 0.997008 g/l KCl 0.498505 g/l MgCl2 x 6 H2O 0.398803 g/l Na2S x 9 H2O 0.299103 g/l NH4Cl 0.249252 g/l KH2PO4 0.199402 g/l CaCl2 x 2 H2O 0.149552 g/l HCl 0.00249252 g/l FeCl2 x 4 H2O 0.00149551 g/l Sodium resazurin 0.000498505 g/l NaOH 0.000498504 g/l Pyridoxine hydrochloride 0.000299103 g/l Nicotinic acid 0.000199402 g/l Thiamine-HCl x 2 H2O 0.000199402 g/l CoCl2 x 6 H2O 0.000189432 g/l Calcium pantothenate 9.97009e-05 g/l MnCl2 x 4 H2O 9.97009e-05 g/l Vitamin B12 9.97009e-05 g/l p-Aminobenzoic acid 7.97607e-05 g/l ZnCl2 6.97906e-05 g/l Na2MoO4 x 2 H2O 3.58923e-05 g/l NiCl2 x 6 H2O 2.39282e-05 g/l D-(+)-biotin 1.99402e-05 g/l H3BO3 5.98205e-06 g/l Na2WO4 x 2 H2O 3.98804e-06 g/l Na2SeO3 x 5 H2O 2.99103e-06 g/l CuCl2 x 2 H2O 1.99402e-06 g/l Distilled water

Culture temp

@ref	Growth	Type	Temperature (°C)
2336	positive	growth	35

Physiology and metabolism

Oxygen tolerance

@ref	Oxygen tolerance	Confidence
2336	anaerobe
125438	anaerobe	90.425
125439	anaerobe	98.1

Pathway annotation

Computationally determined by

@ref	pathway	enzyme coverage	annotated reactions
66794	C4 and CAM-carbon fixation	100	8 of 8
66794	L-lactaldehyde degradation	100	3 of 3
66794	ppGpp biosynthesis	100	4 of 4
66794	palmitate biosynthesis	100	22 of 22
66794	reductive acetyl coenzyme A pathway	100	7 of 7
66794	threonine metabolism	100	10 of 10
66794	adipate degradation	100	2 of 2
66794	cis-vaccenate biosynthesis	100	2 of 2
66794	aminopropanol phosphate biosynthesis	100	2 of 2
66794	coenzyme A metabolism	100	4 of 4
66794	CDP-diacylglycerol biosynthesis	100	2 of 2
66794	UDP-GlcNAc biosynthesis	100	3 of 3
66794	anapleurotic synthesis of oxalacetate	100	1 of 1
66794	folate polyglutamylation	100	1 of 1
66794	suberin monomers biosynthesis	100	2 of 2
66794	lactate fermentation	100	4 of 4
66794	vitamin B1 metabolism	92.31	12 of 13
66794	valine metabolism	88.89	8 of 9
66794	CO2 fixation in Crenarchaeota	88.89	8 of 9
66794	aspartate and asparagine metabolism	88.89	8 of 9
66794	chorismate metabolism	88.89	8 of 9
66794	gluconeogenesis	87.5	7 of 8
66794	alanine metabolism	86.21	25 of 29
66794	propanol degradation	85.71	6 of 7
66794	ubiquinone biosynthesis	85.71	6 of 7
66794	flavin biosynthesis	80	12 of 15
66794	peptidoglycan biosynthesis	80	12 of 15
66794	methylglyoxal degradation	80	4 of 5
66794	pyrimidine metabolism	80	36 of 45
66794	glutamate and glutamine metabolism	78.57	22 of 28
66794	photosynthesis	78.57	11 of 14
66794	citric acid cycle	78.57	11 of 14
66794	tetrahydrofolate metabolism	78.57	11 of 14
66794	molybdenum cofactor biosynthesis	77.78	7 of 9
66794	purine metabolism	77.66	73 of 94
66794	phenylalanine metabolism	76.92	10 of 13
66794	acetate fermentation	75	3 of 4
66794	butanoate fermentation	75	3 of 4
66794	glycogen biosynthesis	75	3 of 4
66794	sulfopterin metabolism	75	3 of 4
66794	6-hydroxymethyl-dihydropterin diphosphate biosynthesis	75	6 of 8
66794	NAD metabolism	72.22	13 of 18
66794	heme metabolism	71.43	10 of 14
66794	cardiolipin biosynthesis	71.43	5 of 7
66794	glycolysis	70.59	12 of 17
66794	Entner Doudoroff pathway	70	7 of 10
66794	myo-inositol biosynthesis	70	7 of 10
66794	formaldehyde oxidation	66.67	2 of 3
66794	serine metabolism	66.67	6 of 9
66794	cyanate degradation	66.67	2 of 3
66794	d-mannose degradation	66.67	6 of 9
66794	acetoin degradation	66.67	2 of 3
66794	selenocysteine biosynthesis	66.67	4 of 6
66794	octane oxidation	66.67	2 of 3
66794	histidine metabolism	65.52	19 of 29
66794	methionine metabolism	65.38	17 of 26
66794	isoleucine metabolism	62.5	5 of 8
66794	isoprenoid biosynthesis	61.54	16 of 26
66794	cysteine metabolism	61.11	11 of 18
66794	tryptophan metabolism	60.53	23 of 38
66794	propionate fermentation	60	6 of 10
66794	phenylacetate degradation (aerobic)	60	3 of 5
66794	glycine betaine biosynthesis	60	3 of 5
66794	cellulose degradation	60	3 of 5
66794	hydrogen production	60	3 of 5
66794	glycogen metabolism	60	3 of 5
66794	lipoate biosynthesis	60	3 of 5
66794	lipid metabolism	58.06	18 of 31
66794	non-pathway related	57.89	22 of 38
66794	oxidative phosphorylation	56.04	51 of 91
66794	d-xylose degradation	54.55	6 of 11
66794	proline metabolism	54.55	6 of 11
66794	vitamin B6 metabolism	54.55	6 of 11
66794	pentose phosphate pathway	54.55	6 of 11
66794	leucine metabolism	53.85	7 of 13
66794	lysine metabolism	52.38	22 of 42
66794	biotin biosynthesis	50	2 of 4
66794	glycine metabolism	50	5 of 10
66794	CMP-KDO biosynthesis	50	2 of 4
66794	4-hydroxyphenylacetate degradation	50	5 of 10
66794	toluene degradation	50	2 of 4
66794	kanosamine biosynthesis II	50	1 of 2
66794	ethanol fermentation	50	1 of 2
66794	pantothenate biosynthesis	50	3 of 6
66794	degradation of aromatic, nitrogen containing compounds	50	6 of 12
66794	glycolate and glyoxylate degradation	50	3 of 6
66794	arginine metabolism	45.83	11 of 24
66794	nitrate assimilation	44.44	4 of 9
66794	polyamine pathway	43.48	10 of 23
66794	tyrosine metabolism	42.86	6 of 14
66794	glutathione metabolism	42.86	6 of 14
66794	vitamin B12 metabolism	41.18	14 of 34
66794	starch degradation	40	4 of 10
66794	coenzyme M biosynthesis	40	4 of 10
66794	arachidonate biosynthesis	40	2 of 5
66794	metabolism of amino sugars and derivatives	40	2 of 5
66794	degradation of hexoses	38.89	7 of 18
66794	sulfate reduction	38.46	5 of 13
66794	phosphatidylethanolamine bioynthesis	38.46	5 of 13
66794	urea cycle	38.46	5 of 13
66794	ketogluconate metabolism	37.5	3 of 8
66794	dTDPLrhamnose biosynthesis	37.5	3 of 8
66794	cholesterol biosynthesis	36.36	4 of 11
66794	metabolism of disaccharids	36.36	4 of 11
66794	4-hydroxymandelate degradation	33.33	3 of 9
66794	enterobactin biosynthesis	33.33	1 of 3
66794	IAA biosynthesis	33.33	1 of 3
66794	acetyl CoA biosynthesis	33.33	1 of 3
66794	lipid A biosynthesis	33.33	3 of 9
66794	phenylpropanoid biosynthesis	30.77	4 of 13
66794	aclacinomycin biosynthesis	28.57	2 of 7
66794	degradation of pentoses	28.57	8 of 28
66794	benzoyl-CoA degradation	28.57	2 of 7
66794	ascorbate metabolism	27.27	6 of 22
66794	degradation of sugar alcohols	25	4 of 16
66794	cyclohexanol degradation	25	1 of 4
66794	androgen and estrogen metabolism	25	4 of 16
66794	degradation of sugar acids	24	6 of 25
66794	bile acid biosynthesis, neutral pathway	23.53	4 of 17

Isolation, sampling and environmental information

Isolation source categories

Cat1	Cat2	Cat3
#Engineered	#Waste	#Sewage sludge
#Condition	#Anoxic (anaerobic)	-

Isolation

@ref	Sample type	Country	Country ISO 3 Code	Continent
2336	anoxic sewage sludge	Germany	DEU	Europe

Taxonmaps

69479

Global distribution of 16S sequence X76744 (>99% sequence identity) for Clostridium homopropionicum from Microbeatlas

Aquatic Samples	329
Soil Samples	172
Animal Samples	8049
Plant Samples	27
Total Samples	8577

Interaction and safety

Risk assessment

@ref	Biosafety level	Biosafety level comment
2336	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
66792	IMG-taxon 2622736521 annotated assembly for Clostridium homopropionicum DSM 5847	scaffold	GCA_900113195	36844.3	2622736521	36844	70.38
66792	ASM126379v1 assembly for Clostridium homopropionicum DSM 5847	contig	GCA_001263795	1121318.3	2645727554	1121318	69.6

16S sequences

@ref	Description	Accession	Length	Database	NCBI tax ID
2336	Clostridium homopropionicum 16S rRNA gene type strain DSM 5847T	X76744	1461		36844

GC content

2336

GC-content (mol%)32.0

Genome-based predictions

Predictions

Predictions from Deep Learning for Genome Sequence Data. R package version 0.3.1 based on: Clostridium homopropionicum DSM 5847
NCBI: GCA_900113195

@ref	Trait	Model	Prediction	Confidence in %	In training data
125439	spore_formation	BacteriaNetⓘ	yes	80.80	no
125439	motility	BacteriaNetⓘ	yes	75.30	no
125439	gram_stain	BacteriaNetⓘ	positive	76.60	no
125439	oxygen_tolerance	BacteriaNetⓘ	anaerobe	98.10	no

Predictions from bacterial phenotypic traits through improved machine learning using high-quality, curated datasets based on: Clostridium homopropionicum DSM 5847
PATRIC: 1121318.3

@ref	Trait	Model	Prediction	Confidence in %	In training data
125438	gram-positive	gram-positiveⓘ	yes	57.77	no
125438	anaerobic	anaerobicⓘ	yes	90.43	yes
125438	spore-forming	spore-formingⓘ	yes	74.22	no
125438	aerobic	aerobicⓘ	no	98.07	yes
125438	thermophilic	thermophileⓘ	no	85.78	yes
125438	flagellated	motile2+ⓘ	yes	79.90	no

Literature

Topic	Title	Authors	Journal	DOI	Year
	Genome Sequence of the Poly-3-Hydroxybutyrate Producer Clostridium acetireducens DSM 10703.	Fluchter S, Poehlein A, Schiel-Bengelsdorf B, Daniel R, Durre P.	Genome Announc	10.1128/genomea.01399-16	2016
	Electron bifurcation and fluoride efflux systems implicated in defluorination of perfluorinated unsaturated carboxylic acids by Acetobacterium spp.	Yu Y, Xu F, Zhao W, Thoma C, Che S, Richman JE, Jin B, Zhu Y, Xing Y, Wackett L, Men Y.	Sci Adv	10.1126/sciadv.ado2957	2024
Phylogeny	Dietary Supplementation With Creatine Pyruvate Alters Rumen Microbiota Protein Function in Heat-Stressed Beef Cattle.	Li Y, Zang Y, Zhao X, Liu L, Qiu Q, Ouyang K, Qu M.	Front Microbiol	10.3389/fmicb.2021.715088	2021
Metabolism	A periplasmic and extracellular c-type cytochrome of Geobacter sulfurreducens acts as a ferric iron reductase and as an electron carrier to other acceptors or to partner bacteria.	Seeliger S, Cord-Ruwisch R, Schink B.	J Bacteriol	10.1128/jb.180.14.3686-3691.1998	1998
	Humic acid reduction by propionibacterium freudenreichii and other fermenting bacteria	Benz M, Schink B, Brune A.	Appl Environ Microbiol	10.1128/aem.64.11.4507-4512.1998	1998
Genetics	Draft Genome Sequence of the Strict Anaerobe Clostridium homopropionicum LuHBu1 (DSM 5847).	Beck MH, Poehlein A, Bengelsdorf FR, Schiel-Bengelsdorf B, Daniel R, Durre P	Genome Announc	10.1128/genomeA.01112-15	2015
Metabolism	Clostridium homopropionicum sp. nov., a new strict anaerobe growing with 2-, 3-, or 4-hydroxybutyrate.	Dorner C, Schink B	Arch Microbiol	10.1007/BF00276529	1990

References

#2336	Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 5847
#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 .
#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 homopropionicum (DSM 5847, ATCC 51426, LuHBu1)

Name and taxonomic classification

Morphology

Culture and growth conditions

Culture medium

Culture temp

Physiology and metabolism

Oxygen tolerance

Pathway annotation

Isolation, sampling and environmental information

Isolation source categories

Isolation

Taxonmaps

Interaction and safety

Risk assessment

Sequence information

Genome sequences

Genome browser: GCA_900113195

16S sequences

GC content

Genome-based predictions

Predictions

Literature

Literature

References

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