Clostridium algidicarnis (DSM 15099, NCFB 2931, NCIMB 702931)

Name: Clostridium algidicarnis (DSM 15099, NCFB 2931, NCIMB 702931)
Creator: BacDive
License: http://creativecommons.org/licenses/by/4.0/

BacDive ID 2813

Type strain

Strain Designation Dainty C

Culture col. no. DSM 15099 NCFB 2931 NCIMB 702931 Dainty C

NCBI tax ID(s) 1121295 37659

Special Collections DSMZ

History <- NCIMB <- NCFB <- R. H. Dainty, Agricultural and Food Research Council, Institute of Food Research, Bristol, UK; Dainty C

Links

Clostridium algidicarnis Dainty C is an anaerobe, psychrophilic prokaryote that was isolated from vacuum-packed refrigerated pork.

anaerobe psychrophilic genome sequence 16S sequence

Name and taxonomic classification

SI-ID 62026

NCIMB 702931,NCFB2931,DSM 15099

@ref 20215

Last LPSN update 2025-12-16 09:47:24

Domain Bacillati

Phylum Bacillota

Class Clostridia

Order Eubacteriales

Family Clostridiaceae

Genus Clostridium

Species Clostridium algidicarnis

Full scientific name Clostridium algidicarnis Lawson et al. 1995

Morphology

Culture and growth conditions

Culture medium

@ref	Name	Growth	Medium link	Composition
5711	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)	Range
5711	positive	growth	22	psychrophilic

Physiology and metabolism

Oxygen tolerance

@ref	Oxygen tolerance	Confidence
5711	anaerobe
125438	anaerobe	91.615
125439	anaerobe	99.5

Pathway annotation

Computationally determined by

@ref	pathway	enzyme coverage	annotated reactions
66794	adipate degradation	100	2 of 2
66794	L-lactaldehyde degradation	100	3 of 3
66794	methylglyoxal degradation	100	5 of 5
66794	ppGpp biosynthesis	100	4 of 4
66794	C4 and CAM-carbon fixation	100	8 of 8
66794	palmitate biosynthesis	100	22 of 22
66794	ethanol fermentation	100	2 of 2
66794	vitamin B1 metabolism	100	13 of 13
66794	cis-vaccenate biosynthesis	100	2 of 2
66794	CDP-diacylglycerol biosynthesis	100	2 of 2
66794	aminopropanol phosphate biosynthesis	100	2 of 2
66794	anapleurotic synthesis of oxalacetate	100	1 of 1
66794	coenzyme A metabolism	100	4 of 4
66794	UDP-GlcNAc biosynthesis	100	3 of 3
66794	folate polyglutamylation	100	1 of 1
66794	chorismate metabolism	88.89	8 of 9
66794	vitamin B12 metabolism	88.24	30 of 34
66794	gluconeogenesis	87.5	7 of 8
66794	peptidoglycan biosynthesis	86.67	13 of 15
66794	glycolysis	82.35	14 of 17
66794	metabolism of amino sugars and derivatives	80	4 of 5
66794	photosynthesis	78.57	11 of 14
66794	aspartate and asparagine metabolism	77.78	7 of 9
66794	CO2 fixation in Crenarchaeota	77.78	7 of 9
66794	phenylalanine metabolism	76.92	10 of 13
66794	pyrimidine metabolism	75.56	34 of 45
66794	butanoate fermentation	75	3 of 4
66794	acetate fermentation	75	3 of 4
66794	biotin biosynthesis	75	3 of 4
66794	sulfopterin metabolism	75	3 of 4
66794	cardiolipin biosynthesis	71.43	5 of 7
66794	heme metabolism	71.43	10 of 14
66794	propanol degradation	71.43	5 of 7
66794	glutamate and glutamine metabolism	71.43	20 of 28
66794	reductive acetyl coenzyme A pathway	71.43	5 of 7
66794	threonine metabolism	70	7 of 10
66794	urea cycle	69.23	9 of 13
66794	purine metabolism	69.15	65 of 94
66794	alanine metabolism	68.97	20 of 29
66794	acetoin degradation	66.67	2 of 3
66794	octane oxidation	66.67	2 of 3
66794	formaldehyde oxidation	66.67	2 of 3
66794	cyanate degradation	66.67	2 of 3
66794	NAD metabolism	66.67	12 of 18
66794	d-mannose degradation	66.67	6 of 9
66794	selenocysteine biosynthesis	66.67	4 of 6
66794	methionine metabolism	65.38	17 of 26
66794	d-xylose degradation	63.64	7 of 11
66794	non-pathway related	63.16	24 of 38
66794	6-hydroxymethyl-dihydropterin diphosphate biosynthesis	62.5	5 of 8
66794	degradation of sugar alcohols	62.5	10 of 16
66794	oxidative phosphorylation	61.54	56 of 91
66794	factor 420 biosynthesis	60	3 of 5
66794	hydrogen production	60	3 of 5
66794	cellulose degradation	60	3 of 5
66794	O-antigen biosynthesis	60	3 of 5
66794	lipoate biosynthesis	60	3 of 5
66794	tetrahydrofolate metabolism	57.14	8 of 14
66794	serine metabolism	55.56	5 of 9
66794	tryptophan metabolism	55.26	21 of 38
66794	lipid metabolism	51.61	16 of 31
66794	glycogen biosynthesis	50	2 of 4
66794	degradation of pentoses	50	14 of 28
66794	citric acid cycle	50	7 of 14
66794	glycolate and glyoxylate degradation	50	3 of 6
66794	isoleucine metabolism	50	4 of 8
66794	Entner Doudoroff pathway	50	5 of 10
66794	ketogluconate metabolism	50	4 of 8
66794	phenylmercury acetate degradation	50	1 of 2
66794	CMP-KDO biosynthesis	50	2 of 4
66794	suberin monomers biosynthesis	50	1 of 2
66794	degradation of aromatic, nitrogen containing compounds	50	6 of 12
66794	dTDPLrhamnose biosynthesis	50	4 of 8
66794	toluene degradation	50	2 of 4
66794	lysine metabolism	47.62	20 of 42
66794	phosphatidylethanolamine bioynthesis	46.15	6 of 13
66794	isoprenoid biosynthesis	46.15	12 of 26
66794	proline metabolism	45.45	5 of 11
66794	histidine metabolism	44.83	13 of 29
66794	valine metabolism	44.44	4 of 9
66794	cysteine metabolism	44.44	8 of 18
66794	nitrate assimilation	44.44	4 of 9
66794	ubiquinone biosynthesis	42.86	3 of 7
66794	glutathione metabolism	42.86	6 of 14
66794	ethylmalonyl-CoA pathway	40	2 of 5
66794	myo-inositol biosynthesis	40	4 of 10
66794	glycine metabolism	40	4 of 10
66794	creatinine degradation	40	2 of 5
66794	bacilysin biosynthesis	40	2 of 5
66794	arachidonate biosynthesis	40	2 of 5
66794	propionate fermentation	40	4 of 10
66794	glycogen metabolism	40	2 of 5
66794	flavin biosynthesis	40	6 of 15
66794	degradation of hexoses	38.89	7 of 18
66794	leucine metabolism	38.46	5 of 13
66794	phenylpropanoid biosynthesis	38.46	5 of 13
66794	vitamin B6 metabolism	36.36	4 of 11
66794	pentose phosphate pathway	36.36	4 of 11
66794	IAA biosynthesis	33.33	1 of 3
66794	acetyl CoA biosynthesis	33.33	1 of 3
66794	methane metabolism	33.33	1 of 3
66794	enterobactin biosynthesis	33.33	1 of 3
66794	lipid A biosynthesis	33.33	3 of 9
66794	molybdenum cofactor biosynthesis	33.33	3 of 9
66794	4-hydroxymandelate degradation	33.33	3 of 9
66794	arachidonic acid metabolism	33.33	6 of 18
66794	sulfate reduction	30.77	4 of 13
66794	coenzyme M biosynthesis	30	3 of 10
66794	arginine metabolism	29.17	7 of 24
66794	benzoyl-CoA degradation	28.57	2 of 7
66794	metabolism of disaccharids	27.27	3 of 11
66794	ascorbate metabolism	27.27	6 of 22
66794	dolichyl-diphosphooligosaccharide biosynthesis	27.27	3 of 11
66794	polyamine pathway	26.09	6 of 23
66794	androgen and estrogen metabolism	25	4 of 16
66794	lactate fermentation	25	1 of 4
66794	cyclohexanol degradation	25	1 of 4
66794	degradation of sugar acids	24	6 of 25
66794	tyrosine metabolism	21.43	3 of 14

Isolation, sampling and environmental information

Isolation source categories

Cat1	Cat2	Cat3
#Engineered	#Food production	#Bottled, canned, packed food
#Engineered	#Food production	#Meat

Isolation

5711

Sample typevacuum-packed refrigerated pork

Taxonmaps

69479

Global distribution of 16S sequence AF127023 (>99% sequence identity) for Clostridium from Microbeatlas

Aquatic Samples	3822
Soil Samples	4363
Animal Samples	10663
Plant Samples	861
Total Samples	19709

Interaction and safety

Risk assessment

@ref	Biosafety level	Biosafety level comment
5711	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	ASM293423v1 assembly for Clostridium algidicarnis DSM 15099	scaffold	GCA_002934235	1121295.3	2695420939	1121295	70.43

16S sequences

@ref	Description	Accession	Length	Database	NCBI tax ID
20218	Clostridium algidicarnis 16S ribosomal RNA gene, partial sequence	AF127023	1481		37659
5711	Clostridium algidicarnis 16S rRNA gene, strain NCFB 2931	X77676	1511		37659

Genome-based predictions

Predictions

Predictions from Deep Learning for Genome Sequence Data. R package version 0.3.1 based on: Clostridium algidicarnis DSM 15099
NCBI: GCA_002934235

@ref	Trait	Model	Prediction	Confidence in %	In training data
125439	spore_formation	BacteriaNetⓘ	yes	80.10	no
125439	motility	BacteriaNetⓘ	yes	78.90	no
125439	gram_stain	BacteriaNetⓘ	positive	80.90	no
125439	oxygen_tolerance	BacteriaNetⓘ	anaerobe	99.50	no

Predictions from bacterial phenotypic traits through improved machine learning using high-quality, curated datasets based on: Clostridium algidicarnis DSM 15099 DSM 15099
NCBI: GCA_002934235.1

@ref	Trait	Model	Prediction	Confidence in %	In training data
125438	gram-positive	gram-positiveⓘ	yes	71.96	no
125438	anaerobic	anaerobicⓘ	yes	91.62	yes
125438	aerobic	aerobicⓘ	no	97.21	yes
125438	spore-forming	spore-formingⓘ	yes	77.02	no
125438	thermophilic	thermophileⓘ	no	92.98	no
125438	flagellated	motile2+ⓘ	yes	78.08	no

Literature

Topic	Title	Authors	Journal	DOI	Year
	Draft Genome Sequences of Two Clostridium algidicarnis Strains Isolated from Meat Juice Samples of Chilled Vacuum-Packed Lamb Meat.	Wambui J, Cernela N, Stevens MJA, Ghielmetti G, Stephan R.	Microbiol Resour Announc	10.1128/mra.00983-20	2020
Pathogenicity	Comparative Genome Analysis and Phenotypic Characterization of Clostridium gasigenes CGAS001 Isolated From Chilled Vacuum-Packed Lamb Meat.	Wambui J, Cernela N, Corti S, Stephan R.	Front Microbiol	10.3389/fmicb.2020.02048	2020
	Diversity and Dynamics of Microbial Community Structure in Different Mangrove, Marine and Freshwater Sediments During Anaerobic Debromination of PBDEs.	Wang YF, Zhu HW, Wang Y, Zhang XL, Tam NFY.	Front Microbiol	10.3389/fmicb.2018.00952	2018
	Influence of plant diversity and elevated atmospheric carbon dioxide levels on belowground bacterial diversity.	Gruter D, Schmid B, Brandl H.	BMC Microbiol	10.1186/1471-2180-6-68	2006
Biotechnology	Selection procedure of bioprotective cultures for their combined use with High Pressure Processing to control spore-forming bacteria in cooked ham.	Ramaroson M, Guillou S, Rossero A, Reze S, Anthoine V, Moriceau N, Martin JL, Duranton F, Zagorec M.	Int J Food Microbiol	10.1016/j.ijfoodmicro.2018.04.010	2018
	Effect of NaCl Concentration on Microbiological Properties in NaCl Assistant Anaerobic Fermentation: Hydrolase Activity and Microbial Community Distribution.	Pang H, Xin X, He J, Cui B, Guo D, Liu S, Yan Z, Liu C, Wang X, Nan J.	Front Microbiol	10.3389/fmicb.2020.589222	2020
	Occurrence of genes encoding spore germination in Clostridium species that cause meat spoilage.	Burgess SA, Palevich FP, Gardner A, Mills J, Brightwell G, Palevich N.	Microb Genom	10.1099/mgen.0.000767	2022
Enzymology	Detection of cold-tolerant clostridia other than Clostridium estertheticum in raw vacuum-packed chill-stored meat.	Cavill L, Renteria-Monterrubio AL, Helps CR, Corry JE.	Food Microbiol	10.1016/j.fm.2011.01.003	2011
	Psychrophilic and psychrotrophic clostridia: sporulation and germination processes and their role in the spoilage of chilled, vacuum-packaged beef, lamb and venison	Adam KH, Flint SH, Brightwell G.	International journal of food science and technology.	10.1111/j.1365-2621.2010.02320.x	2010
	PandaGUT provides new insights into bacterial diversity, function, and resistome landscapes with implications for conservation.	Huang G, Shi W, Wang L, Qu Q, Zuo Z, Wang J, Zhao F, Wei F.	Microbiome	10.1186/s40168-023-01657-0	2023
Enzymology	Sources of psychrophilic and psychrotolerant clostridia causing spoilage of vacuum-packed chilled meats, as determined by PCR amplification procedure.	Broda DM, Boerema JA, Brightwell G.	J Appl Microbiol	10.1111/j.1365-2672.2009.04193.x	2009
Pathogenicity	The structural basis of hyperpromiscuity in a core combinatorial network of type II toxin-antitoxin and related phage defense systems.	Ernits K, Saha CK, Brodiazhenko T, Chouhan B, Shenoy A, Buttress JA, Duque-Pedraza JJ, Bojar V, Nakamoto JA, Kurata T, Egorov AA, Shyrokova L, Johansson MJO, Mets T, Rustamova A, Dzigurski J, Tenson T, Garcia-Pino A, Strahl H, Elofsson A, Hauryliuk V, Atkinson GC.	Proc Natl Acad Sci U S A	10.1073/pnas.2305393120	2023
	Controlling Blown Pack Spoilage Using Anti-Microbial Packaging.	Reid R, Bolton D, Tiuftin AA, Kerry JP, Fanning S, Whyte P.	Foods	10.3390/foods6080067	2017
Biotechnology	PCR detection of psychrotolerant clostridia associated with deep tissue spoilage of vacuum-packed chilled meats.	Boerema JA, Broda DM, Bell RG.	Lett Appl Microbiol	10.1046/j.1472-765x.2002.01205.x	2002
Enzymology	Unraveling the Genotypic and Phenotypic Diversity of the Psychrophilic Clostridium estertheticum Complex, a Meat Spoilage Agent.	Wambui J, Stevens MJA, Cernela N, Stephan R.	Front Microbiol	10.3389/fmicb.2022.856810	2022
Phylogeny	The past, present and future of ancient bacterial DNA.	Arning N, Wilson DJ.	Microb Genom	10.1099/mgen.0.000384	2020
	Analysis of bacterial DNA in skin and muscle of the Tyrolean iceman offers new insight into the mummification process.	Rollo F, Luciani S, Canapa A, Marota I.	Am J Phys Anthropol	10.1002/(sici)1096-8644(200002)111:2<211::aid-ajpa7>3.0.co;2-m	2000
Genetics	Ancient bacteria of the Ötzi's microbiome: a genomic tale from the Copper Age.	Lugli GA, Milani C, Mancabelli L, Turroni F, Ferrario C, Duranti S, van Sinderen D, Ventura M.	Microbiome	10.1186/s40168-016-0221-y	2017
Metabolism	Glycosylated proteins preserved over millennia: N-glycan analysis of Tyrolean Iceman, Scythian Princess and Warrior.	Ozcan S, Kim BJ, Ro G, Kim JH, Bereuter TL, Reiter C, Dimapasoc L, Garrido D, Mills DA, Grimm R, Lebrilla CB, An HJ.	Sci Rep	10.1038/srep04963	2014
	Deciphering intra-species bacterial diversity of meat and seafood spoilage microbiota using gyrB amplicon sequencing: A comparative analysis with 16S rDNA V3-V4 amplicon sequencing.	Poirier S, Rue O, Peguilhan R, Coeuret G, Zagorec M, Champomier-Verges MC, Loux V, Chaillou S.	PLoS One	10.1371/journal.pone.0204629	2018
	Growth of spoilage bacteria during storage and transport of meat.	EFSA Panel on Biological Hazards (BIOHAZ).	EFSA J	10.2903/j.efsa.2016.4523	2016
Phylogeny	Efficacy of heat and ethanol spore treatments for the isolation of psychrotrophic Clostridium spp. associated with the spoilage of chilled vacuum-packed meats.	Broda DM, De Lacy KM, Bell RG	Int J Food Microbiol	10.1016/s0168-1605(97)00119-0	1998
Enzymology	Characterization of a psychrotrophic Clostridium causing spoilage in vacuum-packed cooked pork: description of Clostridium algidicarnis sp. nov.	Lawson P, Dainty RH, Kristiansen N, Berg J, Collins MD.	Lett Appl Microbiol	10.1111/j.1472-765x.1994.tb00930.x	1994

References

#5711	Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 15099
#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 )
#20218	Verslyppe, B., De Smet, W., De Baets, B., De Vos, P., Dawyndt P.: StrainInfo introduces electronic passports for microorganisms.. Syst Appl Microbiol. 37: 42 - 50 2014 ( DOI 10.1016/j.syapm.2013.11.002 , PubMed 24321274 )
#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 algidicarnis (DSM 15099, NCFB 2931, NCIMB 702931)

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_002934235

16S sequences

Genome-based predictions

Predictions

Literature

Literature

References

BacDive

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