Clostridium vincentii (DSM 10228, lac-1)

Name: Clostridium vincentii (DSM 10228, lac-1)
Creator: BacDive
License: http://creativecommons.org/licenses/by/4.0/

BacDive ID 2789

Type strain

Strain Designation lac-1

Culture col. no. DSM 10228 lac-1

NCBI tax ID(s) 52704

Special Collections DSMZ

Links

Clostridium vincentii lac-1 is an anaerobe, psychrophilic prokaryote that was isolated from anaerobic sediment.

anaerobe psychrophilic genome sequence 16S sequence

Name and taxonomic classification

SI-ID 48781

DSM 10228

@ref 20215

Last LPSN update 2025-12-16 09:47:23

Domain Bacillati

Phylum Bacillota

Class Clostridia

Order Eubacteriales

Family Clostridiaceae

Genus Clostridium

Species Clostridium vincentii

Full scientific name Clostridium vincentii Mountfort et al. 1997

Morphology

Culture and growth conditions

Culture medium

@ref	Name	Growth	Medium link	Composition
3853	CLOSTRIDIUM VINCENTII MEDIUM (DSMZ Medium 769)		Medium recipe at MediaDive	Name: CLOSTRIDIUM VINCENTII MEDIUM (DSMZ Medium 769) Composition: Sea Salt 11.988 g/l Lactose 1.998 g/l Yeast extract 0.999001 g/l NaHCO3 0.999001 g/l Trypticase peptone 0.3996 g/l Na2S x 9 H2O 0.2997 g/l L-Cysteine HCl x H2O 0.2997 g/l NH4NO3 0.0999001 g/l Sodium resazurin 0.0004995 g/l Pyridoxine hydrochloride 9.99001e-05 g/l Riboflavin 4.995e-05 g/l Thiamine HCl 4.995e-05 g/l Nicotinic acid 4.995e-05 g/l Calcium D-(+)-pantothenate 4.995e-05 g/l (DL)-alpha-Lipoic acid 4.995e-05 g/l p-Aminobenzoic acid 4.995e-05 g/l Folic acid 1.998e-05 g/l Biotin 1.998e-05 g/l Vitamin B12 9.99001e-07 g/l Na-phosphate buffer Distilled water

Culture temp

@ref	Growth	Type	Temperature (°C)	Range
3853	positive	growth	12	psychrophilic

Physiology and metabolism

Oxygen tolerance

@ref	Oxygen tolerance	Confidence
3853	anaerobe
125439	anaerobe	99.5

Pathway annotation

Computationally determined by

@ref	pathway	enzyme coverage	annotated reactions
66794	coenzyme A metabolism	100	4 of 4
66794	ppGpp biosynthesis	100	4 of 4
66794	C4 and CAM-carbon fixation	100	8 of 8
66794	cis-vaccenate biosynthesis	100	2 of 2
66794	formaldehyde oxidation	100	3 of 3
66794	L-lactaldehyde degradation	100	3 of 3
66794	biotin biosynthesis	100	4 of 4
66794	CDP-diacylglycerol biosynthesis	100	2 of 2
66794	UDP-GlcNAc biosynthesis	100	3 of 3
66794	adipate degradation	100	2 of 2
66794	suberin monomers biosynthesis	100	2 of 2
66794	folate polyglutamylation	100	1 of 1
66794	anapleurotic synthesis of oxalacetate	100	1 of 1
66794	palmitate biosynthesis	100	22 of 22
66794	vitamin B1 metabolism	92.31	12 of 13
66794	threonine metabolism	90	9 of 10
66794	starch degradation	90	9 of 10
66794	chorismate metabolism	88.89	8 of 9
66794	aspartate and asparagine metabolism	88.89	8 of 9
66794	gluconeogenesis	87.5	7 of 8
66794	reductive acetyl coenzyme A pathway	85.71	6 of 7
66794	alanine metabolism	82.76	24 of 29
66794	pyrimidine metabolism	82.22	37 of 45
66794	glutamate and glutamine metabolism	82.14	23 of 28
66794	peptidoglycan biosynthesis	80	12 of 15
66794	metabolism of amino sugars and derivatives	80	4 of 5
66794	cellulose degradation	80	4 of 5
66794	glycine betaine biosynthesis	80	4 of 5
66794	flavin biosynthesis	80	12 of 15
66794	glycogen metabolism	80	4 of 5
66794	hydrogen production	80	4 of 5
66794	tetrahydrofolate metabolism	78.57	11 of 14
66794	photosynthesis	78.57	11 of 14
66794	d-mannose degradation	77.78	7 of 9
66794	serine metabolism	77.78	7 of 9
66794	valine metabolism	77.78	7 of 9
66794	phenylalanine metabolism	76.92	10 of 13
66794	glycolysis	76.47	13 of 17
66794	vitamin E metabolism	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	acetate fermentation	75	3 of 4
66794	NAD metabolism	72.22	13 of 18
66794	glutathione metabolism	71.43	10 of 14
66794	heme metabolism	71.43	10 of 14
66794	propanol degradation	71.43	5 of 7
66794	purine metabolism	71.28	67 of 94
66794	octane oxidation	66.67	2 of 3
66794	methane metabolism	66.67	2 of 3
66794	CO2 fixation in Crenarchaeota	66.67	6 of 9
66794	acetoin degradation	66.67	2 of 3
66794	histidine metabolism	65.52	19 of 29
66794	methionine metabolism	65.38	17 of 26
66794	d-xylose degradation	63.64	7 of 11
66794	metabolism of disaccharids	63.64	7 of 11
66794	isoleucine metabolism	62.5	5 of 8
66794	degradation of sugar alcohols	62.5	10 of 16
66794	dTDPLrhamnose biosynthesis	62.5	5 of 8
66794	ketogluconate metabolism	62.5	5 of 8
66794	oxidative phosphorylation	61.54	56 of 91
66794	non-pathway related	60.53	23 of 38
66794	methylglyoxal degradation	60	3 of 5
66794	Entner Doudoroff pathway	60	6 of 10
66794	factor 420 biosynthesis	60	3 of 5
66794	tryptophan metabolism	57.89	22 of 38
66794	degradation of pentoses	57.14	16 of 28
66794	citric acid cycle	57.14	8 of 14
66794	molybdenum cofactor biosynthesis	55.56	5 of 9
66794	cysteine metabolism	55.56	10 of 18
66794	lysine metabolism	54.76	23 of 42
66794	proline metabolism	54.55	6 of 11
66794	sulfate reduction	53.85	7 of 13
66794	leucine metabolism	53.85	7 of 13
66794	phenylmercury acetate degradation	50	1 of 2
66794	aminopropanol phosphate biosynthesis	50	1 of 2
66794	glycolate and glyoxylate degradation	50	3 of 6
66794	propionate fermentation	50	5 of 10
66794	pantothenate biosynthesis	50	3 of 6
66794	CMP-KDO biosynthesis	50	2 of 4
66794	arginine metabolism	50	12 of 24
66794	degradation of aromatic, nitrogen containing compounds	50	6 of 12
66794	toluene degradation	50	2 of 4
66794	selenocysteine biosynthesis	50	3 of 6
66794	cyclohexanol degradation	50	2 of 4
66794	ethanol fermentation	50	1 of 2
66794	vitamin B12 metabolism	47.06	16 of 34
66794	vitamin B6 metabolism	45.45	5 of 11
66794	pentose phosphate pathway	45.45	5 of 11
66794	lipid metabolism	45.16	14 of 31
66794	degradation of hexoses	44.44	8 of 18
66794	nitrate assimilation	44.44	4 of 9
66794	cardiolipin biosynthesis	42.86	3 of 7
66794	tyrosine metabolism	42.86	6 of 14
66794	isoprenoid biosynthesis	42.31	11 of 26
66794	O-antigen biosynthesis	40	2 of 5
66794	4-hydroxyphenylacetate degradation	40	4 of 10
66794	arachidonate biosynthesis	40	2 of 5
66794	polyamine pathway	39.13	9 of 23
66794	urea cycle	38.46	5 of 13
66794	phenylpropanoid biosynthesis	38.46	5 of 13
66794	ascorbate metabolism	36.36	8 of 22
66794	lipid A biosynthesis	33.33	3 of 9
66794	4-hydroxymandelate degradation	33.33	3 of 9
66794	IAA biosynthesis	33.33	1 of 3
66794	cyanate degradation	33.33	1 of 3
66794	sphingosine metabolism	33.33	2 of 6
66794	allantoin degradation	33.33	3 of 9
66794	androgen and estrogen metabolism	31.25	5 of 16
66794	phosphatidylethanolamine bioynthesis	30.77	4 of 13
66794	glycine metabolism	30	3 of 10
66794	myo-inositol biosynthesis	30	3 of 10
66794	coenzyme M biosynthesis	30	3 of 10
66794	benzoyl-CoA degradation	28.57	2 of 7
66794	arachidonic acid metabolism	27.78	5 of 18
66794	dolichyl-diphosphooligosaccharide biosynthesis	27.27	3 of 11
66794	carnitine metabolism	25	2 of 8
66794	lactate fermentation	25	1 of 4
66794	methanogenesis from CO2	25	3 of 12
66794	alginate biosynthesis	25	1 of 4
66794	degradation of sugar acids	24	6 of 25

Isolation, sampling and environmental information

Isolation source categories

Cat1	Cat2	Cat3
#Environmental	#Aquatic	#Sediment
#Condition	#Anoxic (anaerobic)	-

Isolation

@ref	Sample type	Geographic location	Continent
3853	anaerobic sediment	McMurdo Ice Shelf	Australia and Oceania

Taxonmaps

69479

Global distribution of 16S sequence X97432 (>99% sequence identity) for Clostridium vincentii subclade from Microbeatlas

Aquatic Samples	807
Soil Samples	696
Animal Samples	1724
Plant Samples	122
Total Samples	3349

Interaction and safety

Risk assessment

@ref	Biosafety level	Biosafety level comment
3853	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	ASM299574v1 assembly for Clostridium vincentii DSM 10228	contig	GCA_002995745	52704.3	2916606478	52704	58.88

16S sequences

@ref	Description	Accession	Length	Database	NCBI tax ID
3853	C.vincentii 16S rRNA gene	X97432	1464		52704

Genome-based predictions

Predictions

Predictions from Deep Learning for Genome Sequence Data. R package version 0.3.1 based on: Clostridium vincentii DSM 10228
NCBI: GCA_002995745

@ref	Trait	Model	Prediction	Confidence in %	In training data
125439	spore_formation	BacteriaNetⓘ	yes	83.30	no
125439	motility	BacteriaNetⓘ	yes	84.80	no
125439	gram_stain	BacteriaNetⓘ	positive	68.10	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 vincentii strain DSM 10228
PATRIC: 52704.3

@ref	Trait	Model	Prediction	Confidence in %	In training data
125438	gram-positive	gram-positiveⓘ	yes	67.12	no
125438	anaerobic	anaerobicⓘ	yes	88.93	yes
125438	spore-forming	spore-formingⓘ	yes	72.85	no
125438	aerobic	aerobicⓘ	no	98.27	no
125438	thermophilic	thermophileⓘ	no	91.63	yes
125438	flagellated	motile2+ⓘ	yes	81.46	no

Literature

Topic	Title	Authors	Journal	DOI	Year
	Culture-independent bacterial community analysis of the salty-fermented fish paste products of Thailand and Laos.	Marui J, Boulom S, Panthavee W, Momma M, Kusumoto K, Nakahara K, Saito M.	Biosci Microbiota Food Health	10.12938/bmfh.2014-018	2015
Genetics	First Insight into the Genome Sequence of Clostridium vincentii DSM 10228, Isolated from Sediment of the McMurdo Ice Shelf, Antarctica.	Poehlein A, Bolz S, Fischer B, Daniel R	Genome Announc	10.1128/genomeA.00334-18	2018
Phylogeny	Clostridium vincentii sp. nov., a new obligately anaerobic, saccharolytic, psychrophilic bacterium isolated from low-salinity pond sediment of the McMurdo Ice Shelf, Antarctica.	Mountfort DO, Rainey FA, Burghardt J, Kaspar HF, Stackebrandt E	Arch Microbiol	10.1007/s002030050416	1997

References

#3853	Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 10228
#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 vincentii (DSM 10228, lac-1)

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_002995745

16S sequences

Genome-based predictions

Predictions

Literature

Literature

References

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