Peptoclostridium litorale (DSM 5388, ATCC 49638, W6)

Name: Peptoclostridium litorale (DSM 5388, ATCC 49638, W6)
Creator: BacDive
License: http://creativecommons.org/licenses/by/4.0/

BacDive ID 2741

Type strain

Strain Designation W6

Culture col. no. DSM 5388 ATCC 49638 W6

NCBI tax ID(s) 1121324 1557

Special Collections DSMZ Literature strains

History DSMZ <- C. Fendrich, Universität Göttingen, Institut für Mikrobiologie, Germany; W6 <- C. Fendrich; {1986}

Links

Peptoclostridium litorale W6 is an anaerobe, spore-forming, Gram-negative bacterium that forms circular colonies and was isolated from anoxic marine sediment.

spore-forming Gram-negative motile curved-shaped colony-forming anaerobe genome sequence 16S sequence Bacteria

Name and taxonomic classification

SI-ID 45235

ATCC 49638,DSM 5388

@ref 20215

Last LPSN update 2026-05-29 08:25:32

Domain Bacteria

Phylum Bacillota

Class Clostridia

Order Peptostreptococcales

Family Peptostreptococcaceae

Genus Peptoclostridium

Species Peptoclostridium litorale

Full scientific name Peptoclostridium litorale (Fendrich et al. 1991) Galperin et al. 2016

Synonyms (1)

Clostridium litorale

Morphology

Cell morphology

@ref	Gram stain	Cell length	Cell width	Cell shape	Motility
25060	negative	2.0-8.0 µm	0.5-1.5 µm	curved-shaped

Colony morphology

@ref	Colony color	Colony shape
25060	brown	circular

Culture and growth conditions

Culture medium

@ref	Name	Growth	Medium link	Composition
2132	PEPTOCLOSTRIDIUM MEDIUM (BETAINE) (DSMZ Medium 487)		Medium recipe at MediaDive	Name: PEPTOCLOSTRIDIUM MEDIUM (BETAINE) (DSMZ Medium 487) Composition: NaCl 9.97009 g/l Betaine x H2O 5.98205 g/l NaHCO3 4.98504 g/l L-Alanine 2.19342 g/l Yeast extract 0.997009 g/l NH4Cl 0.997009 g/l MgSO4 x 7 H2O 0.498504 g/l K2HPO4 0.358923 g/l Na2S x 9 H2O 0.299103 g/l KH2PO4 0.229312 g/l CaCl2 x 2 H2O 0.0299103 g/l HCl 0.00249252 g/l FeCl2 x 4 H2O 0.00149551 g/l Sodium resazurin 0.000498504 g/l NaOH 0.000498504 g/l CoCl2 x 6 H2O 0.000189432 g/l Pyridoxine hydrochloride 9.97009e-05 g/l MnCl2 x 4 H2O 9.97009e-05 g/l ZnCl2 6.97906e-05 g/l p-Aminobenzoic acid 4.98504e-05 g/l Riboflavin 4.98504e-05 g/l (DL)-alpha-Lipoic acid 4.98504e-05 g/l Calcium D-(+)-pantothenate 4.98504e-05 g/l Nicotinic acid 4.98504e-05 g/l Thiamine HCl 4.98504e-05 g/l Na2MoO4 x 2 H2O 3.58923e-05 g/l NiCl2 x 6 H2O 2.39282e-05 g/l Biotin 1.99402e-05 g/l Folic acid 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 Vitamin B12 9.97009e-07 g/l Distilled water

Culture temp

@ref	Growth	Type	Temperature (°C)
2132	positive	growth	30
25060	positive	growth	15.0-40.0
25060	negative	growth	42

Culture pH

@ref	Ability	Type	PH
25060	positive	optimum	7.1-7.4
25060	positive	growth	6.5-8.4

Physiology and metabolism

Oxygen tolerance

@ref	Oxygen tolerance	Confidence
2132	anaerobe
25060	obligate anaerobe
125439	obligate anaerobe	99.546

Spore formation

@ref	Spore description	Type of spore	Spore formation
25060	ovoid,subterminal,1.5-2.0 µm in diameter	spore

Halophily

@ref	Salt	Growth	Tested relation	Concentration
25060	NaCl		growth	6 %

Metabolite utilization

@ref	Chebi-ID	Metabolite	Utilization activity	Kind of utilization tested
25060	17632 ChEBI	nitrate	-	reduction
25060	16189 ChEBI	sulfate	-	reduction
25060	16094 ChEBI	thiosulfate	-	reduction

Enzymes

@ref	Value	Activity	Ec
25060	catalase	-	1.11.1.6
25060	cytochrome oxidase	-	1.9.3.1

Pathway annotation

Computationally determined by

@ref	pathway	enzyme coverage	annotated reactions
66794	cellulose degradation	100	5 of 5
66794	biotin biosynthesis	100	4 of 4
66794	phenylmercury acetate degradation	100	2 of 2
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	threonine metabolism	100	10 of 10
66794	cis-vaccenate biosynthesis	100	2 of 2
66794	L-lactaldehyde degradation	100	3 of 3
66794	anapleurotic synthesis of oxalacetate	100	1 of 1
66794	UDP-GlcNAc biosynthesis	100	3 of 3
66794	CDP-diacylglycerol biosynthesis	100	2 of 2
66794	folate polyglutamylation	100	1 of 1
66794	coenzyme A metabolism	100	4 of 4
66794	factor 420 biosynthesis	100	5 of 5
66794	aminopropanol phosphate biosynthesis	100	2 of 2
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	reductive acetyl coenzyme A pathway	85.71	6 of 7
66794	tetrahydrofolate metabolism	85.71	12 of 14
66794	NAD metabolism	83.33	15 of 18
66794	glycolate and glyoxylate degradation	83.33	5 of 6
66794	flavin biosynthesis	80	12 of 15
66794	peptidoglycan biosynthesis	80	12 of 15
66794	alanine metabolism	79.31	23 of 29
66794	photosynthesis	78.57	11 of 14
66794	valine metabolism	77.78	7 of 9
66794	pyrimidine metabolism	77.78	35 of 45
66794	aspartate and asparagine metabolism	77.78	7 of 9
66794	molybdenum cofactor biosynthesis	77.78	7 of 9
66794	phenylalanine metabolism	76.92	10 of 13
66794	vitamin B1 metabolism	76.92	10 of 13
66794	glycolysis	76.47	13 of 17
66794	lactate fermentation	75	3 of 4
66794	glutamate and glutamine metabolism	75	21 of 28
66794	glycogen biosynthesis	75	3 of 4
66794	6-hydroxymethyl-dihydropterin diphosphate biosynthesis	75	6 of 8
66794	pentose phosphate pathway	72.73	8 of 11
66794	heme metabolism	71.43	10 of 14
66794	purine metabolism	71.28	67 of 94
66794	urea cycle	69.23	9 of 13
66794	methionine metabolism	69.23	18 of 26
66794	acetoin degradation	66.67	2 of 3
66794	octane oxidation	66.67	2 of 3
66794	selenocysteine biosynthesis	66.67	4 of 6
66794	serine metabolism	66.67	6 of 9
66794	formaldehyde oxidation	66.67	2 of 3
66794	d-mannose degradation	66.67	6 of 9
66794	citric acid cycle	64.29	9 of 14
66794	proline metabolism	63.64	7 of 11
66794	degradation of sugar alcohols	62.5	10 of 16
66794	isoleucine metabolism	62.5	5 of 8
66794	leucine metabolism	61.54	8 of 13
66794	cysteine metabolism	61.11	11 of 18
66794	glycine betaine biosynthesis	60	3 of 5
66794	glycogen metabolism	60	3 of 5
66794	lipoate biosynthesis	60	3 of 5
66794	starch degradation	60	6 of 10
66794	hydrogen production	60	3 of 5
66794	oxidative phosphorylation	58.24	53 of 91
66794	non-pathway related	57.89	22 of 38
66794	propanol degradation	57.14	4 of 7
66794	tryptophan metabolism	55.26	21 of 38
66794	histidine metabolism	55.17	16 of 29
66794	arginine metabolism	54.17	13 of 24
66794	lysine metabolism	52.38	22 of 42
66794	dTDPLrhamnose biosynthesis	50	4 of 8
66794	CMP-KDO biosynthesis	50	2 of 4
66794	sulfopterin metabolism	50	2 of 4
66794	toluene degradation	50	2 of 4
66794	suberin monomers biosynthesis	50	1 of 2
66794	kanosamine biosynthesis II	50	1 of 2
66794	acetate fermentation	50	2 of 4
66794	ethanol fermentation	50	1 of 2
66794	adipate degradation	50	1 of 2
66794	vitamin E metabolism	50	2 of 4
66794	glycine metabolism	50	5 of 10
66794	butanoate fermentation	50	2 of 4
66794	isoprenoid biosynthesis	50	13 of 26
66794	tyrosine metabolism	50	7 of 14
66794	sulfate reduction	46.15	6 of 13
66794	CO2 fixation in Crenarchaeota	44.44	4 of 9
66794	nitrate assimilation	44.44	4 of 9
66794	allantoin degradation	44.44	4 of 9
66794	ubiquinone biosynthesis	42.86	3 of 7
66794	cardiolipin biosynthesis	42.86	3 of 7
66794	lipid metabolism	41.94	13 of 31
66794	degradation of aromatic, nitrogen containing compounds	41.67	5 of 12
66794	O-antigen biosynthesis	40	2 of 5
66794	arachidonate biosynthesis	40	2 of 5
66794	propionate fermentation	40	4 of 10
66794	ketogluconate metabolism	37.5	3 of 8
66794	metabolism of disaccharids	36.36	4 of 11
66794	polyamine pathway	34.78	8 of 23
66794	acetyl CoA biosynthesis	33.33	1 of 3
66794	lipid A biosynthesis	33.33	3 of 9
66794	pantothenate biosynthesis	33.33	2 of 6
66794	enterobactin biosynthesis	33.33	1 of 3
66794	degradation of hexoses	33.33	6 of 18
66794	cyanate degradation	33.33	1 of 3
66794	IAA biosynthesis	33.33	1 of 3
66794	phenylpropanoid biosynthesis	30.77	4 of 13
66794	4-hydroxyphenylacetate degradation	30	3 of 10
66794	myo-inositol biosynthesis	30	3 of 10
66794	Entner Doudoroff pathway	30	3 of 10
66794	glutathione metabolism	28.57	4 of 14
66794	degradation of pentoses	28.57	8 of 28
66794	vitamin B6 metabolism	27.27	3 of 11
66794	dolichyl-diphosphooligosaccharide biosynthesis	27.27	3 of 11
66794	ascorbate metabolism	27.27	6 of 22
66794	phenol degradation	25	5 of 20
66794	cyclohexanol degradation	25	1 of 4
66794	alginate biosynthesis	25	1 of 4
66794	catecholamine biosynthesis	25	1 of 4
66794	phosphatidylethanolamine bioynthesis	23.08	3 of 13
66794	4-hydroxymandelate degradation	22.22	2 of 9

Isolation, sampling and environmental information

Isolation source categories

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

Isolation

@ref	Sample type	Geographic location	Country	Country ISO 3 Code	Continent
2132	anoxic marine sediment	North Sea coast, Jadebusen	Germany	DEU	Europe

Interaction and safety

Risk assessment

@ref	Biosafety level	Biosafety level comment
2132	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	CLIT1 assembly for Peptoclostridium litorale DSM 5388 W6	contig	GCA_000699585	1121324.10	2561511002	1121324	68.3
66792	IMG-taxon 2585428090 annotated assembly for Peptoclostridium litorale DSM 5388	scaffold	GCA_900141635	1121324.4	2585428090	1121324	65.51
66792	[Clostridium] litorale DSM 5388	contig		1121324.3		1121324	55.4

16S sequences

@ref	Description	Accession	Length	Database	NCBI tax ID
2132	Clostridium litorale 16S rRNA gene, strain DSM 5388	X77845	1507		1557

GC content

@ref	GC-content (mol%)	Method
2132	26.1	thermal denaturation, midpoint method (Tm)
25060	41.3	genome sequence analysis
2132	41.3	sequence analysis

Genome-based predictions

Predictions

Predictions from Deep Learning for Genome Sequence Data. R package version 0.3.1 based on: CLIT1 assembly for Peptoclostridium litorale DSM 5388 W6
NCBI: GCA_000699585

@ref	Trait	Model	Prediction	Confidence in %	In training data
125439	oxygen_tolerance	BacteriaNetⓘ	obligate anaerobe	99.55	no
125439	gram_stain	BacteriaNetⓘ	variable	56.86	no
125439	motility	BacteriaNetⓘ	yes	61.24	no
125439	spore_formation	BacteriaNetⓘ	yes	53.50	no

Predictions from bacterial phenotypic traits through improved machine learning using high-quality, curated datasets based on: Peptoclostridium litorale DSM 5388 DSM 5388
NCBI: GCA_900141635.1

@ref	Trait	Model	Prediction	Confidence in %	In training data
125438	gram-positive	gram-positiveⓘ	yes	52.09	yes
125438	anaerobic	anaerobicⓘ	yes	89.81	no
125438	aerobic	aerobicⓘ	no	92.24	yes
125438	spore-forming	spore-formingⓘ	yes	66.56	yes
125438	thermophilic	thermophileⓘ	no	81.81	yes
125438	flagellated	motile2+ⓘ	yes	79.13	no

Literature

Topic	Title	Authors	Journal	DOI	Year
Phylogeny	Phylogenomic analysis of the family Peptostreptococcaceae (Clostridium cluster XI) and proposal for reclassification of Clostridium litorale (Fendrich et al. 1991) and Eubacterium acidaminophilum (Zindel et al. 1989) as Peptoclostridium litorale gen. nov. comb. nov. and Peptoclostridium acidaminophilum comb. nov.	Galperin MY, Brover V, Tolstoy I, Yutin N.	Int J Syst Evol Microbiol	10.1099/ijsem.0.001548	2016
	Microbiota-Related Changes in Unconjugated Fecal Bile Acids Are Associated With Naturally Occurring, Insulin-Dependent Diabetes Mellitus in Dogs.	Jergens AE, Guard BC, Redfern A, Rossi G, Mochel JP, Pilla R, Chandra L, Seo YJ, Steiner JM, Lidbury J, Allenspach K, Suchodolski J.	Front Vet Sci	10.3389/fvets.2019.00199	2019
Metabolism	A Heterodimeric Reduced-Ferredoxin-Dependent Methylenetetrahydrofolate Reductase from Syngas-Fermenting Clostridium ljungdahlii.	Yi J, Huang H, Liang J, Wang R, Liu Z, Li F, Wang S.	Microbiol Spectr	10.1128/spectrum.00958-21	2021
Metabolism	Changes in the faecal bile acid profile in dogs fed dry food vs high content of beef: a pilot study.	Herstad KMV, Ronning HT, Bakke AM, Moe L, Skancke E.	Acta Vet Scand	10.1186/s13028-018-0383-7	2018
Phylogeny	Phylogenetic relationships of three amino-acid-utilizing anaerobes, Selenomonas acidaminovorans, 'Selenomonas acidaminophila' and Eubacterium acidaminophilum, as inferred from partial 16S rDNA nucleotide sequences and proposal of Thermanaerovibrio acidaminovorans gen. nov., comb. nov. and Anaeromusa acidaminophila gen. nov., comb. nov.	Baena S, Fardeau ML, Woo TH, Ollivier B, Labat M, Patel BK.	Int J Syst Bacteriol	10.1099/00207713-49-3-969	1999
Enzymology	Sarcosine reductase of Tissierella creatinophila: purification and characterization of its components.	Harms C, Ludwig U, Andreesen JR.	Arch Microbiol	10.1007/s002030050665	1998
Enzymology	Fast purification of thioredoxin reductases and of thioredoxins with an unusual redox-active centre from anaerobic, amino-acid-utilizing bacteria.	Harms C, Meyer MA, Andreesen JR.	Microbiology (Reading)	10.1099/00221287-144-3-793	1998
	Two closely linked genes encoding thioredoxin and thioredoxin reductase in Clostridium litorale.	Kreimer S, Sohling B, Andreesen JR.	Arch Microbiol	10.1007/s002030050506	1997
Enzymology	Glycine reductase of Clostridium litorale. Cloning, sequencing, and molecular analysis of the grdAB operon that contains two in-frame TGA codons for selenium incorporation.	Kreimer S, Andreesen JR.	Eur J Biochem	10.1111/j.1432-1033.1995.192_c.x	1995
	Specific alterations in gut microbiota are associated with prognosis of Budd-Chiari syndrome.	Sun YL, Li WQ, Ding PX, Wang ZW, Wei CH, Ma XX, Zhang RF, Wu Y, Zhou L, Liang RP, Zhang YP, Zhao YP, Zhu RT, Li J.	Oncotarget	10.18632/oncotarget.23234	2018
Phylogeny	Visceral hypersensitive rats share common dysbiosis features with irritable bowel syndrome patients.	Zhou XY, Li M, Li X, Long X, Zuo XL, Hou XH, Cong YZ, Li YQ.	World J Gastroenterol	10.3748/wjg.v22.i22.5211	2016
	A diet change from dry food to beef induces reversible changes on the faecal microbiota in healthy, adult client-owned dogs.	Herstad KMV, Gajardo K, Bakke AM, Moe L, Ludvigsen J, Rudi K, Rud I, Sekelja M, Skancke E.	BMC Vet Res	10.1186/s12917-017-1073-9	2017
Enzymology	Thioredoxin elicits a new dihydrolipoamide dehydrogenase activity by interaction with the electron-transferring flavoprotein in Clostridium litoralis and Eubacterium acidaminophilum.	Meyer M, Dietrichs D, Schmidt B, Andreesen JR.	J Bacteriol	10.1128/jb.173.4.1509-1513.1991	1991
Phylogeny	Microbial diversity within early-stage cultured Panulirus ornatus phyllosomas.	Payne MS, Hall MR, Sly L, Bourne DG.	Appl Environ Microbiol	10.1128/aem.02520-06	2007
Metabolism	Purification of NADPH-dependent electron-transferring flavoproteins and N-terminal protein sequence data of dihydrolipoamide dehydrogenases from anaerobic, glycine-utilizing bacteria.	Dietrichs D, Meyer M, Schmidt B, Andreesen JR.	J Bacteriol	10.1128/jb.172.4.2088-2095.1990	1990
Metabolism	Characterization of a defined 2,3,5, 6-tetrachlorobiphenyl-ortho-dechlorinating microbial community by comparative sequence analysis of genes coding for 16S rRNA.	Holoman TR, Elberson MA, Cutter LA, May HD, Sowers KR.	Appl Environ Microbiol	10.1128/aem.64.9.3359-3367.1998	1998
Enzymology	Isolation of an atypically small lipoamide dehydrogenase involved in the glycine decarboxylase complex from Eubacterium acidaminophilum.	Freudenberg W, Dietrichs D, Lebertz H, Andreesen JR.	J Bacteriol	10.1128/jb.171.3.1346-1354.1989	1989
Metabolism	Interaction of selenoprotein PA and the thioredoxin system, components of the NADPH-dependent reduction of glycine in Eubacterium acidaminophilum and Clostridium litorale [corrected].	Dietrichs D, Meyer M, Rieth M, Andreesen JR.	J Bacteriol	10.1128/jb.173.19.5983-5991.1991	1991
	First Insights into the Genome of the Amino Acid-Metabolizing Bacterium Clostridium litorale DSM 5388.	Poehlein A, Alghaithi HS, Chandran L, Chibani CM, Davydova E, Dhamotharan K, Ge W, Gutierrez-Gutierrez DA, Jagirdar A, Khonsari B, Nair KP, Daniel R	Genome Announc	10.1128/genomeA.00754-14	2014

References

#2132	Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 5388
#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 )
#25060	M. Y. B. Galperin, V.,Tolstoy, I.,Yutin, N.: Phylogenomic analysis of the family Peptostreptococcaceae (Clostridium cluster XI) and proposal for reclassification of Clostridium litorale (Fendrich et al. 1991) and Eubacterium acidaminophilum (Zindel et al. 1989) as Peptoclostridium litorale gen. nov. comb. nov. and Peptoclostridium acidaminophilum comb. nov. IJSEM 66: 5506 - 5513 2016 ( DOI 10.1099/ijsem.0.001548 , PubMed 27902180 )
#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 )
#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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Peptoclostridium litorale (DSM 5388, ATCC 49638, W6)

Name and taxonomic classification

Morphology

Cell morphology

Colony morphology

Culture and growth conditions

Culture medium

Culture temp

Culture pH

Physiology and metabolism

Oxygen tolerance

Spore formation

Halophily

Metabolite utilization

Enzymes

Pathway annotation

Isolation, sampling and environmental information

Isolation source categories

Isolation

Interaction and safety

Risk assessment

Sequence information

Genome sequences

Genome browser: GCA_000699585

16S sequences

GC content

Genome-based predictions

Predictions

Literature

Literature

References

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