Name: Peptoclostridium litorale W6
Creator: BacDive
License: https://creativecommons.org/licenses/by/4.0/

Strain identifier

BacDive ID: 2741

Type strain:

Species: Peptoclostridium litorale

Strain Designation: W6

Culture col. no.: DSM 5388, ATCC 49638

Strain history: <- C. Fendrich, Universität Göttingen, Institut für Mikrobiologie, Germany; W6 <- C. Fendrich; {1986}

NCBI tax ID(s): 1121324 (strain), 1557 (species)

SI-ID 45235

ATCC 49638, DSM 5388

Special Collections

Section

When using BacDive for research please cite our paper

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

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

Information on the name and the taxonomic classification. Name and taxonomic classification

	Last LPSN update	09-12-2024 (DD-MM-YYYY)
	Domain	*Bacteria*
	Phylum	*Bacillota*
	Class	*Clostridia*
	Order	*Eubacteriales*
	Family	*Peptostreptococcaceae*
	Genus	*Peptoclostridium*
	Species	**Peptoclostridium litorale**
	Full Scientific Name (LPSN)	Peptoclostridium litorale (Fendrich et al. 1991) Galperin et al. 2016

Synonym

Clostridium litorale

Information on morphological and physiological properties Morphology

[Ref.: #25060]	Gram stain	negative

[Ref.: #25060]	Cell length	2.0-8.0 µm

[Ref.: #25060]	Cell width	0.5-1.5 µm

[Ref.: #25060]	Cell shape	curved-shaped

[Ref.: #25060]	Motility	yes

[Ref.: #25060]	Colony color	brown
[Ref.: #25060]	Colony shape	circular

Information on culture and growth conditions Culture and growth conditions

[Ref.: #2132]

Culture medium

PEPTOCLOSTRIDIUM MEDIUM (BETAINE) (DSMZ Medium 487)

[Ref.: #2132]

Culture medium growth

[Ref.: #2132]

Culture medium link

Medium recipe at MediaDive

[Ref.: #2132]

Culture medium composition

expand / minimize

	Kind of temperature		Temperature
[Ref.: #2132]		growth	30 °C
[Ref.: #25060]		growth	15.0-40.0 °C
[Ref.: #25060]	negative	growth	42 °C

	pH	Kind of pH		pH
[Ref.: #25060]			optimum	7.1-7.4
[Ref.: #25060]			growth	6.5-8.4

Information on physiology and metabolism Physiology and metabolism

[Ref.: #2132]	Oxygen tolerance	anaerobe
[Ref.: #25060]	Oxygen tolerance	obligate anaerobe
[Ref.: #125439]	Oxygen tolerance	anaerobe Confidence in %99.9

[Ref.: #25060]	Spore description	ovoid,subterminal,1.5-2.0 µm in diameter
[Ref.: #25060]	Type of spore	spore
[Ref.: #25060]	Ability of spore formation	yes

	Halophily	Salt	Tested relation		Salt conc.
[Ref.: #25060]		NaCl	no	growth	6	%

	Metabolite	Utilization activity	Kind of utilization tested
[Ref.: #25060]	nitrate ChEBI	-	reduction
[Ref.: #25060]	sulfate ChEBI	-	reduction
[Ref.: #25060]	thiosulfate ChEBI	-	reduction

	Enzymes	Enzyme	Enzyme activity	EC number
[Ref.: #25060]		catalase	-	1.11.1.6
[Ref.: #25060]		cytochrome oxidase	-	1.9.3.1

	Pathway	Enzyme coverage	Annotated reactions
	Pathway annotation	Computationally determined by
[Ref.: #66794]	cellulose degradation	100	5 of 5
[Ref.: #66794]	biotin biosynthesis	100	4 of 4
[Ref.: #66794]	phenylmercury acetate degradation	100	2 of 2
[Ref.: #66794]	methylglyoxal degradation	100	5 of 5
[Ref.: #66794]	ppGpp biosynthesis	100	4 of 4
[Ref.: #66794]	C4 and CAM-carbon fixation	100	8 of 8
[Ref.: #66794]	palmitate biosynthesis	100	22 of 22
[Ref.: #66794]	threonine metabolism	100	10 of 10
[Ref.: #66794]	cis-vaccenate biosynthesis	100	2 of 2
[Ref.: #66794]	L-lactaldehyde degradation	100	3 of 3
[Ref.: #66794]	anapleurotic synthesis of oxalacetate	100	1 of 1
[Ref.: #66794]	UDP-GlcNAc biosynthesis	100	3 of 3
[Ref.: #66794]	CDP-diacylglycerol biosynthesis	100	2 of 2
[Ref.: #66794]	folate polyglutamylation	100	1 of 1
[Ref.: #66794]	coenzyme A metabolism	100	4 of 4
[Ref.: #66794]	factor 420 biosynthesis	100	5 of 5
[Ref.: #66794]	aminopropanol phosphate biosynthesis	100	2 of 2
[Ref.: #66794]	chorismate metabolism	88.89	8 of 9
[Ref.: #66794]	vitamin B12 metabolism	88.24	30 of 34
[Ref.: #66794]	gluconeogenesis	87.5	7 of 8
[Ref.: #66794]	reductive acetyl coenzyme A pathway	85.71	6 of 7
[Ref.: #66794]	tetrahydrofolate metabolism	85.71	12 of 14
[Ref.: #66794]	NAD metabolism	83.33	15 of 18
[Ref.: #66794]	glycolate and glyoxylate degradation	83.33	5 of 6
[Ref.: #66794]	flavin biosynthesis	80	12 of 15
[Ref.: #66794]	peptidoglycan biosynthesis	80	12 of 15
[Ref.: #66794]	alanine metabolism	79.31	23 of 29
[Ref.: #66794]	photosynthesis	78.57	11 of 14
[Ref.: #66794]	valine metabolism	77.78	7 of 9
[Ref.: #66794]	pyrimidine metabolism	77.78	35 of 45
[Ref.: #66794]	aspartate and asparagine metabolism	77.78	7 of 9
[Ref.: #66794]	molybdenum cofactor biosynthesis	77.78	7 of 9
[Ref.: #66794]	phenylalanine metabolism	76.92	10 of 13
[Ref.: #66794]	vitamin B1 metabolism	76.92	10 of 13
[Ref.: #66794]	glycolysis	76.47	13 of 17
[Ref.: #66794]	lactate fermentation	75	3 of 4
[Ref.: #66794]	glutamate and glutamine metabolism	75	21 of 28
[Ref.: #66794]	glycogen biosynthesis	75	3 of 4
[Ref.: #66794]	6-hydroxymethyl-dihydropterin diphosphate biosynthesis	75	6 of 8
[Ref.: #66794]	pentose phosphate pathway	72.73	8 of 11
[Ref.: #66794]	heme metabolism	71.43	10 of 14
[Ref.: #66794]	purine metabolism	71.28	67 of 94
[Ref.: #66794]	urea cycle	69.23	9 of 13
[Ref.: #66794]	methionine metabolism	69.23	18 of 26
[Ref.: #66794]	acetoin degradation	66.67	2 of 3
[Ref.: #66794]	octane oxidation	66.67	2 of 3
[Ref.: #66794]	selenocysteine biosynthesis	66.67	4 of 6
[Ref.: #66794]	serine metabolism	66.67	6 of 9
[Ref.: #66794]	formaldehyde oxidation	66.67	2 of 3
[Ref.: #66794]	d-mannose degradation	66.67	6 of 9
[Ref.: #66794]	citric acid cycle	64.29	9 of 14
[Ref.: #66794]	proline metabolism	63.64	7 of 11
[Ref.: #66794]	degradation of sugar alcohols	62.5	10 of 16
[Ref.: #66794]	isoleucine metabolism	62.5	5 of 8
[Ref.: #66794]	leucine metabolism	61.54	8 of 13
[Ref.: #66794]	cysteine metabolism	61.11	11 of 18
[Ref.: #66794]	glycine betaine biosynthesis	60	3 of 5
[Ref.: #66794]	glycogen metabolism	60	3 of 5
[Ref.: #66794]	lipoate biosynthesis	60	3 of 5
[Ref.: #66794]	starch degradation	60	6 of 10
[Ref.: #66794]	hydrogen production	60	3 of 5
[Ref.: #66794]	oxidative phosphorylation	58.24	53 of 91
[Ref.: #66794]	non-pathway related	57.89	22 of 38
[Ref.: #66794]	propanol degradation	57.14	4 of 7
[Ref.: #66794]	tryptophan metabolism	55.26	21 of 38
[Ref.: #66794]	histidine metabolism	55.17	16 of 29
[Ref.: #66794]	arginine metabolism	54.17	13 of 24
[Ref.: #66794]	lysine metabolism	52.38	22 of 42
[Ref.: #66794]	dTDPLrhamnose biosynthesis	50	4 of 8
[Ref.: #66794]	CMP-KDO biosynthesis	50	2 of 4
[Ref.: #66794]	sulfopterin metabolism	50	2 of 4
[Ref.: #66794]	toluene degradation	50	2 of 4
[Ref.: #66794]	suberin monomers biosynthesis	50	1 of 2
[Ref.: #66794]	kanosamine biosynthesis II	50	1 of 2
[Ref.: #66794]	acetate fermentation	50	2 of 4
[Ref.: #66794]	ethanol fermentation	50	1 of 2
[Ref.: #66794]	adipate degradation	50	1 of 2
[Ref.: #66794]	vitamin E metabolism	50	2 of 4
[Ref.: #66794]	glycine metabolism	50	5 of 10
[Ref.: #66794]	butanoate fermentation	50	2 of 4
[Ref.: #66794]	isoprenoid biosynthesis	50	13 of 26
[Ref.: #66794]	tyrosine metabolism	50	7 of 14
[Ref.: #66794]	sulfate reduction	46.15	6 of 13
[Ref.: #66794]	CO2 fixation in Crenarchaeota	44.44	4 of 9
[Ref.: #66794]	nitrate assimilation	44.44	4 of 9
[Ref.: #66794]	allantoin degradation	44.44	4 of 9
[Ref.: #66794]	ubiquinone biosynthesis	42.86	3 of 7
[Ref.: #66794]	cardiolipin biosynthesis	42.86	3 of 7
[Ref.: #66794]	lipid metabolism	41.94	13 of 31
[Ref.: #66794]	degradation of aromatic, nitrogen containing compounds	41.67	5 of 12
[Ref.: #66794]	O-antigen biosynthesis	40	2 of 5
[Ref.: #66794]	arachidonate biosynthesis	40	2 of 5
[Ref.: #66794]	propionate fermentation	40	4 of 10
[Ref.: #66794]	ketogluconate metabolism	37.5	3 of 8
[Ref.: #66794]	metabolism of disaccharids	36.36	4 of 11
[Ref.: #66794]	polyamine pathway	34.78	8 of 23
[Ref.: #66794]	acetyl CoA biosynthesis	33.33	1 of 3
[Ref.: #66794]	lipid A biosynthesis	33.33	3 of 9
[Ref.: #66794]	pantothenate biosynthesis	33.33	2 of 6
[Ref.: #66794]	enterobactin biosynthesis	33.33	1 of 3
[Ref.: #66794]	degradation of hexoses	33.33	6 of 18
[Ref.: #66794]	cyanate degradation	33.33	1 of 3
[Ref.: #66794]	IAA biosynthesis	33.33	1 of 3
[Ref.: #66794]	phenylpropanoid biosynthesis	30.77	4 of 13
[Ref.: #66794]	4-hydroxyphenylacetate degradation	30	3 of 10
[Ref.: #66794]	myo-inositol biosynthesis	30	3 of 10
[Ref.: #66794]	Entner Doudoroff pathway	30	3 of 10
[Ref.: #66794]	glutathione metabolism	28.57	4 of 14
[Ref.: #66794]	degradation of pentoses	28.57	8 of 28
[Ref.: #66794]	vitamin B6 metabolism	27.27	3 of 11
[Ref.: #66794]	dolichyl-diphosphooligosaccharide biosynthesis	27.27	3 of 11
[Ref.: #66794]	ascorbate metabolism	27.27	6 of 22
[Ref.: #66794]	phenol degradation	25	5 of 20
[Ref.: #66794]	cyclohexanol degradation	25	1 of 4
[Ref.: #66794]	alginate biosynthesis	25	1 of 4
[Ref.: #66794]	catecholamine biosynthesis	25	1 of 4
[Ref.: #66794]	phosphatidylethanolamine bioynthesis	23.08	3 of 13
[Ref.: #66794]	4-hydroxymandelate degradation	22.22	2 of 9
		Only first 10 entries are displayed. Click here to see all.

Information on isolation source, the sampling and environmental conditions Isolation, sampling and environmental information

[Ref.: #2132]	Sample type/isolated from	anoxic marine sediment
[Ref.: #2132]	Geographic location (country and/or sea, region)	North Sea coast, Jadebusen
[Ref.: #2132]	Country	Germany
[Ref.: #2132]	Country ISO 3 Code	DEU
[Ref.: #2132]	Continent	Europe
* marker position based on {}

Isolation sources categories

#Environmental	#Aquatic	#Marine
#Environmental	#Aquatic	#Sediment
#Condition	#Anoxic (anaerobic)	-

What are isolation sources categories?

Information on possible application of the strain and its possible interaction with e.g. potential hosts Safety information

[Ref.: #2132]

Biosafety level

Risk group (German classification)
According to TRBA 466

Information on genomic background e.g. entries in nucleic sequence databass Sequence information

16S Sequence information:

	Sequence accession description	Seq. accession number	Sequence length (bp)	Sequence database	Associated NCBI tax ID
[Ref.: #2132]	Clostridium litorale 16S rRNA gene, strain DSM 5388	X77845	1507	GenBank ENA	1557 tax ID

Genome sequence information:

Only first 5 entries are displayed. Click here to see all.

	Sequence accession description	Seq. accession number	Assembly level	Sequence database	Associated NCBI tax ID
[Ref.: #66792]	Peptoclostridium litorale DSM 5388 W6	GCA_000699585	contig	GenBank ENA	1121324 tax ID	*
[Ref.: #66792]	Peptoclostridium litorale DSM 5388	GCA_900141635	scaffold	GenBank ENA	1121324 tax ID	*
[Ref.: #66792]	[Clostridium] litorale DSM 5388	1121324.3	wgs	PATRIC	1121324 tax ID	*
[Ref.: #66792]	Peptoclostridium litorale DSM 5388	1121324.4	wgs	PATRIC	1121324 tax ID	*
[Ref.: #66792]	Peptoclostridium litorale DSM 5388	2585428090	draft	JGI IMG/M	1121324 tax ID	*
[Ref.: #66792]	Peptoclostridium litorale W6	2561511002	draft	JGI IMG/M	1121324 tax ID	*

[Ref.: #2132]	GC-content	26.1 mol%	thermal denaturation, midpoint method (Tm)
[Ref.: #25060]	GC-content	41.3 mol%	genome sequence analysis
[Ref.: #2132]	GC-content	41.3 mol%	sequence analysis

Data predicted using genome information as a basis Genome-based predictions

	Model	Trait	Prediction	Confidence in %	In training data
	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.: #125438]	gram-positive	gram-positiveⓘ	yes	52.089	yes
[Ref.: #125438]	anaerobic	anaerobicⓘ	yes	89.812	no
[Ref.: #125438]	aerobic	aerobicⓘ	no	92.24	yes
[Ref.: #125438]	spore-forming	spore-formingⓘ	yes	66.558	yes
[Ref.: #125438]	thermophile	thermophilicⓘ	no	81.811	yes
[Ref.: #125438]	motile2+	flagellatedⓘ	yes	79.126	no

	Model	Trait	Prediction	Confidence in %
	Predictions from Deep Learning for Genome Sequence Data. R package version 0.3.1 based on: Peptoclostridium litorale DSM 5388 NCBI: GCA_900141635
[Ref.: #125439]	BacteriaNet	oxygen_toleranceⓘ	anaerobe	99.9
[Ref.: #125439]	BacteriaNet	gram_stainⓘ	variable	73.1
[Ref.: #125439]	BacteriaNet	motilityⓘ	yes	62.8
[Ref.: #125439]	BacteriaNet	spore_formationⓘ	yes	50.1

Availability in culture collections External links

[Ref.: #2132]

Culture collection no.

DSM 5388, ATCC 49638

[Ref.: #72270]

SI-ID 45235

Literature:

	Title	Authors	Journal	DOI	Year
	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 )

#72270

Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.: StrainInfo: A central database for resolving microbial strain identifiers . ( DOI 10.60712/SI-ID45235.1 )

#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 .

* These data were automatically processed and therefore are not curated

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Peptoclostridium litorale DSM 5388 DSM 5388

Peptoclostridium litorale DSM 5388

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