Strain identifier

BacDive ID: 2741

Type strain: Yes

Species: Peptoclostridium litorale

Strain Designation: W6

Strain history: <- C. Fendrich, W6

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

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General

@ref: 2132

BacDive-ID: 2741

DSM-Number: 5388

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

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

NCBI tax id

NCBI tax idMatching level
1121324strain
1557species

strain history

  • @ref: 2132
  • history: <- C. Fendrich, W6

doi: 10.13145/bacdive2741.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/bacillota
  • domain: Bacteria
  • phylum: Bacillota
  • class: Clostridia
  • order: Eubacteriales
  • family: Peptostreptococcaceae
  • genus: Peptoclostridium
  • species: Peptoclostridium litorale
  • full scientific name: Peptoclostridium litorale (Fendrich et al. 1991) Galperin et al. 2016

  • synonyms

    • @ref: 20215
    • synonym: Clostridium litorale

@ref: 2132

domain: Bacteria

phylum: Firmicutes

class: Clostridia

order: Clostridiales

family: Peptostreptococcaceae

genus: Peptoclostridium

species: Peptoclostridium litorale

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

strain designation: W6

type strain: yes

Morphology

cell morphology

  • @ref: 25060
  • gram stain: negative
  • cell length: 2.0-8.0 µm
  • cell width: 0.5-1.5 µm
  • cell shape: curved-shaped
  • motility: yes

colony morphology

  • @ref: 25060
  • colony color: brown
  • colony shape: circular

Culture and growth conditions

culture medium

  • @ref: 2132
  • name: PEPTOCLOSTRIDIUM MEDIUM (BETAINE) (DSMZ Medium 487)
  • growth: yes
  • link: https://mediadive.dsmz.de/medium/487
  • composition: 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

@refgrowthtypetemperaturerange
2132positivegrowth30mesophilic
25060positivegrowth15.0-40.0
25060nogrowth42thermophilic

culture pH

@refabilitytypepH
25060positivegrowth6.5-8.4
25060positiveoptimum7.1-7.4

Physiology and metabolism

oxygen tolerance

@refoxygen tolerance
2132anaerobe
25060obligate anaerobe

spore formation

  • @ref: 25060
  • spore description: ovoid,subterminal,1.5-2.0 µm in diameter
  • type of spore: spore
  • spore formation: yes

halophily

  • @ref: 25060
  • salt: NaCl
  • growth: no
  • tested relation: growth
  • concentration: 6 %

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
2506017632nitrate-reduction
2506016189sulfate-reduction
2506016094thiosulfate-reduction

enzymes

@refvalueactivityec
25060catalase-1.11.1.6
25060cytochrome oxidase-1.9.3.1

Isolation, sampling and environmental information

isolation

  • @ref: 2132
  • sample type: anoxic marine sediment
  • geographic location: North Sea coast, Jadebusen
  • country: Germany
  • origin.country: DEU
  • continent: Europe

isolation source categories

Cat1Cat2Cat3
#Environmental#Aquatic#Marine
#Environmental#Aquatic#Sediment
#Condition#Anoxic (anaerobic)

Safety information

risk assessment

  • @ref: 2132
  • biosafety level: 1
  • biosafety level comment: Risk group (German classification)

Sequence information

16S sequences

  • @ref: 2132
  • description: Clostridium litorale 16S rRNA gene, strain DSM 5388
  • accession: X77845
  • length: 1507
  • database: ena
  • NCBI tax ID: 1557

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Peptoclostridium litorale DSM 5388 W6GCA_000699585contigncbi1121324
66792Peptoclostridium litorale DSM 5388GCA_900141635scaffoldncbi1121324
66792[Clostridium] litorale DSM 53881121324.3wgspatric1121324
66792Peptoclostridium litorale DSM 53881121324.4wgspatric1121324
66792Peptoclostridium litorale DSM 53882585428090draftimg1121324
66792Peptoclostridium litorale W62561511002draftimg1121324

GC content

@refGC-contentmethod
213226.1thermal denaturation, midpoint method (Tm)
2506041.3genome sequence analysis
213241.3sequence analysis

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
motileyes85.29yes
flagellatedno55.96no
gram-positiveyes75.743no
anaerobicyes99.504yes
aerobicno98.734yes
halophileno85.123no
spore-formingyes90.81yes
thermophileno80.307no
glucose-utilyes75.931no
glucose-fermentno55.567no

External links

@ref: 2132

culture collection no.: DSM 5388, ATCC 49638

straininfo link

  • @ref: 72270
  • straininfo: 45235

literature

  • Pubmed-ID: 25081264
  • title: First Insights into the Genome of the Amino Acid-Metabolizing Bacterium Clostridium litorale DSM 5388.
  • authors: 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
  • journal: Genome Announc
  • DOI: 10.1128/genomeA.00754-14
  • year: 2014

Reference

@idauthorscataloguedoi/urltitlejournalpubmed
2132Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 5388)https://www.dsmz.de/collection/catalogue/details/culture/DSM-5388
20215Parte, A.C., Sardà Carbasse, J., Meier-Kolthoff, J.P., Reimer, L.C. and Göker, M.10.1099/ijsem.0.004332List of Prokaryotic names with Standing in Nomenclature (LPSN) moves to the DSMZ
25060M. Y. B. Galperin, V.,Tolstoy, I.,Yutin, N.10.1099/ijsem.0.001548Phylogenomic 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. novIJSEM 66: 5506-5513 201627902180
66792Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmannhttps://diaspora-project.de/progress.html#genomesAutomatically annotated for the DiASPora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information)
66794Antje Chang, Lisa Jeske, Sandra Ulbrich, Julia Hofmann, Julia Koblitz, Ida Schomburg, Meina Neumann-Schaal, Dieter Jahn, Dietmar Schomburg10.1093/nar/gkaa1025BRENDA, the ELIXIR core data resource in 2021: new developments and updatesNucleic Acids Res. 49: D498-D508 202033211880
72270Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID45235.1StrainInfo: A central database for resolving microbial strain identifiers