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Strain identifier

BacDive ID: 2832

Type strain: Yes

Species: Clostridium schirmacherense

Strain Designation: AP15

Strain history: L. Singh AP15.

NCBI tax ID(s): 351628 (species)

For citation purpose refer to the digital object identifier (doi) of the current version.
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General

@ref: 6946

BacDive-ID: 2832

DSM-Number: 17394

keywords: 16S sequence, Bacteria, anaerobe, spore-forming, psychrophilic, Gram-positive, motile, rod-shaped

description: Clostridium schirmacherense AP15 is an anaerobe, spore-forming, psychrophilic bacterium that was isolated from lake sediment.

NCBI tax id

  • NCBI tax id: 351628
  • Matching level: species

strain history

doi: 10.13145/bacdive2832.20221219.7.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/bacillota
  • domain: Bacteria
  • phylum: Bacillota
  • class: Clostridia
  • order: Eubacteriales
  • family: Clostridiaceae
  • genus: Clostridium
  • species: Clostridium schirmacherense
  • full scientific name: Clostridium schirmacherense Alam et al. 2006

@ref: 6946

domain: Bacteria

phylum: Firmicutes

class: Clostridia

order: Clostridiales

family: Clostridiaceae

genus: Clostridium

species: Clostridium schirmacherense

full scientific name: Clostridium schirmacherense Alam et al. 2006

strain designation: AP15

type strain: yes

Morphology

cell morphology

  • @ref: 31559
  • gram stain: positive
  • cell length: 02-04 µm
  • cell width: 0.5-0.7 µm
  • cell shape: rod-shaped
  • motility: yes

pigmentation

  • @ref: 31559
  • production: yes

Culture and growth conditions

culture medium

  • @ref: 6946
  • name: CHOPPED MEAT MEDIUM WITH CARBOHYDRATES (DSMZ Medium 110)
  • growth: yes
  • link: https://mediadive.dsmz.de/medium/110
  • composition: 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

@refgrowthtypetemperaturerange
6946positivegrowth20psychrophilic
31559positivegrowth05-35
31559positiveoptimum05-10psychrophilic
67770positivegrowth30mesophilic

culture pH

@refabilitytypepHPH range
31559positivegrowth06-09alkaliphile
31559positiveoptimum8

Physiology and metabolism

oxygen tolerance

@refoxygen tolerance
6946anaerobe
31559anaerobe

spore formation

  • @ref: 31559
  • spore formation: yes

halophily

  • @ref: 31559
  • salt: NaCl
  • growth: positive
  • tested relation: growth
  • concentration: 0-7.5 %

observation

  • @ref: 31559
  • observation: aggregates in chains

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
3155915963ribitol+carbon source
3155917234glucose+carbon source
3155916634raffinose+carbon source
3155926546rhamnose+carbon source
3155933942ribose+carbon source
315594853esculin+hydrolysis

metabolite production

  • @ref: 31559
  • Chebi-ID: 16136
  • metabolite: hydrogen sulfide
  • production: yes

enzymes

  • @ref: 31559
  • value: gelatinase
  • activity: +

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcontinentcountryorigin.country
6946lake sedimentSchirmacher OasisAustralia and Oceania
67770Lake sediment of Schirmacher OasisAntarcticaAntarcticaATA

isolation source categories

Cat1Cat2Cat3
#Environmental#Aquatic#Lake (large)
#Environmental#Aquatic#Sediment

taxonmaps

  • @ref: 69479
  • File name: preview.99_4630.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_34;96_2305;97_2799;98_3476;99_4630&stattab=map
  • Last taxonomy: Clostridium
  • 16S sequence: AM114453
  • Sequence Identity:
  • Total samples: 2886
  • soil counts: 677
  • aquatic counts: 339
  • animal counts: 1770
  • plant counts: 100

Safety information

risk assessment

  • @ref: 6946
  • biosafety level: 1
  • biosafety level comment: Risk group (German classification)

Sequence information

16S sequences

  • @ref: 6946
  • description: Clostridium schirmacherense partial 16S rRNA gene, type strain AP15T
  • accession: AM114453
  • length: 1457
  • database: ena
  • NCBI tax ID: 351628

GC content

@refGC-contentmethod
694624
6777024thermal denaturation, midpoint method (Tm)

External links

@ref: 6946

culture collection no.: DSM 17394, JCM 13289

straininfo link

@refpassport
20218http://www.straininfo.net/strains/677347
20218http://www.straininfo.net/strains/677348

literature

  • topic: Phylogeny
  • Pubmed-ID: 16585682
  • title: Clostridium schirmacherense sp. nov., an obligately anaerobic, proteolytic, psychrophilic bacterium isolated from lake sediment of Schirmacher Oasis, Antarctica.
  • authors: Alam SI, Dixit A, Reddy GSN, Dube S, Palit M, Shivaji S, Singh L
  • journal: Int J Syst Evol Microbiol
  • DOI: 10.1099/ijs.0.63808-0
  • year: 2006
  • mesh: Amino Acids/metabolism, Bacteria, Anaerobic, Clostridium/*classification/genetics/isolation & purification/metabolism, Cold Temperature, DNA, Bacterial/analysis, Fermentation, Geologic Sediments, Molecular Sequence Data, Peptides/*metabolism, RNA, Ribosomal, 16S/genetics, *Water Microbiology
  • topic2: Metabolism

Reference

@idauthorscataloguedoi/urltitlejournalpubmedID_cross_reference
6946Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 17394)https://www.dsmz.de/collection/catalogue/details/culture/DSM-17394
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
20218Verslyppe, B., De Smet, W., De Baets, B., De Vos, P., Dawyndt P.10.1016/j.syapm.2013.11.002StrainInfo introduces electronic passports for microorganisms.Syst Appl Microbiol. 37: 42-50 201424321274
2784910.1099/ijs.0.63808-016585682
31559Barberan A, Caceres Velazquez H, Jones S, Fierer N.10.1128/mSphere.00237-17Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information2877604127849
67770Curators of the JCMhttps://jcm.brc.riken.jp/en/
69479João 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.https://microbeatlas.org/MicrobeAtlas 1.0 beta