Strain identifier

BacDive ID: 2776

Type strain: Yes

Species: Clostridium estertheticum

Strain Designation: MT1

Strain history: CIP <- 1997, NCIMB <- J.L. Smart: strain MT1

NCBI tax ID(s): 238834 (species)

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General

@ref: 3410

BacDive-ID: 2776

DSM-Number: 8809

keywords: genome sequence, 16S sequence, Bacteria, anaerobe, spore-forming, psychrophilic, motile

description: Clostridium estertheticum MT1 is an anaerobe, spore-forming, psychrophilic bacterium that was isolated from vacuum packed beef.

NCBI tax id

  • NCBI tax id: 238834
  • Matching level: species

strain history

@refhistory
3410<- NCIMB <- J. L. Smart, AFRC, Institute of Food Research, Langford Bristol, U.K.; MT1
119135CIP <- 1997, NCIMB <- J.L. Smart: strain MT1

doi: 10.13145/bacdive2776.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/bacillota
  • domain: Bacteria
  • phylum: Bacillota
  • class: Clostridia
  • order: Eubacteriales
  • family: Clostridiaceae
  • genus: Clostridium
  • species: Clostridium estertheticum
  • full scientific name: Clostridium estertheticum Collins et al. 1993

@ref: 3410

domain: Bacteria

phylum: Firmicutes

class: Clostridia

order: Clostridiales

family: Clostridiaceae

genus: Clostridium

species: Clostridium estertheticum

full scientific name: Clostridium estertheticum Collins et al. 1993 emend. Spring et al. 2003

strain designation: MT1

type strain: yes

Morphology

cell morphology

@refmotilityconfidencegram staincell shape
69480yes94.855
69480100positive
119135nopositiverod-shaped

colony morphology

  • @ref: 3410
  • incubation period: >14 days

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
3410RCM MEDIUM (N2/CO2) (DSMZ Medium 634c)yeshttps://mediadive.dsmz.de/medium/634cName: RCM MEDIUM (N2/CO2) (DSMZ Medium 634c) Composition: dehydrated RCM medium 38.0 g/l Sodium carbonate 1.0 g/l Sodium resazurin 0.0005 g/l Distilled water
39195MEDIUM 20 - for Anaerobic bacteriayesAgar (15.000 g);Glucose (5.000 g);Yeast extract (20.000 g);Tryptone (30.000 g);Cysteine hydrochloride (0.500 g);distilled water (1000.000 ml);Hemin solution -M00149 (25.000 ml)
119135CIP Medium 20yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=20

culture temp

@refgrowthtypetemperaturerange
3410positivegrowth10psychrophilic
39195positivegrowth10psychrophilic

Physiology and metabolism

oxygen tolerance

@refoxygen toleranceconfidence
3410anaerobe
69480anaerobe99.513

spore formation

@refspore formationconfidence
69481yes100
69480yes99.999
119135yes

Isolation, sampling and environmental information

isolation

@refsample type
3410vacuum packed beef
119135Food, Vacuum packed beef

isolation source categories

Cat1Cat2Cat3
#Engineered#Food production#Bottled, canned, packed food
#Engineered#Food production#Meat

taxonmaps

  • @ref: 69479
  • File name: preview.99_505.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_34;96_327;97_364;98_413;99_505&stattab=map
  • Last taxonomy: Clostridium
  • 16S sequence: S46734
  • Sequence Identity:
  • Total samples: 18467
  • soil counts: 9246
  • aquatic counts: 5428
  • animal counts: 1548
  • plant counts: 2245

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
34101Risk group (German classification)
1191352Risk group (French classification)

Sequence information

16S sequences

@refdescriptionaccessionlengthdatabaseNCBI tax ID
20218Clostridium estertheticum subsp. estertheticum strain DSM 8809 16S ribosomal RNA gene, partial sequenceDQ911250328ena1552
20218Clostridium estertheticum strain NCIBM 12511 16S ribosomal RNA gene, partial sequenceS467341427ena238834

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Clostridium estertheticum subsp. estertheticum DSM 8809GCA_001877035completencbi1552
66792Clostridium estertheticum subsp. estertheticum strain DSM 88091552.13completepatric1552
66792Clostridium estertheticum subsp. estertheticum strain DSM 88091552.14plasmidpatric1552
66792Clostridium estertheticum estertheticum DSM 88092721755605completeimg1552

GC content

  • @ref: 3410
  • GC-content: 30.9
  • method: sequence analysis

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingyes100no
flagellatedyes59.82no
gram-positiveyes70.488no
anaerobicyes96.978yes
aerobicno96.679yes
halophileno97.172no
spore-formingyes93.302no
thermophileno98.599no
glucose-utilyes92.181no
motileyes80.756no
glucose-fermentyes68.948no

External links

@ref: 3410

culture collection no.: DSM 8809, ATCC 51377, NCIMB 12511, CIP 105093

straininfo link

  • @ref: 72306
  • straininfo: 42959

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny1383083Taxonomic studies on a psychrophilic Clostridium from vacuum-packed beef: description of Clostridium estertheticum sp. nov.Collins MD, Rodrigues UM, Dainty RH, Edwards RA, Roberts TAFEMS Microbiol Lett10.1016/0378-1097(92)90410-p1992Animals, Base Sequence, Cattle, Clostridium/*classification/genetics/isolation & purification, *Food Microbiology, Food Preservation, Meat/*microbiology, Molecular Sequence Data, Phylogeny, RNA, Bacterial/genetics, RNA, Ribosomal, 16S/genetics, VacuumBiotechnology
Phylogeny12892121Characterization of novel psychrophilic clostridia from an Antarctic microbial mat: description of Clostridium frigoris sp. nov., Clostridium lacusfryxellense sp. nov., Clostridium bowmanii sp. nov. and Clostridium psychrophilum sp. nov. and reclassification of Clostridium laramiense as Clostridium estertheticum subsp. laramiense subsp. nov.Spring S, Merkhoffer B, Weiss N, Kroppenstedt RM, Hippe H, Stackebrandt EInt J Syst Evol Microbiol10.1099/ijs.0.02554-02003Antarctic Regions, Clostridium/*classification/genetics/isolation & purification/metabolism, DNA, Bacterial/genetics, DNA, Ribosomal/genetics, Fresh Water/microbiology, Genotype, Molecular Sequence Data, Phenotype, Phylogeny, RNA, Bacterial/genetics, RNA, Ribosomal, 16S/genetics, Species Specificity, Terminology as TopicGenetics
Metabolism19027974Substrate utilization by Clostridium estertheticum cultivated in meat juice medium.Yang X, Balamurugan S, Gill COInt J Food Microbiol10.1016/j.ijfoodmicro.2008.10.0242008Acetates/metabolism, Animals, Butyrates/metabolism, Clostridium/*growth & development/*metabolism, Colony Count, Microbial, Fermentation, Food Contamination/*analysis/prevention & control, Food Packaging/methods, Food Preservation/*methods, Glucose/*metabolism, Hydrogen-Ion Concentration, Kinetics, Lactic Acid/metabolism, Meat/*microbiology, RNA, Ribosomal, 16S/chemistry/genetics, Temperature, Time Factors, VacuumEnzymology
Biotechnology19903404Effects of temperature and pH on the growth of bacteria isolated from blown packs of vacuum-packaged beef.Yang X, Gill CO, Balamurugan SJ Food Prot10.4315/0362-028x-72.11.23802009Animals, Carnobacterium/growth & development, Cattle, Clostridium/growth & development, Colony Count, Microbial, Food Contamination/*analysis, Food Handling/methods, Food Microbiology, Food Packaging/*methods, Food Preservation/*methods, Gram-Positive Bacteria/*growth & development, Humans, Hydrogen-Ion Concentration, Kinetics, Lactococcus lactis/growth & development, Leuconostoc/growth & development, Meat/*microbiology, Temperature, VacuumPathogenicity
Genetics27891116Complete Genome Sequence of Clostridium estertheticum DSM 8809, a Microbe Identified in Spoiled Vacuum Packed Beef.Yu Z, Gunn L, Brennan E, Reid R, Wall PG, Gaora PO, Hurley D, Bolton D, Fanning SFront Microbiol10.3389/fmicb.2016.017642016

Reference

@idauthorscataloguedoi/urltitlejournalpubmed
3410Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 8809)https://www.dsmz.de/collection/catalogue/details/culture/DSM-8809
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
39195Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/17073
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)
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
69480Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmannhttps://diaspora-project.de/progress.html#genomesPredictions based on genome sequence made in the Diaspora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information)
69481Xiao-Yin To, René Mreches, Martin Binder, Alice C. McHardy, Philipp C. Münch10.21203/rs.3.rs-2527258/v1Predictions based on the model GenomeNet Sporulation v. 1
72306Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID42959.1StrainInfo: A central database for resolving microbial strain identifiers
119135Curators of the CIPCollection of Institut Pasteur (CIP 105093)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20105093