Strain identifier

BacDive ID: 2558

Type strain: No

Species: Paraclostridium bifermentans

Strain Designation: TYR6

Strain history: CIP <- 2000, J.L. Garcia, IRD, Marseille, France: strain TYR6, Clostridium bifermentans

NCBI tax ID(s): 1490 (species)

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General

@ref: 5088

BacDive-ID: 2558

DSM-Number: 13560

keywords: 16S sequence, Bacteria, anaerobe, spore-forming, mesophilic, Gram-positive, rod-shaped, human pathogen

description: Paraclostridium bifermentans TYR6 is an anaerobe, spore-forming, mesophilic human pathogen that was isolated from olive mill wastewaters.

NCBI tax id

  • NCBI tax id: 1490
  • Matching level: species

strain history

@refhistory
5088<- J.-L. Garcia, Lab. Microbiol. de l'IRD/ESIL, Univ. de Provence et de la Méditerranée, Marseille, France; TYR6 <- M. Chamkha
116805CIP <- 2000, J.L. Garcia, IRD, Marseille, France: strain TYR6, Clostridium bifermentans

doi: 10.13145/bacdive2558.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/bacillota
  • domain: Bacteria
  • phylum: Bacillota
  • class: Clostridia
  • order: Eubacteriales
  • family: Clostridiaceae
  • genus: Paraclostridium
  • species: Paraclostridium bifermentans
  • full scientific name: Paraclostridium bifermentans (Weinberg and Séguin 1918) Sasi Jyothsna et al. 2016

  • synonyms

    @refsynonym
    20215Clostridium bifermentans
    20215Bacillus bifermentans

@ref: 5088

domain: Bacteria

phylum: Firmicutes

class: Clostridia

order: Clostridiales

family: Clostridiaceae

genus: Paraclostridium

species: Paraclostridium bifermentans

full scientific name: Paraclostridium bifermentans (Weinberg and Séguin 1918) Sasi Jyothsna et al. 2016 emend. Kutsuna et al. 2018

strain designation: TYR6

type strain: no

Morphology

cell morphology

  • @ref: 116805
  • gram stain: positive
  • cell shape: rod-shaped
  • motility: no

colony morphology

  • @ref: 116805

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
5088PY + X MEDIUM (DSMZ Medium 104b)yeshttps://mediadive.dsmz.de/medium/104bName: PY + X MEDIUM (DSMZ Medium 104b) Composition: Yeast extract 10.0 g/l D-Glucose 5.0 g/l Trypticase peptone 5.0 g/l Meat peptone 5.0 g/l L-Cysteine HCl x H2O 0.5 g/l NaHCO3 0.4 g/l NaCl 0.08 g/l KH2PO4 0.04 g/l K2HPO4 0.04 g/l MgSO4 x 7 H2O 0.02 g/l CaCl2 x 2 H2O 0.01 g/l Sodium resazurin 0.0005 g/l Distilled water
32997MEDIUM 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)
116805CIP Medium 20yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=20

culture temp

@refgrowthtypetemperaturerange
5088positivegrowth37mesophilic
32997positivegrowth37mesophilic

Physiology and metabolism

oxygen tolerance

@refoxygen tolerance
5088anaerobe
116805anaerobe

spore formation

  • @ref: 116805
  • spore formation: yes

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
11680517108D-arabinose-degradation
11680515824D-fructose+/-degradation
11680517634D-glucose+/-degradation
11680565327D-xylose-degradation
11680517057cellobiose-degradation
11680517716lactose-degradation
11680517306maltose+/-degradation
11680517814salicin-degradation
11680517992sucrose-degradation
1168054853esculin+hydrolysis
11680517632nitrate-reduction
11680516301nitrite+reduction
11680517632nitrate+respiration

antibiotic resistance

  • @ref: 116805
  • ChEBI: 6909
  • metabolite: metronidazole
  • is antibiotic: yes
  • is sensitive: yes
  • is resistant: no

metabolite production

  • @ref: 116805
  • Chebi-ID: 35581
  • metabolite: indole
  • production: no

enzymes

@refvalueactivityec
68382alpha-fucosidase-3.2.1.51
68382alpha-mannosidase-3.2.1.24
68382N-acetyl-beta-glucosaminidase-3.2.1.52
68382beta-glucosidase+3.2.1.21
68382alpha-glucosidase-3.2.1.20
68382beta-glucuronidase-3.2.1.31
68382beta-galactosidase-3.2.1.23
68382alpha-galactosidase-3.2.1.22
68382naphthol-AS-BI-phosphohydrolase+
68382acid phosphatase+3.1.3.2
68382alpha-chymotrypsin-3.4.21.1
68382trypsin-3.4.21.4
68382cystine arylamidase-3.4.11.3
68382valine arylamidase-
68382leucine arylamidase+3.4.11.1
68382lipase (C 14)-
68382esterase lipase (C 8)+
68382esterase (C 4)+
68382alkaline phosphatase+3.1.3.1
116805oxidase-
116805beta-galactosidase-3.2.1.23
116805gelatinase+/-
116805amylase-
116805DNase-
116805caseinase+3.4.21.50
116805catalase-1.11.1.6
116805tween esterase-
116805lecithinase+
116805lipase-
116805protease+
116805urease-3.5.1.5

API zym

@refControlAlkaline phosphataseEsteraseEsterase LipaseLipaseLeucine arylamidaseValine arylamidaseCystine arylamidaseTrypsinalpha- ChymotrypsinAcid phosphataseNaphthol-AS-BI-phosphohydrolasealpha- Galactosidasebeta- Galactosidasebeta- Glucuronidasealpha- Glucosidasebeta- GlucosidaseN-acetyl-beta- glucosaminidasealpha- Mannosidasealpha- Fucosidase
116805-+++-+----++----+---

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinentisolation date
5088olive mill wastewatersMarseilleFranceFRAEurope
116805Environment, Olive mill, wastewaterMarseilleFranceFRAEurope1998

isolation source categories

  • Cat1: #Engineered
  • Cat2: #Waste
  • Cat3: #Industrial wastewater

taxonmaps

  • @ref: 69479
  • File name: preview.99_532.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_2;96_337;97_376;98_432;99_532&stattab=map
  • Last taxonomy: Paeniclostridium
  • 16S sequence: AF320283
  • Sequence Identity:
  • Total samples: 51554
  • soil counts: 14269
  • aquatic counts: 9424
  • animal counts: 25127
  • plant counts: 2734

Safety information

risk assessment

@refpathogenicity humanpathogenicity animalbiosafety levelbiosafety level comment
5088yesyes2Risk group (German classification)
1168052Risk group (French classification)

Sequence information

16S sequences

  • @ref: 20218
  • description: Clostridium bifermentans 16S ribosomal RNA gene, partial sequence
  • accession: AF320283
  • length: 1488
  • database: ena
  • NCBI tax ID: 1490

GC content

  • @ref: 5088
  • GC-content: 29.1
  • method: high performance liquid chromatography (HPLC)

External links

@ref: 5088

culture collection no.: DSM 13560, CIP 106673

straininfo link

  • @ref: 72091
  • straininfo: 87973

Reference

@idauthorscataloguedoi/urltitlejournalpubmed
5088Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 13560)https://www.dsmz.de/collection/catalogue/details/culture/DSM-13560
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
32997Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/18829
68382Automatically annotated from API zym
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
72091Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID87973.1StrainInfo: A central database for resolving microbial strain identifiers
116805Curators of the CIPCollection of Institut Pasteur (CIP 106673)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20106673