Strain identifier

BacDive ID: 2559

Type strain: Yes

Species: Paraclostridium bifermentans

Strain Designation: 76, 10028

Strain history: CIP <- 1994, J.P. Carlier, Inst. Pasteur, Paris, France: strain 10028 <- ATCC <- I.C. Hall: strain 76, Bacillus centrosporogenes

NCBI tax ID(s): 1490 (species)

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General

@ref: 5658

BacDive-ID: 2559

DSM-Number: 14991

keywords: genome sequence, 16S sequence, Bacteria, anaerobe, spore-forming, mesophilic, motile, human pathogen

description: Paraclostridium bifermentans 76 is an anaerobe, spore-forming, mesophilic human pathogen that was isolated from soil.

NCBI tax id

  • NCBI tax id: 1490
  • Matching level: species

strain history

@refhistory
5658<- JCM; JCM 1386 <- ATCC; ATCC 638 <- I. C. Hall; 76
67770ATCC 638 <-- I. C. Hall 76.
116804CIP <- 1994, J.P. Carlier, Inst. Pasteur, Paris, France: strain 10028 <- ATCC <- I.C. Hall: strain 76, Bacillus centrosporogenes

doi: 10.13145/bacdive2559.20230509.8.1

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: 5658

domain: Bacteria

phylum: Firmicutes

class: Clostridia

order: Clostridiales

family: Clostridiaceae

genus: Paraclostridium

species: Paraclostridium bifermentans subsp. bifermentans

full scientific name: Paraclostridium bifermentans subsp. bifermentans (Weinberg and Séguin 1918) Kutsuna et al. 2019

strain designation: 76, 10028

type strain: yes

Morphology

cell morphology

@refmotilityconfidencegram staincell shape
69480yes94.142
69480100positive
116804yespositiverod-shaped

colony morphology

  • @ref: 116804
  • hemolysis ability: 1

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
5658CHOPPED MEAT MEDIUM WITH CARBOHYDRATES (DSMZ Medium 110)yeshttps://mediadive.dsmz.de/medium/110Name: 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
5658FASTIDIOUS ANAEROBE BROTH (DSMZ Medium 1203a)yeshttps://www.dsmz.de/microorganisms/medium/pdf/DSMZ_Medium1203a.pdf
5658COLUMBIA BLOOD MEDIUM (DSMZ Medium 693)yeshttps://www.dsmz.de/microorganisms/medium/pdf/DSMZ_Medium693.pdf
41797MEDIUM 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)
116804CIP Medium 20yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=20

culture temp

@refgrowthtypetemperaturerange
5658positivegrowth37mesophilic
41797positivegrowth37mesophilic
67770positivegrowth37mesophilic

Physiology and metabolism

oxygen tolerance

@refoxygen toleranceconfidence
5658anaerobe
69480anaerobe99.533

spore formation

@refspore formationconfidence
69481yes99
69480yes100
116804yes

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
1168044853esculin+hydrolysis
11680417632nitrate+reduction
11680416301nitrite+reduction
116804132112sodium thiosulfate+builds gas from
6838016199urea-hydrolysis
6838029016arginine-hydrolysis
6838016024D-mannose-fermentation
6838016634raffinose-fermentation
6838029985L-glutamate-degradation
6838017632nitrate-reduction
6838027897tryptophan+energy source

metabolite production

@refChebi-IDmetaboliteproduction
11680435581indoleno
6838035581indoleyes

metabolite tests

  • @ref: 68380
  • Chebi-ID: 35581
  • metabolite: indole
  • indole test: +

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
68380serine arylamidase-
68380glutamyl-glutamate arylamidase-
68380histidine arylamidase-
68380glycin arylamidase-
68380alanine arylamidase-3.4.11.2
68380tyrosine arylamidase-
68380pyrrolidonyl arylamidase-3.4.19.3
68380leucine arylamidase-3.4.11.1
68380phenylalanine arylamidase-
68380leucyl glycin arylamidase-3.4.11.1
68380proline-arylamidase+3.4.11.5
68380L-arginine arylamidase-
68380alkaline phosphatase-3.1.3.1
68380tryptophan deaminase+4.1.99.1
68380alpha-fucosidase-3.2.1.51
68380glutamate decarboxylase-4.1.1.15
68380N-acetyl-beta-glucosaminidase-3.2.1.52
68380beta-glucuronidase-3.2.1.31
68380alpha-arabinosidase-3.2.1.55
68380beta-glucosidase-3.2.1.21
68380alpha-glucosidase-3.2.1.20
68380beta-Galactosidase 6-phosphate-
68380beta-galactosidase-3.2.1.23
68380alpha-galactosidase-3.2.1.22
68380arginine dihydrolase-3.5.3.6
68380urease-3.5.1.5
116804alcohol dehydrogenase-1.1.1.1
116804gelatinase-
116804DNase+
116804catalase-1.11.1.6
116804lecithinase+
116804lysine decarboxylase-4.1.1.18
116804ornithine decarboxylase-4.1.1.17
116804urease-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
116804-+++-+----++---+----

API rID32A

@refUREADH Argalpha GALbeta GALbeta GPalpha GLUbeta GLUalpha ARAbeta GURbeta NAGMNERAFGDCalpha FUCNITINDPALArgAProALGAPheALeuAPyrATyrAAlaAGlyAHisAGGASerA
5658---------------+--+----------

Isolation, sampling and environmental information

isolation

@refsample type
5658soil
53282Soil
67770Soil

isolation source categories

  • Cat1: #Environmental
  • Cat2: #Terrestrial
  • Cat3: #Soil

Safety information

risk assessment

@refpathogenicity humanpathogenicity animalbiosafety levelbiosafety level comment
5658yesyes2Risk group (German classification)
1168042Risk group (French classification)

Sequence information

16S sequences

@refdescriptionaccessionlengthdatabaseNCBI tax ID
20218Clostridium bifermentans gene for 16S rRNA, partial sequence, strain: ATCC 638AB0757691476ena1490
20218[Clostridium] bifermentans gene for 16S ribosomal RNA, partial cds, strain: JCM 1386AB6187871463ena1490
20218Clostridium bifermentans strain DSM 14991 16S ribosomal RNA gene, partial sequenceHM245932841ena1490
20218Clostridium bifermentans 16S rRNA geneX759061451ena1490
5658Clostridium bifermentans 16S rRNA gene, strain DSM 10716X734371498ena1490

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Paraclostridium bifermentans DSM 14991GCA_019916025completencbi1490
66792Clostridium bifermentans ATCC 6381233171.3wgspatric1233171
66792Paraclostridium bifermentans strain ATCC 6381490.25wgspatric1490
66792Paraclostridium bifermentans strain DSM 149911490.72completepatric1490
66792Paraclostridium bifermentans ATCC 6382541047518draftimg1233171
67770Paraclostridium bifermentans ATCC 638 = DSM 14991GCA_000452245contigncbi1233171
67770Paraclostridium bifermentans ATCC 638GCA_006802875scaffoldncbi1490
66792Paraclostridium bifermentans strain DSM 149911490.78completepatric1490
66792Paraclostridium bifermentans strain DSM 149911490.81completepatric1490
66792Paraclostridium bifermentans strain DSM 149911490.75completepatric1490

GC content

@refGC-contentmethod
565827thermal denaturation, midpoint method (Tm)
6777029.2high performance liquid chromatography (HPLC)

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingyes99no
flagellatedno55.414no
gram-positiveyes90.549no
anaerobicyes97.723no
aerobicno97.055yes
halophileno92.211no
spore-formingyes94.705no
motileyes78.08no
thermophileno97.546yes
glucose-utilyes88.291no
glucose-fermentyes64.958no

External links

@ref: 5658

culture collection no.: DSM 14991, ATCC 638, JCM 1386, CCUG 36626, NCIMB 10716, Hall 76, BCRC 14542, CIP 104309, NCTC 13019, PAGU 2008

straininfo link

  • @ref: 72092
  • straininfo: 34627

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phenotype3911662Correlative properties for a differentiation of two Clostridium sordellii phenotypes and their distinction from Clostridium bifermentans.Roggentin P, Gutschker-Gdaniec G, Schauer R, Hobrecht RZentralbl Bakteriol Mikrobiol Hyg A10.1016/s0176-6724(85)80020-11985Animals, Bacteriological Techniques, Clostridium/classification/*genetics/pathogenicity, Culture Media, Humans, Mice, Phenotype, VirulenceCultivation
Metabolism25002034Biohydrogenation of C20 polyunsaturated fatty acids by anaerobic bacteria.Sakurama H, Kishino S, Mihara K, Ando A, Kita K, Takahashi S, Shimizu S, Ogawa JJ Lipid Res10.1194/jlr.M0454502014Anaerobiosis, Arachidonic Acid/*metabolism, Clostridium bifermentans/*metabolism, Eicosapentaenoic Acid/*metabolism, Hydrogenation, Linoleic Acids/metabolism
Phylogeny26738915Paraclostridium benzoelyticum gen. nov., sp. nov., isolated from marine sediment and reclassification of Clostridium bifermentans as Paraclostridium bifermentans comb. nov. Proposal of a new genus Paeniclostridium gen. nov. to accommodate Clostridium sordellii and Clostridium ghonii.Sasi Jyothsna TS, Tushar L, Sasikala C, Ramana CVInt J Syst Evol Microbiol10.1099/ijsem.0.0008742016
Phylogeny30549099Description of Paraclostridium bifermentans subsp. muricolitidis subsp. nov., emended description of Paraclostridium bifermentans (Sasi Jyothsna et al., 2016), and creation of Paraclostridium bifermentans subsp. bifermentans subsp. nov.Kutsuna R, Miyoshi-Akiyama T, Mori K, Hayashi M, Tomida J, Morita Y, Tanaka K, Kawamura YMicrobiol Immunol10.1111/1348-0421.126632019Bacterial Typing Techniques, Clostridiales/*classification/cytology/genetics/physiology, DNA, Bacterial/genetics, Fatty Acids/analysis, Hydrogen Sulfide/metabolism, Nucleic Acid Hybridization, Phenotype, Phospholipids/metabolism, *Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Species SpecificityMetabolism

Reference

@idauthorscataloguedoi/urltitlejournalpubmed
5658Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 14991)https://www.dsmz.de/collection/catalogue/details/culture/DSM-14991
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
41797Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/16204
53282Curators of the CCUGCulture Collection University of Gothenburg (CCUG) (CCUG 36626)https://www.ccug.se/strain?id=36626
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)
67770Curators of the JCMhttps://jcm.brc.riken.jp/en/
68380Automatically annotated from API rID32A
68382Automatically annotated from API zym
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
72092Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID34627.1StrainInfo: A central database for resolving microbial strain identifiers
116804Curators of the CIPCollection of Institut Pasteur (CIP 104309)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20104309