Strain identifier

BacDive ID: 2706

Type strain: Yes

Species: Thomasclavelia spiroformis

Strain history: CIP <- 2001, J.P. Carlier, Inst. Pasteur, France, Paris: strain AIP 10141 <- DSMZ <- C. Kaneuchi <- E.P. Cato: VPI C28-23-1A

NCBI tax ID(s): 428126 (strain), 29348 (species)

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General

@ref: 819

BacDive-ID: 2706

DSM-Number: 1552

keywords: genome sequence, 16S sequence, Bacteria, anaerobe, mesophilic, human pathogen

description: Thomasclavelia spiroformis DSM 1552 is an anaerobe, mesophilic human pathogen that was isolated from human faeces.

NCBI tax id

NCBI tax idMatching level
428126strain
29348species

strain history

@refhistory
819<- C. Kaneuchi, Institute of Physical and Chemical Research, Wako, Saitama, Japan; VPI C28-23-1A <- E. P. Cato, Virginia Polytechnical Institute and State University, Blacksburg, V., USA
67770C. Kaneuchi <-- E. P. Cato VPI C28-23-1A.
123267CIP <- 2001, J.P. Carlier, Inst. Pasteur, France, Paris: strain AIP 10141 <- DSMZ <- C. Kaneuchi <- E.P. Cato: VPI C28-23-1A

doi: 10.13145/bacdive2706.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/bacillota
  • domain: Bacteria
  • phylum: Bacillota
  • class: Erysipelotrichia
  • order: Erysipelotrichales
  • family: Coprobacillaceae
  • genus: Thomasclavelia
  • species: Thomasclavelia spiroformis
  • full scientific name: Thomasclavelia spiroformis (Kaneuchi et al. 1979) Lawson et al. 2023

  • synonyms

    • @ref: 20215
    • synonym: Clostridium spiroforme

@ref: 819

domain: Bacteria

phylum: Firmicutes

class: Clostridia

order: Clostridiales

family: Clostridiaceae

genus: Clostridium

species: Clostridium spiroforme

full scientific name: Clostridium spiroforme Kaneuchi et al. 1979

type strain: yes

Morphology

cell morphology

@refmotilityconfidencegram staincell shape
69480no90.51
69480100positive
123267nopositiverod-shaped

colony morphology

  • @ref: 123267

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
819CMC MEDIUM (N2/CO2) (DSMZ Medium 110a)yeshttps://mediadive.dsmz.de/medium/110aName: CMC MEDIUM (N2/CO2) (DSMZ Medium 110a) Composition: Ground beef 500.0 g/l Casitone 30.0 g/l Yeast extract 5.0 g/l K2HPO4 5.0 g/l D-Glucose 4.0 g/l Na2CO3 1.5 g/l Cellobiose 1.0 g/l Maltose 1.0 g/l Starch 1.0 g/l L-Cysteine HCl x H2O 0.5 g/l Sodium resazurin 0.0005 g/l NaOH Distilled water
33027MEDIUM 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)
819PY + X MEDIUM (N2/CO2) (DSMZ Medium 104c)yeshttps://mediadive.dsmz.de/medium/104cName: PY + X MEDIUM (N2/CO2) (DSMZ Medium 104c) 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 Na2CO3 1.0 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
123267CIP Medium 20yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=20

culture temp

@refgrowthtypetemperaturerange
819positivegrowth37mesophilic
33027positivegrowth37mesophilic
67770positivegrowth37mesophilic
123267positivegrowth37mesophilic

Physiology and metabolism

oxygen tolerance

@refoxygen toleranceconfidence
819anaerobe
69480anaerobe99.999
123267anaerobe

spore formation

  • @ref: 69480
  • spore formation: no
  • confidence: 99.954

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
1232674853esculin-hydrolysis
12326717632nitrate-reduction
12326716301nitrite-reduction
12326717632nitrate+respiration

metabolite production

  • @ref: 123267
  • 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
123267oxidase-
123267beta-galactosidase+3.2.1.23
123267gelatinase-
123267catalase-1.11.1.6
123267urease-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
123267--+-------++-----+--

Isolation, sampling and environmental information

isolation

@refsample typecountryorigin.countrycontinent
819human faecesUSAUSANorth America
67770Human feces
123267Human, Feces

isolation source categories

Cat1Cat2Cat3
#Host#Human
#Host Body Product#Gastrointestinal tract#Feces (Stool)

taxonmaps

  • @ref: 69479
  • File name: preview.99_9609.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_15821;96_1444;97_1723;98_2107;99_9609&stattab=map
  • Last taxonomy: [Clostridium] spiroforme subclade
  • 16S sequence: X75908
  • Sequence Identity:
  • Total samples: 82020
  • soil counts: 558
  • aquatic counts: 1756
  • animal counts: 79526
  • plant counts: 180

Safety information

risk assessment

@refpathogenicity humanbiosafety levelbiosafety level comment
819yes, in single cases1Risk group (German classification)
1232672Risk group (French classification)

Sequence information

16S sequences

@refdescriptionaccessionlengthdatabaseNCBI tax ID
20218Clostridium spiroforme DSM 1552 16S ribosomal RNA gene, partial sequenceHM245952821ena428126
20218C.spiroforme 16S rRNA geneX759081388ena428126
819Clostridium spiroforme 16S rRNA gene, strain DSM 1552X734411519ena428126
67770Clostridium spiroforme gene for 16S ribosomal RNA, partial sequence, strain: JCM 1432AB8189481486ena29348

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Clostridium spiroforme DSM 1552428126.7wgspatric428126
66792Erysipelatoclostridium spiroforme DSM 1552641736169draftimg428126
67770Thomasclavelia spiroformis DSM 1552GCA_000154805scaffoldncbi428126
66792Thomasclavelia spiroformis DSM 1552GCA_025149465completencbi428126
66792[Clostridium] spiroforme DSM 1552428126.20completepatric428126

GC content

  • @ref: 819
  • GC-content: 27.4

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno84no
motileno93.749no
flagellatedno96.36no
gram-positiveyes97.792no
anaerobicyes99.042yes
aerobicno99.011yes
halophileno74.752no
spore-formingno84.957no
glucose-fermentyes73.109no
thermophileno94.394no
glucose-utilyes87.549no

External links

@ref: 819

culture collection no.: DSM 1552, ATCC 29900, NCTC 11211, VPI C28-23-1A, JCM 1432, BCRC 14526, CCM 6168, CECT 4322, CIP 106966, AIP 10141

straininfo link

  • @ref: 72234
  • straininfo: 45881

literature

  • topic: Pathogenicity
  • Pubmed-ID: 36058421
  • title: Altered gut microbiota correlates with behavioral problems but not gastrointestinal symptoms in individuals with autism.
  • authors: Chen YC, Lin HY, Chien Y, Tung YH, Ni YH, Gau SS
  • journal: Brain Behav Immun
  • DOI: 10.1016/j.bbi.2022.08.015
  • year: 2022
  • mesh: *Autism Spectrum Disorder/metabolism, *Autistic Disorder, Biomarkers, *Gastrointestinal Diseases/complications, *Gastrointestinal Microbiome/genetics, Humans, *Problem Behavior
  • topic2: Metabolism

Reference

@idauthorscataloguedoi/urltitlejournalpubmed
819Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 1552)https://www.dsmz.de/collection/catalogue/details/culture/DSM-1552
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
33027Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/19154
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
67770Curators of the JCMhttps://jcm.brc.riken.jp/en/
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
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)
72234Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID45881.1StrainInfo: A central database for resolving microbial strain identifiers
123267Curators of the CIPCollection of Institut Pasteur (CIP 106966)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20106966