Strain identifier

BacDive ID: 2721

Type strain: Yes

Species: Clostridium symbiosum

Strain Designation: 2

Strain history: C. Kaneuchi <-- ATCC 14940 <-- R. E. Reeves ("Bacteroides symbiosus") <-- J. Shaffer 2 (M. Sebald strain LSU).

NCBI tax ID(s): 411472 (strain), 1512 (species)

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General

@ref: 472

BacDive-ID: 2721

DSM-Number: 934

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

description: Clostridium symbiosum 2 is an anaerobe, mesophilic bacterium of the family Clostridiaceae.

NCBI tax id

NCBI tax idMatching level
411472strain
1512species

strain history

@refhistory
472<- C. Kaneuchi; ATCC 14940 <- ATCC; ATCC 14940 <- R.E. Reeves; LSU (M. Sebald) (Bacteroides symbiosus) <- J. Shaffer; 2
67770C. Kaneuchi <-- ATCC 14940 <-- R. E. Reeves ("Bacteroides symbiosus") <-- J. Shaffer 2 (M. Sebald strain LSU).

doi: 10.13145/bacdive2721.20250331.9.3

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 symbiosum
  • full scientific name: Clostridium symbiosum (Stevens 1956) Kaneuchi et al. 1976 (Approved Lists 1980)

  • synonyms

    • @ref: 20215
    • synonym: Bacteroides symbiosus

@ref: 472

domain: Bacteria

phylum: Firmicutes

class: Clostridia

order: Clostridiales

family: Clostridiaceae

genus: Clostridium

species: Clostridium symbiosum

full scientific name: Clostridium symbiosum (Stevens 1956) Kaneuchi et al. 1976

strain designation: 2

type strain: yes

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
472FASTIDIOUS ANAEROBE BROTH (DSMZ Medium 1203a)yeshttps://www.dsmz.de/microorganisms/medium/pdf/DSMZ_Medium1203a.pdf
472COLUMBIA BLOOD MEDIUM (DSMZ Medium 693)yeshttps://www.dsmz.de/microorganisms/medium/pdf/DSMZ_Medium693.pdf
472CHOPPED 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

culture temp

@refgrowthtypetemperature
472positivegrowth37
67770positivegrowth37

Physiology and metabolism

oxygen tolerance

@refoxygen toleranceconfidence
472anaerobe
125439anaerobe97.6

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
6838027897tryptophan-energy source
6838016199urea-hydrolysis
6838017632nitrate-reduction
6838029985L-glutamate-degradation
6838016634raffinose-fermentation
6838016024D-mannose-fermentation
6838029016arginine-hydrolysis

metabolite production

  • @ref: 68380
  • Chebi-ID: 35581
  • metabolite: indole
  • production: no

metabolite tests

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

enzymes

@refvalueactivityec
68380pyrrolidonyl arylamidase-3.4.19.3
68380phenylalanine arylamidase-
68380N-acetyl-beta-glucosaminidase-3.2.1.52
68380alpha-glucosidase-3.2.1.20
68380serine arylamidase-
68380glutamyl-glutamate arylamidase-
68380histidine arylamidase-
68380glycin arylamidase-
68380alanine arylamidase-3.4.11.2
68380tyrosine arylamidase-
68380leucine arylamidase-3.4.11.1
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
68380beta-glucuronidase-3.2.1.31
68380alpha-arabinosidase-3.2.1.55
68380beta-glucosidase-3.2.1.21
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

API rID32A

@refUREADH Argalpha GALbeta GALbeta GPalpha GLUbeta GLUalpha ARAbeta GURbeta NAGMNERAFGDCalpha FUCNITINDPALArgAProALGAPheALeuAPyrATyrAAlaAGlyAHisAGGASerA
472---+-------------------------

Isolation, sampling and environmental information

taxonmaps

  • @ref: 69479
  • File name: preview.99_5102.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_16;96_2483;97_3033;98_3808;99_5102&stattab=map
  • Last taxonomy: [Clostridium] symbiosum subclade
  • 16S sequence: LC036311
  • Sequence Identity:
  • Total samples: 189499
  • soil counts: 1377
  • aquatic counts: 3039
  • animal counts: 184529
  • plant counts: 554

Safety information

risk assessment

  • @ref: 472
  • biosafety level: 2
  • biosafety level comment: Risk group (German classification)

Sequence information

16S sequences

@refdescriptionaccessionlengthdatabaseNCBI tax ID
20218Clostridium symbiosum strain ATCC 14940 16S ribosomal RNA gene, partial sequenceM591121478nuccore1512
472Clostridium symbiosum strain DSM 934 16S ribosomal RNA gene, partial sequenceHM245954845nuccore1512
67770[Clostridium] symbiosum gene for 16S ribosomal RNA, partial sequence, strain: JCM 1297LC0363111492nuccore1512

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792[Clostridium] symbiosum strain NCTC132331512.13wgspatric1512
66792Clostridium symbiosum ATCC 14940411472.5wgspatric411472
66792Lachnoclostridium symbiosum ATCC 149402597490298draftimg411472
66792Lachnoclostridium symbiosum NCTC 132332814123396draftimg1512
67770[Clostridium] symbiosum ATCC 14940GCA_000466485scaffoldncbi411472
67770[Clostridium] symbiosum NCTC13233GCA_900461275contigncbi1512

GC content

@refGC-contentmethod
47246.1
6777046.1thermal denaturation, midpoint method (Tm)

Genome-based predictions

predictions

@refmodeltraitdescriptionpredictionconfidencetraining_data
125438gram-positivegram-positivePositive reaction to Gram-stainingyes63.189no
125438anaerobicanaerobicAbility to grow under anoxygenic conditions (including facultative anaerobes)yes89.941yes
125438spore-formingspore-formingAbility to form endo- or exosporesyes70.556no
125438aerobicaerobicAbility to grow under oxygenic conditions (including facultative aerobes)no94.86yes
125438thermophilethermophilicAbility to grow at temperatures above or equal to 45°Cno92.976yes
125438motile2+flagellatedAbility to perform flagellated movementyes70.532no
125439BacteriaNetspore_formationAbility to form endo- or exosporesyes80.8
125439BacteriaNetmotilityAbility to perform movementyes82.8
125439BacteriaNetgram_stainReaction to gram-stainingvariable83.3
125439BacteriaNetoxygen_toleranceOxygenic conditions needed for growthanaerobe97.6

External links

@ref: 472

culture collection no.: DSM 934, ATCC 14940, LSU (M. Sebald), JCM 1297, BCRC 14487, CCM 6065, NCTC 13233, VTT E-981051

straininfo link

  • @ref: 72249
  • straininfo: 36207

Reference

@idauthorscataloguedoi/urltitlejournalpubmed
472Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 934)https://www.dsmz.de/collection/catalogue/details/culture/DSM-934
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
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
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
72249Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID36207.1StrainInfo: A central database for resolving microbial strain identifiers
125438Julia Koblitz, Lorenz Christian Reimer, Rüdiger Pukall, Jörg Overmann10.1101/2024.08.12.607695Predicting bacterial phenotypic traits through improved machine learning using high-quality, curated datasets
125439Philipp Münch, René Mreches, Martin Binder, Hüseyin Anil Gündüz, Xiao-Yin To, Alice McHardyhttps://github.com/GenomeNet/deepGdeepG: Deep Learning for Genome Sequence Data. R package version 0.3.1