Strain identifier

BacDive ID: 140317

Type strain: Yes

Species: Clostridium tepidum

Strain history: <- A. Dobritsa, Institute for Environmental Health, 15300 Bothell Way NE, Lake Forest Park, WA 98155, USA; IEH 97212 <- G. Ma {2016}

NCBI tax ID(s): 1962263 (species)

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General

@ref: 42924

BacDive-ID: 140317

DSM-Number: 104389

keywords: 16S sequence, Bacteria, anaerobe, spore-forming, thermophilic, Gram-positive, motile, rod-shaped, colony-forming

description: Clostridium tepidum DSM 104389 is an anaerobe, spore-forming, thermophilic bacterium that forms circular colonies and was isolated from bloated bottle of non-dairy protein shake.

NCBI tax id

  • NCBI tax id: 1962263
  • Matching level: species

strain history

  • @ref: 42924
  • history: <- A. Dobritsa, Institute for Environmental Health, 15300 Bothell Way NE, Lake Forest Park, WA 98155, USA; IEH 97212 <- G. Ma {2016}

doi: 10.13145/bacdive140317.20230509.8.1

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 tepidum
  • full scientific name: Clostridium tepidum Dobritsa et al. 2017

@ref: 42924

domain: Bacteria

phylum: Firmicutes

class: Clostridia

order: Anaeroplasmatales

family: Clostridiaceae

genus: Clostridium

species: Clostridium tepidum

full scientific name: Clostridium tepidum Dobritsa et al. 2017

type strain: yes

Morphology

cell morphology

  • @ref: 43310
  • gram stain: positive
  • cell length: 2.2-6.2 µm
  • cell width: 1.3-1.6 µm
  • cell shape: rod-shaped
  • motility: yes

colony morphology

  • @ref: 43310
  • colony shape: circular
  • medium used: pre-reduced tryptic soy agar with 5% sheep blood

Culture and growth conditions

culture medium

@refnamegrowthcompositionlink
43310pre-reduced tryptic soy agar with 5% sheep bloodyes
43310DSMZ medium 104b (PY+X)yes5g Tryptone, 5g peptone, 10g yeast extract, 0.5 ml 0.1% sodium resazurin solution, 0.5g L-cysteine hydrochloride, 2g K2HPO4 per 1 litre of deionized water
42924PY + X MEDIUM (N2/CO2) (DSMZ Medium 104c)yesName: 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 waterhttps://mediadive.dsmz.de/medium/104c
42924COLUMBIA BLOOD MEDIUM (DSMZ Medium 693)yesName: COLUMBIA BLOOD MEDIUM (DSMZ Medium 693) Composition: Defibrinated sheep blood 50.0 g/l Columbia agar basehttps://mediadive.dsmz.de/medium/693
42924FASTIDIOUS ANAEROBE BROTH (DSMZ Medium 1203a)yesName: FASTIDIOUS ANAEROBE BROTH (DSMZ Medium 1203a) Composition: Fastidious Anaerobe Basal Broth 35.4 g/l Distilled waterhttps://mediadive.dsmz.de/medium/1203a

culture temp

@refgrowthtypetemperaturerange
43310positiveoptimum45-50thermophilic
43310positivegrowth30-55
42924positivegrowth37mesophilic

culture pH

  • @ref: 43310
  • ability: positive
  • type: growth
  • pH: 6-9.5
  • PH range: alkaliphile

Physiology and metabolism

oxygen tolerance

  • @ref: 43310
  • oxygen tolerance: anaerobe

spore formation

  • @ref: 43310
  • spore description: oval, located subterminally and swell cells
  • spore formation: yes

halophily

  • @ref: 43310
  • salt: NaCl
  • growth: positive
  • tested relation: growth
  • concentration: 0-2.5 %

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
4331017634D-glucose+builds acid from
4331017306maltose+builds acid from
4331027082trehalose+builds acid from
433105291gelatin+hydrolysis
433104853esculin-hydrolysis
4331016899D-mannitol-builds acid from
4331017716lactose-builds acid from
4331017992sucrose-builds acid from
4331017814salicin-builds acid from
4331065327D-xylose-builds acid from
4331030849L-arabinose-builds acid from
4331017754glycerol-builds acid from
4331017057cellobiose-builds acid from
4331016024D-mannose-builds acid from
433106731melezitose-builds acid from
4331016634raffinose-builds acid from
4331017924D-sorbitol-builds acid from
4331062345L-rhamnose-builds acid from

metabolite production

@refChebi-IDmetaboliteproduction
4331035581indoleno
4331030089acetateyes
4331017272propionateyes
4331017968butyrateyes
4331048944isobutyrateyes
4331031011valerateyes
4331048942isovalerateyes
43310510573-phenylpropionateyes
4331074904isocaproateyes
4331077761piperidin-2-oneyes
4331036592pyrrolidin-2-oneyes

enzymes

@refvalueactivityec
43310catalase-1.11.1.6
43310cytochrome oxidase-1.9.3.1
43310urease-3.5.1.5
43310pyrrolidonyl arylamidase-3.4.19.3
43310phenylalanine arylamidase+
43310proline-arylamidase+3.4.11.5

Isolation, sampling and environmental information

isolation

@refsample typecountryorigin.countrycontinent
42924bloated bottle of non-dairy protein shakeUSAUSANorth America
43310non-dairy protein shake in bloated bottles

isolation source categories

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

taxonmaps

  • @ref: 69479
  • File name: preview.99_6861.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_34;96_226;97_248;98_277;99_6861&stattab=map
  • Last taxonomy: Clostridium
  • 16S sequence: KY322707
  • Sequence Identity:
  • Total samples: 5328
  • soil counts: 1240
  • aquatic counts: 1069
  • animal counts: 2733
  • plant counts: 286

Safety information

risk assessment

  • @ref: 42924
  • biosafety level: 1
  • biosafety level comment: Risk group (German classification)

Sequence information

16S sequences

@refdescriptionaccessiondatabase
4331016S rRNA, rpoB, recA, dnaA and gyrB gene sequencesKY322707nuccore
4331016S rRNA, rpoB, recA, dnaA and gyrB gene sequencesKY322708nuccore
4331016S rRNA, rpoB, recA, dnaA and gyrB gene sequencesKY322709nuccore
4331016S rRNA, rpoB, recA, dnaA and gyrB gene sequencesKY322710nuccore
4331016S rRNA, rpoB, recA, dnaA and gyrB gene sequencesKY322711nuccore

GC content

@refGC-contentmethod
4331026.7genome sequence analysis
4292426.9sequence analysis

External links

@ref: 42924

culture collection no.: DSM 104389, NRRL B-65463, IEH 97212

straininfo link

  • @ref: 96621
  • straininfo: 400564

literature

  • topic: Phylogeny
  • Pubmed-ID: 28693684
  • title: Clostridium tepidum sp. nov., a close relative of Clostridium sporogenes and Clostridium botulinum Group I.
  • authors: Dobritsa AP, Kutumbaka KK, Werner K, Wiedmann M, Asmus A, Samadpour M
  • journal: Int J Syst Evol Microbiol
  • DOI: 10.1099/ijsem.0.001948
  • year: 2017
  • mesh: Bacterial Typing Techniques, Base Composition, Clostridium/*classification/genetics/isolation & purification, DNA, Bacterial/genetics, Electrophoresis, Gel, Pulsed-Field, Fatty Acids/chemistry, *Food Microbiology, Nucleic Acid Hybridization, *Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA
  • topic2: Enzymology

Reference

@idauthorstitledoi/urlcataloguejournalpubmed
20215Parte, A.C., Sardà Carbasse, J., Meier-Kolthoff, J.P., Reimer, L.C. and Göker, M.List of Prokaryotic names with Standing in Nomenclature (LPSN) moves to the DSMZ10.1099/ijsem.0.004332
42924Curators of the DSMZhttps://www.dsmz.de/collection/catalogue/details/culture/DSM-104389Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 104389)
43310Anatoly P. Dobritsa, Kirthi K. Kutumbaka, Kirsten Werner, Martin Wiedmann, Aaron Asmus, Mansour SamadpourClostridium tepidum sp. nov., a close relative of Clostridium sporogenes and Clostridium botulinum Group I10.1099/ijsem.0.001948IJSEM 67: 2317-2322 201728693684
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.MicrobeAtlas 1.0 betahttps://microbeatlas.org/
96621Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.StrainInfo: A central database for resolving microbial strain identifiers10.60712/SI-ID400564.1