Strain identifier

BacDive ID: 2811

Type strain: Yes

Species: Clostridium hylemonae

Strain Designation: TN-271, TN271

Strain history: CIP <- 2000, JCM <- F. Takamine: strain TN271

NCBI tax ID(s): 553973 (strain), 89153 (species)

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General

@ref: 5686

BacDive-ID: 2811

DSM-Number: 15053

keywords: genome sequence, 16S sequence, Bacteria, anaerobe, spore-forming, mesophilic, Gram-positive

description: Clostridium hylemonae TN-271 is an anaerobe, spore-forming, mesophilic bacterium that was isolated from human faeces.

NCBI tax id

NCBI tax idMatching level
553973strain
89153species

strain history

@refhistory
5686<- JCM <- F. Takamine, University of the Ryukyus, Okinawa, Japan; TN-271
67770F. Takamine TN271.
120027CIP <- 2000, JCM <- F. Takamine: strain TN271

doi: 10.13145/bacdive2811.20230509.8.1

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 hylemonae
  • full scientific name: Clostridium hylemonae Kitahara et al. 2000

@ref: 5686

domain: Bacteria

phylum: Firmicutes

class: Clostridia

order: Clostridiales

family: Clostridiaceae

genus: Clostridium

species: Clostridium hylemonae

full scientific name: Clostridium hylemonae Kitahara et al. 2000

strain designation: TN-271, TN271

type strain: yes

Morphology

cell morphology

@refgram stainconfidencecell shapemotility
69480positive99.998
120027positiverod-shapedno

colony morphology

  • @ref: 120027

Culture and growth conditions

culture medium

  • @ref: 5686
  • name: CHOPPED MEAT MEDIUM WITH CARBOHYDRATES (DSMZ Medium 110)
  • growth: yes
  • link: https://mediadive.dsmz.de/medium/110
  • composition: Name: 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

@refgrowthtypetemperaturerange
5686positivegrowth37mesophilic
67770positivegrowth37mesophilic

Physiology and metabolism

oxygen tolerance

@refoxygen toleranceconfidence
5686anaerobe
69480anaerobe100
120027anaerobe

spore formation

@refspore formationconfidence
69481yes91
69480no92.014
120027yes

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
12002717108D-arabinose-degradation
12002715824D-fructose+degradation
12002717634D-glucose+degradation
12002765327D-xylose+degradation
12002717057cellobiose-degradation
12002717716lactose-degradation
12002717306maltose+degradation
12002717814salicin-degradation
12002717992sucrose-degradation
1200274853esculin-hydrolysis
12002717632nitrate-reduction
12002716301nitrite-reduction
12002717632nitrate+respiration

metabolite production

  • @ref: 120027
  • 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
120027oxidase-
120027beta-galactosidase-3.2.1.23
120027gelatinase-
120027amylase+
120027DNase-
120027caseinase-3.4.21.50
120027catalase-1.11.1.6
120027urease-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
120027----------++--------

Isolation, sampling and environmental information

isolation

@refsample typecountryorigin.countrycontinent
5686human faeces
67770Human feces
120027Human, FecesJapanJPNAsia

isolation source categories

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

taxonmaps

  • @ref: 69479
  • File name: preview.99_81916.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_16;96_34341;97_43550;98_56937;99_81916&stattab=map
  • Last taxonomy: [Clostridium] hylemonae subclade
  • 16S sequence: AB910737
  • Sequence Identity:
  • Total samples: 21798
  • soil counts: 103
  • aquatic counts: 281
  • animal counts: 21377
  • plant counts: 37

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
56861Risk group (German classification)
1200272Risk group (French classification)

Sequence information

16S sequences

@refdescriptionaccessionlengthdatabaseNCBI tax ID
20218Clostridium hylemonae gene for 16S ribosomal RNA, partial sequenceAB9107371504ena553973
5686Clostridium hylemonae gene for 16S rRNA, partial sequence, strain:TN-271AB0239721377ena553973

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792[Clostridium] hylemonae DSM 15053GCA_008281175completencbi553973
66792Clostridium hylemonae DSM 15053553973.6wgspatric553973
66792[Clostridium] hylemonae DSM 15053553973.19completepatric553973
66792Lachnoclostridium hylemonae DSM 15053642979359draftimg553973
67770[Clostridium] hylemonae DSM 15053GCA_000156515scaffoldncbi553973

GC content

  • @ref: 5686
  • GC-content: 48.6
  • method: high performance liquid chromatography (HPLC)

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingyes91no
motileyes80.469no
flagellatedno69.699no
gram-positiveyes90.488no
anaerobicyes99.262yes
aerobicno98.416yes
halophileno83.694no
spore-formingyes70.791no
glucose-utilyes90.592no
thermophileno97.685yes
glucose-fermentyes72.88no

External links

@ref: 5686

culture collection no.: CCUG 45367, CIP 106689, DSM 15053, JCM 10539

straininfo link

  • @ref: 72337
  • straininfo: 100604

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny10843034Assignment of Eubacterium sp. VPI 12708 and related strains with high bile acid 7alpha-dehydroxylating activity to Clostridium scindens and proposal of Clostridium hylemonae sp. nov., isolated from human faeces.Kitahara M, Takamine F, Imamura T, Benno YInt J Syst Evol Microbiol10.1099/00207713-50-3-9712000Base Composition, Bile Acids and Salts/metabolism, Clostridium/*classification/enzymology/isolation & purification, DNA, Ribosomal/chemistry/genetics, Eubacterium/*classification/*enzymology, Feces/*microbiology, Genes, rRNA, Humans, *Hydroxysteroid Dehydrogenases, Molecular Sequence Data, *Oxidoreductases, Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Homology, Nucleic Acid, Steroid Hydroxylases/*metabolismEnzymology
Metabolism29684065Biochemical properties of L-arabinose isomerase from Clostridium hylemonae to produce D-tagatose as a functional sweetener.Nguyen TK, Hong MG, Chang PS, Lee BH, Yoo SHPLoS One10.1371/journal.pone.01960992018Aldose-Ketose Isomerases/*genetics/*metabolism, Bacterial Proteins/genetics/metabolism, Cloning, Molecular, Clostridium/*enzymology, Hexoses/*metabolism, Hydrogen-Ion Concentration, Magnesium/metabolism, Molecular Weight, Sweetening Agents/metabolism, TemperatureEnzymology
Metabolism31177942The 'in vivo lifestyle' of bile acid 7alpha-dehydroxylating bacteria: comparative genomics, metatranscriptomic, and bile acid metabolomics analysis of a defined microbial community in gnotobiotic mice.Ridlon JM, Devendran S, Alves JM, Doden H, Wolf PG, Pereira GV, Ly L, Volland A, Takei H, Nittono H, Murai T, Kurosawa T, Chlipala GE, Green SJ, Hernandez AG, Fields CJ, Wright CL, Kakiyama G, Cann I, Kashyap P, McCracken V, Gaskins HRGut Microbes10.1080/19490976.2019.16181732019Animals, Bacteria, Anaerobic/*genetics/*metabolism, Bacteroides/genetics/metabolism, Bile Acids and Salts/*metabolism, Bilophila/genetics/metabolism, Cecum/*microbiology, Cholic Acids/metabolism, Clostridium/genetics/metabolism, Gene Expression Regulation, Bacterial, Genome, Bacterial, Genomics, Germ-Free Life, Humans, *Metabolome, Mice, Mice, Inbred C57BL, Microbiota, Operon, RNA-Seq, *Transcriptome, Up-RegulationGenetics

Reference

@idauthorscataloguedoi/urltitlejournalpubmed
5686Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 15053)https://www.dsmz.de/collection/catalogue/details/culture/DSM-15053
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)
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)
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
72337Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID100604.1StrainInfo: A central database for resolving microbial strain identifiers
120027Curators of the CIPCollection of Institut Pasteur (CIP 106689)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20106689