Strain identifier

BacDive ID: 2797

Type strain: Yes

Species: Anaerocolumna xylanovorans

Strain Designation: HESP1

Strain history: DSM 12503 <-- J. L. Garcia; HESP1.

For citation purpose refer to the digital object identifier (doi) of the current version.
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General

@ref: 4749

BacDive-ID: 2797

DSM-Number: 12503

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

description: Anaerocolumna xylanovorans HESP1 is an anaerobe, spore-forming, mesophilic bacterium that was isolated from anaerobic digester fed with olive mill wastewater.

NCBI tax id

NCBI tax idMatching level
1121345strain
100134species

strain history

@refhistory
4749<- J. L. Garcia, Université de Provence, Marseille, France; HESP1 <- T. Mechichi {1998}
67770DSM 12503 <-- J. L. Garcia; HESP1.

doi: 10.13145/bacdive2797.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/bacillota
  • domain: Bacteria
  • phylum: Bacillota
  • class: Clostridia
  • order: Eubacteriales
  • family: Lachnospiraceae
  • genus: Anaerocolumna
  • species: Anaerocolumna xylanovorans
  • full scientific name: Anaerocolumna xylanovorans (Mechichi et al. 2000) Ueki et al. 2016
  • synonyms

    • @ref: 20215
    • synonym: Clostridium xylanovorans

@ref: 4749

domain: Bacteria

phylum: Firmicutes

class: Clostridia

order: Clostridiales

family: Lachnospiraceae

genus: Anaerocolumna

species: Anaerocolumna xylanovorans

full scientific name: Anaerocolumna xylanovorans (Mechichi et al. 2000) Ueki et al. 2016

strain designation: HESP1

type strain: yes

Morphology

cell morphology

@refmotilityconfidencegram stain
69480yes90.35
69480100positive

Culture and growth conditions

culture medium

  • @ref: 4749
  • name: ANAEROCOLUMNA MEDIUM (DSMZ Medium 860)
  • growth: yes
  • link: https://mediadive.dsmz.de/medium/860
  • composition: Name: ANAEROCOLUMNA MEDIUM (DSMZ Medium 860) Composition: D-Fructose 3.99202 g/l Na2CO3 1.49701 g/l NH4Cl 0.998004 g/l Yeast extract 0.998004 g/l NaCl 0.598802 g/l L-Cysteine HCl x H2O 0.499002 g/l K2HPO4 0.299401 g/l KH2PO4 0.299401 g/l Na2S x 9 H2O 0.299401 g/l MgCl2 x 6 H2O 0.199601 g/l CaCl2 x 2 H2O 0.0998004 g/l KCl 0.0998004 g/l HCl 0.00374251 g/l FeCl2 x 4 H2O 0.00224551 g/l Sodium resazurin 0.000499002 g/l CoCl2 x 6 H2O 0.000284431 g/l MnCl2 x 4 H2O 0.000149701 g/l ZnCl2 0.00010479 g/l Na2MoO4 x 2 H2O 5.38922e-05 g/l NiCl2 x 6 H2O 3.59281e-05 g/l H3BO3 8.98204e-06 g/l CuCl2 x 2 H2O 2.99401e-06 g/l Distilled water

culture temp

@refgrowthtypetemperaturerange
4749positivegrowth35mesophilic
67770positivegrowth35mesophilic

Physiology and metabolism

oxygen tolerance

@refoxygen toleranceconfidence
4749anaerobe
69480anaerobe100

spore formation

@refspore formationconfidence
69481yes91
69480yes99.447

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinent
4749anaerobic digester fed with olive mill wastewaterSfaxTunisiaTUNAfrica
67770Methanogenic digester

isolation source categories

Cat1Cat2Cat3
#Engineered#Biodegradation#Anaerobic digestor
#Engineered#Industrial
#Engineered#Waste#Industrial wastewater
#Condition#Anoxic (anaerobic)

Safety information

risk assessment

  • @ref: 4749
  • biosafety level: 1
  • biosafety level comment: Risk group (German classification)

Sequence information

16S sequences

  • @ref: 4749
  • description: Clostridium xylanovorans 16S ribosomal RNA gene, partial sequence
  • accession: AF116920
  • length: 1533
  • database: ena
  • NCBI tax ID: 100134

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Anaerocolumna cellulosilytica strain SN021433286.4completepatric433286
66792Anaerocolumna xylanovorans DSM 125031121345.3wgspatric1121345
66792Anaerocolumna xylanovorans DSM 125032582580727draftimg1121345
67770Anaerocolumna xylanovorans DSM 12503GCA_900143645scaffoldncbi1121345

GC content

@refGC-contentmethod
474940.0high performance liquid chromatography (HPLC)
6777040high performance liquid chromatography (HPLC)

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingyes91no
gram-positiveyes87.637no
anaerobicyes98.102yes
halophileno95.799no
spore-formingyes93.903no
glucose-utilyes88.836no
aerobicno97.386yes
flagellatedyes61.811no
thermophileno98.431yes
motileyes82.494no
glucose-fermentyes64.848no

External links

@ref: 4749

culture collection no.: DSM 12503, JCM 31057

straininfo link

  • @ref: 72323
  • straininfo: 49306

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny10553289Characterization of a new xylanolytic bacterium, Clostridium xylanovorans sp. nov.Mechichi T, Labat M, Garcia JL, Thomas P, Patel BKSyst Appl Microbiol10.1016/S0723-2020(99)80044-71999Base Sequence, Biodegradation, Environmental, Carbohydrate Metabolism, Chromatography, High Pressure Liquid, Clostridium/*classification/cytology/physiology, Fermentation, Fumarates/metabolism, Methanol/metabolism, Molecular Sequence Data, Phylogeny, Polymerase Chain Reaction, RNA, Bacterial/chemistry, RNA, Ribosomal, 16S/chemistry, Xylans/*metabolismMetabolism
Phylogeny27126251Descriptions of Anaerotaenia torta gen. nov., sp. nov. and Anaerocolumna cellulosilytica gen. nov., sp. nov. isolated from a methanogenic reactor of cattle waste and reclassification of Clostridium aminovalericum, Clostridium jejuense and Clostridium xylanovorans as Anaerocolumna species.Ueki A, Ohtaki Y, Kaku N, Ueki KInt J Syst Evol Microbiol10.1099/ijsem.0.0011232016Animals, Bacteria, Anaerobic/classification/genetics/isolation & purification, Bacterial Typing Techniques, Base Composition, Bioreactors/*microbiology, Cattle, Cellulose/metabolism, Clostridiales/*classification/genetics/isolation & purification, DNA, Bacterial/genetics, Fatty Acids/chemistry, Fermentation, Manure/*microbiology, *Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNAEnzymology

Reference

@idauthorscataloguedoi/urltitlejournalpubmed
4749Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 12503)https://www.dsmz.de/collection/catalogue/details/culture/DSM-12503
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
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/
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
72323Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID49306.1StrainInfo: A central database for resolving microbial strain identifiers