Strain identifier

BacDive ID: 2758

Type strain: Yes

Species: Lacrimispora xylanolytica

Strain history: DSM 6555 <-- G. M. Rogers.

NCBI tax ID(s): 29375 (species)

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General

@ref: 2729

BacDive-ID: 2758

DSM-Number: 6555

keywords: 16S sequence, Bacteria, anaerobe, mesophilic

description: Lacrimispora xylanolytica DSM 6555 is an anaerobe, mesophilic bacterium that was isolated from decayed Pinus patula wood chips.

NCBI tax id

  • NCBI tax id: 29375
  • Matching level: species

strain history

@refhistory
2729<- G. M. Rogers, University of the Witwaterstrand, Department of Microbiology, Johannesburg, South Africa <- G. M. Rogers {1987}
67770DSM 6555 <-- G. M. Rogers.

doi: 10.13145/bacdive2758.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/bacillota
  • domain: Bacteria
  • phylum: Bacillota
  • class: Clostridia
  • order: Eubacteriales
  • family: Lachnospiraceae
  • genus: Lacrimispora
  • species: Lacrimispora xylanolytica
  • full scientific name: Lacrimispora xylanolytica (Rogers and Baecker 1991) Haas and Blanchard 2020
  • synonyms

    • @ref: 20215
    • synonym: Clostridium xylanolyticum

@ref: 2729

domain: Bacteria

phylum: Firmicutes

class: Clostridia

order: Clostridiales

family: Lachnospiraceae

genus: Lacrimispora

species: Lacrimispora xylanolytica

full scientific name: Lacrimispora xylanolytica (Rogers and Baecker 1991) Haas and Blanchard 2020

type strain: yes

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
2729CHOPPED 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
2729PY + X MEDIUM (DSMZ Medium 104b)yeshttps://mediadive.dsmz.de/medium/104bName: PY + X MEDIUM (DSMZ Medium 104b; with strain-specific modifications) Composition: Yeast extract 10.0 g/l Xylan 5.0 g/l Trypticase peptone 5.0 g/l Meat peptone 5.0 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

culture temp

@refgrowthtypetemperaturerange
2729positivegrowth37mesophilic
67770positivegrowth37mesophilic

Physiology and metabolism

oxygen tolerance

  • @ref: 2729
  • oxygen tolerance: anaerobe

Isolation, sampling and environmental information

isolation

@refsample typehost speciescountryorigin.countrycontinent
2729decayed Pinus patula wood chipsPinus patulaSouth AfricaZAFAfrica
67770Decayed Pinus patula wood chipsPinus patula

isolation source categories

Cat1Cat2Cat3
#Host#Plants#Decomposing plant
#Host#Plants#Tree

taxonmaps

  • @ref: 69479
  • File name: preview.99_423.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_16;96_286;97_316;98_351;99_423&stattab=map
  • Last taxonomy: Lacrimispora
  • 16S sequence: X76739
  • Sequence Identity:
  • Total samples: 1645
  • soil counts: 221
  • aquatic counts: 156
  • animal counts: 1072
  • plant counts: 196

Safety information

risk assessment

  • @ref: 2729
  • biosafety level: 1
  • biosafety level comment: Risk group (German classification)

Sequence information

16S sequences

@refdescriptionaccessionlengthdatabaseNCBI tax ID
20218C.xylanolyticum gene for 16S ribosomal RNAX718551501ena29375
2729Clostridium xylanolyticum 16S rRNA gene, type strain DSM 6555TX767391448ena29375

GC content

@refGC-contentmethod
272940.0
6777040thermal denaturation, midpoint method (Tm)

External links

@ref: 2729

culture collection no.: DSM 6555, ATCC 49623, JCM 15735

straininfo link

  • @ref: 72288
  • straininfo: 42587

literature

  • topic: Metabolism
  • Pubmed-ID: 11760953
  • title: Metabolism of cinnamic acids by some Clostridiales and emendation of the descriptions of Clostridium aerotolerans, Clostridium celerecrescens and Clostridium xylanolyticum.
  • authors: Chamkha M, Garcia JL, Labat M
  • journal: Int J Syst Evol Microbiol
  • DOI: 10.1099/00207713-51-6-2105
  • year: 2001
  • mesh: Bacterial Typing Techniques, Cinnamates/*metabolism, Clostridium/*classification/growth & development/*metabolism, Culture Media, Glucose/metabolism
  • topic2: Cultivation

Reference

@idauthorscataloguedoi/urltitlejournalpubmed
2729Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 6555)https://www.dsmz.de/collection/catalogue/details/culture/DSM-6555
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
67770Curators of the JCMhttps://jcm.brc.riken.jp/en/
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
72288Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID42587.1StrainInfo: A central database for resolving microbial strain identifiers