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Strain identifier

BacDive ID: 2282

Type strain: Yes

Species: Trichococcus palustris

Strain Designation: Z-7189

Strain history: <- T.N. Zhilina, Z-7189

NCBI tax ID(s): 140314 (species)

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

@ref: 3503

BacDive-ID: 2282

DSM-Number: 9172

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

description: Trichococcus palustris Z-7189 is a microaerophile, mesophilic bacterium that was isolated from swamp.

NCBI tax id

  • NCBI tax id: 140314
  • Matching level: species

strain history: <- T.N. Zhilina, Z-7189

doi: 10.13145/bacdive2282.20221219.7.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/bacillota
  • domain: Bacteria
  • phylum: Bacillota
  • class: Bacilli
  • order: Lactobacillales
  • family: Carnobacteriaceae
  • genus: Trichococcus
  • species: Trichococcus palustris
  • full scientific name: Trichococcus palustris (Zhilina et al. 1997) Liu et al. 2002
  • synonyms

    • @ref: 20215
    • synonym: Ruminococcus palustris

@ref: 3503

domain: Bacteria

phylum: Firmicutes

class: Bacilli

order: Lactobacillales

family: Carnobacteriaceae

genus: Trichococcus

species: Trichococcus palustris

full scientific name: Trichococcus palustris (Zhilina et al. 1997) Liu et al. 2002

strain designation: Z-7189

type strain: yes

Morphology

cell morphology

  • @ref: 69480
  • gram stain: positive
  • confidence: 80.13

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
3503TRYPTICASE SOY YEAST EXTRACT MEDIUM (DSMZ Medium 92)yeshttps://mediadive.dsmz.de/medium/92Name: TRYPTICASE SOY YEAST EXTRACT MEDIUM (DSMZ Medium 92) Composition: Trypticase soy broth 30.0 g/l Agar 15.0 g/l Yeast extract 3.0 g/l Distilled water
39276MEDIUM 118 - for Pasteurella, Actinobacillus and Psychrobacter frigidicolayesDistilled water make up to (1000.000 ml);Yeast extract (1.000 g);Tryptocasein soy agar (40.000 g)

culture temp

@refgrowthtypetemperaturerange
3503positivegrowth30mesophilic
39276positivegrowth30mesophilic

Physiology and metabolism

oxygen tolerance

  • @ref: 3503
  • oxygen tolerance: microaerophile

spore formation

  • @ref: 69480
  • spore formation: no
  • confidence: 98.15

halophily

  • @ref: 69480
  • halophily level: non-halophilic
  • confidence: 43.416

murein

  • @ref: 3503
  • murein short key: A11.31
  • type: A4alpha L-Lys-D-Asp

Isolation, sampling and environmental information

isolation

  • @ref: 3503
  • sample type: swamp
  • geographic location: Russia, near Abramtsevo settlement
  • country: Russia
  • origin.country: RUS
  • continent: Europe

isolation source categories

  • Cat1: #Environmental
  • Cat2: #Terrestrial
  • Cat3: #Wetland (Swamp)

taxonmaps

  • @ref: 69479
  • File name: preview.99_24449.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_13;96_12252;97_14862;98_18388;99_24449&stattab=map
  • Last taxonomy: Trichococcus
  • 16S sequence: AJ296179
  • Sequence Identity:
  • Total samples: 38677
  • soil counts: 4890
  • aquatic counts: 19650
  • animal counts: 13208
  • plant counts: 929

Safety information

risk assessment

  • @ref: 3503
  • biosafety level: 1
  • biosafety level comment: Risk group (German classification)

Sequence information

16S sequences

  • @ref: 3503
  • description: Ruminococcus palustris 16S rRNA gene, strain DSM 9172T
  • accession: AJ296179
  • length: 1520
  • database: ena
  • NCBI tax ID: 140314

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Trichococcus palustris DSM 9172GCA_900114465scaffoldncbi140314
66792Trichococcus palustris strain DSM 9172140314.8wgspatric140314
66792Trichococcus palustris DSM 91722619618822draftimg140314

GC content

  • @ref: 3503
  • GC-content: 47.5
  • method: thermal denaturation, midpoint method (Tm)

External links

@ref: 3503

culture collection no.: DSM 9172, CIP 105359

straininfo link

@refpassport
20218http://www.straininfo.net/strains/154728
20218http://www.straininfo.net/strains/154727

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny12148615Emended description of the genus Trichococcus, description of Trichococcus collinsii sp. nov., and reclassification of Lactosphaera pasteurii as Trichococcus pasteurii comb. nov. and of Ruminococcus palustris as Trichococcus palustris comb. nov. in the low-G+C gram-positive bacteria.Liu JR, Tanner RS, Schumann P, Weiss N, McKenzie CA, Janssen PH, Seviour EM, Lawson PA, Allen TD, Seviour RJInt J Syst Evol Microbiol10.1099/00207713-52-4-11132002Bacteria/*classification/genetics/metabolism/ultrastructure, Bacterial Typing Techniques, Base Composition, Cell Wall/chemistry, DNA, Bacterial/analysis/genetics, DNA, Ribosomal/analysis/genetics, Fatty Acids/analysis, Genes, rRNA, Molecular Sequence Data, Nucleic Acid Hybridization, Phenotype, RNA, Ribosomal, 16S/genetics, RNA, Ribosomal, 23S/geneticsGenetics
Metabolism24126154Enhanced start-up of anaerobic facultatively autotrophic biocathodes in bioelectrochemical systems.Zaybak Z, Pisciotta JM, Tokash JC, Logan BEJ Biotechnol10.1016/j.jbiotec.2013.10.0012013Anaerobiosis/genetics, *Autotrophic Processes, Bacteria, Anaerobic/classification/genetics/*metabolism, Bioelectric Energy Sources/microbiology, Carbon Cycle, Carbon Dioxide/*metabolism, Electrodes, Electrons, Fresh Water/*microbiology, Geologic Sediments/microbiology, Hydrogen/metabolism, RNA, Ribosomal, 16S/geneticsPhylogeny

Reference

@idauthorscataloguedoi/urltitlejournalpubmed
3503Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 9172)https://www.dsmz.de/collection/catalogue/details/culture/DSM-9172
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
39276Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/17370
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
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)