Strain identifier

BacDive ID: 2282

Type strain: Yes

Species: Trichococcus palustris

Strain Designation: Z-7189

Strain history: CIP <- 1997, DSM <- T.N. Zhilina: strain 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, Gram-positive, oval-shaped

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

NCBI tax id

  • NCBI tax id: 140314
  • Matching level: species

strain history

@refhistory
3503<- T.N. Zhilina, Z-7189
121521CIP <- 1997, DSM <- T.N. Zhilina: strain Z-7189

doi: 10.13145/bacdive2282.20230509.8.1

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: 121521
  • gram stain: positive
  • cell shape: oval-shaped
  • motility: no

colony morphology

  • @ref: 121521

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)
121521CIP Medium 118-byeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=118-b
121521CIP Medium 187yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=187

culture temp

@refgrowthtypetemperaturerange
3503positivegrowth30mesophilic
39276positivegrowth30mesophilic
121521positivegrowth5-30
121521nogrowth37mesophilic
121521nogrowth41thermophilic

Physiology and metabolism

oxygen tolerance

@refoxygen tolerance
3503microaerophile
121521facultative anaerobe

murein

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

metabolite utilization

@refmetaboliteutilization activitykind of utilization testedChebi-ID
68371Potassium 5-ketogluconate-builds acid from
68371Potassium 2-ketogluconate-builds acid from
68371L-arabitol-builds acid from18403
68371D-arabitol-builds acid from18333
68371L-fucose-builds acid from18287
68371D-fucose-builds acid from28847
68371D-lyxose-builds acid from62318
68371gentiobiose+builds acid from28066
68371xylitol-builds acid from17151
68371glycogen-builds acid from28087
68371starch-builds acid from28017
68371raffinose+builds acid from16634
68371melezitose+builds acid from6731
68371inulin+builds acid from15443
68371trehalose-builds acid from27082
68371sucrose+builds acid from17992
68371melibiose+builds acid from28053
68371lactose+builds acid from17716
68371maltose+builds acid from17306
68371cellobiose+builds acid from17057
68371salicin+builds acid from17814
68371esculin+builds acid from4853
68371arbutin+builds acid from18305
68371amygdalin+builds acid from27613
68371N-acetylglucosamine+builds acid from59640
68371methyl alpha-D-glucopyranoside-builds acid from320061
68371methyl alpha-D-mannoside-builds acid from43943
68371D-sorbitol+builds acid from17924
68371D-mannitol+builds acid from16899
68371myo-inositol-builds acid from17268
68371galactitol-builds acid from16813
68371L-rhamnose-builds acid from62345
68371L-sorbose-builds acid from17266
68371D-mannose+builds acid from16024
68371D-fructose+builds acid from15824
68371D-glucose+builds acid from17634
68371D-galactose+builds acid from12936
68371methyl beta-D-xylopyranoside-builds acid from74863
68371ribitol-builds acid from15963
68371L-xylose-builds acid from65328
68371D-xylose-builds acid from65327
68371D-ribose+builds acid from16988
68371L-arabinose-builds acid from30849
68371D-arabinose-builds acid from17108
68371erythritol-builds acid from17113
68371glycerol-builds acid from17754
121521esculin+hydrolysis4853
121521hippurate+hydrolysis606565
121521nitrate-reduction17632
121521nitrite-reduction16301

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
121521oxidase-
121521beta-galactosidase+3.2.1.23
121521alcohol dehydrogenase-1.1.1.1
121521gelatinase-
121521amylase-
121521DNase-
121521caseinase-3.4.21.50
121521catalase-1.11.1.6
121521tween esterase-
121521gamma-glutamyltransferase-2.3.2.2
121521lecithinase-
121521lipase-
121521lysine decarboxylase-4.1.1.18
121521ornithine decarboxylase-4.1.1.17

API zym

@refControlAlkaline phosphataseEsteraseEsterase LipaseLipaseLeucine arylamidaseValine arylamidaseCystine arylamidaseTrypsinalpha- ChymotrypsinAcid phosphataseNaphthol-AS-BI-phosphohydrolasealpha- Galactosidasebeta- Galactosidasebeta- Glucuronidasealpha- Glucosidasebeta- GlucosidaseN-acetyl-beta- glucosaminidasealpha- Mannosidasealpha- Fucosidase
121521--++------+++-+-+---

API 50CHac

@refGLYERYDARALARARIBDXYLLXYLADOMDXGALGLUFRUMNESBERHADULINOMANSORMDMMDGNAGAMYARBESCSALCELMALLACMELSACTREINUMLZRAFAMDGLYGXLTGENTURLYXTAGDFUCLFUCDARLLARLGNT2KG5KG
121521----+----++++----++--++++++++++-+++---++/--+/-----+/---

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinent
3503swampRussia, near Abramtsevo settlementRussiaRUSEurope
121521SwampRussian FederationRUSEurope

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

@refbiosafety levelbiosafety level comment
35031Risk group (German classification)
1215211Risk group (French 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)

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
motileno58.486no
flagellatedno77.364no
gram-positiveyes82.253no
anaerobicno70.073no
aerobicno96.508no
halophileno55.261no
spore-formingno77.161no
glucose-fermentyes79.771no
thermophileno99.378yes
glucose-utilyes87.43no

External links

@ref: 3503

culture collection no.: DSM 9172, CIP 105359

straininfo link

  • @ref: 71840
  • straininfo: 48588

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
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
68371Automatically annotated from API 50CH acid
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
71840Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID48588.1StrainInfo: A central database for resolving microbial strain identifiers
121521Curators of the CIPCollection of Institut Pasteur (CIP 105359)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20105359