Strain identifier

BacDive ID: 5253

Type strain: No

Species: Tetragenococcus halophilus subsp. halophilus

Strain Designation: dl 2, TVA 7-16

Strain history: IAM 1683 <-- K. Sakaguchi dl-2 ("Pediococcus soyae").

NCBI tax ID(s): 1513897 (subspecies)

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General

@ref: 8728

BacDive-ID: 5253

DSM-Number: 20337

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

description: Tetragenococcus halophilus subsp. halophilus dl 2 is a mesophilic bacterium that was isolated from soy sauce brewing mash.

NCBI tax id

  • NCBI tax id: 1513897
  • Matching level: subspecies

strain history

@refhistory
8728<- K. Kitahara, TVA 7-16 <- K. Sakaguchi, dl 2 (Pediococcus soyae)
67770IAM 1683 <-- K. Sakaguchi dl-2 ("Pediococcus soyae").

doi: 10.13145/bacdive5253.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/bacillota
  • domain: Bacteria
  • phylum: Bacillota
  • class: Bacilli
  • order: Lactobacillales
  • family: Enterococcaceae
  • genus: Tetragenococcus
  • species: Tetragenococcus halophilus subsp. halophilus
  • full scientific name: Tetragenococcus halophilus subsp. halophilus (Mees 1934) Justé et al. 2012

@ref: 8728

domain: Bacteria

phylum: Firmicutes

class: Bacilli

order: Lactobacillales

family: Enterococcaceae

genus: Tetragenococcus

species: Tetragenococcus halophilus subsp. halophilus

full scientific name: Tetragenococcus halophilus subsp. halophilus (Mees 1934) Justé et al. 2012

strain designation: dl 2, TVA 7-16

type strain: no

Culture and growth conditions

culture medium

  • @ref: 8728
  • name: PEDIOCOCCUS HALOPHILUS MEDIUM (DSMZ Medium 227)
  • growth: yes
  • link: https://mediadive.dsmz.de/medium/227
  • composition: Name: PEDIOCOCCUS HALOPHILUS MEDIUM (DSMZ Medium 227) Composition: NaCl 65.0 g/l Glucose 20.0 g/l Meat extract 10.0 g/l Casein peptone 10.0 g/l Yeast extract 5.0 g/l Na-acetate 5.0 g/l (NH4)3 citrate 2.0 g/l K2HPO4 2.0 g/l Tween 80 1.0 g/l MgSO4 x 7 H2O 0.2 g/l MnSO4 x H2O 0.05 g/l Distilled water

culture temp

@refgrowthtypetemperaturerange
8728positivegrowth30mesophilic
67770positivegrowth30mesophilic

Physiology and metabolism

murein

  • @ref: 8728
  • 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
68371gluconate-builds acid from24265
68371L-arabitol-builds acid from18403
68371D-arabitol-builds acid from18333
68371L-fucose-builds acid from18287
68371D-fucose-builds acid from28847
68371D-tagatose-builds acid from16443
68371D-lyxose-builds acid from62318
68371turanose-builds acid from32528
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

API 50CHac

@refQGLYERYDARALARARIBDXYLLXYLADOMDXGALGLUFRUMNESBERHADULINOMANSORMDMMDGNAGAMYARBESCSALCELMALLACMELSACTREINUMLZRAFAMDGLYGXLTGENTURLYXTAGDFUCLFUCDARLLARLGNT2KG5KG
8728----+-------------+------+----+-------------------

Isolation, sampling and environmental information

isolation

@refsample type
8728soy sauce brewing mash
67770Soy sauce brewing mashes

isolation source categories

  • Cat1: #Engineered
  • Cat2: #Food production
  • Cat3: #Food

taxonmaps

  • @ref: 69479
  • File name: preview.99_261.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_13;96_184;97_200;98_223;99_261&stattab=map
  • Last taxonomy: Tetragenococcus halophilus
  • 16S sequence: AB911549
  • Sequence Identity:
  • Total samples: 23236
  • soil counts: 861
  • aquatic counts: 1678
  • animal counts: 20165
  • plant counts: 532

Safety information

risk assessment

  • @ref: 8728
  • biosafety level: 1
  • biosafety level comment: Risk group (German classification)

Sequence information

16S sequences

  • @ref: 67770
  • description: Tetragenococcus halophilus gene for 16S rRNA, partial sequence, strain: JCM 20252
  • accession: AB911549
  • length: 1515
  • database: ena
  • NCBI tax ID: 51669

Genome sequences

  • @ref: 66792
  • description: Tetragenococcus halophilus DSM 20337
  • accession: GCA_024137205
  • assembly level: contig
  • database: ncbi
  • NCBI tax ID: 51669

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
flagellatedno97.784no
gram-positiveyes91.563no
anaerobicno90.056no
aerobicno96.746no
halophileyes94.352no
spore-formingno92.293no
motileno94.072no
glucose-fermentyes88.947no
thermophileno98.296no
glucose-utilyes91.019no

External links

@ref: 8728

culture collection no.: DSM 20337, JCM 20252, IAM 1683, NISL 7128

straininfo link

  • @ref: 74743
  • straininfo: 49608

Reference

@idauthorscataloguedoi/urltitle
8728Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 20337)https://www.dsmz.de/collection/catalogue/details/culture/DSM-20337
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)
67770Curators of the JCMhttps://jcm.brc.riken.jp/en/
68371Automatically annotated from API 50CH acid
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
74743Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID49608.1StrainInfo: A central database for resolving microbial strain identifiers