Strain identifier

BacDive ID: 5260

Type strain: Yes

Species: Tetragenococcus halophilus subsp. flandriensis

Strain Designation: T5

Strain history: LMG 26042 <-- A. Justé; Scientia Terrae Res. Inst., Belgium; T5.

NCBI tax ID(s): 1513898 (subspecies)

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General

@ref: 17366

BacDive-ID: 5260

DSM-Number: 23766

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

description: Tetragenococcus halophilus subsp. flandriensis T5 is a microaerophile, mesophilic bacterium that was isolated from degraded sugar thick juice.

NCBI tax id

  • NCBI tax id: 1513898
  • Matching level: subspecies

strain history

@refhistory
17366<- A. Justé, Lessius University College, De Nayer Campus, Sint-Katelijne Waver, Belgium; T5
67770LMG 26042 <-- A. Justé; Scientia Terrae Res. Inst., Belgium; T5.

doi: 10.13145/bacdive5260.20230509.8.1

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. flandriensis
  • full scientific name: Tetragenococcus halophilus subsp. flandriensis Justé et al. 2012

@ref: 17366

domain: Bacteria

phylum: Firmicutes

class: Bacilli

order: Lactobacillales

family: Enterococcaceae

genus: Tetragenococcus

species: Tetragenococcus halophilus subsp. flandriensis

full scientific name: Tetragenococcus halophilus subsp. flandriensis Justé et al. 2012

strain designation: T5

type strain: yes

Morphology

cell morphology

@refmotilityconfidencegram stain
69480no95.923
69480100positive

Culture and growth conditions

culture medium

  • @ref: 17366
  • name: TRYPTICASE SOY YEAST EXTRACT MEDIUM (DSMZ Medium 92)
  • growth: yes
  • link: https://mediadive.dsmz.de/medium/92
  • composition: Name: 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

culture temp

@refgrowthtypetemperaturerange
17366positivegrowth30mesophilic
67770positivegrowth28mesophilic

Physiology and metabolism

oxygen tolerance

  • @ref: 17366
  • oxygen tolerance: microaerophile

spore formation

  • @ref: 69480
  • spore formation: no
  • confidence: 99.943

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
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-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

API 50CHac

@refQGLYERYDARALARARIBDXYLLXYLADOMDXGALGLUFRUMNESBERHADULINOMANSORMDMMDGNAGAMYARBESCSALCELMALLACMELSACTREINUMLZRAFAMDGLYGXLTGENTURLYXTAGDFUCLFUCDARLLARLGNT2KG5KG
17366-+/-+/-+-+----++++-----+-+/-+++++++-+++------++----+/-----

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinent
17366degraded sugar thick juiceTienen, FlandersBelgiumBELEurope
67770Degraded sugar thick juice

isolation source categories

Cat1Cat2Cat3
#Host#Plants#Herbaceous plants (Grass,Crops)
#Host Body Product#Plant#Juice (natural)

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: EU522087
  • Sequence Identity:
  • Total samples: 23236
  • soil counts: 861
  • aquatic counts: 1678
  • animal counts: 20165
  • plant counts: 532

Safety information

risk assessment

  • @ref: 17366
  • biosafety level: 1
  • biosafety level comment: Risk group (German classification)

Sequence information

16S sequences

  • @ref: 17366
  • description: Tetragenococcus halophilus subsp. flandriensis strain T5 16S ribosomal RNA gene, partial sequence
  • accession: EU522087
  • length: 1388
  • database: ena
  • NCBI tax ID: 1513898

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Tetragenococcus halophilus LMG 26042GCA_003795105completencbi51669
66792Tetragenococcus halophilus strain LMG 2604251669.19completepatric51669
66792Tetragenococcus halophilus subsp. flandriensis strain DSM 237661513898.3wgspatric1513898
66792Tetragenococcus halophilus LMG 260422841061659completeimg51669
67770Tetragenococcus halophilus subsp. flandriensis DSM 23766GCA_002922845contigncbi1513898

GC content

  • @ref: 17366
  • GC-content: 36.7
  • method: high performance liquid chromatography (HPLC)

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingyes67no
motileno95.063no
flagellatedno97.735no
gram-positiveyes90.997no
anaerobicno93.645yes
aerobicno96.702yes
halophileyes93.626no
spore-formingno93.228no
glucose-utilyes90.733no
thermophileno98.434yes
glucose-fermentyes90.68no

External links

@ref: 17366

culture collection no.: DSM 23766, LMG 26042, JCM 31127

straininfo link

  • @ref: 74750
  • straininfo: 374285

Reference

@idauthorscataloguedoi/urltitle
17366Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 23766)https://www.dsmz.de/collection/catalogue/details/culture/DSM-23766
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
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)
74750Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID374285.1StrainInfo: A central database for resolving microbial strain identifiers