Strain identifier

BacDive ID: 5255

Type strain: Yes

Species: Tetragenococcus halophilus subsp. halophilus

Strain Designation: T11

Strain history: CIP <- 1986, NCFB, Pediococcus halophilus <- 1962, B. Coster, Queen Elizabeth College, London, UK, Pediococcus halophilus <- Tech. Hoogeschool Delft, The Netherlands: strain TC1

NCBI tax ID(s): 1123358 (strain), 51669 (species), 1513897 (subspecies)

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General

@ref: 8744

BacDive-ID: 5255

DSM-Number: 20339

keywords: genome sequence, 16S sequence, Bacteria, facultative anaerobe, mesophilic, Gram-positive, coccus-shaped

description: Tetragenococcus halophilus subsp. halophilus T11 is a facultative anaerobe, mesophilic, Gram-positive bacterium that was isolated from salted anchovy.

NCBI tax id

NCBI tax idMatching level
51669species
1123358strain
1513897subspecies

strain history

@refhistory
8744<- NCDO <- B. Coster, TC 1
67770ATCC 33315 <-- NCDO 1635 <-- B. Coster <-- Tech. Hogesch., Delft.
119820CIP <- 1986, NCFB, Pediococcus halophilus <- 1962, B. Coster, Queen Elizabeth College, London, UK, Pediococcus halophilus <- Tech. Hoogeschool Delft, The Netherlands: strain TC1

doi: 10.13145/bacdive5255.20250331.9.3

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: 8744

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: T11

type strain: yes

Morphology

cell morphology

@refgram staincell shapemotilityconfidence
119820positivecoccus-shapedno
125438positive91.674

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
8744PEDIOCOCCUS HALOPHILUS MEDIUM (DSMZ Medium 227)yeshttps://mediadive.dsmz.de/medium/227Name: 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
34907MEDIUM 63 - for Tetragenococcus halophilusyesDistilled water make up to (1000.000 ml);Sodium chloride (30.000 g);ManRogosa Sharp broth (55.000 g)
119820CIP Medium 63yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=63

culture temp

@refgrowthtypetemperature
8744positivegrowth30
34907positivegrowth30
50895positivegrowth30
67770positivegrowth30
119820positivegrowth22-37
119820nogrowth10
119820nogrowth41
119820nogrowth45

Physiology and metabolism

oxygen tolerance

@refoxygen toleranceconfidence
119820facultative anaerobe
125439obligate aerobe96.5

halophily

@refsaltgrowthtested relationconcentration
50895NaClpositivegrowth5 %
119820NaClpositivegrowth0-10 %

murein

  • @ref: 8744
  • murein short key: A11.31
  • type: A4alpha L-Lys-D-Asp

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
119820606565hippurate+hydrolysis
11982017632nitrate-reduction
11982016301nitrite-reduction
68371Potassium 5-ketogluconate-builds acid from
6837127613amygdalin+builds acid from
68371320061methyl alpha-D-glucopyranoside-builds acid from
6837112936D-galactose+builds acid from
68371Potassium 2-ketogluconate-builds acid from
6837124265gluconate-builds acid from
6837118403L-arabitol-builds acid from
6837118333D-arabitol-builds acid from
6837118287L-fucose-builds acid from
6837128847D-fucose-builds acid from
6837116443D-tagatose+builds acid from
6837162318D-lyxose-builds acid from
6837132528turanose+builds acid from
6837128066gentiobiose+builds acid from
6837117151xylitol-builds acid from
6837128087glycogen-builds acid from
6837128017starch-builds acid from
6837116634raffinose-builds acid from
683716731melezitose-builds acid from
6837115443inulin-builds acid from
6837127082trehalose+builds acid from
6837117992sucrose-builds acid from
6837128053melibiose-builds acid from
6837117716lactose-builds acid from
6837117306maltose+builds acid from
6837117057cellobiose+builds acid from
6837117814salicin+builds acid from
683714853esculin+builds acid from
6837118305arbutin+builds acid from
6837159640N-acetylglucosamine+builds acid from
6837143943methyl alpha-D-mannoside-builds acid from
6837117924D-sorbitol-builds acid from
6837116899D-mannitol-builds acid from
6837117268myo-inositol-builds acid from
6837116813galactitol-builds acid from
6837162345L-rhamnose-builds acid from
6837117266L-sorbose-builds acid from
6837116024D-mannose+builds acid from
6837115824D-fructose+builds acid from
6837117634D-glucose+builds acid from
6837174863methyl beta-D-xylopyranoside-builds acid from
6837115963ribitol-builds acid from
6837165328L-xylose-builds acid from
6837165327D-xylose-builds acid from
6837116988D-ribose+builds acid from
6837130849L-arabinose+builds acid from
6837117108D-arabinose-builds acid from
6837117113erythritol-builds acid from
6837117754glycerol-builds acid from

metabolite production

  • @ref: 119820
  • Chebi-ID: 35581
  • metabolite: indole
  • production: no

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
68382beta-glucuronidase-3.2.1.31
68382alpha-glucosidase+3.2.1.20
68382alpha-galactosidase-3.2.1.22
68382beta-galactosidase-3.2.1.23
68382naphthol-AS-BI-phosphohydrolase+
68382acid phosphatase+3.1.3.2
68382alpha-chymotrypsin-3.4.21.1
68382trypsin-3.4.21.4
68382leucine arylamidase+3.4.11.1
68382lipase (C 14)-
68382esterase (C 4)+
68382esterase lipase (C 8)-
119820oxidase-
119820beta-galactosidase+3.2.1.23
119820alcohol dehydrogenase-1.1.1.1
119820gelatinase-
119820amylase-
119820DNase-
119820caseinase-3.4.21.50
119820catalase-1.11.1.6
119820tween esterase-
119820gamma-glutamyltransferase+2.3.2.2
119820lecithinase-
119820lipase-
119820lysine decarboxylase-4.1.1.18
119820ornithine decarboxylase-4.1.1.17
119820phenylalanine ammonia-lyase-4.3.1.24
119820urease-3.5.1.5
68382cystine arylamidase-3.4.11.3
68382valine arylamidase+
68382alkaline phosphatase-3.1.3.1

API zym

@refControlAlkaline phosphataseEsteraseEsterase LipaseLipaseLeucine arylamidaseValine arylamidaseCystine arylamidaseTrypsinalpha- ChymotrypsinAcid phosphataseNaphthol-AS-BI-phosphohydrolasealpha- Galactosidasebeta- Galactosidasebeta- Glucuronidasealpha- Glucosidasebeta- GlucosidaseN-acetyl-beta- glucosaminidasealpha- Mannosidasealpha- Fucosidase
119820--+--++---++---++---

API 50CHac

@refQGLYERYDARALARARIBDXYLLXYLADOMDXGALGLUFRUMNESBERHADULINOMANSORMDMMDGNAGAMYARBESCSALCELMALLACMELSACTREINUMLZRAFAMDGLYGXLTGENTURLYXTAGDFUCLFUCDARLLARLGNT2KG5KG
8744----++----++++--------+++++++---+------++-+-------

Isolation, sampling and environmental information

isolation

  • @ref: 8744
  • sample type: salted anchovy

isolation source categories

Cat1Cat2
#Host#Fishes
#Condition#Saline

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: LC071840
  • Sequence Identity:
  • Total samples: 23236
  • soil counts: 861
  • aquatic counts: 1678
  • animal counts: 20165
  • plant counts: 532

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
87441Risk group (German classification)
1198201Risk group (French classification)

Sequence information

16S sequences

@refdescriptionaccessionlengthdatabaseNCBI tax ID
20218Tetragenococcus halophilus 16S rRNA gene, strain DSM 20339AJ3018431653nuccore1123358
8744Tetragenococcus halophilus subsp. halophilus gene for 16S ribosomal RNAD886681522nuccore1513897
8744Tetragenococcus halophilus strain LMG 11490 16S ribosomal RNA gene, partial sequenceEU6890521357nuccore1123358
67770Tetragenococcus halophilus gene for 16S rRNA, partial sequence, strain: JCM 5888AB5969381481nuccore1123358
67770Tetragenococcus halophilus subsp. halophilus gene for 16S ribosomal RNA, partial sequence, strain: JCM 5888LC0718401486nuccore1513897

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Tetragenococcus halophilus subsp. halophilus DSM 203391123358.5wgspatric1123358
66792Tetragenococcus halophilus DSM 203392574179712draftimg1123358
66792Tetragenococcus halophilus DSM 203392835202559draftimg1123358
67770Tetragenococcus halophilus subsp. halophilus DSM 20339GCA_003841405contigncbi1123358

GC content

@refGC-content
874436
6777036.8

Genome-based predictions

predictions

@refmodeltraitdescriptionpredictionconfidencetraining_data
125439BacteriaNetoxygen_toleranceOxygenic conditions needed for growthobligate aerobe96.5
125439BacteriaNetgram_stainReaction to gram-stainingvariable75.4
125439BacteriaNetmotilityAbility to perform movementyes79.6
125439BacteriaNetspore_formationAbility to form endo- or exosporesyes88.6
125438gram-positivegram-positivePositive reaction to Gram-stainingyes91.674no
125438anaerobicanaerobicAbility to grow under anoxygenic conditions (including facultative anaerobes)no85.215yes
125438spore-formingspore-formingAbility to form endo- or exosporesno82.441no
125438aerobicaerobicAbility to grow under oxygenic conditions (including facultative aerobes)no90.747no
125438thermophilethermophilicAbility to grow at temperatures above or equal to 45°Cno94.5yes
125438motile2+flagellatedAbility to perform flagellated movementno88.5no

External links

@ref: 8744

culture collection no.: DSM 20339, ATCC 33315, IAM 1676, LMG 11490, NCDO 1635, CCUG 32204, CCM 3458, TC 1, JCM 5888, BCRC 12550, CECT 4792, CIP 102263, IAM 12284, NBRC 100498, NCFB 1635, NCIMB 12011

straininfo link

  • @ref: 74745
  • straininfo: 343333

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Genetics7750734pUCL287 plasmid from Tetragenococcus halophila (Pediococcus halophilus) ATCC 33315 represents a new theta-type replicon family of lactic acid bacteria.Benachour A, Frere J, Novel GFEMS Microbiol Lett10.1111/j.1574-6968.1995.tb07518.x1995Base Sequence, Lactobacillaceae/genetics, Molecular Sequence Data, Pediococcus/*genetics, Plasmids/classification/genetics/*isolation & purification, Replicon/*geneticsPhylogeny
Genetics8824766Characterization and replication mode determination of the minimal replicon of Tetragenococcus halophila ATCC33315 plasmid pUCL287.Benachour A, Frere J, Boutibonnes P, Auffray YBiochimie10.1016/0300-9084(95)90005-51995Amino Acid Sequence, Base Sequence, DNA, Bacterial/*genetics, Molecular Sequence Data, Pediococcus/*genetics, Plasmids/genetics, Replication Origin/genetics, Replicon/*genetics
Genetics9294035Molecular analysis of the replication region of the theta-replicating plasmid pUCL287 from Tetragenococcus (Pediococcus) halophilus ATCC33315.Benachour A, Frere J, Flahaut S, Novel G, Auffray YMol Gen Genet10.1007/s0043800505231997Amino Acid Sequence, Bacterial Proteins/biosynthesis/genetics, Base Sequence, *DNA Helicases, DNA Primers/genetics, DNA Replication/genetics, *DNA-Binding Proteins, Escherichia coli/genetics/metabolism, Gene Expression, Genes, Bacterial, Molecular Sequence Data, Open Reading Frames, Pediococcus/*genetics/metabolism, Plasmids/*genetics, Polymerase Chain Reaction, Protein Biosynthesis, Proteins/genetics, Replication Origin, *Replicon, Restriction Mapping, Sequence Homology, Amino Acid, *Trans-ActivatorsMetabolism
Phylogeny16014460Tetragenococcus koreensis sp. nov., a novel rhamnolipid-producing bacterium.Lee M, Kim MK, Vancanneyt M, Swings J, Kim SH, Kang MS, Lee STInt J Syst Evol Microbiol10.1099/ijs.0.63448-02005Bacterial Typing Techniques, Base Composition, DNA, Bacterial/analysis, DNA, Ribosomal/analysis, Fatty Acids/analysis, Fermentation, Genes, rRNA, Glycolipids/*biosynthesis, Gram-Positive Cocci/chemistry/*classification/genetics/isolation & purification, Korea, Molecular Sequence Data, Nucleic Acid Hybridization, Phenotype, Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Vegetables/*microbiologyGenetics
16233497Effect of heterologous expression of molecular chaperone DnaK from Tetragenococcus halophilus on salinity adaptation of Escherichia coli.Sugimoto S, Nakayama J, Fukuda D, Sonezaki S, Watanabe M, Tosukhowong A, Sonomoto KJ Biosci Bioeng10.1016/s1389-1723(03)90114-92003
Metabolism20541276Proteinase-producing halophilic lactic acid bacteria isolated from fish sauce fermentation and their ability to produce volatile compounds.Udomsil N, Rodtong S, Tanasupawat S, Yongsawatdigul JInt J Food Microbiol10.1016/j.ijfoodmicro.2010.05.0162010Animals, Bacterial Proteins/*metabolism, Enterococcaceae/classification/enzymology/*isolation & purification/*metabolism, *Fermentation, Fish Products/analysis/*microbiology, Fishes, Lactic Acid/*metabolism, Molecular Sequence Data, Peptide Hydrolases/*metabolism, Phylogeny, Sodium Chloride/*metabolism, Volatile Organic Compounds/*metabolismPhylogeny
Phylogeny21357458Characterization of Tetragenococcus strains from sugar thick juice reveals a novel species, Tetragenococcus osmophilus sp. nov., and divides Tetragenococcus halophilus into two subspecies, T. halophilus subsp. halophilus subsp. nov. and T. halophilus subsp. flandriensis subsp. nov.Juste A, Van Trappen S, Verreth C, Cleenwerck I, De Vos P, Lievens B, Willems KAInt J Syst Evol Microbiol10.1099/ijs.0.029157-02011Bacterial Typing Techniques, Base Composition, Belgium, Cluster Analysis, DNA, Bacterial/chemistry/genetics, DNA, Ribosomal/chemistry/genetics, Enterococcaceae/*classification/genetics/*isolation & purification/physiology, *Food Microbiology, Molecular Sequence Data, Nucleic Acid Hybridization, Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNABiotechnology
Genetics31202417Genomic and metabolic features of Tetragenococcus halophilus as revealed by pan-genome and transcriptome analyses.Chun BH, Han DM, Kim KH, Jeong SE, Park D, Jeon COFood Microbiol10.1016/j.fm.2019.04.0092019Biogenic Amines/metabolism, Enterococcaceae/*genetics/*metabolism, *Gene Expression Profiling, *Genome, Bacterial, Genomics, *Metabolic Networks and Pathways, Osmotic Pressure, Phylogeny, RNA, Ribosomal, 16S/genetics, SalinityPhylogeny

Reference

@idauthorscataloguedoi/urltitlejournalpubmed
8744Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 20339)https://www.dsmz.de/collection/catalogue/details/culture/DSM-20339
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
34907Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/13930
50895Curators of the CCUGCulture Collection University of Gothenburg (CCUG) (CCUG 32204)https://www.ccug.se/strain?id=32204
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
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
74745Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID343333.1StrainInfo: A central database for resolving microbial strain identifiers
119820Curators of the CIPCollection of Institut Pasteur (CIP 102263)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20102263
125438Julia Koblitz, Lorenz Christian Reimer, Rüdiger Pukall, Jörg Overmann10.1101/2024.08.12.607695Predicting bacterial phenotypic traits through improved machine learning using high-quality, curated datasets
125439Philipp Münch, René Mreches, Martin Binder, Hüseyin Anil Gündüz, Xiao-Yin To, Alice McHardyhttps://github.com/GenomeNet/deepGdeepG: Deep Learning for Genome Sequence Data. R package version 0.3.1