Strain identifier
BacDive ID: 5255
Type strain:
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)
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 id | Matching level |
---|---|
51669 | species |
1123358 | strain |
strain history
@ref | history |
---|---|
8744 | <- NCDO <- B. Coster, TC 1 |
67770 | ATCC 33315 <-- NCDO 1635 <-- B. Coster <-- Tech. Hogesch., Delft. |
119820 | CIP <- 1986, NCFB, Pediococcus halophilus <- 1962, B. Coster, Queen Elizabeth College, London, UK, Pediococcus halophilus <- Tech. Hoogeschool Delft, The Netherlands: strain TC1 |
doi: 10.13145/bacdive5255.20230509.8.1
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: 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
- @ref: 119820
- gram stain: positive
- cell shape: coccus-shaped
- motility: no
Culture and growth conditions
culture medium
@ref | name | growth | link | composition |
---|---|---|---|---|
8744 | PEDIOCOCCUS HALOPHILUS MEDIUM (DSMZ Medium 227) | yes | https://mediadive.dsmz.de/medium/227 | 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 |
34907 | MEDIUM 63 - for Tetragenococcus halophilus | yes | Distilled water make up to (1000.000 ml);Sodium chloride (30.000 g);ManRogosa Sharp broth (55.000 g) | |
119820 | CIP Medium 63 | yes | https://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=63 |
culture temp
@ref | growth | type | temperature | range |
---|---|---|---|---|
8744 | positive | growth | 30 | mesophilic |
34907 | positive | growth | 30 | mesophilic |
50895 | positive | growth | 30 | mesophilic |
67770 | positive | growth | 30 | mesophilic |
119820 | positive | growth | 22-37 | |
119820 | no | growth | 10 | psychrophilic |
119820 | no | growth | 41 | thermophilic |
119820 | no | growth | 45 | thermophilic |
Physiology and metabolism
oxygen tolerance
- @ref: 119820
- oxygen tolerance: facultative anaerobe
halophily
@ref | salt | growth | tested relation | concentration |
---|---|---|---|---|
50895 | NaCl | positive | growth | 5 % |
119820 | NaCl | positive | growth | 0-10 % |
murein
- @ref: 8744
- murein short key: A11.31
- type: A4alpha L-Lys-D-Asp
metabolite utilization
@ref | metabolite | utilization activity | kind of utilization tested | Chebi-ID |
---|---|---|---|---|
68371 | Potassium 5-ketogluconate | - | builds acid from | |
68371 | Potassium 2-ketogluconate | - | builds acid from | |
68371 | gluconate | - | builds acid from | 24265 |
68371 | L-arabitol | - | builds acid from | 18403 |
68371 | D-arabitol | - | builds acid from | 18333 |
68371 | L-fucose | - | builds acid from | 18287 |
68371 | D-fucose | - | builds acid from | 28847 |
68371 | D-tagatose | + | builds acid from | 16443 |
68371 | D-lyxose | - | builds acid from | 62318 |
68371 | turanose | + | builds acid from | 32528 |
68371 | gentiobiose | + | builds acid from | 28066 |
68371 | xylitol | - | builds acid from | 17151 |
68371 | glycogen | - | builds acid from | 28087 |
68371 | starch | - | builds acid from | 28017 |
68371 | raffinose | - | builds acid from | 16634 |
68371 | melezitose | - | builds acid from | 6731 |
68371 | inulin | - | builds acid from | 15443 |
68371 | trehalose | + | builds acid from | 27082 |
68371 | sucrose | - | builds acid from | 17992 |
68371 | melibiose | - | builds acid from | 28053 |
68371 | lactose | - | builds acid from | 17716 |
68371 | maltose | + | builds acid from | 17306 |
68371 | cellobiose | + | builds acid from | 17057 |
68371 | salicin | + | builds acid from | 17814 |
68371 | esculin | + | builds acid from | 4853 |
68371 | arbutin | + | builds acid from | 18305 |
68371 | amygdalin | + | builds acid from | 27613 |
68371 | N-acetylglucosamine | + | builds acid from | 59640 |
68371 | methyl alpha-D-glucopyranoside | - | builds acid from | 320061 |
68371 | methyl alpha-D-mannoside | - | builds acid from | 43943 |
68371 | D-sorbitol | - | builds acid from | 17924 |
68371 | D-mannitol | - | builds acid from | 16899 |
68371 | myo-inositol | - | builds acid from | 17268 |
68371 | galactitol | - | builds acid from | 16813 |
68371 | L-rhamnose | - | builds acid from | 62345 |
68371 | L-sorbose | - | builds acid from | 17266 |
68371 | D-mannose | + | builds acid from | 16024 |
68371 | D-fructose | + | builds acid from | 15824 |
68371 | D-glucose | + | builds acid from | 17634 |
68371 | D-galactose | + | builds acid from | 12936 |
68371 | methyl beta-D-xylopyranoside | - | builds acid from | 74863 |
68371 | ribitol | - | builds acid from | 15963 |
68371 | L-xylose | - | builds acid from | 65328 |
68371 | D-xylose | - | builds acid from | 65327 |
68371 | D-ribose | + | builds acid from | 16988 |
68371 | L-arabinose | + | builds acid from | 30849 |
68371 | D-arabinose | - | builds acid from | 17108 |
68371 | erythritol | - | builds acid from | 17113 |
68371 | glycerol | - | builds acid from | 17754 |
119820 | hippurate | + | hydrolysis | 606565 |
119820 | nitrate | - | reduction | 17632 |
119820 | nitrite | - | reduction | 16301 |
metabolite production
- @ref: 119820
- Chebi-ID: 35581
- metabolite: indole
- production: no
enzymes
@ref | value | activity | ec |
---|---|---|---|
68382 | alpha-fucosidase | - | 3.2.1.51 |
68382 | alpha-mannosidase | - | 3.2.1.24 |
68382 | N-acetyl-beta-glucosaminidase | - | 3.2.1.52 |
68382 | beta-glucosidase | + | 3.2.1.21 |
68382 | alpha-glucosidase | + | 3.2.1.20 |
68382 | beta-glucuronidase | - | 3.2.1.31 |
68382 | beta-galactosidase | - | 3.2.1.23 |
68382 | alpha-galactosidase | - | 3.2.1.22 |
68382 | naphthol-AS-BI-phosphohydrolase | + | |
68382 | acid phosphatase | + | 3.1.3.2 |
68382 | alpha-chymotrypsin | - | 3.4.21.1 |
68382 | trypsin | - | 3.4.21.4 |
68382 | cystine arylamidase | - | 3.4.11.3 |
68382 | valine arylamidase | + | |
68382 | leucine arylamidase | + | 3.4.11.1 |
68382 | lipase (C 14) | - | |
68382 | esterase lipase (C 8) | - | |
68382 | esterase (C 4) | + | |
68382 | alkaline phosphatase | - | 3.1.3.1 |
119820 | oxidase | - | |
119820 | beta-galactosidase | + | 3.2.1.23 |
119820 | alcohol dehydrogenase | - | 1.1.1.1 |
119820 | gelatinase | - | |
119820 | amylase | - | |
119820 | DNase | - | |
119820 | caseinase | - | 3.4.21.50 |
119820 | catalase | - | 1.11.1.6 |
119820 | tween esterase | - | |
119820 | gamma-glutamyltransferase | + | 2.3.2.2 |
119820 | lecithinase | - | |
119820 | lipase | - | |
119820 | lysine decarboxylase | - | 4.1.1.18 |
119820 | ornithine decarboxylase | - | 4.1.1.17 |
119820 | phenylalanine ammonia-lyase | - | 4.3.1.24 |
119820 | urease | - | 3.5.1.5 |
API zym
@ref | Control | Alkaline phosphatase | Esterase | Esterase Lipase | Lipase | Leucine arylamidase | Valine arylamidase | Cystine arylamidase | Trypsin | alpha- Chymotrypsin | Acid phosphatase | Naphthol-AS-BI-phosphohydrolase | alpha- Galactosidase | beta- Galactosidase | beta- Glucuronidase | alpha- Glucosidase | beta- Glucosidase | N-acetyl-beta- glucosaminidase | alpha- Mannosidase | alpha- Fucosidase |
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
119820 | - | - | + | - | - | + | + | - | - | - | + | + | - | - | - | + | + | - | - | - |
API 50CHac
@ref | Q | GLY | ERY | DARA | LARA | RIB | DXYL | LXYL | ADO | MDX | GAL | GLU | FRU | MNE | SBE | RHA | DUL | INO | MAN | SOR | MDM | MDG | NAG | AMY | ARB | ESC | SAL | CEL | MAL | LAC | MEL | SAC | TRE | INU | MLZ | RAF | AMD | GLYG | XLT | GEN | TUR | LYX | TAG | DFUC | LFUC | DARL | LARL | GNT | 2KG | 5KG |
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
8744 | - | - | - | - | + | + | - | - | - | - | + | + | + | + | - | - | - | - | - | - | - | - | + | + | + | + | + | + | + | - | - | - | + | - | - | - | - | - | - | + | + | - | + | - | - | - | - | - | - | - |
Isolation, sampling and environmental information
isolation
- @ref: 8744
- sample type: salted anchovy
isolation source categories
Cat1 | Cat2 |
---|---|
#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
@ref | biosafety level | biosafety level comment |
---|---|---|
8744 | 1 | Risk group (German classification) |
119820 | 1 | Risk group (French classification) |
Sequence information
16S sequences
@ref | description | accession | length | database | NCBI tax ID |
---|---|---|---|---|---|
20218 | Tetragenococcus halophilus 16S rRNA gene, strain DSM 20339 | AJ301843 | 1653 | ena | 1123358 |
8744 | Tetragenococcus halophilus subsp. halophilus gene for 16S ribosomal RNA | D88668 | 1522 | ena | 1513897 |
8744 | Tetragenococcus halophilus strain LMG 11490 16S ribosomal RNA gene, partial sequence | EU689052 | 1357 | ena | 1123358 |
67770 | Tetragenococcus halophilus gene for 16S rRNA, partial sequence, strain: JCM 5888 | AB596938 | 1481 | ena | 1123358 |
67770 | Tetragenococcus halophilus subsp. halophilus gene for 16S ribosomal RNA, partial sequence, strain: JCM 5888 | LC071840 | 1486 | ena | 1513897 |
Genome sequences
@ref | description | accession | assembly level | database | NCBI tax ID |
---|---|---|---|---|---|
66792 | Tetragenococcus halophilus subsp. halophilus DSM 20339 | 1123358.5 | wgs | patric | 1123358 |
66792 | Tetragenococcus halophilus DSM 20339 | 2574179712 | draft | img | 1123358 |
66792 | Tetragenococcus halophilus DSM 20339 | 2835202559 | draft | img | 1123358 |
67770 | Tetragenococcus halophilus subsp. halophilus DSM 20339 | GCA_003841405 | contig | ncbi | 1123358 |
GC content
@ref | GC-content |
---|---|
8744 | 36 |
67770 | 36.8 |
Genome-based predictions
predictions
trait | prediction | confidence | training_data |
---|---|---|---|
motile | no | 94.717 | no |
flagellated | no | 98.191 | no |
gram-positive | yes | 91.04 | no |
anaerobic | no | 92.761 | no |
aerobic | no | 96.599 | no |
halophile | yes | 92.861 | no |
spore-forming | no | 93.724 | no |
thermophile | no | 97.526 | yes |
glucose-util | yes | 90.826 | no |
glucose-ferment | yes | 87.766 | no |
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
topic | Pubmed-ID | title | authors | journal | DOI | year | mesh | topic2 |
---|---|---|---|---|---|---|---|---|
Genetics | 7750734 | pUCL287 plasmid from Tetragenococcus halophila (Pediococcus halophilus) ATCC 33315 represents a new theta-type replicon family of lactic acid bacteria. | Benachour A, Frere J, Novel G | FEMS Microbiol Lett | 10.1111/j.1574-6968.1995.tb07518.x | 1995 | Base Sequence, Lactobacillaceae/genetics, Molecular Sequence Data, Pediococcus/*genetics, Plasmids/classification/genetics/*isolation & purification, Replicon/*genetics | Phylogeny |
Genetics | 8824766 | Characterization and replication mode determination of the minimal replicon of Tetragenococcus halophila ATCC33315 plasmid pUCL287. | Benachour A, Frere J, Boutibonnes P, Auffray Y | Biochimie | 10.1016/0300-9084(95)90005-5 | 1995 | Amino Acid Sequence, Base Sequence, DNA, Bacterial/*genetics, Molecular Sequence Data, Pediococcus/*genetics, Plasmids/genetics, Replication Origin/genetics, Replicon/*genetics | |
Genetics | 9294035 | Molecular 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 Y | Mol Gen Genet | 10.1007/s004380050523 | 1997 | Amino 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-Activators | Metabolism |
Phylogeny | 16014460 | Tetragenococcus koreensis sp. nov., a novel rhamnolipid-producing bacterium. | Lee M, Kim MK, Vancanneyt M, Swings J, Kim SH, Kang MS, Lee ST | Int J Syst Evol Microbiol | 10.1099/ijs.0.63448-0 | 2005 | Bacterial 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/*microbiology | Genetics |
16233497 | Effect 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 K | J Biosci Bioeng | 10.1016/s1389-1723(03)90114-9 | 2003 | |||
Metabolism | 20541276 | Proteinase-producing halophilic lactic acid bacteria isolated from fish sauce fermentation and their ability to produce volatile compounds. | Udomsil N, Rodtong S, Tanasupawat S, Yongsawatdigul J | Int J Food Microbiol | 10.1016/j.ijfoodmicro.2010.05.016 | 2010 | Animals, 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/*metabolism | Phylogeny |
Phylogeny | 21357458 | Characterization 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 KA | Int J Syst Evol Microbiol | 10.1099/ijs.0.029157-0 | 2011 | Bacterial 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, DNA | Biotechnology |
Genetics | 31202417 | Genomic 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 CO | Food Microbiol | 10.1016/j.fm.2019.04.009 | 2019 | Biogenic Amines/metabolism, Enterococcaceae/*genetics/*metabolism, *Gene Expression Profiling, *Genome, Bacterial, Genomics, *Metabolic Networks and Pathways, Osmotic Pressure, Phylogeny, RNA, Ribosomal, 16S/genetics, Salinity | Phylogeny |
Reference
@id | authors | catalogue | doi/url | title | journal | pubmed |
---|---|---|---|---|---|---|
8744 | Curators of the DSMZ | Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 20339) | https://www.dsmz.de/collection/catalogue/details/culture/DSM-20339 | |||
20215 | Parte, A.C., Sardà Carbasse, J., Meier-Kolthoff, J.P., Reimer, L.C. and Göker, M. | 10.1099/ijsem.0.004332 | List of Prokaryotic names with Standing in Nomenclature (LPSN) moves to the DSMZ | |||
20218 | Verslyppe, B., De Smet, W., De Baets, B., De Vos, P., Dawyndt P. | 10.1016/j.syapm.2013.11.002 | StrainInfo introduces electronic passports for microorganisms. | Syst Appl Microbiol. 37: 42-50 2014 | 24321274 | |
34907 | Curators of the CIP | https://brclims.pasteur.fr/brcWeb/souche/detail/1/13930 | ||||
50895 | Curators of the CCUG | Culture Collection University of Gothenburg (CCUG) (CCUG 32204) | https://www.ccug.se/strain?id=32204 | |||
66792 | Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmann | https://diaspora-project.de/progress.html#genomes | Automatically annotated for the DiASPora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information) | |||
67770 | Curators of the JCM | https://jcm.brc.riken.jp/en/ | ||||
68371 | Automatically annotated from API 50CH acid | |||||
68382 | Automatically annotated from API zym | |||||
69479 | João 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 | |||
74745 | Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J. | 10.60712/SI-ID343333.1 | StrainInfo: A central database for resolving microbial strain identifiers | |||
119820 | Curators of the CIP | Collection of Institut Pasteur (CIP 102263) | https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20102263 |