Strain identifier

BacDive ID: 5256

Type strain: Yes

Species: Tetragenococcus solitarius

Strain Designation: 885/78, 885-78

Strain history: CIP <- 1989, NCTC <- 1988, J.A.E. Farrow, AFRC, Reading, UK <- R.R. Facklam, CDC: strain 885-78

NCBI tax ID(s): 1223494 (strain), 71453 (species)

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General

@ref: 2140

BacDive-ID: 5256

DSM-Number: 5634

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

description: Tetragenococcus solitarius 885/78 is an anaerobe, mesophilic, Gram-positive bacterium that was isolated from ear exudate.

NCBI tax id

NCBI tax idMatching level
1223494strain
71453species

strain history

@refhistory
2140<- NCTC <- J.A.E. Farrow <- R.R. Facklam, 885/78
67770ATCC 49428 <-- NCTC 12193 <-- J. A. E. Farrow 885/78 <-- R. R. Facklam.
122673CIP <- 1989, NCTC <- 1988, J.A.E. Farrow, AFRC, Reading, UK <- R.R. Facklam, CDC: strain 885-78

doi: 10.13145/bacdive5256.20250331.9.3

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 solitarius
  • full scientific name: Tetragenococcus solitarius (Collins et al. 1989) Ennahar and Cai 2005

  • synonyms

    • @ref: 20215
    • synonym: Enterococcus solitarius

@ref: 2140

domain: Bacteria

phylum: Firmicutes

class: Bacilli

order: Lactobacillales

family: Enterococcaceae

genus: Tetragenococcus

species: Tetragenococcus solitarius

full scientific name: Tetragenococcus solitarius (Collins et al. 1989) Ennahar and Cai 2005

strain designation: 885/78, 885-78

type strain: yes

Morphology

cell morphology

  • @ref: 122673
  • gram stain: positive
  • cell shape: coccus-shaped
  • motility: no

colony morphology

  • @ref: 122673
  • hemolysis ability: 1

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
2140TRYPTICASE 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
40633MEDIUM 29- Brain heart agaryesDistilled water make up to (1000.000 ml);Brain heart infusion agar (52.000 g)
122673CIP Medium 29yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=29

culture temp

@refgrowthtypetemperature
2140positivegrowth37
40633positivegrowth37
67770positivegrowth37
122673positivegrowth10-45

Physiology and metabolism

oxygen tolerance

@refoxygen toleranceconfidence
2140anaerobe
2140microaerophile
122673facultative anaerobe
125439obligate aerobe99.3

halophily

  • @ref: 122673
  • salt: NaCl
  • growth: positive
  • tested relation: growth
  • concentration: 6.5 %

murein

  • @ref: 2140
  • murein short key: A11.31
  • type: A4alpha L-Lys-D-Asp

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
1226734853esculin+hydrolysis
122673606565hippurate+hydrolysis
12267317632nitrate-reduction
12267316301nitrite-reduction
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
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
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
6837127613amygdalin+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 tests

  • @ref: 122673
  • Chebi-ID: 15688
  • metabolite: acetoin
  • voges-proskauer-test: -

enzymes

@refvalueactivityec
68382alpha-fucosidase-3.2.1.51
68382alpha-mannosidase-3.2.1.24
68382beta-glucosidase+3.2.1.21
68382N-acetyl-beta-glucosaminidase-3.2.1.52
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
68382trypsin-3.4.21.4
68382alpha-chymotrypsin-3.4.21.1
68382cystine arylamidase-3.4.11.3
68382valine arylamidase-
68382leucine arylamidase+3.4.11.1
68382lipase (C 14)-
68382esterase lipase (C 8)+
68382alkaline phosphatase-3.1.3.1
122673oxidase-
122673beta-galactosidase+3.2.1.23
122673alcohol dehydrogenase+1.1.1.1
122673catalase-1.11.1.6
122673gamma-glutamyltransferase-2.3.2.2
122673lysine decarboxylase-4.1.1.18
122673ornithine decarboxylase-4.1.1.17
68382esterase (C 4)+

API zym

@refControlAlkaline phosphataseEsteraseEsterase LipaseLipaseLeucine arylamidaseValine arylamidaseCystine arylamidaseTrypsinalpha- ChymotrypsinAcid phosphataseNaphthol-AS-BI-phosphohydrolasealpha- Galactosidasebeta- Galactosidasebeta- Glucuronidasealpha- Glucosidasebeta- GlucosidaseN-acetyl-beta- glucosaminidasealpha- Mannosidasealpha- Fucosidase
122673--++-+------+---+---

API 50CHac

@refGLYERYDARALARARIBDXYLLXYLADOMDXGALGLUFRUMNESBERHADULINOMANSORMDMMDGNAGAMYARBESCSALCELMALLACMELSACTREINUMLZRAFAMDGLYGXLTGENTURLYXTAGDFUCLFUCDARLLARLGNT2KG5KG
122673+---+----++++-+--++--++++++++-++-+/-++--++-+--+/--+-+/-

API biotype100

@refGLUFRUGALTREMNESBEMELSACRAFMTEMALLACLTEMbGaMaGaCELGENMbGuESCRIBARAXYLPLERHAFUCMLZDARLLARLXLTDULTAGGLYINOMANMTLTURSORADOHBGLYXERYMDG3MDGSATMUCLTATDTATMTATDMLTLMLTCATETATETTECITGRTGAT2KG5KGTRYNAGGNTPACPATpOBEQATGTEmOBEBATPPATCMTTGEBETPCEABTHINLATCAPCYTHISSUCFUMGREGYTAVTETNTTNGLNITA3OBUAPTGTTPRODALALALASERMNTPROPTYR2KT
122673------------------+----------------------------------------+---------------------------------------

Isolation, sampling and environmental information

isolation

@refsample type
2140ear exudate
67770Ear exudate
122673Human, Ear exudate

isolation source categories

Cat1Cat2Cat3
#Host Body-Site#Organ#Ear
#Host Body Product#Fluids

taxonmaps

  • @ref: 69479
  • File name: preview.99_56325.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_13;96_184;97_200;98_40204;99_56325&stattab=map
  • Last taxonomy: Tetragenococcus
  • 16S sequence: Y18338
  • Sequence Identity:
  • Total samples: 587
  • soil counts: 179
  • aquatic counts: 102
  • animal counts: 266
  • plant counts: 40

Safety information

risk assessment

@refpathogenicity humanbiosafety levelbiosafety level comment
2140yes, in single cases1Risk group (German classification)
1226732Risk group (French classification)

Sequence information

16S sequences

@refdescriptionaccessionlengthdatabaseNCBI tax ID
20218Enterococcus solitarius 16S ribosomal RNA gene, partial sequenceAF0610101340nuccore71453
20218E.solitarius 16S rRNA gene, partial (strain CCUG 29293)Y12915367nuccore71453
20218Enterococcus solitarius 16S rRNA gene, strain DSM 5634AJ3018401653nuccore71453
20218Tetragenococcus solitarius gene for 16S rRNA, partial sequence, strain: NBRC 100494AB6811921448nuccore71453
20218Enterococcus solitarius 16S rRNA geneY183381411nuccore71453
67770Tetragenococcus solitarius gene for 16S ribosomal RNA, partial sequence, strain: JCM 8736LC0970731412nuccore71453

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Tetragenococcus solitarius NBRC 1004941223494.3wgspatric1223494
66792Tetragenococcus solitarius NBRC 1004942731957563draftimg1223494
67770Tetragenococcus solitarius NBRC 100494GCA_001544195contigncbi1223494

GC content

@refGC-contentmethod
214040.0thermal denaturation, midpoint method (Tm)
6777038thermal denaturation, midpoint method (Tm)

Genome-based predictions

predictions

@refmodeltraitdescriptionpredictionconfidencetraining_data
125439BacteriaNetoxygen_toleranceOxygenic conditions needed for growthobligate aerobe99.3
125439BacteriaNetgram_stainReaction to gram-stainingvariable74.1
125439BacteriaNetmotilityAbility to perform movementyes72.9
125439BacteriaNetspore_formationAbility to form endo- or exosporesyes82.3
125438gram-positivegram-positivePositive reaction to Gram-stainingyes84.138no
125438anaerobicanaerobicAbility to grow under anoxygenic conditions (including facultative anaerobes)no87.855no
125438spore-formingspore-formingAbility to form endo- or exosporesno81.071no
125438aerobicaerobicAbility to grow under oxygenic conditions (including facultative aerobes)no93.169yes
125438thermophilethermophilicAbility to grow at temperatures above or equal to 45°Cno96yes
125438motile2+flagellatedAbility to perform flagellated movementno87no

External links

@ref: 2140

culture collection no.: CCUG 29293, LMG 12890, CIP 103330, JCM 8736, DSM 5634, ATCC 49428, NCTC 12193, CCM 4217, CDC 885-78, KCTC 3553, KCTC 3923, NBRC 100494, NCIMB 12902

straininfo link

  • @ref: 74746
  • straininfo: 10345

literature

  • topic: Phylogeny
  • Pubmed-ID: 15774629
  • title: Biochemical and genetic evidence for the transfer of Enterococcus solitarius Collins et al. 1989 to the genus Tetragenococcus as Tetragenococcus solitarius comb. nov.
  • authors: Ennahar S, Cai Y
  • journal: Int J Syst Evol Microbiol
  • DOI: 10.1099/ijs.0.63205-0
  • year: 2005
  • mesh: Bacterial Typing Techniques, Carbohydrate Metabolism, Enterococcus/*classification/genetics/metabolism, Gram-Positive Cocci/*classification/genetics/*metabolism, Lactose/*metabolism, Molecular Sequence Data, Nucleic Acid Hybridization, Phenotype, *Phylogeny, RNA, Ribosomal, 16S/*genetics, Sequence Analysis, DNA
  • topic2: Metabolism

Reference

@idauthorscataloguedoi/urltitlejournalpubmed
2140Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 5634)https://www.dsmz.de/collection/catalogue/details/culture/DSM-5634
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
40633Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/15116
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
74746Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID10345.1StrainInfo: A central database for resolving microbial strain identifiers
122673Curators of the CIPCollection of Institut Pasteur (CIP 103330)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20103330
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