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, human pathogen

description: Tetragenococcus solitarius 885/78 is an anaerobe, mesophilic, Gram-positive human pathogen 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/bacdive5256.20230509.8.1

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 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

@refgrowthtypetemperaturerange
2140positivegrowth37mesophilic
40633positivegrowth37mesophilic
67770positivegrowth37mesophilic
122673positivegrowth10-45

Physiology and metabolism

oxygen tolerance

@refoxygen tolerance
2140anaerobe
2140microaerophile
122673facultative anaerobe

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

@refmetaboliteutilization activitykind of utilization testedChebi-ID
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
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
122673esculin+hydrolysis4853
122673hippurate+hydrolysis606565
122673nitrate-reduction17632
122673nitrite-reduction16301

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
68382N-acetyl-beta-glucosaminidase-3.2.1.52
68382beta-glucosidase+3.2.1.21
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
68382alpha-chymotrypsin-3.4.21.1
68382trypsin-3.4.21.4
68382cystine arylamidase-3.4.11.3
68382valine arylamidase-
68382leucine arylamidase+3.4.11.1
68382lipase (C 14)-
68382esterase lipase (C 8)+
68382esterase (C 4)+
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

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 sequenceAF0610101340ena71453
20218E.solitarius 16S rRNA gene, partial (strain CCUG 29293)Y12915367ena71453
20218Enterococcus solitarius 16S rRNA gene, strain DSM 5634AJ3018401653ena71453
20218Tetragenococcus solitarius gene for 16S rRNA, partial sequence, strain: NBRC 100494AB6811921448ena71453
20218Enterococcus solitarius 16S rRNA geneY183381411ena71453
67770Tetragenococcus solitarius gene for 16S ribosomal RNA, partial sequence, strain: JCM 8736LC0970731412ena71453

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

traitpredictionconfidencetraining_data
motileno95.691no
gram-positiveyes90.54no
anaerobicno95.981no
aerobicno96.337yes
halophileyes93.875no
spore-formingno94.064no
glucose-utilyes91.317no
flagellatedno97.646no
thermophileno96.718yes
glucose-fermentyes89.353no

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