Strain identifier

BacDive ID: 14763

Type strain: Yes

Species: Streptococcus ratti

Strain Designation: FA1, FA-1

Strain history: CIP <- 1986, ATCC <- R.J. Fitzgerald: strain FA-1

NCBI tax ID(s): 699248 (strain), 1341 (species)

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General

@ref: 8914

BacDive-ID: 14763

DSM-Number: 20564

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

description: Streptococcus ratti FA1 is a microaerophile, mesophilic bacterium that was isolated from caries lesion in rat.

NCBI tax id

NCBI tax idMatching level
1341species
699248strain

strain history

@refhistory
8914<- ATCC <- R.J. Fitzgerald, FA1
122146CIP <- 1986, ATCC <- R.J. Fitzgerald: strain FA-1

doi: 10.13145/bacdive14763.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/bacillota
  • domain: Bacteria
  • phylum: Bacillota
  • class: Bacilli
  • order: Lactobacillales
  • family: Streptococcaceae
  • genus: Streptococcus
  • species: Streptococcus ratti
  • full scientific name: Streptococcus ratti corrig. Coykendall 1977 (Approved Lists 1980)

  • synonyms

    • @ref: 20215
    • synonym: Streptococcus rattus

@ref: 8914

domain: Bacteria

phylum: Firmicutes

class: Bacilli

order: Lactobacillales

family: Streptococcaceae

genus: Streptococcus

species: Streptococcus ratti

full scientific name: Streptococcus ratti Coykendall 1977

strain designation: FA1, FA-1

type strain: yes

Morphology

cell morphology

@refmotilityconfidencegram staincell shape
69480no92.076
69480100positive
122146nopositivecoccus-shaped

colony morphology

  • @ref: 122146
  • hemolysis ability: 1

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
8914TRYPTICASE 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
38976MEDIUM 29- Brain heart agaryesDistilled water make up to (1000.000 ml);Brain heart infusion agar (52.000 g)
122146CIP Medium 72yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=72
122146CIP Medium 29yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=29

culture temp

@refgrowthtypetemperaturerange
8914positivegrowth37mesophilic
38976positivegrowth37mesophilic
122146positivegrowth30-37mesophilic

Physiology and metabolism

oxygen tolerance

@refoxygen tolerance
8914microaerophile
122146facultative anaerobe

spore formation

@refspore formationconfidence
69481no100
69480no99.951

murein

  • @ref: 8914
  • murein short key: A11.05
  • type: A3alpha L-Lys-L-Ala2

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-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
122146esculin+hydrolysis4853
122146nitrate-reduction17632
122146nitrite-reduction16301
68381arginine+hydrolysis29016
68381D-ribose-builds acid from16988
68381D-mannitol+builds acid from16899
68381sorbitol+builds acid from30911
68381lactose+builds acid from17716
68381trehalose+builds acid from27082
68381raffinose+builds acid from16634
68381sucrose+builds acid from17992
68381L-arabinose-builds acid from30849
68381D-arabitol-builds acid from18333
68381alpha-cyclodextrin-builds acid from40585
68381hippurate-hydrolysis606565
68381glycogen-builds acid from28087
68381pullulan-builds acid from27941
68381maltose+builds acid from17306
68381melibiose+builds acid from28053
68381melezitose-builds acid from6731
68381methyl beta-D-glucopyranoside+builds acid from320055
68381D-tagatose+builds acid from16443
68381urea-hydrolysis16199

metabolite production

  • @ref: 68381
  • Chebi-ID: 15688
  • metabolite: acetoin
  • production: yes

metabolite tests

  • @ref: 68381
  • Chebi-ID: 15688
  • metabolite: acetoin
  • voges-proskauer-test: +

enzymes

@refvalueactivityec
68381urease-3.5.1.5
68381beta-mannosidase-3.2.1.25
68381glycyl tryptophan arylamidase-
68381N-acetyl-beta-glucosaminidase-3.2.1.52
68381pyrrolidonyl arylamidase-3.4.19.3
68381beta-galactosidase-3.2.1.23
68381Alanyl-Phenylalanyl-Proline arylamidase+
68381alkaline phosphatase-3.1.3.1
68381alpha-galactosidase+3.2.1.22
68381beta-glucuronidase-3.2.1.31
68381beta-glucosidase+3.2.1.21
68381arginine dihydrolase+3.5.3.6
122146oxidase-
122146beta-galactosidase+3.2.1.23
122146alcohol dehydrogenase+1.1.1.1
122146catalase-1.11.1.6
122146lysine decarboxylase-4.1.1.18
122146ornithine decarboxylase-4.1.1.17
68382alkaline phosphatase-3.1.3.1
68382esterase (C 4)+
68382esterase lipase (C 8)-
68382lipase (C 14)-
68382leucine arylamidase+3.4.11.1
68382valine arylamidase-
68382cystine arylamidase-3.4.11.3
68382trypsin-3.4.21.4
68382alpha-chymotrypsin-3.4.21.1
68382acid phosphatase-3.1.3.2
68382naphthol-AS-BI-phosphohydrolase-
68382alpha-galactosidase-3.2.1.22
68382beta-galactosidase-3.2.1.23
68382beta-glucuronidase-3.2.1.31
68382alpha-glucosidase+3.2.1.20
68382beta-glucosidase+3.2.1.21
68382N-acetyl-beta-glucosaminidase-3.2.1.52
68382alpha-mannosidase-3.2.1.24
68382alpha-fucosidase-3.2.1.51

API zym

@refControlAlkaline phosphataseEsteraseEsterase LipaseLipaseLeucine arylamidaseValine arylamidaseCystine arylamidaseTrypsinalpha- ChymotrypsinAcid phosphataseNaphthol-AS-BI-phosphohydrolasealpha- Galactosidasebeta- Galactosidasebeta- Glucuronidasealpha- Glucosidasebeta- GlucosidaseN-acetyl-beta- glucosaminidasealpha- Mannosidasealpha- Fucosidase
122146--+--+---------++---

API 50CHac

@refGLYERYDARALARARIBDXYLLXYLADOMDXGALGLUFRUMNESBERHADULINOMANSORMDMMDGNAGAMYARBESCSALCELMALLACMELSACTREINUMLZRAFAMDGLYGXLTGENTURLYXTAGDFUCLFUCDARLLARLGNT2KG5KG
122146---------++++----++--+++++++++++--+---+--+--+/----+

API rID32STR

@refADH Argbeta GLUbeta GARbeta GURalpha GALPALRIBMANSORLACTRERAFSACLARADARLCDEXVPAPPAbeta GALPyrAbeta NAGGTAHIPGLYGPULMALMELMLZMbeta DGTAGbeta MANURE
8914++--+--++++++---++-------++-++--

Isolation, sampling and environmental information

isolation

@refsample type
8914caries lesion in rat
122146Animal, Rat, caries lesion

isolation source categories

Cat1Cat2Cat3
#Host#Mammals#Muridae (Mouse/Rat)
#Host Body-Site#Oral cavity and airways#Tooth
#Host Body-Site#Other#Wound

taxonmaps

  • @ref: 69479
  • File name: preview.99_3703.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_4;96_1909;97_2297;98_2830;99_3703&stattab=map
  • Last taxonomy: Streptococcus ratti
  • 16S sequence: AJ420201
  • Sequence Identity:
  • Total samples: 4713
  • soil counts: 6
  • aquatic counts: 18
  • animal counts: 4655
  • plant counts: 34

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
89141Risk group (German classification)
1221462Risk group (French classification)

Sequence information

16S sequences

@refdescriptionaccessionlengthdatabaseNCBI tax ID
20218Streptococcus ratti partial 16S rRNA gene, strain ATCC19645AJ4202011444ena1341
20218Streptococcus ratti strain CCUG 27642 16S-23S ribosomal RNA intergenic spacer, partial sequenceDQ204497527ena1341
20218S.rattus 16S rRNAX583041334ena1341

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Streptococcus ratti FA-1 = DSM 20564GCA_000286075contigncbi699248
66792Streptococcus ratti FA-1 = DSM 20564GCA_000347915contigncbi699248
66792Streptococcus ratti FA-1 = DSM 20564699248.4wgspatric699248
66792Streptococcus ratti FA-1 = DSM 20564699248.3wgspatric699248

GC content

  • @ref: 8914
  • GC-content: 42.2

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno100no
gram-positiveyes90.666no
anaerobicno92.647yes
halophileyes74.123no
spore-formingno94.797no
glucose-utilyes87.355no
thermophileno99.409no
flagellatedno96.95no
motileno95.849no
aerobicno97.941yes
glucose-fermentyes80.836no

External links

@ref: 8914

culture collection no.: DSM 20564, ATCC 19645, CIP 102509, CCM 6068, CCUG 27642, IMET 3280, NCDO 2723, NCTC 10920

straininfo link

  • @ref: 83880
  • straininfo: 8069

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Genetics15031528Molecular characterization of dextranase from Streptococcus rattus.Igarashi T, Morisaki H, Goto NMicrobiol Immunol10.1111/j.1348-0421.2004.tb03501.x2004Amino Acid Sequence, Base Sequence, Dextranase/chemistry/*genetics/metabolism, Escherichia coli/genetics, Molecular Sequence Data, Streptococcus/chemistry/*enzymology/genetics, TemperatureMetabolism
Phylogeny20139281Streptococcus ursoris sp. nov., isolated from the oral cavities of bears.Shinozaki-Kuwahara N, Takada K, Hirasawa MInt J Syst Evol Microbiol10.1099/ijs.0.019638-02010Animals, Bacterial Typing Techniques, Cluster Analysis, Culture Media/chemistry, DNA, Bacterial/chemistry/genetics, DNA, Ribosomal/chemistry/genetics, Molecular Sequence Data, Mouth/*microbiology, Nucleic Acid Hybridization, Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Streptococcus/*classification/genetics/*isolation & purification/physiology, Ursidae/*microbiologyGenetics
Phylogeny21924372Rapid detection and identification of Streptococcus ratti by a species-specific PCR method.Nishio J, Taniguchi M, Higashi J, Takahashi M, Ando T, Hasegawa T, Igarashi TAnaerobe10.1016/j.anaerobe.2011.09.0012011Bacterial Typing Techniques, DNA, Bacterial, Dextranase/genetics, *Polymerase Chain Reaction, Sensitivity and Specificity, Sequence Analysis, DNA, Species Specificity, Streptococcus/classification/genetics/*isolation & purificationTranscriptome

Reference

@idauthorscataloguedoi/urltitlejournalpubmed
8914Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 20564)https://www.dsmz.de/collection/catalogue/details/culture/DSM-20564
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
38976Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/14204
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)
68371Automatically annotated from API 50CH acid
68381Automatically annotated from API rID32STR
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
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)
69481Xiao-Yin To, René Mreches, Martin Binder, Alice C. McHardy, Philipp C. Münch10.21203/rs.3.rs-2527258/v1Predictions based on the model GenomeNet Sporulation v. 1
83880Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID8069.1StrainInfo: A central database for resolving microbial strain identifiers
122146Curators of the CIPCollection of Institut Pasteur (CIP 102509)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20102509