Strain identifier

BacDive ID: 18122

Type strain: Yes

Species: Gemella cuniculi

Strain Designation: M60449/99/1

Strain history: CIP <- 2000, CCUG <- M.D. Collins, IFR, Reading, UK: strain M60449/99/1 <- L. Hoyles, Reading, UK <- G. Foster, Inverness, UK

NCBI tax ID(s): 1121914 (strain), 150240 (species)

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General

@ref: 6040

BacDive-ID: 18122

DSM-Number: 15828

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

description: Gemella cuniculi M60449/99/1 is a microaerophile, mesophilic animal pathogen that was isolated from rabbit, sub-mandibular abscess.

NCBI tax id

NCBI tax idMatching level
150240species
1121914strain

strain history

@refhistory
6040<- CCUG <- M. D. Collins <- L. Hoxles <- G. Foster
118816CIP <- 2000, CCUG <- M.D. Collins, IFR, Reading, UK: strain M60449/99/1 <- L. Hoyles, Reading, UK <- G. Foster, Inverness, UK

doi: 10.13145/bacdive18122.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/bacillota
  • domain: Bacteria
  • phylum: Bacillota
  • class: Bacilli
  • order: Caryophanales
  • family: Gemellaceae
  • genus: Gemella
  • species: Gemella cuniculi
  • full scientific name: Gemella cuniculi Hoyles et al. 2000

@ref: 6040

domain: Bacteria

phylum: Firmicutes

class: Bacilli

order: Bacillales

family: Bacilli, not assigned to family

genus: Gemella

species: Gemella cuniculi

full scientific name: Gemella cuniculi Hoyles et al. 2000

strain designation: M60449/99/1

type strain: yes

Morphology

cell morphology

@refmotilityconfidencegram staincell shape
69480no95.36
69480100positive
118816nopositivecoccus-shaped

colony morphology

  • @ref: 118816
  • hemolysis ability: 1

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
6040MRS MEDIUM (DSMZ Medium 11)yeshttps://mediadive.dsmz.de/medium/11Name: MRS MEDIUM (DSMZ Medium 11) Composition: Glucose 20.0 g/l Casein peptone 10.0 g/l Meat extract 10.0 g/l Na-acetate 5.0 g/l Yeast extract 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
6040COLUMBIA BLOOD MEDIUM (DSMZ Medium 693)yeshttps://mediadive.dsmz.de/medium/693Name: COLUMBIA BLOOD MEDIUM (DSMZ Medium 693) Composition: Defibrinated sheep blood 50.0 g/l Columbia agar base
38629MEDIUM 6 - Columbia agar with 10 % horse bloodyesDistilled water make up to (1000.000 ml);Columbia agar (39.000 g);Horseblood (100.000 ml)
118816CIP Medium 6yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=6

culture temp

@refgrowthtypetemperaturerange
6040positivegrowth37mesophilic
38629positivegrowth37mesophilic
55532positivegrowth37mesophilic
118816positivegrowth10-41
118816nogrowth45thermophilic

Physiology and metabolism

oxygen tolerance

@refoxygen tolerance
6040microaerophile
55532anaerobe
55532microaerophile
118816facultative anaerobe

spore formation

  • @ref: 69480
  • spore formation: no
  • confidence: 99.997

halophily

  • @ref: 118816
  • salt: NaCl
  • growth: no
  • tested relation: growth
  • concentration: 6.5 %

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
68371D-arabitol-builds acid from18333
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
118816esculin-hydrolysis4853
118816hippurate-hydrolysis606565
118816nitrate-reduction17632
118816nitrite-reduction16301

metabolite tests

  • @ref: 118816
  • Chebi-ID: 15688
  • metabolite: acetoin
  • voges-proskauer-test: -

enzymes

@refvalueactivityec
118816oxidase-
118816beta-galactosidase-3.2.1.23
118816alcohol dehydrogenase-1.1.1.1
118816catalase-1.11.1.6
118816gamma-glutamyltransferase-2.3.2.2
118816lysine decarboxylase-4.1.1.18
118816ornithine 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
118816-+++-+----++--------

API 50CHac

@refGLYERYDARALARARIBDXYLLXYLADOMDXGALGLUFRUMNESBERHADULINOMANSORMDMMDGNAGAMYARBESCSALCELMALLACMELSACTREINUMLZRAFAMDGLYGXLTGENTURLYXTAGDFUCLFUCDARLLARLGNT2KG5KG
118816----------+++----++--+-----+--+------+-----------

Isolation, sampling and environmental information

isolation

@refsample typesampling dategeographic locationcountryorigin.countrycontinent
6040rabbit, sub-mandibular abscess
55532Rabbit sub-mandibular abscess1999InvernessUnited KingdomGBREurope
118816Animal, Rabbit, sub-mandibular abscess

isolation source categories

Cat1Cat2Cat3
#Host#Mammals#Leporidae (Rabbit/Hare)
#Host Body-Site#Oral cavity and airways
#Host Body-Site#Other#Abscess

taxonmaps

  • @ref: 69479
  • File name: preview.99_7624.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_238;96_3551;97_4361;98_5580;99_7624&stattab=map
  • Last taxonomy: Gemella cuniculi subclade
  • 16S sequence: AJ251987
  • Sequence Identity:
  • Total samples: 10599
  • soil counts: 63
  • aquatic counts: 121
  • animal counts: 10393
  • plant counts: 22

Safety information

risk assessment

@refpathogenicity animalbiosafety levelbiosafety level comment
6040yes2Risk group (German classification)
1188161Risk group (French classification)

Sequence information

16S sequences

@refdescriptionaccessionlengthdatabaseNCBI tax ID
20218Gemella cuniculi strain CCUG 42726 16S-23S ribosomal RNA intergenic spacer, complete sequenceJQ012767199ena150240
6040Gemella sp. M60449/99/1 T partial 16S rRNA geneAJ2519871451ena1121914

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Gemella cuniculi DSM 15828GCA_000425665scaffoldncbi1121914
66792Gemella cuniculi DSM 158281121914.3wgspatric1121914
66792Gemella cuniculi DSM 158282523533578draftimg1121914

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingyes82no
motileno94.526no
flagellatedno97.24no
gram-positiveyes94.178no
anaerobicno81.605no
halophileyes87.983no
spore-formingno90.023no
thermophileno99.151no
glucose-utilyes83.98no
aerobicno95.171no
glucose-fermentyes79.534no

External links

@ref: 6040

culture collection no.: DSM 15828, CCUG 42726, CIP 106481, ATCC BAA 287

straininfo link

  • @ref: 87110
  • straininfo: 44344

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny11155978Characterization of a Gemella-like organism isolated from an abscess of a rabbit: description of Gemella cunicula sp. nov.Hoyles L, Foster G, Falsen E, Collins MDInt J Syst Evol Microbiol10.1099/00207713-50-6-20372000*Abscess, Animals, Bacterial Proteins/analysis, DNA, Ribosomal/analysis, Genes, rRNA, Gram-Positive Bacterial Infections/*microbiology, Gram-Positive Cocci/chemistry/*classification/genetics/*isolation & purification, *Mandible, Molecular Sequence Data, Phenotype, Phylogeny, RNA, Ribosomal, 16S/genetics, Rabbits, Sequence Analysis, DNAGenetics
Phylogeny24664577Gemella parahaemolysans sp. nov. and Gemella taiwanensis sp. nov., isolated from human clinical specimens.Hung WC, Chen HJ, Tsai JC, Tseng SP, Lee TF, Hsueh PR, Shieh WY, Teng LJInt J Syst Evol Microbiol10.1099/ijs.0.052795-02014Aged, Aged, 80 and over, Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, Fatty Acids/chemistry, Female, Gemella/*classification/genetics/isolation & purification, Genes, Bacterial, Humans, Male, Middle Aged, Molecular Sequence Data, Multilocus Sequence Typing, Nucleic Acid Hybridization, *Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, TaiwanPathogenicity

Reference

@idauthorscataloguedoi/urltitlejournalpubmed
6040Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 15828)https://www.dsmz.de/collection/catalogue/details/culture/DSM-15828
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
38629Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/18616
55532Curators of the CCUGCulture Collection University of Gothenburg (CCUG) (CCUG 42726)https://www.ccug.se/strain?id=42726
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
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)
87110Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID44344.1StrainInfo: A central database for resolving microbial strain identifiers
118816Curators of the CIPCollection of Institut Pasteur (CIP 106481)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20106481