Strain identifier

BacDive ID: 2274

Type strain: Yes

Species: Granulicatella adiacens

Strain Designation: GaD

Strain history: CIP <- 1988, A. Bouvet, Hôtel-Dieu Hosp., Paris, France: strain GaD, Streptococcus adjacens <- P. Cayeux, Inst. Pasteur, Paris, France <- J. Acar, Broussais Hosp., France

NCBI tax ID(s): 638301 (strain), 46124 (species)

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General

@ref: 3743

BacDive-ID: 2274

DSM-Number: 9848

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

description: Granulicatella adiacens GaD is an anaerobe, mesophilic bacterium that was isolated from Aortic valve.

NCBI tax id

NCBI tax idMatching level
46124species
638301strain

strain history

@refhistory
3743<- A. Bouvet, GaD <- J.F. Acar
116044CIP <- 1988, A. Bouvet, Hôtel-Dieu Hosp., Paris, France: strain GaD, Streptococcus adjacens <- P. Cayeux, Inst. Pasteur, Paris, France <- J. Acar, Broussais Hosp., France

doi: 10.13145/bacdive2274.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/bacillota
  • domain: Bacteria
  • phylum: Bacillota
  • class: Bacilli
  • order: Lactobacillales
  • family: Carnobacteriaceae
  • genus: Granulicatella
  • species: Granulicatella adiacens
  • full scientific name: Granulicatella adiacens (Bouvet et al. 1989) Collins and Lawson 2000

  • synonyms

    @refsynonym
    20215Abiotrophia adiacens
    20215Streptococcus adjacens

@ref: 3743

domain: Bacteria

phylum: Firmicutes

class: Bacilli

order: Lactobacillales

family: Carnobacteriaceae

genus: Granulicatella

species: Granulicatella adiacens

full scientific name: Granulicatella adiacens (Bouvet et al. 1989) Collins and Lawson 2000

strain designation: GaD

type strain: yes

Morphology

cell morphology

@refmotilityconfidencegram staincell shape
69480no92.816
69480100positive
116044nopositivecoccus-shaped

colony morphology

  • @ref: 116044

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
3743PYG MEDIUM (MODIFIED) (DSMZ Medium 104)yeshttps://mediadive.dsmz.de/medium/104Name: PYG MEDIUM (modified) (DSMZ Medium 104) Composition: Yeast extract 10.0 g/l Peptone 5.0 g/l Trypticase peptone 5.0 g/l Beef extract 5.0 g/l Glucose 5.0 g/l L-Cysteine HCl x H2O 0.5 g/l NaHCO3 0.4 g/l NaCl 0.08 g/l K2HPO4 0.04 g/l KH2PO4 0.04 g/l MgSO4 x 7 H2O 0.02 g/l CaCl2 x 2 H2O 0.01 g/l Hemin 0.005 g/l Ethanol 0.0038 g/l Resazurin 0.001 g/l Tween 80 Vitamin K1 NaOH Distilled water
40610MEDIUM 27 - for Capnocytophaga gingivalis and Abiotrophia genusyesDistilled water make up to (489.000 ml);Horse serum (200.000 ml);Brain heart infusion (37.000 g);Maltose 10 % solution - M0173 (200.000 ml);Cysteine hydrochloride 5% solution - M0172 (111.000 ml)
116044CIP Medium 27yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=27

culture temp

@refgrowthtypetemperaturerange
3743positivegrowth37mesophilic
40610positivegrowth37
48956positivegrowth37
116044positivegrowth30-37mesophilic
116044nogrowth5psychrophilic
116044nogrowth10psychrophilic

Physiology and metabolism

oxygen tolerance

@refoxygen tolerance
3743anaerobe
48956anaerobe
48956microaerophile
116044facultative anaerobe

spore formation

  • @ref: 69480
  • spore formation: no
  • confidence: 99.987

halophily

  • @ref: 116044
  • salt: NaCl
  • growth: no
  • tested relation: growth
  • concentration: 6.5 %

murein

  • @ref: 3743
  • murein short key: A11.04
  • type: A3alpha L-Lys-L-Ala

metabolite utilization

@refmetaboliteutilization activitykind of utilization testedChebi-ID
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
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
116044esculin-hydrolysis4853
116044hippurate-hydrolysis606565
116044nitrate-reduction17632
116044nitrite-reduction16301
68380urea-hydrolysis16199
68380arginine-hydrolysis29016
68380L-glutamate-degradation29985
68380nitrate-reduction17632
68380tryptophan-energy source27897

metabolite production

  • @ref: 68380
  • Chebi-ID: 35581
  • metabolite: indole
  • production: no

metabolite tests

@refChebi-IDmetaboliteindole testvoges-proskauer-test
6838035581indole-
11604415688acetoin-

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
68380serine arylamidase+
68380histidine arylamidase+
68380glycin arylamidase+
68380alanine arylamidase+3.4.11.2
68380tyrosine arylamidase+
68380leucyl glycin arylamidase-3.4.11.1
68380proline-arylamidase+3.4.11.5
68380L-arginine arylamidase+
68380alkaline phosphatase-3.1.3.1
68380tryptophan deaminase-4.1.99.1
68380glutamate decarboxylase-4.1.1.15
68380N-acetyl-beta-glucosaminidase-3.2.1.52
68380beta-glucuronidase-3.2.1.31
68380alpha-arabinosidase-3.2.1.55
68380beta-glucosidase-3.2.1.21
68380alpha-glucosidase-3.2.1.20
68380beta-Galactosidase 6-phosphate-
68380beta-galactosidase-3.2.1.23
68380alpha-galactosidase-3.2.1.22
68380arginine dihydrolase-3.5.3.6
68380urease-3.5.1.5
116044oxidase-
116044beta-galactosidase+3.2.1.23
116044alcohol dehydrogenase-1.1.1.1
116044catalase-1.11.1.6
116044gamma-glutamyltransferase-2.3.2.2
116044lysine decarboxylase-4.1.1.18
116044ornithine 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
116044-++-----+--+--------

API 50CHac

@refGLYERYDARALARARIBDXYLLXYLADOMDXGALGLUFRUMNESBERHADULINOMANSORMDMMDGNAGAMYARBESCSALCELMALLACMELSACTREINUMLZRAFAMDGLYGXLTGENTURLYXTAGDFUCLFUCDARLLARLGNT2KG5KG
116044+/-------+/---+++--------+-----+--+-+--++--+-+-+----+/-

API rID32A

@refUREADH Argalpha GALbeta GALbeta GPalpha GLUbeta GLUalpha ARAbeta GURbeta NAGMNERAFGDCalpha FUCNITINDPALArgAProALGAPheALeuAPyrATyrAAlaAGlyAHisAGGASerA
3743----------++-+/----++-+++/-+++++/-+
3743----------+/-+/--+---++-+/-+/--++++-+

API biotype100

@refGLUFRUGALTREMNESBEMELSACRAFMTEMALLACLTEMbGaMaGaCELGENMbGuESCRIBARAXYLPLERHAFUCMLZDARLLARLXLTDULTAGGLYINOMANMTLTURSORADOHBGLYXERYMDG3MDGSATMUCLTATDTATMTATDMLTLMLTCATETATETTECITGRTGAT2KG5KGTRYNAGGNTPACPATpOBEQATGTEmOBEBATPPATCMTTGEBETPCEABTHINLATCAPCYTHISSUCFUMGREGYTAVTETNTTNGLNITA3OBUAPTGTTPRODALALALASERMNTPROPTYR2KT
116044---------------------------------------------------------------------------------------------------

Isolation, sampling and environmental information

isolation

@refsample typecountryorigin.countrycontinent
3743Aortic valve
48859Human cardiac valves,endocarditis
48956Human blood,endocarditisFranceFRAEurope
116044Human, Aortic valves

isolation source categories

Cat1Cat2Cat3
#Host Body-Site#Organ#Heart
#Host#Human
#Host Body Product#Fluids#Blood
#Infection#Inflammation
#Infection#Patient

taxonmaps

  • @ref: 69479
  • File name: preview.99_2628.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_13;96_1400;97_1671;98_2034;99_2628&stattab=map
  • Last taxonomy: Granulicatella adiacens subclade
  • 16S sequence: D50540
  • Sequence Identity:
  • Total samples: 165582
  • soil counts: 3152
  • aquatic counts: 5374
  • animal counts: 155545
  • plant counts: 1511

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
37432Risk group (German classification)
1160442Risk group (French classification)

Sequence information

16S sequences

@refdescriptionaccessionlengthdatabaseNCBI tax ID
20218Granulicatella adiacens strain ATCC 49175 16S-23S ribosomal RNA intergenic spacer, complete sequenceAY353083222ena638301
20218Granulicatella adiacens strain ATCC 49175 clone 2 16S-23S ribosomal RNA intergenic spacer, partial sequenceDQ204536222ena638301
3743Granulicatella adiacens gene for 16S rRNA, strain: GIFU12706D505401406ena46124

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Granulicatella adiacens ATCC 49175GCA_000160675scaffoldncbi638301
66792Granulicatella adiacens ATCC 49175638301.3wgspatric638301
66792Granulicatella adiacens strain FDAARGOS_147746124.66completepatric46124
66792Granulicatella adiacens ATCC 49175645951817draftimg638301
66792Granulicatella adiacens ATCC 49175GCA_025150565completencbi638301
66792Granulicatella adiacens strain FDAARGOS_147746124.71completepatric46124
66792Granulicatella adiacens strain FDAARGOS_147746124.72completepatric46124
66792Granulicatella adiacens ATCC 49175638301.55completepatric638301
66792Granulicatella adiacens strain FDAARGOS_147746124.67completepatric46124

GC content

  • @ref: 3743
  • GC-content: 36.6
  • method: thermal denaturation, midpoint method (Tm)

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingyes72no
motileno95.776no
flagellatedno97.262no
gram-positiveyes91.878no
anaerobicno86.232no
aerobicno95.746no
halophileyes88.152no
spore-formingno95.325no
glucose-fermentyes83.506no
thermophileno99.079no
glucose-utilyes85.349no

External links

@ref: 3743

culture collection no.: DSM 9848, ATCC 49175, CIP 103243, CCUG 27637 A, CCUG 27809

straininfo link

  • @ref: 71832
  • straininfo: 10348

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Pathogenicity11574566Granulicatella and Abiotrophia species from human clinical specimens.Christensen JJ, Facklam RRJ Clin Microbiol10.1128/JCM.39.10.3520-3523.20012001Adolescent, Adult, Aged, Aged, 80 and over, Bacterial Typing Techniques/methods, Child, Child, Preschool, Gram-Positive Bacterial Infections/*microbiology, Humans, Infant, Male, Middle Aged, Phenotype, Streptococcaceae/*classification/physiologyPhenotype
Metabolism29174702Cytokine induction of peripheral blood mononuclear cells by biofilms and biofilm supernatants of Granulicatella and Abiotrophia spp.Bhardwaj RG, Al-Khabbaz A, Karched MMicrob Pathog10.1016/j.micpath.2017.11.0372017Abiotrophia/*immunology, Arachidonic Acids/metabolism, *Biofilms, Carnobacteriaceae/*immunology, Chemokine CCL3/metabolism, Chemokine CCL4/metabolism, Chemokines/metabolism, Cytokines/*metabolism, Endocarditis, Bacterial/microbiology, Humans, Interleukin-17/metabolism, Interleukin-1beta/metabolism, Interleukin-6/metabolism, Interleukin-8/metabolism, Leukocytes, Mononuclear/*metabolism, Peptide Fragments/metabolism, Tumor Necrosis Factor-alpha/metabolismPathogenicity
Metabolism33216751Proteomics of extracellular vesicles produced by Granulicatella adiacens, which causes infective endocarditis.Alkandari SA, Bhardwaj RG, Ellepola A, Karched MPLoS One10.1371/journal.pone.02276572020Carnobacteriaceae/isolation & purification/*metabolism, Cytokines/metabolism, Endocarditis, Bacterial/*microbiology, Extracellular Vesicles/*metabolism/microbiology, Humans, Leukocytes, Mononuclear/*metabolism/microbiology, Proteome/*analysis/metabolism, Proteomics/*methods, Virulence Factors/*metabolismPathogenicity

Reference

@idauthorscataloguedoi/urltitlejournalpubmed
3743Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 9848)https://www.dsmz.de/collection/catalogue/details/culture/DSM-9848
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
40610Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/15019
48859Curators of the CCUGCulture Collection University of Gothenburg (CCUG) (CCUG 27637 A)https://www.ccug.se/strain?id=27637
48956Curators of the CCUGCulture Collection University of Gothenburg (CCUG) (CCUG 27809)https://www.ccug.se/strain?id=27809
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)
66794Antje Chang, Lisa Jeske, Sandra Ulbrich, Julia Hofmann, Julia Koblitz, Ida Schomburg, Meina Neumann-Schaal, Dieter Jahn, Dietmar Schomburg10.1093/nar/gkaa1025BRENDA, the ELIXIR core data resource in 2021: new developments and updatesNucleic Acids Res. 49: D498-D508 202033211880
68371Automatically annotated from API 50CH acid
68380Automatically annotated from API rID32A
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)
71832Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID10348.1StrainInfo: A central database for resolving microbial strain identifiers
116044Curators of the CIPCollection of Institut Pasteur (CIP 103243)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20103243