Strain identifier

BacDive ID: 223

Type strain: Yes

Species: Aerococcus urinae

Strain Designation: E2

Strain history: CIP <- 1996, CCUG <- 1991, NCFB <- J.J. Christensen, Denmark: strain E2

NCBI tax ID(s): 1216979 (strain), 1376 (species)

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General

@ref: 3153

BacDive-ID: 223

DSM-Number: 7446

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

description: Aerococcus urinae E2 is a facultative anaerobe, mesophilic bacterium that was isolated from urinary tract infection; human.

NCBI tax id

NCBI tax idMatching level
1376species
1216979strain

strain history

@refhistory
3153<- NCDO; NCFB 2893 <- M. D. Collins; <- J. J. Christensen; E2 (Aerococcus-like organism)
67770CIP 104688 <-- CCUG 34223 <-- NCFB 2893 <-- J. J. Christensen E2.
123750CIP <- 1996, CCUG <- 1991, NCFB <- J.J. Christensen, Denmark: strain E2

doi: 10.13145/bacdive223.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/bacillota
  • domain: Bacteria
  • phylum: Bacillota
  • class: Bacilli
  • order: Lactobacillales
  • family: Aerococcaceae
  • genus: Aerococcus
  • species: Aerococcus urinae
  • full scientific name: Aerococcus urinae Aguirre and Collins 1992

@ref: 3153

domain: Bacteria

phylum: Firmicutes

class: Bacilli

order: Lactobacillales

family: Aerococcaceae

genus: Aerococcus

species: Aerococcus urinae

full scientific name: Aerococcus urinae Aguirre and Collins 1992 emend. Tohno et al. 2014

strain designation: E2

type strain: yes

Morphology

cell morphology

@refmotilityconfidencegram staincell shape
69480no97.493
69480100positive
123750positivecoccus-shaped

colony morphology

  • @ref: 123750

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
3153TRYPTICASE 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
22982MRS mediumyes
3153COLUMBIA 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
123750CIP Medium 72yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=72
123750CIP Medium 3yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=3

culture temp

@refgrowthtypetemperaturerange
3153positivegrowth37mesophilic
67770positivegrowth30mesophilic
123750positivegrowth37mesophilic
123750nogrowth10psychrophilic
123750nogrowth45thermophilic

Physiology and metabolism

oxygen tolerance

  • @ref: 123750
  • oxygen tolerance: facultative anaerobe

spore formation

@refspore formationconfidence
69481no100
69480no99.912

halophily

@refsaltgrowthtested relationconcentration
123750NaClpositivegrowth0-4 %
123750NaClnogrowth6 %
123750NaClnogrowth8 %
123750NaClnogrowth10 %

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
22982168082-dehydro-D-gluconate-builds acid from
22982174265-dehydro-D-gluconate-builds acid from
2298227613amygdalin-builds acid from
2298218305arbutin-builds acid from
2298217057cellobiose-builds acid from
2298215963ribitol-builds acid from
2298217108D-arabinose-builds acid from
2298228847D-fucose-builds acid from
2298212936D-galactose-builds acid from
2298262318D-lyxose-builds acid from
2298216024D-mannose-builds acid from
2298216443D-tagatose-builds acid from
2298265327D-xylose-builds acid from
2298216813galactitol-builds acid from
2298217113erythritol-builds acid from
2298228066gentiobiose-builds acid from
2298224265gluconate-builds acid from
2298217754glycerol-builds acid from
2298228087glycogen-builds acid from
2298217268myo-inositol-builds acid from
2298215443inulin-builds acid from
2298230849L-arabinose-builds acid from
2298218403L-arabitol-builds acid from
2298218287L-fucose-builds acid from
2298262345L-rhamnose-builds acid from
2298217266L-sorbose-builds acid from
2298265328L-xylose-builds acid from
2298217716lactose-builds acid from
2298217306maltose-builds acid from
229826731melezitose-builds acid from
2298228053melibiose-builds acid from
22982320061methyl alpha-D-glucopyranoside-builds acid from
2298243943methyl alpha-D-mannoside-builds acid from
2298274863methyl beta-D-xylopyranoside-builds acid from
2298216634raffinose-builds acid from
2298217814salicin-builds acid from
2298228017starch-builds acid from
2298227082trehalose-builds acid from
2298232528turanose-builds acid from
2298218333D-arabitol+builds acid from
2298215824D-fructose+builds acid from
2298217634D-glucose+builds acid from
2298216899D-mannitol+builds acid from
2298216988D-ribose+builds acid from
2298217924D-sorbitol+builds acid from
22982506227N-acetylglucosamine+builds acid from
2298217992sucrose+builds acid from
2298217151xylitol+builds acid from
1237504853esculin-hydrolysis
12375017632nitrate-reduction
12375016301nitrite-reduction
6838129016arginine-hydrolysis
6838117716lactose-builds acid from
6838127082trehalose-builds acid from
6838116634raffinose-builds acid from
6838130849L-arabinose-builds acid from
6838140585alpha-cyclodextrin-builds acid from
68381606565hippurate+hydrolysis
6838128087glycogen-builds acid from
6838127941pullulan-builds acid from
6838117306maltose-builds acid from
6838128053melibiose-builds acid from
683816731melezitose-builds acid from
68381320055methyl beta-D-glucopyranoside-builds acid from
6838116443D-tagatose-builds acid from
6838116199urea-hydrolysis

metabolite production

@refChebi-IDmetaboliteproduction
2298215688acetoinyes
12375035581indoleno
6838115688acetoinno

metabolite tests

@refChebi-IDmetabolitevoges-proskauer-test
6838115688acetoin-
12375015688acetoin-

enzymes

@refvalueactivityec
22982acid phosphatase+3.1.3.2
22982alkaline phosphatase+3.1.3.1
22982alpha-fucosidase-3.2.1.51
22982alpha-galactosidase-3.2.1.22
22982alpha-glucosidase-3.2.1.20
22982alpha-mannosidase-3.2.1.24
22982beta-galactosidase-3.2.1.23
22982beta-glucosidase-3.2.1.21
22982beta-glucuronidase+3.2.1.31
22982beta-mannosidase-3.2.1.25
22982chymotrypsin-3.4.4.5
22982cystine arylamidase-3.4.11.3
22982esterase (C 4)+
22982esterase lipase (C 8)-
22982glycyl tryptophan arylamidase+
22982leucine arylamidase+3.4.11.1
22982lipase (C 14)-
22982N-acetyl-beta-glucosaminidase-3.2.1.52
22982naphthol-AS-BI-phosphohydrolase+
22982pyroglutamic acid arylamidase-
22982pyrrolidonyl arylamidase-3.4.19.3
22982tripeptide aminopeptidase+3.4.11.4
22982trypsin-3.4.21.4
22982urease-3.5.1.5
22982valine arylamidase-
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
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
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
123750oxidase-
123750alcohol dehydrogenase-1.1.1.1
123750gelatinase-
123750DNase-
123750catalase-1.11.1.6
123750lecithinase-
123750lysine decarboxylase-4.1.1.18
123750ornithine decarboxylase-4.1.1.17
123750urease-3.5.1.5

API zym

@refControlAlkaline phosphataseEsteraseEsterase LipaseLipaseLeucine arylamidaseValine arylamidaseCystine arylamidaseTrypsinalpha- ChymotrypsinAcid phosphataseNaphthol-AS-BI-phosphohydrolasealpha- Galactosidasebeta- Galactosidasebeta- Glucuronidasealpha- Glucosidasebeta- GlucosidaseN-acetyl-beta- glucosaminidasealpha- Mannosidasealpha- Fucosidase
123750--+--+-----+--+-----

API rID32STR

@refADH Argbeta GLUbeta GARbeta GURalpha GALPALRIBMANSORLACTRERAFSACLARADARLCDEXVPAPPAbeta GALPyrAbeta NAGGTAHIPGLYGPULMALMELMLZMbeta DGTAGbeta MANURE
3153---+--+++/----+-+--+----+---------
3153---+--+/-+/-+/------+/--------+---------

API biotype100

@refGLUFRUGALTREMNESBEMELSACRAFMTEMALLACLTEMbGaMaGaCELGENMbGuESCRIBARAXYLPLERHAFUCMLZDARLLARLXLTDULTAGGLYINOMANMTLTURSORADOHBGLYXERYMDG3MDGSATMUCLTATDTATMTATDMLTLMLTCATETATETTECITGRTGAT2KG5KGTRYNAGGNTPACPATpOBEQATGTEmOBEBATPPATCMTTGEBETPCEABTHINLATCAPCYTHISSUCFUMGREGYTAVTETNTTNGLNITA3OBUAPTGTTPRODALALALASERMNTPROPTYR2KT
123750---------------------------------------------------------------------------------------------------

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinent
3153urinary tract infection; human
67770Human sources (urinary tract specimens)
123750Human, Urinary tractEsbjergDenmarkDNKEurope

isolation source categories

Cat1Cat2
#Infection#Disease
#Host Body-Site#Urogenital tract

taxonmaps

  • @ref: 69479
  • File name: preview.99_1288.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_13;96_748;97_871;98_1017;99_1288&stattab=map
  • Last taxonomy: Aerococcus urinae subclade
  • 16S sequence: LC589209
  • Sequence Identity:
  • Total samples: 5265
  • soil counts: 94
  • aquatic counts: 249
  • animal counts: 4861
  • plant counts: 61

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
31532Risk group (German classification)
1237501Risk group (French classification)

Sequence information

16S sequences

@refdescriptionaccessionlengthdatabaseNCBI tax ID
20218Aerococcus urinae strain CCUG 36881 16S-23S ribosomal RNA intergenic spacer, partial sequenceJN977132207ena1376
20218Aerococcus urinae gene for 16S rRNA, partial sequence, strain: NBRC 15544AB6808951415ena1376
3153Aerococcus urinae strain NCFB 2893 16S ribosomal RNA gene, partial sequenceM778191481ena1376
67770Aerococcus urinae JCM 18986 gene for 16S rRNA, partial sequenceLC5892091487ena1376

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Aerococcus urinae CCUG 36881GCA_001543175completencbi1376
66792Aerococcus urinae NBRC 15544 = CCUG 368811216979.3wgspatric1216979
66792Aerococcus urinae strain ATCC 512681376.307wgspatric1376
66792Aerococcus urinae strain CCUG368811376.123completepatric1376
66792Aerococcus urinae strain FDAARGOS_9111376.448completepatric1376
66792Aerococcus urinae NBRC 155442681812972draftimg1216979
66792Aerococcus urinae CCUG 368812687453482completeimg1376
67770Aerococcus urinae NBRC 15544 = CCUG 36881GCA_001544335contigncbi1216979
67770Aerococcus urinae ATCC 51268GCA_002087935scaffoldncbi1376

GC content

@refGC-contentmethod
315344.0thermal denaturation, midpoint method (Tm)
315344.1high performance liquid chromatography (HPLC)
6777044.4thermal denaturation, midpoint method (Tm)

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno100no
flagellatedno98.039no
gram-positiveyes92.341no
anaerobicno93.656no
halophileyes94.1no
spore-formingno92.389no
thermophileno99.614no
glucose-utilyes85.844no
motileno96.322no
aerobicno93.794no
glucose-fermentyes81.307no

External links

@ref: 3153

culture collection no.: DSM 7446, ATCC 51268, JCM 18986, NCFB 2893, NCTC 12142, CCM 4310, CCUG 29291, CCUG 29564, CCUG 34223, CCUG 36881, CIP 104688, IFO 15544, LMG 17750, LMG 19527, NBRC 15544, NCIMB 702893

straininfo link

  • @ref: 69906
  • straininfo: 363644

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny1373437Phylogenetic analysis of some Aerococcus-like organisms from urinary tract infections: description of Aerococcus urinae sp. nov.Aguirre M, Collins MDJ Gen Microbiol10.1099/00221287-138-2-4011992Base Sequence, Humans, Molecular Sequence Data, Phylogeny, RNA, Bacterial/*genetics, RNA, Ribosomal, 16S/*genetics, Sequence Homology, Nucleic Acid, Streptococcaceae/classification/*genetics, Streptococcal Infections/*microbiology, Urinary Tract Infections/*microbiologyPathogenicity
Phylogeny8995798Aerococcus urinae: intraspecies genetic and phenotypic relatedness.Christensen JJ, Whitney AM, Teixeira LM, Steigerwalt AG, Facklam RR, Korner B, Brenner DJInt J Syst Bacteriol10.1099/00207713-47-1-281997Bacteriological Techniques, DNA, Bacterial/*analysis, Esculin/metabolism, Molecular Sequence Data, Nucleic Acid Hybridization, Phylogeny, Polymerase Chain Reaction, RNA, Ribosomal, 16S/analysis, Sequence Analysis, DNA, Sequence Analysis, RNA, Sequence Homology, Nucleic Acid, Streptococcaceae/*classification/*geneticsTranscriptome
Genetics27103727Complete Genome Sequences of Aerococcus christensenii CCUG 28831T, Aerococcus sanguinicola CCUG 43001T, Aerococcus urinae CCUG 36881T, Aerococcus urinaeequi CCUG 28094T, Aerococcus urinaehominis CCUG 42038 BT, and Aerococcus viridans CCUG 4311T.Carkaci D, Dargis R, Nielsen XC, Skovgaard O, Fuursted K, Christensen JJGenome Announc10.1128/genomeA.00302-162016

Reference

@idauthorscataloguedoi/urltitlejournalpubmed
3153Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 7446)https://www.dsmz.de/collection/catalogue/details/culture/DSM-7446
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
22982Masanori Tohno,Maki Kitahara,Shuichi Matsuyama,Koji Kimura,Moriya Ohkuma,Kiyoshi Tajima10.1099/ijs.0.058081-0Aerococcus vaginalis sp. nov., isolated from the vaginal mucosa of a beef cow, and emended descriptions of Aerococcus suis, Aerococcus viridans, Aerococcus urinaeequi, Aerococcus urinaehominis, Aerococcus urinae, Aerococcus christensenii and Aerococcus sanguinicolaIJSEM 64: 1229-1236 201424421273
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/
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
69906Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID363644.1StrainInfo: A central database for resolving microbial strain identifiers
123750Curators of the CIPCollection of Institut Pasteur (CIP 104688)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20104688