Strain identifier

BacDive ID: 225

Type strain: Yes

Species: Aerococcus urinaehominis

Strain history: CIP <- 2000, CCUG <- 1999, Y. Wyon, PHLS, Lindköping, Sweden

NCBI tax ID(s): 128944 (species)

« back to strain detail view
For citation purpose refer to the digital object identifier (doi) of the current version.
Archive
version 9.3 (current version):
version 9.2:
version 9.1:
version 9:
version 8.1:
version 8:
version 7.1:
version 7:
version 6:
version 5:
version 4.1:
version 4:
version 3:
version 2.1:
version 2:
version 1:
version 9.3 (current version)

General

@ref: 5921

BacDive-ID: 225

DSM-Number: 15634

keywords: genome sequence, 16S sequence, Bacteria, microaerophile, mesophilic, Gram-positive, coccus-shaped

description: Aerococcus urinaehominis CCUG 42038 B is a microaerophile, mesophilic, Gram-positive bacterium that was isolated from human urine.

NCBI tax id

  • NCBI tax id: 128944
  • Matching level: species

strain history

@refhistory
5921<- CIP <- CCUG <- Y. Wyon, PHLS
67770CIP 106675 <-- CCUG 42038 B <-- Y. Wyon.
123751CIP <- 2000, CCUG <- 1999, Y. Wyon, PHLS, Lindköping, Sweden

doi: 10.13145/bacdive225.20250331.9.3

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 urinaehominis
  • full scientific name: Aerococcus urinaehominis Lawson et al. 2001

@ref: 5921

domain: Bacteria

phylum: Firmicutes

class: Bacilli

order: Lactobacillales

family: Aerococcaceae

genus: Aerococcus

species: Aerococcus urinaehominis

full scientific name: Aerococcus urinaehominis Lawson et al. 2001 emend. Tohno et al. 2014

type strain: yes

Morphology

cell morphology

@refgram staincell shapemotility
22978positivecoccus-shaped
123751positiveovoid-shapedno

colony morphology

@reftype of hemolysishemolysis abilitycolony sizeincubation periodmedium used
22978alpha1<1.0 mm1 dayColumbia horse blood agar
1237511

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
5921BHI MEDIUM (DSMZ Medium 215)yeshttps://mediadive.dsmz.de/medium/215Name: BHI MEDIUM (DSMZ Medium 215) Composition: Brain heart infusion 37.0 g/l Distilled water
5921COLUMBIA 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
22978Columbia horse blood agaryes
36413MEDIUM 6 - Columbia agar with 10 % horse bloodyesDistilled water make up to (1000.000 ml);Columbia agar (39.000 g);Horseblood (100.000 ml)
123751CIP Medium 6yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=6

culture temp

@refgrowthtypetemperature
5921positivegrowth37
36413positivegrowth37
55315positivegrowth37
67770positivegrowth30
123751positivegrowth25-41
123751nogrowth10
123751nogrowth45

Physiology and metabolism

oxygen tolerance

@refoxygen toleranceconfidence
5921microaerophile
22978facultative anaerobe
55315microaerophile
123751facultative anaerobe
125439microaerophile98.2

spore formation

@refspore formationconfidence
22978no
125439no98.3

halophily

  • @ref: 123751
  • salt: NaCl
  • growth: no
  • tested relation: growth
  • concentration: 6.5 %

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
2297823456cyclodextrin-builds acid from
2297818333D-arabitol-builds acid from
2297865327D-xylose-builds acid from
2297828087glycogen-builds acid from
2297830849L-arabinose-builds acid from
2297817716lactose-builds acid from
2297829864mannitol-builds acid from
229786731melezitose-builds acid from
2297828053melibiose-builds acid from
2297827941pullulan-builds acid from
2297816634raffinose-builds acid from
2297830911sorbitol-builds acid from
2297833954tagatose-builds acid from
2297827082trehalose-builds acid from
229785291gelatin-hydrolysis
2297817632nitrate-reduction
2297816988D-ribose+builds acid from
2297817234glucose+builds acid from
2297817306maltose+builds acid from
22978320055methyl beta-D-glucopyranoside+builds acid from
2297817992sucrose+builds acid from
229784853esculin+hydrolysis
22978606565hippurate+hydrolysis
1237514853esculin+hydrolysis
123751606565hippurate+hydrolysis
12375117632nitrate-reduction
12375116301nitrite-reduction

metabolite production

@refChebi-IDmetaboliteproduction
2297816301nitriteno
2297815688acetoinno

metabolite tests

  • @ref: 123751
  • Chebi-ID: 15688
  • metabolite: acetoin
  • voges-proskauer-test: -

enzymes

@refvalueactivityec
22978acid phosphatase+3.1.3.2
22978alpha-fucosidase-3.2.1.51
22978alpha-galactosidase-3.2.1.22
22978alpha-glucosidase-3.2.1.20
22978alpha-mannosidase-3.2.1.24
22978arginine dihydrolase-3.5.3.6
22978beta-galactosidase-3.2.1.23
22978beta-glucuronidase+3.2.1.31
22978beta-mannosidase-3.2.1.25
22978catalase-1.11.1.6
22978chymotrypsin-3.4.4.5
22978cystine arylamidase-3.4.11.3
22978cytochrome oxidase-1.9.3.1
22978esterase (C 4)+
22978esterase lipase (C 8)-
22978glycyl tryptophan arylamidase-
22978leucine arylamidase-3.4.11.1
22978lipase (C 14)-
22978N-acetyl-beta-glucosaminidase-3.2.1.52
22978phosphoamidase-3.9.1.1
22978pyrazinamidase+3.5.1.B15
22978pyroglutamic acid arylamidase-
22978pyrrolidonyl arylamidase-3.4.19.3
22978tripeptide aminopeptidase-3.4.11.4
22978trypsin-3.4.21.4
22978urease-3.5.1.5
22978valine 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
68382beta-glucuronidase+3.2.1.31
68382alpha-glucosidase+3.2.1.20
68382alpha-galactosidase-3.2.1.22
68382beta-galactosidase-3.2.1.23
68382naphthol-AS-BI-phosphohydrolase+
68382alpha-chymotrypsin-3.4.21.1
68382trypsin-3.4.21.4
68382valine arylamidase-
68382cystine arylamidase-3.4.11.3
68382leucine arylamidase-3.4.11.1
68382lipase (C 14)-
68382esterase (C 4)+
68382esterase lipase (C 8)+
123751oxidase-
123751beta-galactosidase-3.2.1.23
123751alcohol dehydrogenase-1.1.1.1
123751catalase-1.11.1.6
123751gamma-glutamyltransferase-2.3.2.2
123751lysine decarboxylase-4.1.1.18
123751ornithine decarboxylase-4.1.1.17
68382acid phosphatase+3.1.3.2
68382alkaline phosphatase-3.1.3.1

API zym

@refControlAlkaline phosphataseEsteraseEsterase LipaseLipaseLeucine arylamidaseValine arylamidaseCystine arylamidaseTrypsinalpha- ChymotrypsinAcid phosphataseNaphthol-AS-BI-phosphohydrolasealpha- Galactosidasebeta- Galactosidasebeta- Glucuronidasealpha- Glucosidasebeta- GlucosidaseN-acetyl-beta- glucosaminidasealpha- Mannosidasealpha- Fucosidase
123751--++------++--+++---

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinentsampling date
5921human urineLinköpingSwedenSWEEurope
55315Human urine,84-yr-old womanLinköpingSwedenSWEEurope1999-03-22
67770Human urine
123751Human, UrineLinköpingSwedenSWEEurope

isolation source categories

Cat1Cat2Cat3
#Host#Human
#Host Body Product#Fluids#Urine

taxonmaps

  • @ref: 69479
  • File name: preview.99_5444.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_13;96_2642;97_3236;98_4067;99_5444&stattab=map
  • Last taxonomy: Aerococcus urinaehominis subclade
  • 16S sequence: LC589210
  • Sequence Identity:
  • Total samples: 1784
  • soil counts: 204
  • aquatic counts: 104
  • animal counts: 1435
  • plant counts: 41

Safety information

risk assessment

@refpathogenicity humanbiosafety levelbiosafety level comment
5921yes, in single cases1Risk group (German classification)
1237511Risk group (French classification)

Sequence information

16S sequences

@refdescriptionaccessionlengthdatabaseNCBI tax ID
5921Aerococcus urinaehominis 16S rRNA gene, strain CCUG 42038bAJ2783411367nuccore128944
67770Aerococcus urinaehominis JCM 18987 gene for 16S rRNA, partial sequenceLC5892101487nuccore128944

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Aerococcus urinaehominis DSM 15634GCA_900103385scaffoldncbi128944
66792Aerococcus urinaehominis strain DSM 15634128944.7wgspatric128944
66792Aerococcus urinaehominis DSM 156342619619005draftimg128944
67770Aerococcus urinaehominis CCUG42038BGCA_001543245completencbi128944

GC content

  • @ref: 5921
  • GC-content: 43.5
  • method: high performance liquid chromatography (HPLC)

Genome-based predictions

predictions

@refmodeltraitdescriptionpredictionconfidencetraining_data
125439BacteriaNetoxygen_toleranceOxygenic conditions needed for growthmicroaerophile98.2
125439BacteriaNetgram_stainReaction to gram-stainingpositive87
125439BacteriaNetmotilityAbility to perform movementno82.3
125439BacteriaNetspore_formationAbility to form endo- or exosporesno98.3
125438gram-positivegram-positivePositive reaction to Gram-stainingyes89.78no
125438anaerobicanaerobicAbility to grow under anoxygenic conditions (including facultative anaerobes)no86.217yes
125438aerobicaerobicAbility to grow under oxygenic conditions (including facultative aerobes)no94.853yes
125438spore-formingspore-formingAbility to form endo- or exosporesno84.199yes
125438thermophilethermophilicAbility to grow at temperatures above or equal to 45°Cno96.971no
125438motile2+flagellatedAbility to perform flagellated movementno88no

External links

@ref: 5921

culture collection no.: CCUG 42038 B, CCM 7338, DSM 15634, ATCC BAA-464, CIP 106675, JCM 18987, CCUG 42038, CCUG 42038b

straininfo link

  • @ref: 69908
  • straininfo: 87796

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny11321115Aerococcus urinaehominis sp. nov., isolated from human urine.Lawson PA, Falsen E, Ohlen M, Collins MDInt J Syst Evol Microbiol10.1099/00207713-51-2-6832001Bacterial Typing Techniques, Bacteriuria/*microbiology, Genes, rRNA/genetics, Humans, Molecular Sequence Data, Phylogeny, RNA, Ribosomal, 16S/genetics, Streptococcaceae/*classification/isolation & purification, Terminology as TopicPathogenicity
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
5921Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 15634)https://www.dsmz.de/collection/catalogue/details/culture/DSM-15634
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
22978P. A. Lawson,E. Falsen,M. Ohlén,M. D. Collins10.1099/00207713-51-2-683Aerococcus urinaehominis sp. nov., isolated from human urineIJSEM 51: 683-686 200111321115
36413Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/18831
55315Curators of the CCUGCulture Collection University of Gothenburg (CCUG) (CCUG 42038 B)https://www.ccug.se/strain?id=42038
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
67770Curators of the JCMhttps://jcm.brc.riken.jp/en/
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
69908Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID87796.1StrainInfo: A central database for resolving microbial strain identifiers
123751Curators of the CIPCollection of Institut Pasteur (CIP 106675)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20106675
125438Julia Koblitz, Lorenz Christian Reimer, Rüdiger Pukall, Jörg Overmann10.1101/2024.08.12.607695Predicting bacterial phenotypic traits through improved machine learning using high-quality, curated datasets
125439Philipp Münch, René Mreches, Martin Binder, Hüseyin Anil Gündüz, Xiao-Yin To, Alice McHardyhttps://github.com/GenomeNet/deepGdeepG: Deep Learning for Genome Sequence Data. R package version 0.3.1