Strain identifier
BacDive ID: 225
Type strain:
Species: Aerococcus urinaehominis
Strain history: CIP <- 2000, CCUG <- 1999, Y. Wyon, PHLS, Lindköping, Sweden
NCBI tax ID(s): 128944 (species)
General
@ref: 5921
BacDive-ID: 225
DSM-Number: 15634
keywords: genome sequence, 16S sequence, Bacteria, microaerophile, mesophilic, Gram-positive, coccus-shaped, human pathogen
description: Aerococcus urinaehominis CCUG 42038 B is a microaerophile, mesophilic, Gram-positive human pathogen that was isolated from human urine.
NCBI tax id
- NCBI tax id: 128944
- Matching level: species
strain history
@ref | history |
---|---|
5921 | <- CIP <- CCUG <- Y. Wyon, PHLS |
67770 | CIP 106675 <-- CCUG 42038 B <-- Y. Wyon. |
123751 | CIP <- 2000, CCUG <- 1999, Y. Wyon, PHLS, Lindköping, Sweden |
doi: 10.13145/bacdive225.20230509.8.1
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 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
@ref | gram stain | cell shape | motility | confidence |
---|---|---|---|---|
22978 | positive | coccus-shaped | ||
69480 | no | 97.777 | ||
69480 | positive | 100 | ||
123751 | positive | ovoid-shaped | no |
colony morphology
@ref | type of hemolysis | hemolysis ability | colony size | incubation period | medium used |
---|---|---|---|---|---|
22978 | alpha | 1 | <1.0 mm | 1 day | Columbia horse blood agar |
123751 | 1 |
Culture and growth conditions
culture medium
@ref | name | growth | link | composition |
---|---|---|---|---|
5921 | BHI MEDIUM (DSMZ Medium 215) | yes | https://mediadive.dsmz.de/medium/215 | Name: BHI MEDIUM (DSMZ Medium 215) Composition: Brain heart infusion 37.0 g/l Distilled water |
5921 | COLUMBIA BLOOD MEDIUM (DSMZ Medium 693) | yes | https://mediadive.dsmz.de/medium/693 | Name: COLUMBIA BLOOD MEDIUM (DSMZ Medium 693) Composition: Defibrinated sheep blood 50.0 g/l Columbia agar base |
22978 | Columbia horse blood agar | yes | ||
36413 | MEDIUM 6 - Columbia agar with 10 % horse blood | yes | Distilled water make up to (1000.000 ml);Columbia agar (39.000 g);Horseblood (100.000 ml) | |
123751 | CIP Medium 6 | yes | https://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=6 |
culture temp
@ref | growth | type | temperature | range |
---|---|---|---|---|
5921 | positive | growth | 37 | mesophilic |
36413 | positive | growth | 37 | mesophilic |
55315 | positive | growth | 37 | mesophilic |
67770 | positive | growth | 30 | mesophilic |
123751 | positive | growth | 25-41 | |
123751 | no | growth | 10 | psychrophilic |
123751 | no | growth | 45 | thermophilic |
Physiology and metabolism
oxygen tolerance
@ref | oxygen tolerance |
---|---|
5921 | microaerophile |
22978 | facultative anaerobe |
55315 | microaerophile |
123751 | facultative anaerobe |
spore formation
@ref | spore formation | confidence |
---|---|---|
22978 | no | |
69481 | no | 100 |
69480 | no | 99.984 |
halophily
- @ref: 123751
- salt: NaCl
- growth: no
- tested relation: growth
- concentration: 6.5 %
metabolite utilization
@ref | Chebi-ID | metabolite | utilization activity | kind of utilization tested |
---|---|---|---|---|
22978 | 23456 | cyclodextrin | - | builds acid from |
22978 | 18333 | D-arabitol | - | builds acid from |
22978 | 65327 | D-xylose | - | builds acid from |
22978 | 28087 | glycogen | - | builds acid from |
22978 | 30849 | L-arabinose | - | builds acid from |
22978 | 17716 | lactose | - | builds acid from |
22978 | 29864 | mannitol | - | builds acid from |
22978 | 6731 | melezitose | - | builds acid from |
22978 | 28053 | melibiose | - | builds acid from |
22978 | 27941 | pullulan | - | builds acid from |
22978 | 16634 | raffinose | - | builds acid from |
22978 | 30911 | sorbitol | - | builds acid from |
22978 | 33954 | tagatose | - | builds acid from |
22978 | 27082 | trehalose | - | builds acid from |
22978 | 5291 | gelatin | - | hydrolysis |
22978 | 17632 | nitrate | - | reduction |
22978 | 16988 | D-ribose | + | builds acid from |
22978 | 17234 | glucose | + | builds acid from |
22978 | 17306 | maltose | + | builds acid from |
22978 | 320055 | methyl beta-D-glucopyranoside | + | builds acid from |
22978 | 17992 | sucrose | + | builds acid from |
22978 | 4853 | esculin | + | hydrolysis |
22978 | 606565 | hippurate | + | hydrolysis |
123751 | 4853 | esculin | + | hydrolysis |
123751 | 606565 | hippurate | + | hydrolysis |
123751 | 17632 | nitrate | - | reduction |
123751 | 16301 | nitrite | - | reduction |
metabolite production
@ref | Chebi-ID | metabolite | production |
---|---|---|---|
22978 | 16301 | nitrite | no |
22978 | 15688 | acetoin | no |
metabolite tests
- @ref: 123751
- Chebi-ID: 15688
- metabolite: acetoin
- voges-proskauer-test: -
enzymes
@ref | value | activity | ec |
---|---|---|---|
22978 | acid phosphatase | + | 3.1.3.2 |
22978 | alpha-fucosidase | - | 3.2.1.51 |
22978 | alpha-galactosidase | - | 3.2.1.22 |
22978 | alpha-glucosidase | - | 3.2.1.20 |
22978 | alpha-mannosidase | - | 3.2.1.24 |
22978 | arginine dihydrolase | - | 3.5.3.6 |
22978 | beta-galactosidase | - | 3.2.1.23 |
22978 | beta-glucuronidase | + | 3.2.1.31 |
22978 | beta-mannosidase | - | 3.2.1.25 |
22978 | catalase | - | 1.11.1.6 |
22978 | chymotrypsin | - | 3.4.4.5 |
22978 | cystine arylamidase | - | 3.4.11.3 |
22978 | cytochrome oxidase | - | 1.9.3.1 |
22978 | esterase (C 4) | + | |
22978 | esterase lipase (C 8) | - | |
22978 | glycyl tryptophan arylamidase | - | |
22978 | leucine arylamidase | - | 3.4.11.1 |
22978 | lipase (C 14) | - | |
22978 | N-acetyl-beta-glucosaminidase | - | 3.2.1.52 |
22978 | phosphoamidase | - | 3.9.1.1 |
22978 | pyrazinamidase | + | 3.5.1.B15 |
22978 | pyroglutamic acid arylamidase | - | |
22978 | pyrrolidonyl arylamidase | - | 3.4.19.3 |
22978 | tripeptide aminopeptidase | - | 3.4.11.4 |
22978 | trypsin | - | 3.4.21.4 |
22978 | urease | - | 3.5.1.5 |
22978 | valine arylamidase | - | |
68382 | alpha-fucosidase | - | 3.2.1.51 |
68382 | alpha-mannosidase | - | 3.2.1.24 |
68382 | N-acetyl-beta-glucosaminidase | - | 3.2.1.52 |
68382 | beta-glucosidase | + | 3.2.1.21 |
68382 | alpha-glucosidase | + | 3.2.1.20 |
68382 | beta-glucuronidase | + | 3.2.1.31 |
68382 | beta-galactosidase | - | 3.2.1.23 |
68382 | alpha-galactosidase | - | 3.2.1.22 |
68382 | naphthol-AS-BI-phosphohydrolase | + | |
68382 | acid phosphatase | + | 3.1.3.2 |
68382 | alpha-chymotrypsin | - | 3.4.21.1 |
68382 | trypsin | - | 3.4.21.4 |
68382 | cystine arylamidase | - | 3.4.11.3 |
68382 | valine arylamidase | - | |
68382 | leucine arylamidase | - | 3.4.11.1 |
68382 | lipase (C 14) | - | |
68382 | esterase lipase (C 8) | + | |
68382 | esterase (C 4) | + | |
68382 | alkaline phosphatase | - | 3.1.3.1 |
123751 | oxidase | - | |
123751 | beta-galactosidase | - | 3.2.1.23 |
123751 | alcohol dehydrogenase | - | 1.1.1.1 |
123751 | catalase | - | 1.11.1.6 |
123751 | gamma-glutamyltransferase | - | 2.3.2.2 |
123751 | lysine decarboxylase | - | 4.1.1.18 |
123751 | ornithine decarboxylase | - | 4.1.1.17 |
API zym
@ref | Control | Alkaline phosphatase | Esterase | Esterase Lipase | Lipase | Leucine arylamidase | Valine arylamidase | Cystine arylamidase | Trypsin | alpha- Chymotrypsin | Acid phosphatase | Naphthol-AS-BI-phosphohydrolase | alpha- Galactosidase | beta- Galactosidase | beta- Glucuronidase | alpha- Glucosidase | beta- Glucosidase | N-acetyl-beta- glucosaminidase | alpha- Mannosidase | alpha- Fucosidase |
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
123751 | - | - | + | + | - | - | - | - | - | - | + | + | - | - | + | + | + | - | - | - |
Isolation, sampling and environmental information
isolation
@ref | sample type | geographic location | country | origin.country | continent | sampling date |
---|---|---|---|---|---|---|
5921 | human urine | Linköping | Sweden | SWE | Europe | |
55315 | Human urine,84-yr-old woman | Linköping | Sweden | SWE | Europe | 1999-03-22 |
67770 | Human urine | |||||
123751 | Human, Urine | Linköping | Sweden | SWE | Europe |
isolation source categories
Cat1 | Cat2 | Cat3 |
---|---|---|
#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
@ref | pathogenicity human | biosafety level | biosafety level comment |
---|---|---|---|
5921 | yes, in single cases | 1 | Risk group (German classification) |
123751 | 1 | Risk group (French classification) |
Sequence information
16S sequences
@ref | description | accession | length | database | NCBI tax ID |
---|---|---|---|---|---|
5921 | Aerococcus urinaehominis 16S rRNA gene, strain CCUG 42038b | AJ278341 | 1367 | ena | 128944 |
67770 | Aerococcus urinaehominis JCM 18987 gene for 16S rRNA, partial sequence | LC589210 | 1487 | ena | 128944 |
Genome sequences
@ref | description | accession | assembly level | database | NCBI tax ID |
---|---|---|---|---|---|
66792 | Aerococcus urinaehominis DSM 15634 | GCA_900103385 | scaffold | ncbi | 128944 |
66792 | Aerococcus urinaehominis strain DSM 15634 | 128944.7 | wgs | patric | 128944 |
66792 | Aerococcus urinaehominis DSM 15634 | 2619619005 | draft | img | 128944 |
67770 | Aerococcus urinaehominis CCUG42038B | GCA_001543245 | complete | ncbi | 128944 |
GC content
- @ref: 5921
- GC-content: 43.5
- method: high performance liquid chromatography (HPLC)
Genome-based predictions
predictions
trait | prediction | confidence | training_data |
---|---|---|---|
spore-forming | no | 100 | no |
motile | no | 97.214 | no |
flagellated | no | 97.529 | no |
gram-positive | yes | 95.095 | yes |
anaerobic | no | 93.893 | yes |
aerobic | no | 95.408 | yes |
halophile | yes | 93.76 | no |
spore-forming | no | 96.167 | yes |
glucose-ferment | yes | 86.734 | no |
thermophile | no | 99.455 | yes |
glucose-util | yes | 84.2 | no |
External links
@ref: 5921
culture collection no.: CCUG 42038 B, CCM 7338, DSM 15634, ATCC BAA 464, CIP 106675, JCM 18987, CCUG 42038
straininfo link
- @ref: 69908
- straininfo: 87796
literature
topic | Pubmed-ID | title | authors | journal | DOI | year | mesh | topic2 |
---|---|---|---|---|---|---|---|---|
Phylogeny | 11321115 | Aerococcus urinaehominis sp. nov., isolated from human urine. | Lawson PA, Falsen E, Ohlen M, Collins MD | Int J Syst Evol Microbiol | 10.1099/00207713-51-2-683 | 2001 | Bacterial Typing Techniques, Bacteriuria/*microbiology, Genes, rRNA/genetics, Humans, Molecular Sequence Data, Phylogeny, RNA, Ribosomal, 16S/genetics, Streptococcaceae/*classification/isolation & purification, Terminology as Topic | Pathogenicity |
Genetics | 27103727 | Complete 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 JJ | Genome Announc | 10.1128/genomeA.00302-16 | 2016 |
Reference
@id | authors | catalogue | doi/url | title | journal | pubmed |
---|---|---|---|---|---|---|
5921 | Curators of the DSMZ | Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 15634) | https://www.dsmz.de/collection/catalogue/details/culture/DSM-15634 | |||
20215 | Parte, A.C., Sardà Carbasse, J., Meier-Kolthoff, J.P., Reimer, L.C. and Göker, M. | 10.1099/ijsem.0.004332 | List of Prokaryotic names with Standing in Nomenclature (LPSN) moves to the DSMZ | |||
22978 | P. A. Lawson,E. Falsen,M. Ohlén,M. D. Collins | 10.1099/00207713-51-2-683 | Aerococcus urinaehominis sp. nov., isolated from human urine | IJSEM 51: 683-686 2001 | 11321115 | |
36413 | Curators of the CIP | https://brclims.pasteur.fr/brcWeb/souche/detail/1/18831 | ||||
55315 | Curators of the CCUG | Culture Collection University of Gothenburg (CCUG) (CCUG 42038 B) | https://www.ccug.se/strain?id=42038 | |||
66792 | Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmann | https://diaspora-project.de/progress.html#genomes | Automatically annotated for the DiASPora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information) | |||
66794 | Antje Chang, Lisa Jeske, Sandra Ulbrich, Julia Hofmann, Julia Koblitz, Ida Schomburg, Meina Neumann-Schaal, Dieter Jahn, Dietmar Schomburg | 10.1093/nar/gkaa1025 | BRENDA, the ELIXIR core data resource in 2021: new developments and updates | Nucleic Acids Res. 49: D498-D508 2020 | 33211880 | |
67770 | Curators of the JCM | https://jcm.brc.riken.jp/en/ | ||||
68382 | Automatically annotated from API zym | |||||
69479 | João 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 | |||
69480 | Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmann | https://diaspora-project.de/progress.html#genomes | Predictions based on genome sequence made in the Diaspora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information) | |||
69481 | Xiao-Yin To, René Mreches, Martin Binder, Alice C. McHardy, Philipp C. Münch | 10.21203/rs.3.rs-2527258/v1 | Predictions based on the model GenomeNet Sporulation v. 1 | |||
69908 | Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J. | 10.60712/SI-ID87796.1 | StrainInfo: A central database for resolving microbial strain identifiers | |||
123751 | Curators of the CIP | Collection of Institut Pasteur (CIP 106675) | https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20106675 |