Strain identifier
BacDive ID: 14664
Type strain:
Species: Mammaliicoccus sciuri
Strain Designation: R1-33, BM 12492
Strain history: CIP <- 1999, N. El Solh, Inst. Pasteur, Paris, France: strain BM 12492 <- W. Kloos: strain R1-33
NCBI tax ID(s): 1296 (species)
General
@ref: 6619
BacDive-ID: 14664
DSM-Number: 16827
keywords: genome sequence, 16S sequence, Bacteria, aerobe, mesophilic, Gram-positive, human pathogen
description: Mammaliicoccus sciuri R1-33 is an aerobe, mesophilic, Gram-positive human pathogen that was isolated from skin of a Norway rat.
NCBI tax id
- NCBI tax id: 1296
- Matching level: species
strain history
@ref | history |
---|---|
6619 | <- CIP <- W. E. Kloos; R1-33 |
122520 | CIP <- 1999, N. El Solh, Inst. Pasteur, Paris, France: strain BM 12492 <- W. Kloos: strain R1-33 |
doi: 10.13145/bacdive14664.20230509.8.1
Name and taxonomic classification
LPSN
- @ref: 20215
- description: domain/bacteria
- keyword: phylum/bacillota
- domain: Bacteria
- phylum: Bacillota
- class: Bacilli
- order: Caryophanales
- family: Staphylococcaceae
- genus: Mammaliicoccus
- species: Mammaliicoccus sciuri
- full scientific name: Mammaliicoccus sciuri (Kloos et al. 1976) Madhaiyan et al. 2020
synonyms
@ref synonym 20215 Staphylococcus sciuri 20215 Staphylococcus sciuri subsp. rodentium 20215 Staphylococcus sciuri subsp. carnaticus
@ref: 6619
domain: Bacteria
phylum: Firmicutes
class: Bacilli
order: Caryophanales
family: Staphylococcaceae
genus: Mammaliicoccus
species: Mammaliicoccus sciuri
full scientific name: Mammaliicoccus sciuri (Kloos et al. 1976) Madhaiyan et al. 2020
strain designation: R1-33, BM 12492
type strain: no
Morphology
cell morphology
@ref | gram stain | confidence | cell shape | motility |
---|---|---|---|---|
69480 | positive | 100 | ||
122520 | positive | coccus-shaped | no |
colony morphology
@ref | type of hemolysis | hemolysis ability |
---|---|---|
6619 | gamma | |
122520 | 1 |
Culture and growth conditions
culture medium
@ref | name | growth | link | composition |
---|---|---|---|---|
6619 | 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 |
6619 | TRYPTICASE SOY YEAST EXTRACT MEDIUM (DSMZ Medium 92) | yes | https://mediadive.dsmz.de/medium/92 | Name: 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 |
42116 | MEDIUM 3 - Columbia agar | yes | Columbia agar (39.000 g);distilled water (1000.000 ml) | |
122520 | CIP Medium 3 | yes | https://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=3 |
culture temp
@ref | growth | type | temperature | range |
---|---|---|---|---|
6619 | positive | growth | 37 | mesophilic |
42116 | positive | growth | 37 | mesophilic |
53957 | positive | growth | 37 | mesophilic |
122520 | positive | growth | 10-45 |
Physiology and metabolism
oxygen tolerance
@ref | oxygen tolerance |
---|---|
53957 | aerobe |
122520 | facultative anaerobe |
spore formation
@ref | spore formation | confidence |
---|---|---|
69481 | no | 93 |
69480 | no | 99.63 |
murein
- @ref: 6619
- murein short key: A11.63
- type: A3alpha L-Lys-L-Ala-Gly3, L-Ser0-1
metabolite utilization
@ref | metabolite | utilization activity | kind of utilization tested | Chebi-ID |
---|---|---|---|---|
68371 | Potassium 5-ketogluconate | - | builds acid from | |
68371 | Potassium 2-ketogluconate | - | builds acid from | |
68371 | L-arabitol | - | builds acid from | 18403 |
68371 | D-arabitol | - | builds acid from | 18333 |
68371 | L-fucose | - | builds acid from | 18287 |
68371 | D-tagatose | - | builds acid from | 16443 |
68371 | D-lyxose | - | builds acid from | 62318 |
68371 | turanose | + | builds acid from | 32528 |
68371 | gentiobiose | + | builds acid from | 28066 |
68371 | xylitol | - | builds acid from | 17151 |
68371 | glycogen | - | builds acid from | 28087 |
68371 | starch | - | builds acid from | 28017 |
68371 | raffinose | - | builds acid from | 16634 |
68371 | melezitose | - | builds acid from | 6731 |
68371 | inulin | - | builds acid from | 15443 |
68371 | trehalose | + | builds acid from | 27082 |
68371 | sucrose | + | builds acid from | 17992 |
68371 | melibiose | - | builds acid from | 28053 |
68371 | lactose | - | builds acid from | 17716 |
68371 | maltose | + | builds acid from | 17306 |
68371 | cellobiose | + | builds acid from | 17057 |
68371 | salicin | + | builds acid from | 17814 |
68371 | esculin | + | builds acid from | 4853 |
68371 | arbutin | + | builds acid from | 18305 |
68371 | methyl alpha-D-glucopyranoside | - | builds acid from | 320061 |
68371 | methyl alpha-D-mannoside | - | builds acid from | 43943 |
68371 | D-sorbitol | + | builds acid from | 17924 |
68371 | D-mannitol | + | builds acid from | 16899 |
68371 | galactitol | - | builds acid from | 16813 |
68371 | L-rhamnose | - | builds acid from | 62345 |
68371 | L-sorbose | - | builds acid from | 17266 |
68371 | D-mannose | + | builds acid from | 16024 |
68371 | D-fructose | + | builds acid from | 15824 |
68371 | D-glucose | + | builds acid from | 17634 |
68371 | methyl beta-D-xylopyranoside | - | builds acid from | 74863 |
68371 | ribitol | - | builds acid from | 15963 |
68371 | L-xylose | - | builds acid from | 65328 |
68371 | D-xylose | - | builds acid from | 65327 |
68371 | D-ribose | + | builds acid from | 16988 |
68371 | L-arabinose | - | builds acid from | 30849 |
68371 | D-arabinose | - | builds acid from | 17108 |
68371 | erythritol | - | builds acid from | 17113 |
68371 | glycerol | + | builds acid from | 17754 |
122520 | hippurate | + | hydrolysis | 606565 |
122520 | nitrate | + | reduction | 17632 |
122520 | nitrite | - | reduction | 16301 |
68375 | urea | - | hydrolysis | 16199 |
68375 | arginine | - | hydrolysis | 29016 |
68375 | ornithine | - | degradation | 18257 |
68375 | esculin | + | hydrolysis | 4853 |
68375 | D-glucose | + | fermentation | 17634 |
68375 | D-fructose | + | fermentation | 15824 |
68375 | D-mannose | + | fermentation | 16024 |
68375 | maltose | + | fermentation | 17306 |
68375 | lactose | - | fermentation | 17716 |
68375 | trehalose | + | fermentation | 27082 |
68375 | D-mannitol | + | fermentation | 16899 |
68375 | raffinose | - | fermentation | 16634 |
68375 | D-ribose | + | fermentation | 16988 |
68375 | cellobiose | + | fermentation | 17057 |
68375 | nitrate | + | reduction | 17632 |
68375 | sucrose | + | fermentation | 17992 |
68375 | N-acetylglucosamine | + | fermentation | 59640 |
68375 | turanose | + | fermentation | 32528 |
68375 | arabinose | - | fermentation | 22599 |
antibiotic resistance
- @ref: 68375
- ChEBI: 28368
- metabolite: novobiocin
- is antibiotic: yes
- is resistant: yes
- resistance conc.: 1.8 µg
metabolite production
@ref | Chebi-ID | metabolite | production |
---|---|---|---|
68375 | 15688 | acetoin | no |
122520 | 35581 | indole | no |
metabolite tests
@ref | Chebi-ID | metabolite | voges-proskauer-test |
---|---|---|---|
68375 | 15688 | acetoin | - |
122520 | 15688 | acetoin | - |
enzymes
@ref | value | activity | ec |
---|---|---|---|
68375 | beta-glucuronidase | + | 3.2.1.31 |
68375 | pyrrolidonyl arylamidase | - | 3.4.19.3 |
68375 | L-arginine arylamidase | - | |
68375 | beta-galactosidase | - | 3.2.1.23 |
68375 | beta-glucosidase | + | 3.2.1.21 |
68375 | ornithine decarboxylase | - | 4.1.1.17 |
68375 | arginine dihydrolase | - | 3.5.3.6 |
68375 | urease | - | 3.5.1.5 |
122520 | oxidase | - | |
122520 | beta-galactosidase | - | 3.2.1.23 |
122520 | alcohol dehydrogenase | - | 1.1.1.1 |
122520 | gelatinase | - | |
122520 | amylase | - | |
122520 | DNase | - | |
122520 | caseinase | + | 3.4.21.50 |
122520 | catalase | + | 1.11.1.6 |
122520 | coagulase | - | |
122520 | tween esterase | + | |
122520 | gamma-glutamyltransferase | - | 2.3.2.2 |
122520 | lecithinase | - | |
122520 | lipase | - | |
122520 | lysine decarboxylase | - | 4.1.1.18 |
122520 | ornithine decarboxylase | - | 4.1.1.17 |
122520 | phenylalanine ammonia-lyase | - | 4.3.1.24 |
122520 | protease | + | |
122520 | tryptophan deaminase | - | |
122520 | urease | - | 3.5.1.5 |
68382 | alkaline phosphatase | + | 3.1.3.1 |
68382 | esterase (C 4) | + | |
68382 | esterase lipase (C 8) | + | |
68382 | lipase (C 14) | - | |
68382 | leucine arylamidase | + | 3.4.11.1 |
68382 | valine arylamidase | - | |
68382 | cystine arylamidase | - | 3.4.11.3 |
68382 | trypsin | - | 3.4.21.4 |
68382 | alpha-chymotrypsin | - | 3.4.21.1 |
68382 | acid phosphatase | + | 3.1.3.2 |
68382 | naphthol-AS-BI-phosphohydrolase | + | |
68382 | alpha-galactosidase | - | 3.2.1.22 |
68382 | beta-galactosidase | - | 3.2.1.23 |
68382 | beta-glucuronidase | + | 3.2.1.31 |
68382 | alpha-glucosidase | + | 3.2.1.20 |
68382 | beta-glucosidase | + | 3.2.1.21 |
68382 | N-acetyl-beta-glucosaminidase | + | 3.2.1.52 |
68382 | alpha-mannosidase | - | 3.2.1.24 |
68382 | alpha-fucosidase | - | 3.2.1.51 |
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 |
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
122520 | - | + | + | + | - | + | - | - | - | - | + | + | - | - | + | + | + | + | - | - |
API 50CHac
@ref | GLY | ERY | DARA | LARA | RIB | DXYL | LXYL | ADO | MDX | GAL | GLU | FRU | MNE | SBE | RHA | DUL | INO | MAN | SOR | MDM | MDG | NAG | AMY | ARB | ESC | SAL | CEL | MAL | LAC | MEL | SAC | TRE | INU | MLZ | RAF | AMD | GLYG | XLT | GEN | TUR | LYX | TAG | DFUC | LFUC | DARL | LARL | GNT | 2KG | 5KG |
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
122520 | + | - | - | - | + | - | - | - | - | +/- | + | + | + | - | - | - | +/- | + | + | - | - | +/- | +/- | + | + | + | + | + | - | - | + | + | - | - | - | - | - | - | + | + | - | - | +/- | - | - | - | +/- | - | - |
API ID32STA
@ref | URE | ADH Arg | ODC | ESC | GLU | FRU | MNE | MAL | LAC | TRE | MAN | RAF | RIB | CEL | NIT | VP | beta GAL | ArgA | PAL | PyrA | NOVO | SAC | NAG | TUR | ARA | beta GUR |
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
6619 | - | - | - | + | + | + | + | + | - | + | + | - | + | + | + | - | - | - | +/- | - | + | + | + | + | - | + |
API biotype100
@ref | GLU | FRU | GAL | TRE | MNE | SBE | MEL | SAC | RAF | MTE | MAL | LAC | LTE | MbGa | MaGa | CEL | GEN | MbGu | ESC | RIB | ARA | XYL | PLE | RHA | FUC | MLZ | DARL | LARL | XLT | DUL | TAG | GLY | INO | MAN | MTL | TUR | SOR | ADO | HBG | LYX | ERY | MDG | 3MDG | SAT | MUC | LTAT | DTAT | MTAT | DMLT | LMLT | CATE | TATE | TTE | CIT | GRT | GAT | 2KG | 5KG | TRY | NAG | GNT | PAC | PAT | pOBE | QAT | GTE | mOBE | BAT | PPAT | CMT | TGE | BET | PCE | ABT | HIN | LAT | CAP | CYT | HIS | SUC | FUM | GRE | GYT | AVT | ETN | TTN | GLN | ITA | 3OBU | APT | GTT | PRO | DALA | LALA | SER | MNT | PROP | TYR | 2KT |
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
122520 | + | + | - | + | - | - | - | + | - | + | + | - | - | - | - | + | + | + | + | + | - | - | + | - | - | - | - | - | - | - | - | + | + | + | + | + | + | - | - | - | - | + | - | - | - | + | - | - | - | + | - | - | - | - | + | - | - | - | - | + | + | - | - | - | - | - | - | - | - | - | - | - | - | + | - | + | - | - | + | + | + | - | - | - | - | - | + | - | - | + | + | - | - | - | - | - | - | - | - |
Isolation, sampling and environmental information
isolation
@ref | sample type | country | origin.country | continent | sampling date |
---|---|---|---|---|---|
6619 | skin of a Norway rat | USA | USA | North America | |
53957 | Norway rat | 1992 | |||
122520 | Animal, Rat |
isolation source categories
Cat1 | Cat2 | Cat3 |
---|---|---|
#Host | #Mammals | #Muridae (Mouse/Rat) |
#Host Body-Site | #Organ | #Skin, Nail, Hair |
taxonmaps
- @ref: 69479
- File name: preview.99_116.png
- url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_3;96_3;97_96;98_105;99_116&stattab=map
- Last taxonomy: Staphylococcus
- 16S sequence: AB233332
- Sequence Identity:
- Total samples: 7505
- soil counts: 269
- aquatic counts: 251
- animal counts: 6869
- plant counts: 116
Safety information
risk assessment
@ref | pathogenicity human | pathogenicity animal | biosafety level | biosafety level comment |
---|---|---|---|---|
6619 | yes, in single cases | yes | 1 | Risk group (German classification) |
122520 | 1 | Risk group (French classification) |
Sequence information
16S sequences
@ref | description | accession | length | database | NCBI tax ID |
---|---|---|---|---|---|
20218 | Staphylococcus sciuri subsp. rodentium strain ATCC 700061 16S ribosomal RNA gene, partial sequence | AY688096 | 465 | ena | 147469 |
6619 | Staphylococcus sciuri subsp. rodentium gene for 16S rRNA, partial sequence, strain: GTC 844 | AB233332 | 1460 | ena | 147469 |
Genome sequences
@ref | description | accession | assembly level | database | NCBI tax ID |
---|---|---|---|---|---|
66792 | Mammaliicoccus sciuri CCUG 37923 | GCA_003968855 | scaffold | ncbi | 1296 |
66792 | Staphylococcus sciuri subsp. rodentium strain CCUG 37923 | 147469.3 | wgs | patric | 1296 |
GC content
- @ref: 6619
- GC-content: 35.2
- method: thermal denaturation, midpoint method (Tm)
Genome-based predictions
predictions
trait | prediction | confidence | training_data |
---|---|---|---|
spore-forming | no | 93 | no |
flagellated | no | 94.074 | no |
gram-positive | yes | 92.965 | no |
anaerobic | no | 99.629 | yes |
aerobic | yes | 94.73 | no |
halophile | yes | 92.618 | no |
spore-forming | no | 86.578 | no |
thermophile | no | 99.816 | yes |
glucose-util | yes | 86.741 | no |
motile | no | 88.204 | no |
glucose-ferment | yes | 73.07 | yes |
External links
@ref: 6619
culture collection no.: DSM 16827, ATCC 700061, CIP 105829, CCUG 37923, CCM 4657
straininfo link
- @ref: 83790
- straininfo: 45397
Reference
@id | authors | catalogue | doi/url | title | journal | pubmed |
---|---|---|---|---|---|---|
6619 | Curators of the DSMZ | Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 16827) | https://www.dsmz.de/collection/catalogue/details/culture/DSM-16827 | |||
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 | |||
20218 | Verslyppe, B., De Smet, W., De Baets, B., De Vos, P., Dawyndt P. | 10.1016/j.syapm.2013.11.002 | StrainInfo introduces electronic passports for microorganisms. | Syst Appl Microbiol. 37: 42-50 2014 | 24321274 | |
42116 | Curators of the CIP | https://brclims.pasteur.fr/brcWeb/souche/detail/1/17892 | ||||
53957 | Curators of the CCUG | Culture Collection University of Gothenburg (CCUG) (CCUG 37923) | https://www.ccug.se/strain?id=37923 | |||
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) | |||
68371 | Automatically annotated from API 50CH acid | |||||
68375 | Automatically annotated from API ID32STA | |||||
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 | |||
83790 | Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J. | 10.60712/SI-ID45397.1 | StrainInfo: A central database for resolving microbial strain identifiers | |||
122520 | Curators of the CIP | Collection of Institut Pasteur (CIP 105829) | https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20105829 |