Strain identifier
BacDive ID: 14681
Type strain:
Species: Nosocomiicoccus ampullae
Strain Designation: TRF-1
Strain history: CIP <- 2007, M. Alves, Coimbra Univ., Coimbra, Portugal: strain TRF-1, "Jeotgalicoccus genus"
NCBI tax ID(s): 489910 (species)
General
@ref: 7944
BacDive-ID: 14681
DSM-Number: 19163
keywords: genome sequence, 16S sequence, Bacteria, aerobe, mesophilic, Gram-positive, coccus-shaped, human pathogen
description: Nosocomiicoccus ampullae TRF-1 is an aerobe, mesophilic, Gram-positive human pathogen that was isolated from transfer spike, physiological saline flask in a health care center.
NCBI tax id
- NCBI tax id: 489910
- Matching level: species
strain history
@ref | history |
---|---|
7944 | <- M. Alves and C. Nogueira, Institute of Microbiolgy, University of Coimbra, Portugal; TRF-1 |
67772 | Alves, M. University of Coimbra |
116345 | CIP <- 2007, M. Alves, Coimbra Univ., Coimbra, Portugal: strain TRF-1, "Jeotgalicoccus genus" |
doi: 10.13145/bacdive14681.20230509.8.1
Name and taxonomic classification
LPSN
- @ref: 20215
- description: domain/bacteria
- keyword: phylum/bacillota
- domain: Bacteria
- phylum: Bacillota
- class: Bacilli
- order: Caryophanales
- family: Staphylococcaceae
- genus: Nosocomiicoccus
- species: Nosocomiicoccus ampullae
- full scientific name: Nosocomiicoccus ampullae Morais et al. 2008
@ref: 7944
domain: Bacteria
phylum: Firmicutes
class: Bacilli
order: Bacillales
family: Staphylococcaceae
genus: Nosocomiicoccus
species: Nosocomiicoccus ampullae
full scientific name: Nosocomiicoccus ampullae Morais et al. 2008
strain designation: TRF-1
type strain: yes
Morphology
cell morphology
@ref | gram stain | cell shape | motility | confidence |
---|---|---|---|---|
32599 | positive | coccus-shaped | no | |
69480 | no | 94.228 | ||
69480 | positive | 100 | ||
116345 | positive | coccus-shaped | no |
pigmentation
- @ref: 32599
- production: yes
Culture and growth conditions
culture medium
@ref | name | growth | link | composition |
---|---|---|---|---|
7944 | 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 |
39787 | MEDIUM 45 - for Columbia agar with sheep blood | yes | Distilled water make up to (1000.000 ml);Columbia agar (39.000 g);Sheepblood (100.000 ml) | |
116345 | CIP Medium 45 | yes | https://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=45 |
culture temp
@ref | growth | type | temperature | range |
---|---|---|---|---|
7944 | positive | growth | 30 | mesophilic |
32599 | positive | growth | 30-45 | |
32599 | positive | optimum | 37 | mesophilic |
39787 | positive | growth | 37 | mesophilic |
67772 | positive | optimum | 30-37 | mesophilic |
67772 | positive | minimum | 30 | mesophilic |
67772 | positive | maximum | 37 | mesophilic |
culture pH
@ref | ability | type | pH |
---|---|---|---|
32599 | positive | growth | 7.5-8 |
32599 | positive | optimum | 7.5-8 |
67772 | positive | maximum | 8.0 |
67772 | positive | minimum | 7.5 |
Physiology and metabolism
oxygen tolerance
@ref | oxygen tolerance |
---|---|
32599 | aerobe |
116345 | obligate aerobe |
spore formation
@ref | spore formation | confidence |
---|---|---|
32599 | no | |
69481 | no | 100 |
69480 | no | 99.973 |
halophily
- @ref: 32599
- salt: NaCl
- growth: positive
- tested relation: growth
- concentration: 0-10 %
murein
- @ref: 7944
- murein short key: A11.03
- type: A3alpha L-Lys-Gly2-4-L-Ser1-2-Gly
observation
- @ref: 32599
- observation: aggregates in chains
metabolite utilization
@ref | Chebi-ID | metabolite | utilization activity | kind of utilization tested |
---|---|---|---|---|
32599 | 22599 | arabinose | + | carbon source |
116345 | 17632 | nitrate | - | reduction |
116345 | 16301 | nitrite | - | reduction |
metabolite production
- @ref: 116345
- Chebi-ID: 35581
- metabolite: indole
- production: no
enzymes
@ref | value | activity | ec |
---|---|---|---|
32599 | alkaline phosphatase | + | 3.1.3.1 |
32599 | catalase | + | 1.11.1.6 |
32599 | gelatinase | + | |
32599 | cytochrome oxidase | + | 1.9.3.1 |
116345 | oxidase | - | |
116345 | catalase | + | 1.11.1.6 |
116345 | 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 |
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
116345 | - | - | + | + | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - |
Isolation, sampling and environmental information
isolation
@ref | sample type | country | origin.country | continent | sampling date | isolation date |
---|---|---|---|---|---|---|
7944 | transfer spike, physiological saline flask in a health care center | Portugal | PRT | Europe | ||
67772 | Surface of bottles of saline solution used in wound cleansing | Portugal | PRT | Europe | 2005 | |
116345 | Saline flask | Portugal | PRT | Europe | 2005 |
isolation source categories
Cat1 | Cat2 |
---|---|
#Infection | #Medical device |
#Infection | #Medical environment |
taxonmaps
- @ref: 69479
- File name: preview.99_9129.png
- url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_3;96_735;97_858;98_6709;99_9129&stattab=map
- Last taxonomy: Nosocomiicoccus ampullae subclade
- 16S sequence: EU240886
- Sequence Identity:
- Total samples: 18375
- soil counts: 1543
- aquatic counts: 1152
- animal counts: 15338
- plant counts: 342
Safety information
risk assessment
@ref | pathogenicity human | biosafety level | biosafety level comment |
---|---|---|---|
7944 | yes, in single cases | 1 | Risk group (German classification) |
67772 | 1 | ||
116345 | 1 | Risk group (French classification) |
Sequence information
16S sequences
- @ref: 7944
- description: Nosocomiicoccus ampullae strain TRF-1 16S ribosomal RNA gene, partial sequence
- accession: EU240886
- length: 1502
- database: ena
- NCBI tax ID: 489910
Genome sequences
@ref | description | accession | assembly level | database | NCBI tax ID |
---|---|---|---|---|---|
66792 | Nosocomiicoccus ampullae DSM 19163 | GCA_019357495 | complete | ncbi | 489910 |
66792 | Nosocomiicoccus ampullae DSM 19163 | GCA_014202595 | scaffold | ncbi | 489910 |
66792 | Nosocomiicoccus ampullae strain DSM 19163 | 489910.8 | complete | patric | 489910 |
66792 | Nosocomiicoccus ampullae strain DSM 19163 | 489910.5 | wgs | patric | 489910 |
66792 | Nosocomiicoccus ampullae DSM 19163 | 2861585789 | draft | img | 489910 |
67772 | Nosocomiicoccus ampullae LUREC | GCA_001696685 | scaffold | ncbi | 489910 |
GC content
- @ref: 7944
- GC-content: 33.5
Genome-based predictions
predictions
trait | prediction | confidence | training_data |
---|---|---|---|
spore-forming | no | 100 | no |
flagellated | no | 98.253 | yes |
gram-positive | yes | 91.226 | yes |
anaerobic | no | 98.185 | yes |
aerobic | yes | 93.161 | yes |
halophile | yes | 96.442 | no |
spore-forming | no | 90.357 | yes |
motile | no | 91.74 | yes |
thermophile | no | 99.586 | no |
glucose-util | yes | 84.121 | no |
glucose-ferment | no | 64.801 | no |
External links
@ref: 7944
culture collection no.: DSM 19163, CIP 109506, LMG 24060, UCCCB22
straininfo link
- @ref: 83807
- straininfo: 302705
literature
topic | Pubmed-ID | title | authors | journal | DOI | year | mesh | topic2 |
---|---|---|---|---|---|---|---|---|
Phylogeny | 19060087 | Nosocomiicoccus ampullae gen. nov., sp. nov., isolated from the surface of bottles of saline solution used in wound cleansing. | Alves M, Nogueira C, de Magalhaes-Sant'ana A, Chung AP, Morais PV, da Costa MS | Int J Syst Evol Microbiol | 10.1099/ijs.0.65753-0 | 2008 | *Environmental Microbiology, Fatty Acids/analysis, Molecular Sequence Data, Phenotype, Phylogeny, RNA, Ribosomal, 16S/genetics, *Sodium Chloride, Species Specificity, Staphylococcaceae/chemistry/*classification/genetics/*physiology, Wounds and Injuries/therapy | Genetics |
Genetics | 34913718 | Complete Genome Sequences of Two Nosocomiicoccus ampullae Strains and a Growth-Adapted Mutant. | Schuster CF, Sommer F, Strommenger B, Werner G, Layer F | Microbiol Resour Announc | 10.1128/MRA.00747-21 | 2021 |
Reference
@id | authors | catalogue | doi/url | title | ID_cross_reference | pubmed |
---|---|---|---|---|---|---|
7944 | Curators of the DSMZ | Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 19163) | https://www.dsmz.de/collection/catalogue/details/culture/DSM-19163 | |||
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 | |||
32599 | Barberan A, Caceres Velazquez H, Jones S, Fierer N. | 10.1128/mSphere.00237-17 | Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information | 28812 | 28776041 | |
39787 | Curators of the CIP | https://brclims.pasteur.fr/brcWeb/souche/detail/1/7257 | ||||
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) | |||
67772 | Curators of the UCCCB | https://ucccb.uc.pt/ | ||||
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 | |||
83807 | Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J. | 10.60712/SI-ID302705.1 | StrainInfo: A central database for resolving microbial strain identifiers | |||
116345 | Curators of the CIP | Collection of Institut Pasteur (CIP 109506) | https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20109506 |