Strain identifier
BacDive ID: 157225
Type strain: 
Species: Vagococcus bubulae
Strain Designation: SS1994
NCBI tax ID(s): 1977868 (species)
version 8.1 (current version)
General
@ref: 63753
BacDive-ID: 157225
keywords: genome sequence, 16S sequence, Bacteria, microaerophile, mesophilic, Gram-positive, rod-shaped, colony-forming
description: Vagococcus bubulae SS1994 is a microaerophile, mesophilic, Gram-positive bacterium that forms circular colonies and was isolated from Ground beef.
NCBI tax id
- NCBI tax id: 1977868
- Matching level: species
doi: 10.13145/bacdive157225.20230509.8.1
Name and taxonomic classification
LPSN
- @ref: 20215
- description: domain/bacteria
- keyword: phylum/bacillota
- domain: Bacteria
- phylum: Bacillota
- class: Bacilli
- order: Lactobacillales
- family: Enterococcaceae
- genus: Vagococcus
- species: Vagococcus bubulae
- full scientific name: Vagococcus bubulae Shewmaker et al. 2019
@ref: 63753
domain: Bacteria
phylum: Firmicutes
class: Bacilli
order: Lactobacillales
family: Enterococcaceae
genus: Vagococcus
species: Vagococcus bubulae
strain designation: SS1994
type strain: yes
Morphology
cell morphology
| @ref | gram stain | cell shape | motility |
|---|---|---|---|
| 67899 | positive | rod-shaped | no |
| 67899 | coccus-shaped |
colony morphology
- @ref: 67899
- type of hemolysis: alpha
- hemolysis ability: 1
- colony size: 1 mm
- colony color: grey-white
- colony shape: circular
- incubation period: 1 days
- medium used: trypticase soy agar supplemented with 5 % sheep blood
Culture and growth conditions
culture temp
| @ref | growth | type | temperature | range |
|---|---|---|---|---|
| 63753 | positive | growth | 37 | mesophilic |
| 67899 | positive | growth | 35 | mesophilic |
| 67899 | positive | growth | 30 | mesophilic |
| 67899 | positive | growth | 10 | psychrophilic |
| 67899 | no | growth | 45 | thermophilic |
Physiology and metabolism
oxygen tolerance
- @ref: 63753
- oxygen tolerance: microaerophile
halophily
- @ref: 67899
- salt: NaCl
- growth: positive
- tested relation: growth
- concentration: 6.5 %
observation
- @ref: 67899
- observation: No gas is produced in Mann-Rogosa-Sharp broth.
metabolite utilization
| @ref | Chebi-ID | metabolite | utilization activity | kind of utilization tested |
|---|---|---|---|---|
| 67899 | 3098 | bile acid | + | growth |
| 67899 | 15361 | pyruvate | + | growth |
| 67899 | 30477 | tellurite | - | growth |
| 67899 | 4853 | esculin | + | hydrolysis |
| 67899 | 606565 | hippurate | + | hydrolysis |
| 67899 | 29016 | arginine | - | hydrolysis |
| 67899 | 16199 | urea | - | hydrolysis |
| 67899 | 28017 | starch | - | hydrolysis |
| 67899 | 17306 | maltose | + | builds acid from |
| 67899 | 27082 | trehalose | + | builds acid from |
| 67899 | 17992 | sucrose | + | builds acid from |
| 67899 | 28053 | melibiose | + | builds acid from |
| 67899 | 16634 | raffinose | + | builds acid from |
| 67899 | 16988 | D-ribose | + | builds acid from |
| 67899 | 17754 | glycerol | + | builds acid from |
| 67899 | 320061 | methyl alpha-D-glucopyranoside | + | builds acid from |
| 67899 | 65327 | D-xylose | + | builds acid from |
| 67899 | 17716 | lactose | + | builds acid from |
| 67899 | 16899 | D-mannitol | + | builds acid from |
| 67899 | 30849 | L-arabinose | + | builds acid from |
| 67899 | 16443 | D-tagatose | + | builds acid from |
| 67899 | 17108 | D-arabinose | + | builds acid from |
| 67899 | 17924 | D-sorbitol | + | builds acid from |
| 67899 | 65328 | L-xylose | + | builds acid from |
| 67899 | 17266 | L-sorbose | - | builds acid from |
| 67899 | 15443 | inulin | + | builds acid from |
| 67899 | 320055 | methyl beta-D-glucopyranoside | + | builds acid from |
| 67899 | 27941 | pullulan | + | builds acid from |
| 67899 | 18333 | D-arabitol | - | builds acid from |
| 67899 | 40585 | alpha-cyclodextrin | - | builds acid from |
| 67899 | 28087 | glycogen | - | builds acid from |
metabolite production
- @ref: 67899
- Chebi-ID: 15688
- metabolite: acetoin
- production: no
enzymes
| @ref | value | activity | ec |
|---|---|---|---|
| 67899 | catalase | - | 1.11.1.6 |
| 67899 | leucine aminopeptidase | + | 3.4.1.1 |
| 67899 | pyrrolidonyl arylamidase | + | 3.4.19.3 |
| 67899 | beta-galactosidase | + | 3.2.1.23 |
| 67899 | beta-glucosidase | + | 3.2.1.21 |
| 67899 | alpha-galactosidase | + | 3.2.1.22 |
| 67899 | beta-glucuronidase | - | 3.2.1.31 |
| 67899 | alkaline phosphatase | - | 3.1.3.1 |
| 67899 | N-acetyl-beta-glucosaminidase | - | 3.2.1.52 |
| 67899 | beta-mannosidase | - | 3.2.1.25 |
Isolation, sampling and environmental information
isolation
| @ref | sample type | sampling date | geographic location | country | origin.country | continent |
|---|---|---|---|---|---|---|
| 63753 | Ground beef | 2002 | Oregon | USA | USA | North America |
| 67899 | ground beef |
isolation source categories
- Cat1: #Engineered
- Cat2: #Food production
- Cat3: #Meat
taxonmaps
- @ref: 69479
- File name: preview.99_70130.png
- url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_13;96_1881;97_2259;98_2772;99_70130&stattab=map
- Last taxonomy: Vagococcus
- 16S sequence: KY937952
- Sequence Identity:
- Total samples: 268
- soil counts: 43
- aquatic counts: 4
- animal counts: 221
Sequence information
16S sequences
- @ref: 67899
- description: Vagococcus sp. strain SS1994T 16S ribosomal RNA gene, partial sequence
- accession: KY937952
- length: 1480
- database: ena
- NCBI tax ID: 1977868
Genome sequences
- @ref: 67899
- description: Vagococcus bubulae SS1994
- accession: GCA_003950315
- assembly level: contig
- database: ncbi
- NCBI tax ID: 1977868
GC content
- @ref: 67899
- GC-content: 33.6
- method: genome sequence analysis
Genome-based predictions
predictions
| trait | prediction | confidence | training_data |
|---|---|---|---|
| motile | no | 94.974 | yes |
| flagellated | no | 96.517 | yes |
| gram-positive | yes | 94.215 | yes |
| anaerobic | no | 88.664 | yes |
| aerobic | no | 96.004 | yes |
| halophile | yes | 65.366 | no |
| spore-forming | no | 84.841 | no |
| glucose-util | yes | 89.771 | no |
| thermophile | no | 97.245 | no |
| glucose-ferment | yes | 77.216 | no |
External links
@ref: 63753
culture collection no.: CCUG 70831, LMG 30164
straininfo link
- @ref: 110324
- straininfo: 411579
literature
- topic: Phylogeny
- Pubmed-ID: 31125302
- title: Vagococcus bubulae sp. nov., isolated from ground beef, and Vagococcus vulneris sp. nov., isolated from a human foot wound.
- authors: Shewmaker PL, Whitney AM, Gulvik CA, Humrighouse BW, Gartin J, Moura H, Barr JR, Moore ERB, Karlsson R, Pinto TCA, Teixeira LM
- journal: Int J Syst Evol Microbiol
- DOI: 10.1099/ijsem.0.003459
- year: 2019
- mesh: Animals, Bacterial Typing Techniques, Base Composition, Cattle, DNA, Bacterial/genetics, Enterococcaceae/*classification/isolation & purification, Fatty Acids/chemistry, Foot/*microbiology, Genes, Bacterial, Humans, Male, Nucleic Acid Hybridization, *Phylogeny, RNA, Ribosomal, 16S/genetics, Red Meat/*microbiology, Sequence Analysis, DNA, Wounds and Injuries/*microbiology
- topic2: Pathogenicity
Reference
| @id | authors | title | doi/url | catalogue | journal |
|---|---|---|---|---|---|
| 20215 | Parte, A.C., Sardà Carbasse, J., Meier-Kolthoff, J.P., Reimer, L.C. and Göker, M. | List of Prokaryotic names with Standing in Nomenclature (LPSN) moves to the DSMZ | 10.1099/ijsem.0.004332 | ||
| 63753 | Curators of the CCUG | https://www.ccug.se/strain?id=70831 | Culture Collection University of Gothenburg (CCUG) (CCUG 70831) | ||
| 67899 | Patricia L. Shewmaker, Anne M. Whitney, Christopher A. Gulvik, Ben W. Humrighouse, Jarrett Gartin, Hercules Moura, John R. Barr, Edward R. B. Moore, Roger Karlsson, Tatiana C. A. Pinto, Lucia M. Teixeira | Vagococcus bubulae sp. nov., isolated from ground beef, and Vagococcus vulneris sp. nov., isolated from a human foot wound | 10.1099/ijsem.0.003459 | IJSEM 69: 2268-2276 2019 | |
| 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. | MicrobeAtlas 1.0 beta | https://microbeatlas.org/ | ||
| 110324 | Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J. | StrainInfo: A central database for resolving microbial strain identifiers | 10.60712/SI-ID411579.1 |