Strain identifier
BacDive ID: 14683
Type strain:
Species: Lactococcus garvieae subsp. garvieae
Strain Designation: YT-3
Strain history: CIP <- 1995, DSM, Enterococcus seriolicida <- ATCC <- R. Kusuda: strain YT-3
NCBI tax ID(s): 1890280 (subspecies)
General
@ref: 2816
BacDive-ID: 14683
DSM-Number: 6783
keywords: genome sequence, 16S sequence, Bacteria, facultative anaerobe, mesophilic, Gram-positive, coccus-shaped, human pathogen
description: Lactococcus garvieae subsp. garvieae YT-3 is a facultative anaerobe, mesophilic, Gram-positive human pathogen that was isolated from kidney of yellowtail.
NCBI tax id
- NCBI tax id: 1890280
- Matching level: subspecies
strain history
@ref | history |
---|---|
2816 | <- ATCC <- R. Kusuda, YT-3 (Enterococcus seriolicida) |
67770 | ATCC 49156 <-- R. Kusuda YT-3. |
119537 | CIP <- 1995, DSM, Enterococcus seriolicida <- ATCC <- R. Kusuda: strain YT-3 |
doi: 10.13145/bacdive14683.20230509.8.1
Name and taxonomic classification
LPSN
- @ref: 20215
- description: domain/bacteria
- keyword: phylum/bacillota
- domain: Bacteria
- phylum: Bacillota
- class: Bacilli
- order: Lactobacillales
- family: Streptococcaceae
- genus: Lactococcus
- species: Lactococcus garvieae subsp. garvieae
- full scientific name: Lactococcus garvieae subsp. garvieae (Collins et al. 1984) Varsha and Nampoothiri 2016
@ref: 2816
domain: Bacteria
phylum: Firmicutes
class: Bacilli
order: Lactobacillales
family: Streptococcaceae
genus: Lactococcus
species: Lactococcus garvieae subsp. garvieae
full scientific name: Lactococcus garvieae subsp. garvieae (Collins et al. 1984) Varsha and Nampoothiri 2016
strain designation: YT-3
type strain: no
Morphology
cell morphology
- @ref: 119537
- gram stain: positive
- cell shape: coccus-shaped
- motility: no
Culture and growth conditions
culture medium
@ref | name | growth | link | composition |
---|---|---|---|---|
2816 | 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 |
34688 | MEDIUM 29- Brain heart agar | yes | Distilled water make up to (1000.000 ml);Brain heart infusion agar (52.000 g) | |
119537 | CIP Medium 29 | yes | https://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=29 |
culture temp
@ref | growth | type | temperature | range |
---|---|---|---|---|
2816 | positive | growth | 37 | mesophilic |
34688 | positive | growth | 37 | mesophilic |
67770 | positive | growth | 37 | mesophilic |
Physiology and metabolism
oxygen tolerance
- @ref: 119537
- oxygen tolerance: facultative anaerobe
murein
- @ref: 2816
- murein short key: A11.12
- type: A3alpha L-Lys-L-Ala2-Gly-L-Ala
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 | gluconate | + | builds acid from | 24265 |
68371 | L-arabitol | - | builds acid from | 18403 |
68371 | D-arabitol | - | builds acid from | 18333 |
68371 | L-fucose | - | builds acid from | 18287 |
68371 | D-fucose | - | builds acid from | 28847 |
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 | amygdalin | + | builds acid from | 27613 |
68371 | N-acetylglucosamine | + | builds acid from | 59640 |
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 | myo-inositol | - | builds acid from | 17268 |
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 | D-galactose | + | builds acid from | 12936 |
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 |
119537 | nitrate | - | reduction | 17632 |
119537 | nitrite | - | reduction | 16301 |
68380 | urea | - | hydrolysis | 16199 |
68380 | arginine | + | hydrolysis | 29016 |
68380 | D-mannose | + | fermentation | 16024 |
68380 | raffinose | - | fermentation | 16634 |
68380 | L-glutamate | - | degradation | 29985 |
68380 | nitrate | - | reduction | 17632 |
68380 | tryptophan | - | energy source | 27897 |
68381 | arginine | + | hydrolysis | 29016 |
68381 | D-ribose | - | builds acid from | 16988 |
68381 | D-mannitol | + | builds acid from | 16899 |
68381 | sorbitol | - | builds acid from | 30911 |
68381 | lactose | - | builds acid from | 17716 |
68381 | trehalose | + | builds acid from | 27082 |
68381 | raffinose | - | builds acid from | 16634 |
68381 | sucrose | - | builds acid from | 17992 |
68381 | L-arabinose | - | builds acid from | 30849 |
68381 | D-arabitol | - | builds acid from | 18333 |
68381 | alpha-cyclodextrin | - | builds acid from | 40585 |
68381 | hippurate | - | hydrolysis | 606565 |
68381 | glycogen | - | builds acid from | 28087 |
68381 | pullulan | - | builds acid from | 27941 |
68381 | maltose | + | builds acid from | 17306 |
68381 | melibiose | - | builds acid from | 28053 |
68381 | melezitose | - | builds acid from | 6731 |
68381 | methyl beta-D-glucopyranoside | + | builds acid from | 320055 |
68381 | D-tagatose | - | builds acid from | 16443 |
68381 | urea | - | hydrolysis | 16199 |
metabolite production
@ref | Chebi-ID | metabolite | production |
---|---|---|---|
119537 | 35581 | indole | no |
68380 | 35581 | indole | no |
68381 | 15688 | acetoin | yes |
metabolite tests
@ref | Chebi-ID | metabolite | voges-proskauer-test | indole test |
---|---|---|---|---|
68381 | 15688 | acetoin | + | |
68380 | 35581 | indole | - |
enzymes
@ref | value | activity | ec |
---|---|---|---|
68381 | urease | - | 3.5.1.5 |
68381 | beta-mannosidase | - | 3.2.1.25 |
68381 | glycyl tryptophan arylamidase | - | |
68381 | N-acetyl-beta-glucosaminidase | - | 3.2.1.52 |
68381 | beta-galactosidase | - | 3.2.1.23 |
68381 | Alanyl-Phenylalanyl-Proline arylamidase | + | |
68381 | alkaline phosphatase | - | 3.1.3.1 |
68381 | alpha-galactosidase | - | 3.2.1.22 |
68381 | beta-glucuronidase | - | 3.2.1.31 |
68381 | beta-glucosidase | + | 3.2.1.21 |
68381 | arginine dihydrolase | + | 3.5.3.6 |
68380 | serine arylamidase | + | |
68380 | glutamyl-glutamate arylamidase | - | |
68380 | histidine arylamidase | + | |
68380 | glycin arylamidase | + | |
68380 | alanine arylamidase | + | 3.4.11.2 |
68380 | tyrosine arylamidase | + | |
68380 | pyrrolidonyl arylamidase | + | 3.4.19.3 |
68380 | leucine arylamidase | + | 3.4.11.1 |
68380 | phenylalanine arylamidase | + | |
68380 | proline-arylamidase | - | 3.4.11.5 |
68380 | L-arginine arylamidase | + | |
68380 | alkaline phosphatase | - | 3.1.3.1 |
68380 | tryptophan deaminase | - | 4.1.99.1 |
68380 | alpha-fucosidase | - | 3.2.1.51 |
68380 | glutamate decarboxylase | - | 4.1.1.15 |
68380 | N-acetyl-beta-glucosaminidase | + | 3.2.1.52 |
68380 | beta-glucuronidase | - | 3.2.1.31 |
68380 | alpha-arabinosidase | - | 3.2.1.55 |
68380 | beta-glucosidase | + | 3.2.1.21 |
68380 | beta-Galactosidase 6-phosphate | - | |
68380 | beta-galactosidase | - | 3.2.1.23 |
68380 | alpha-galactosidase | - | 3.2.1.22 |
68380 | arginine dihydrolase | + | 3.5.3.6 |
68380 | urease | - | 3.5.1.5 |
119537 | oxidase | - | |
119537 | catalase | - | 1.11.1.6 |
119537 | 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 |
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
119537 | - | - | - | + | - | + | - | - | - | + | + | + | - | - | - | + | + | - | - | - |
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 |
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
119537 | + | - | - | - | + | - | - | - | - | + | + | + | + | - | - | - | - | + | - | - | - | + | + | + | + | + | + | + | - | - | - | + | - | - | - | - | - | - | + | - | - | - | - | - | - | - | + | - | + |
API rID32A
@ref | URE | ADH Arg | alpha GAL | beta GAL | beta GP | alpha GLU | beta GLU | alpha ARA | beta GUR | beta NAG | MNE | RAF | GDC | alpha FUC | NIT | IND | PAL | ArgA | ProA | LGA | PheA | LeuA | PyrA | TyrA | AlaA | GlyA | HisA | GGA | SerA |
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
2816 | - | + | - | - | - | +/- | + | - | - | + | + | - | - | - | - | - | - | + | - | +/- | + | + | + | + | + | + | + | - | + |
API rID32STR
@ref | ADH Arg | beta GLU | beta GAR | beta GUR | alpha GAL | PAL | RIB | MAN | SOR | LAC | TRE | RAF | SAC | LARA | DARL | CDEX | VP | APPA | beta GAL | PyrA | beta NAG | GTA | HIP | GLYG | PUL | MAL | MEL | MLZ | Mbeta DG | TAG | beta MAN | URE |
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
2816 | + | + | - | - | - | - | - | + | - | - | + | - | - | - | - | - | + | + | - | +/- | - | - | - | - | - | + | - | - | + | - | - | - |
2816 | + | + | - | - | - | - | - | + | - | - | + | - | - | - | - | - | + | + | - | - | - | - | - | - | - | + | - | - | + | - | - | - |
Isolation, sampling and environmental information
isolation
@ref | sample type | geographic location | country | origin.country | continent |
---|---|---|---|---|---|
2816 | kidney of yellowtail | Kochi | Japan | JPN | Asia |
67770 | Kidney of yellowtail | ||||
119537 | Kidney of yellowtail |
isolation source categories
Cat1 | Cat2 | Cat3 |
---|---|---|
#Host | #Fishes | |
#Host Body-Site | #Urogenital tract | #Kidney |
taxonmaps
- @ref: 69479
- File name: preview.99_274.png
- url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_58;96_192;97_208;98_233;99_274&stattab=map
- Last taxonomy: Lactococcus
- 16S sequence: AB026843
- Sequence Identity:
- Total samples: 95930
- soil counts: 3482
- aquatic counts: 8187
- animal counts: 81994
- plant counts: 2267
Safety information
risk assessment
@ref | pathogenicity human | pathogenicity animal | biosafety level | biosafety level comment |
---|---|---|---|---|
2816 | yes | yes | 2 | Risk group (German classification) |
119537 | 2 | Risk group (French classification) |
Sequence information
16S sequences
@ref | description | accession | length | database | NCBI tax ID |
---|---|---|---|---|---|
20218 | Lactococcus garvieae gene for 16S ribosomal RNA | AB026843 | 1007 | ena | 420889 |
20218 | Enterococcus seriolicida 16S ribosomal RNA gene, partial sequence | AF061005 | 1485 | ena | 420889 |
20218 | Enterococcus seriolicida 16S ribosomal RNA (16S rRNA) | L32813 | 1497 | ena | 1363 |
Genome sequences
@ref | description | accession | assembly level | database | NCBI tax ID |
---|---|---|---|---|---|
67770 | Lactococcus garvieae ATCC 49156 | GCA_000407125 | scaffold | ncbi | 420889 |
67770 | Lactococcus garvieae ATCC 49156 | GCA_000269925 | complete | ncbi | 420889 |
67770 | Lactococcus garvieae ATCC 49156 | GCA_000407645 | contig | ncbi | 420889 |
GC content
@ref | GC-content | method |
---|---|---|
2816 | 44.0 | thermal denaturation, midpoint method (Tm) |
67770 | 44 | thermal denaturation, midpoint method (Tm) |
Genome-based predictions
predictions
trait | prediction | confidence | training_data |
---|---|---|---|
motile | no | 93.816 | no |
flagellated | no | 97.464 | no |
gram-positive | yes | 94.668 | no |
anaerobic | no | 97.565 | no |
aerobic | no | 97.109 | no |
halophile | yes | 85.704 | no |
spore-forming | no | 95.32 | no |
thermophile | no | 99.84 | yes |
glucose-util | yes | 91.187 | no |
glucose-ferment | yes | 87.26 | no |
External links
@ref: 2816
culture collection no.: DSM 6783, ATCC 49156, CIP 104369, JCM 8735, CECT 4828, CECT 5274, LMG 12889, NCIMB 13208
straininfo link
- @ref: 83809
- straininfo: 92580
literature
- topic: Phylogeny
- Pubmed-ID: 27498541
- title: Lactococcus garvieae subsp. bovis subsp. nov., lactic acid bacteria isolated from wild gaur (Bos gaurus) dung, and description of Lactococcus garvieae subsp. garvieae subsp. nov.
- authors: Varsha KK, Nampoothiri KM
- journal: Int J Syst Evol Microbiol
- DOI: 10.1099/ijsem.0.001268
- year: 2016
- mesh: Animals, Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, Fatty Acids/chemistry, Feces/microbiology, Genes, Bacterial, India, Lactic Acid, Lactococcus/*classification/genetics/isolation & purification, Nucleic Acid Hybridization, *Phylogeny, RNA, Ribosomal, 16S/genetics, Ruminants/*microbiology, Sequence Analysis, DNA
- topic2: Transcriptome
Reference
@id | authors | catalogue | doi/url | title | journal | pubmed |
---|---|---|---|---|---|---|
2816 | Curators of the DSMZ | Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 6783) | https://www.dsmz.de/collection/catalogue/details/culture/DSM-6783 | |||
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 | |
34688 | Curators of the CIP | https://brclims.pasteur.fr/brcWeb/souche/detail/1/16270 | ||||
67770 | Curators of the JCM | https://jcm.brc.riken.jp/en/ | ||||
68371 | Automatically annotated from API 50CH acid | |||||
68380 | Automatically annotated from API rID32A | |||||
68381 | Automatically annotated from API rID32STR | |||||
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 | |||
83809 | Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J. | 10.60712/SI-ID92580.1 | StrainInfo: A central database for resolving microbial strain identifiers | |||
119537 | Curators of the CIP | Collection of Institut Pasteur (CIP 104369) | https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20104369 |