Strain identifier
BacDive ID: 14686
Type strain:
Species: Lactococcus garvieae
Strain Designation: 0159, O159
Strain history: CIP <- 1986, NCFB <- 1979, A.J. Bramley: strain O159
NCBI tax ID(s): 1363 (species)
General
@ref: 9006
BacDive-ID: 14686
DSM-Number: 20684
keywords: genome sequence, 16S sequence, Bacteria, anaerobe, mesophilic, human pathogen
description: Lactococcus garvieae 0159 is an anaerobe, mesophilic human pathogen that was isolated from bovine mastitis.
NCBI tax id
- NCBI tax id: 1363
- Matching level: species
strain history
@ref | history |
---|---|
9006 | <- NCDO <- J. Bramley, 0159 |
67770 | DSM 20684 <-- NCDO 2155 <-- J. Bramley 0159. |
119536 | CIP <- 1986, NCFB <- 1979, A.J. Bramley: strain O159 |
doi: 10.13145/bacdive14686.20230509.8.1
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
- full scientific name: Lactococcus garvieae (Collins et al. 1984) Schleifer et al. 1986
synonyms
@ref synonym 20215 Enterococcus seriolicida 20215 Streptococcus garvieae
@ref: 9006
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: 0159, O159
type strain: yes
Morphology
cell morphology
@ref | motility | confidence | gram stain | cell shape |
---|---|---|---|---|
69480 | no | 96.704 | ||
69480 | 100 | positive | ||
119536 | no | positive | coccus-shaped |
colony morphology
@ref | incubation period |
---|---|
50898 | 3 days |
119536 |
Culture and growth conditions
culture medium
@ref | name | growth | link | composition |
---|---|---|---|---|
9006 | 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 |
38974 | MEDIUM 29- Brain heart agar | yes | Distilled water make up to (1000.000 ml);Brain heart infusion agar (52.000 g) | |
119536 | CIP Medium 29 | yes | https://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=29 | |
119536 | CIP Medium 45 | yes | https://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=45 |
culture temp
@ref | growth | type | temperature | range |
---|---|---|---|---|
9006 | positive | growth | 30 | mesophilic |
38974 | positive | growth | 30 | mesophilic |
50898 | positive | growth | 30 | mesophilic |
50898 | positive | growth | 37 | mesophilic |
67770 | positive | growth | 30 | mesophilic |
119536 | positive | growth | 10-41 | |
119536 | no | growth | 45 | thermophilic |
Physiology and metabolism
oxygen tolerance
@ref | oxygen tolerance |
---|---|
50898 | anaerobe |
50898 | microaerophile |
119536 | facultative anaerobe |
spore formation
@ref | spore formation | confidence |
---|---|---|
69481 | no | 95 |
69480 | no | 99.993 |
halophily
- @ref: 119536
- salt: NaCl
- growth: no
- tested relation: growth
- concentration: 6.5 %
murein
- @ref: 9006
- murein short key: A11.12
- type: A3alpha L-Lys-L-Ala2-Gly-L-Ala
observation
- @ref: 67770
- observation: quinones: MK-9, MK-8
metabolite utilization
@ref | metabolite | utilization activity | kind of utilization tested | Chebi-ID |
---|---|---|---|---|
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 | 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 |
119536 | esculin | + | hydrolysis | 4853 |
119536 | hippurate | + | hydrolysis | 606565 |
119536 | nitrate | - | reduction | 17632 |
119536 | nitrite | - | reduction | 16301 |
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 | 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: 68381
- Chebi-ID: 15688
- metabolite: acetoin
- production: yes
metabolite tests
@ref | Chebi-ID | metabolite | voges-proskauer-test |
---|---|---|---|
68381 | 15688 | acetoin | + |
119536 | 15688 | acetoin | + |
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 |
119536 | oxidase | - | |
119536 | beta-galactosidase | - | 3.2.1.23 |
119536 | alcohol dehydrogenase | + | 1.1.1.1 |
119536 | catalase | - | 1.11.1.6 |
119536 | gamma-glutamyltransferase | - | 2.3.2.2 |
119536 | lysine decarboxylase | - | 4.1.1.18 |
119536 | ornithine decarboxylase | - | 4.1.1.17 |
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 |
fatty acid profile
fatty acids
@ref fatty acid percentage ECL 50898 C14:0 16.6 14 50898 C16:0 26.1 16 50898 C18:0 2.9 18 50898 C13:0 ISO 2OH 1.5 13.814 50898 C16:1 ω7c 6.4 15.819 50898 C18:1 ω7c /12t/9t 25.7 17.824 50898 C18:1 ω9c 3 17.769 50898 C18:2 ω6,9c/C18:0 ANTE 7.3 17.724 50898 C19:0 CYCLO ω8c 10.6 18.9 - type of FA analysis: whole cell analysis
- method/protocol: CCUG
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 |
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
119536 | - | - | + | + | - | + | - | - | - | + | + | - | - | - | - | + | + | - | - | - |
API 50CHac
@ref | Q | 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 |
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
9006 | - | - | - | - | - | + | - | - | - | - | + | + | + | + | - | - | - | - | + | - | - | - | + | + | + | + | + | + | + | - | - | - | + | - | - | - | - | - | - | + | - | - | - | - | - | - | - | + | - | - |
119536 | - | - | - | - | + | - | - | - | - | + | + | + | + | - | - | - | - | + | - | - | - | + | + | + | + | + | + | + | + | - | - | + | - | - | - | - | - | - | + | - | - | - | - | - | - | - | + | - | + |
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 |
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
9006 | + | + | - | - | - | - | + | + | - | +/- | + | - | - | - | - | + | + | + | - | +/- | + | - | - | - | - | + | - | - | + | - | - | - |
Isolation, sampling and environmental information
isolation
@ref | sample type | sampling date | isolation date |
---|---|---|---|
9006 | bovine mastitis | ||
50898 | Mastitis | 1973 | |
67770 | Bovine mastitis | ||
119536 | Animal, Bovine mastitis | 1973 |
isolation source categories
Cat1 | Cat2 | Cat3 |
---|---|---|
#Host | #Mammals | #Bovinae (Cow, Cattle) |
#Infection | #Disease | |
#Infection | #Inflammation | |
#Host Body-Site | #Organ | #Mammary gland |
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: LC145570
- 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 |
---|---|---|---|---|
9006 | yes | yes | 2 | Risk group (German classification) |
119536 | 1 | Risk group (French classification) |
Sequence information
16S sequences
@ref | description | accession | length | database | NCBI tax ID |
---|---|---|---|---|---|
20218 | Lactococcus garvieae culture-collection CECT:4531 16S ribosomal RNA gene, partial sequence | KF012886 | 805 | ena | 1363 |
20218 | Lactococcus garvieae strain DSM 20684 16S-23S intergenic spacer region, and tRNA-Ala gene, complete sequence | AF225967 | 350 | ena | 1363 |
20218 | Lactococcus garvieae gene for 16S rRNA, partial sequence, strain: JCM 10343 | AB598994 | 1510 | ena | 1363 |
20218 | Lactococcus garvieae strain KCTC 3772 16S ribosomal RNA gene, partial sequence; 16S-23S ribosomal RNA intergenic spacer, complete sequence; and 23S ribosomal RNA gene, partial sequence | HM241913 | 560 | ena | 1363 |
20218 | Lactococcus garvieae strain NIZO2415T 16S ribosomal RNA gene, partial sequence | EU091459 | 652 | ena | 1363 |
20218 | Lactococcus garvieae gene for 16S rRNA, partial sequence, strain: NBRC 100934 | AB681296 | 1474 | ena | 1363 |
67770 | Lactococcus garvieae gene for 16S ribosomal RNA, partial sequence, strain: JCM 10343 | LC096229 | 1458 | ena | 1363 |
67770 | Lactococcus garvieae gene for 16S ribosomal RNA, partial sequence, strain: JCM 12256 | LC145570 | 1488 | ena | 1363 |
Genome sequences
@ref | description | accession | assembly level | database | NCBI tax ID |
---|---|---|---|---|---|
66792 | Lactococcus garvieae NBRC 100934 | 1223498.3 | wgs | patric | 1223498 |
66792 | Lactococcus garvieae strain DSM 20684 | 1363.60 | wgs | patric | 1363 |
66792 | Lactococcus garvieae strain FDAARGOS_929 | 1363.315 | complete | patric | 1363 |
66792 | Lactococcus garvieae DSM 20684 | 2876473875 | draft | img | 1363 |
66792 | Lactococcus garvieae garvieae CCUG 32208 | 2906019534 | draft | img | 1890280 |
66792 | Lactococcus garvieae NBRC 100934 | 2600255050 | draft | img | 1223498 |
67770 | Lactococcus garvieae NBRC 100934 | GCA_000739975 | contig | ncbi | 1223498 |
67770 | Lactococcus garvieae DSM 20684 | GCA_002441675 | contig | ncbi | 1363 |
67770 | Lactococcus garvieae subsp. garvieae CCUG 32208T | GCA_008692985 | contig | ncbi | 1890280 |
GC content
@ref | GC-content | method |
---|---|---|
9006 | 38.3 | |
67770 | 38.3-38.7 | thermal denaturation, midpoint method (Tm) |
Genome-based predictions
predictions
trait | prediction | confidence | training_data |
---|---|---|---|
spore-forming | no | 95 | no |
motile | no | 94.496 | no |
gram-positive | yes | 95.263 | no |
anaerobic | no | 97.925 | no |
halophile | yes | 85.551 | no |
spore-forming | no | 95.047 | no |
thermophile | no | 99.801 | yes |
glucose-util | yes | 91.343 | no |
flagellated | no | 98.016 | no |
aerobic | no | 96.579 | no |
glucose-ferment | yes | 87.711 | no |
External links
@ref: 9006
culture collection no.: DSM 20684, ATCC 43921, JCM 10343, NCDO 2155, CCUG 32208, NCIMB 702155, BCRC 17074, CECT 4531, CIP 102507, HAMBI 1592, JCM 12256, KCTC 3772, LMG 8893, NBRC 100934, NCFB 2155, LMG 9893
straininfo link
- @ref: 83812
- straininfo: 3390
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 |
---|---|---|---|---|---|---|
9006 | Curators of the DSMZ | Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 20684) | https://www.dsmz.de/collection/catalogue/details/culture/DSM-20684 | |||
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 | |
38974 | Curators of the CIP | https://brclims.pasteur.fr/brcWeb/souche/detail/1/14202 | ||||
50898 | Curators of the CCUG | Culture Collection University of Gothenburg (CCUG) (CCUG 32208) | https://www.ccug.se/strain?id=32208 | |||
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) | |||
67770 | Curators of the JCM | https://jcm.brc.riken.jp/en/ | ||||
68371 | Automatically annotated from API 50CH acid | |||||
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 | |||
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 | |||
83812 | Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J. | 10.60712/SI-ID3390.1 | StrainInfo: A central database for resolving microbial strain identifiers | |||
119536 | Curators of the CIP | Collection of Institut Pasteur (CIP 102507) | https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20102507 |