Strain identifier

BacDive ID: 14686

Type strain: Yes

Species: Lactococcus garvieae

Strain Designation: 0159, O159

Strain history: CIP <- 1986, NCFB <- 1979, A.J. Bramley: strain O159

NCBI tax ID(s): 1363 (species)

For citation purpose refer to the digital object identifier (doi) of the current version.
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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

@refhistory
9006<- NCDO <- J. Bramley, 0159
67770DSM 20684 <-- NCDO 2155 <-- J. Bramley 0159.
119536CIP <- 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

    @refsynonym
    20215Enterococcus seriolicida
    20215Streptococcus 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

@refmotilityconfidencegram staincell shape
69480no96.704
69480100positive
119536nopositivecoccus-shaped

colony morphology

@refincubation period
508983 days
119536

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
9006TRYPTICASE SOY YEAST EXTRACT MEDIUM (DSMZ Medium 92)yeshttps://mediadive.dsmz.de/medium/92Name: 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
38974MEDIUM 29- Brain heart agaryesDistilled water make up to (1000.000 ml);Brain heart infusion agar (52.000 g)
119536CIP Medium 29yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=29
119536CIP Medium 45yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=45

culture temp

@refgrowthtypetemperaturerange
9006positivegrowth30mesophilic
38974positivegrowth30mesophilic
50898positivegrowth30mesophilic
50898positivegrowth37mesophilic
67770positivegrowth30mesophilic
119536positivegrowth10-41
119536nogrowth45thermophilic

Physiology and metabolism

oxygen tolerance

@refoxygen tolerance
50898anaerobe
50898microaerophile
119536facultative anaerobe

spore formation

@refspore formationconfidence
69481no95
69480no99.993

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

@refmetaboliteutilization activitykind of utilization testedChebi-ID
68371Potassium 2-ketogluconate-builds acid from
68371gluconate+builds acid from24265
68371L-arabitol-builds acid from18403
68371D-arabitol-builds acid from18333
68371L-fucose-builds acid from18287
68371D-fucose-builds acid from28847
68371D-tagatose-builds acid from16443
68371D-lyxose-builds acid from62318
68371turanose-builds acid from32528
68371gentiobiose+builds acid from28066
68371xylitol-builds acid from17151
68371glycogen-builds acid from28087
68371starch-builds acid from28017
68371raffinose-builds acid from16634
68371melezitose-builds acid from6731
68371inulin-builds acid from15443
68371trehalose+builds acid from27082
68371sucrose-builds acid from17992
68371melibiose-builds acid from28053
68371maltose+builds acid from17306
68371cellobiose+builds acid from17057
68371salicin+builds acid from17814
68371esculin+builds acid from4853
68371arbutin+builds acid from18305
68371amygdalin+builds acid from27613
68371N-acetylglucosamine+builds acid from59640
68371methyl alpha-D-glucopyranoside-builds acid from320061
68371methyl alpha-D-mannoside-builds acid from43943
68371D-sorbitol-builds acid from17924
68371D-mannitol+builds acid from16899
68371myo-inositol-builds acid from17268
68371galactitol-builds acid from16813
68371L-rhamnose-builds acid from62345
68371L-sorbose-builds acid from17266
68371D-mannose+builds acid from16024
68371D-fructose+builds acid from15824
68371D-glucose+builds acid from17634
68371D-galactose+builds acid from12936
68371methyl beta-D-xylopyranoside-builds acid from74863
68371ribitol-builds acid from15963
68371L-xylose-builds acid from65328
68371D-xylose-builds acid from65327
68371D-ribose+builds acid from16988
68371L-arabinose-builds acid from30849
68371D-arabinose-builds acid from17108
68371erythritol-builds acid from17113
68371glycerol-builds acid from17754
119536esculin+hydrolysis4853
119536hippurate+hydrolysis606565
119536nitrate-reduction17632
119536nitrite-reduction16301
68381arginine+hydrolysis29016
68381D-ribose+builds acid from16988
68381D-mannitol+builds acid from16899
68381sorbitol-builds acid from30911
68381trehalose+builds acid from27082
68381raffinose-builds acid from16634
68381sucrose-builds acid from17992
68381L-arabinose-builds acid from30849
68381D-arabitol-builds acid from18333
68381alpha-cyclodextrin+builds acid from40585
68381hippurate-hydrolysis606565
68381glycogen-builds acid from28087
68381pullulan-builds acid from27941
68381maltose+builds acid from17306
68381melibiose-builds acid from28053
68381melezitose-builds acid from6731
68381methyl beta-D-glucopyranoside+builds acid from320055
68381D-tagatose-builds acid from16443
68381urea-hydrolysis16199

metabolite production

  • @ref: 68381
  • Chebi-ID: 15688
  • metabolite: acetoin
  • production: yes

metabolite tests

@refChebi-IDmetabolitevoges-proskauer-test
6838115688acetoin+
11953615688acetoin+

enzymes

@refvalueactivityec
68381urease-3.5.1.5
68381beta-mannosidase-3.2.1.25
68381glycyl tryptophan arylamidase-
68381N-acetyl-beta-glucosaminidase+3.2.1.52
68381beta-galactosidase-3.2.1.23
68381Alanyl-Phenylalanyl-Proline arylamidase+
68381alkaline phosphatase-3.1.3.1
68381alpha-galactosidase-3.2.1.22
68381beta-glucuronidase-3.2.1.31
68381beta-glucosidase+3.2.1.21
68381arginine dihydrolase+3.5.3.6
119536oxidase-
119536beta-galactosidase-3.2.1.23
119536alcohol dehydrogenase+1.1.1.1
119536catalase-1.11.1.6
119536gamma-glutamyltransferase-2.3.2.2
119536lysine decarboxylase-4.1.1.18
119536ornithine decarboxylase-4.1.1.17
68382alkaline phosphatase-3.1.3.1
68382esterase (C 4)+
68382esterase lipase (C 8)+
68382lipase (C 14)-
68382leucine arylamidase+3.4.11.1
68382valine arylamidase-
68382cystine arylamidase-3.4.11.3
68382trypsin-3.4.21.4
68382alpha-chymotrypsin+3.4.21.1
68382acid phosphatase+3.1.3.2
68382naphthol-AS-BI-phosphohydrolase-
68382alpha-galactosidase-3.2.1.22
68382beta-galactosidase-3.2.1.23
68382beta-glucuronidase-3.2.1.31
68382alpha-glucosidase+3.2.1.20
68382beta-glucosidase+3.2.1.21
68382N-acetyl-beta-glucosaminidase-3.2.1.52
68382alpha-mannosidase-3.2.1.24
68382alpha-fucosidase-3.2.1.51

fatty acid profile

  • fatty acids

    @reffatty acidpercentageECL
    50898C14:016.614
    50898C16:026.116
    50898C18:02.918
    50898C13:0 ISO 2OH1.513.814
    50898C16:1 ω7c6.415.819
    50898C18:1 ω7c /12t/9t25.717.824
    50898C18:1 ω9c317.769
    50898C18:2 ω6,9c/C18:0 ANTE7.317.724
    50898C19:0 CYCLO ω8c10.618.9
  • type of FA analysis: whole cell analysis
  • method/protocol: CCUG

API zym

@refControlAlkaline phosphataseEsteraseEsterase LipaseLipaseLeucine arylamidaseValine arylamidaseCystine arylamidaseTrypsinalpha- ChymotrypsinAcid phosphataseNaphthol-AS-BI-phosphohydrolasealpha- Galactosidasebeta- Galactosidasebeta- Glucuronidasealpha- Glucosidasebeta- GlucosidaseN-acetyl-beta- glucosaminidasealpha- Mannosidasealpha- Fucosidase
119536--++-+---++----++---

API 50CHac

@refQGLYERYDARALARARIBDXYLLXYLADOMDXGALGLUFRUMNESBERHADULINOMANSORMDMMDGNAGAMYARBESCSALCELMALLACMELSACTREINUMLZRAFAMDGLYGXLTGENTURLYXTAGDFUCLFUCDARLLARLGNT2KG5KG
9006-----+----++++----+---+++++++---+------+-------+--
119536----+----++++----+---++++++++--+------+-------+-+

API rID32STR

@refADH Argbeta GLUbeta GARbeta GURalpha GALPALRIBMANSORLACTRERAFSACLARADARLCDEXVPAPPAbeta GALPyrAbeta NAGGTAHIPGLYGPULMALMELMLZMbeta DGTAGbeta MANURE
9006++----++-+/-+----+++-+/-+----+--+---

Isolation, sampling and environmental information

isolation

@refsample typesampling dateisolation date
9006bovine mastitis
50898Mastitis1973
67770Bovine mastitis
119536Animal, Bovine mastitis1973

isolation source categories

Cat1Cat2Cat3
#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

@refpathogenicity humanpathogenicity animalbiosafety levelbiosafety level comment
9006yesyes2Risk group (German classification)
1195361Risk group (French classification)

Sequence information

16S sequences

@refdescriptionaccessionlengthdatabaseNCBI tax ID
20218Lactococcus garvieae culture-collection CECT:4531 16S ribosomal RNA gene, partial sequenceKF012886805ena1363
20218Lactococcus garvieae strain DSM 20684 16S-23S intergenic spacer region, and tRNA-Ala gene, complete sequenceAF225967350ena1363
20218Lactococcus garvieae gene for 16S rRNA, partial sequence, strain: JCM 10343AB5989941510ena1363
20218Lactococcus garvieae strain KCTC 3772 16S ribosomal RNA gene, partial sequence; 16S-23S ribosomal RNA intergenic spacer, complete sequence; and 23S ribosomal RNA gene, partial sequenceHM241913560ena1363
20218Lactococcus garvieae strain NIZO2415T 16S ribosomal RNA gene, partial sequenceEU091459652ena1363
20218Lactococcus garvieae gene for 16S rRNA, partial sequence, strain: NBRC 100934AB6812961474ena1363
67770Lactococcus garvieae gene for 16S ribosomal RNA, partial sequence, strain: JCM 10343LC0962291458ena1363
67770Lactococcus garvieae gene for 16S ribosomal RNA, partial sequence, strain: JCM 12256LC1455701488ena1363

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Lactococcus garvieae NBRC 1009341223498.3wgspatric1223498
66792Lactococcus garvieae strain DSM 206841363.60wgspatric1363
66792Lactococcus garvieae strain FDAARGOS_9291363.315completepatric1363
66792Lactococcus garvieae DSM 206842876473875draftimg1363
66792Lactococcus garvieae garvieae CCUG 322082906019534draftimg1890280
66792Lactococcus garvieae NBRC 1009342600255050draftimg1223498
67770Lactococcus garvieae NBRC 100934GCA_000739975contigncbi1223498
67770Lactococcus garvieae DSM 20684GCA_002441675contigncbi1363
67770Lactococcus garvieae subsp. garvieae CCUG 32208TGCA_008692985contigncbi1890280

GC content

@refGC-contentmethod
900638.3
6777038.3-38.7thermal denaturation, midpoint method (Tm)

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno95no
motileno94.496no
gram-positiveyes95.263no
anaerobicno97.925no
halophileyes85.551no
spore-formingno95.047no
thermophileno99.801yes
glucose-utilyes91.343no
flagellatedno98.016no
aerobicno96.579no
glucose-fermentyes87.711no

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

@idauthorscataloguedoi/urltitlejournalpubmed
9006Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 20684)https://www.dsmz.de/collection/catalogue/details/culture/DSM-20684
20215Parte, A.C., Sardà Carbasse, J., Meier-Kolthoff, J.P., Reimer, L.C. and Göker, M.10.1099/ijsem.0.004332List of Prokaryotic names with Standing in Nomenclature (LPSN) moves to the DSMZ
20218Verslyppe, B., De Smet, W., De Baets, B., De Vos, P., Dawyndt P.10.1016/j.syapm.2013.11.002StrainInfo introduces electronic passports for microorganisms.Syst Appl Microbiol. 37: 42-50 201424321274
38974Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/14202
50898Curators of the CCUGCulture Collection University of Gothenburg (CCUG) (CCUG 32208)https://www.ccug.se/strain?id=32208
66792Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmannhttps://diaspora-project.de/progress.html#genomesAutomatically annotated for the DiASPora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information)
67770Curators of the JCMhttps://jcm.brc.riken.jp/en/
68371Automatically annotated from API 50CH acid
68381Automatically annotated from API rID32STR
68382Automatically annotated from API zym
69479João 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
69480Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmannhttps://diaspora-project.de/progress.html#genomesPredictions based on genome sequence made in the Diaspora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information)
69481Xiao-Yin To, René Mreches, Martin Binder, Alice C. McHardy, Philipp C. Münch10.21203/rs.3.rs-2527258/v1Predictions based on the model GenomeNet Sporulation v. 1
83812Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID3390.1StrainInfo: A central database for resolving microbial strain identifiers
119536Curators of the CIPCollection of Institut Pasteur (CIP 102507)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20102507