Strain identifier

BacDive ID: 14683

Type strain: No

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)

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

@refhistory
2816<- ATCC <- R. Kusuda, YT-3 (Enterococcus seriolicida)
67770ATCC 49156 <-- R. Kusuda YT-3.
119537CIP <- 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

@refnamegrowthlinkcomposition
2816TRYPTICASE 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
34688MEDIUM 29- Brain heart agaryesDistilled water make up to (1000.000 ml);Brain heart infusion agar (52.000 g)
119537CIP Medium 29yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=29

culture temp

@refgrowthtypetemperaturerange
2816positivegrowth37mesophilic
34688positivegrowth37mesophilic
67770positivegrowth37mesophilic

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

@refmetaboliteutilization activitykind of utilization testedChebi-ID
68371Potassium 5-ketogluconate+builds acid from
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
68371lactose-builds acid from17716
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
119537nitrate-reduction17632
119537nitrite-reduction16301
68380urea-hydrolysis16199
68380arginine+hydrolysis29016
68380D-mannose+fermentation16024
68380raffinose-fermentation16634
68380L-glutamate-degradation29985
68380nitrate-reduction17632
68380tryptophan-energy source27897
68381arginine+hydrolysis29016
68381D-ribose-builds acid from16988
68381D-mannitol+builds acid from16899
68381sorbitol-builds acid from30911
68381lactose-builds acid from17716
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

@refChebi-IDmetaboliteproduction
11953735581indoleno
6838035581indoleno
6838115688acetoinyes

metabolite tests

@refChebi-IDmetabolitevoges-proskauer-testindole test
6838115688acetoin+
6838035581indole-

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
68380serine arylamidase+
68380glutamyl-glutamate arylamidase-
68380histidine arylamidase+
68380glycin arylamidase+
68380alanine arylamidase+3.4.11.2
68380tyrosine arylamidase+
68380pyrrolidonyl arylamidase+3.4.19.3
68380leucine arylamidase+3.4.11.1
68380phenylalanine arylamidase+
68380proline-arylamidase-3.4.11.5
68380L-arginine arylamidase+
68380alkaline phosphatase-3.1.3.1
68380tryptophan deaminase-4.1.99.1
68380alpha-fucosidase-3.2.1.51
68380glutamate decarboxylase-4.1.1.15
68380N-acetyl-beta-glucosaminidase+3.2.1.52
68380beta-glucuronidase-3.2.1.31
68380alpha-arabinosidase-3.2.1.55
68380beta-glucosidase+3.2.1.21
68380beta-Galactosidase 6-phosphate-
68380beta-galactosidase-3.2.1.23
68380alpha-galactosidase-3.2.1.22
68380arginine dihydrolase+3.5.3.6
68380urease-3.5.1.5
119537oxidase-
119537catalase-1.11.1.6
119537urease-3.5.1.5
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

API zym

@refControlAlkaline phosphataseEsteraseEsterase LipaseLipaseLeucine arylamidaseValine arylamidaseCystine arylamidaseTrypsinalpha- ChymotrypsinAcid phosphataseNaphthol-AS-BI-phosphohydrolasealpha- Galactosidasebeta- Galactosidasebeta- Glucuronidasealpha- Glucosidasebeta- GlucosidaseN-acetyl-beta- glucosaminidasealpha- Mannosidasealpha- Fucosidase
119537---+-+---+++---++---

API 50CHac

@refGLYERYDARALARARIBDXYLLXYLADOMDXGALGLUFRUMNESBERHADULINOMANSORMDMMDGNAGAMYARBESCSALCELMALLACMELSACTREINUMLZRAFAMDGLYGXLTGENTURLYXTAGDFUCLFUCDARLLARLGNT2KG5KG
119537+---+----++++----+---+++++++---+------+-------+-+

API rID32A

@refUREADH Argalpha GALbeta GALbeta GPalpha GLUbeta GLUalpha ARAbeta GURbeta NAGMNERAFGDCalpha FUCNITINDPALArgAProALGAPheALeuAPyrATyrAAlaAGlyAHisAGGASerA
2816-+---+/-+--++------+-+/-+++++++-+

API rID32STR

@refADH Argbeta GLUbeta GARbeta GURalpha GALPALRIBMANSORLACTRERAFSACLARADARLCDEXVPAPPAbeta GALPyrAbeta NAGGTAHIPGLYGPULMALMELMLZMbeta DGTAGbeta MANURE
2816++-----+--+-----++-+/------+--+---
2816++-----+--+-----++-------+--+---

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinent
2816kidney of yellowtailKochiJapanJPNAsia
67770Kidney of yellowtail
119537Kidney of yellowtail

isolation source categories

Cat1Cat2Cat3
#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

@refpathogenicity humanpathogenicity animalbiosafety levelbiosafety level comment
2816yesyes2Risk group (German classification)
1195372Risk group (French classification)

Sequence information

16S sequences

@refdescriptionaccessionlengthdatabaseNCBI tax ID
20218Lactococcus garvieae gene for 16S ribosomal RNAAB0268431007ena420889
20218Enterococcus seriolicida 16S ribosomal RNA gene, partial sequenceAF0610051485ena420889
20218Enterococcus seriolicida 16S ribosomal RNA (16S rRNA)L328131497ena1363

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
67770Lactococcus garvieae ATCC 49156GCA_000407125scaffoldncbi420889
67770Lactococcus garvieae ATCC 49156GCA_000269925completencbi420889
67770Lactococcus garvieae ATCC 49156GCA_000407645contigncbi420889

GC content

@refGC-contentmethod
281644.0thermal denaturation, midpoint method (Tm)
6777044thermal denaturation, midpoint method (Tm)

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
motileno93.816no
flagellatedno97.464no
gram-positiveyes94.668no
anaerobicno97.565no
aerobicno97.109no
halophileyes85.704no
spore-formingno95.32no
thermophileno99.84yes
glucose-utilyes91.187no
glucose-fermentyes87.26no

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

@idauthorscataloguedoi/urltitlejournalpubmed
2816Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 6783)https://www.dsmz.de/collection/catalogue/details/culture/DSM-6783
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
34688Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/16270
67770Curators of the JCMhttps://jcm.brc.riken.jp/en/
68371Automatically annotated from API 50CH acid
68380Automatically annotated from API rID32A
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
83809Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID92580.1StrainInfo: A central database for resolving microbial strain identifiers
119537Curators of the CIPCollection of Institut Pasteur (CIP 104369)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20104369