Strain identifier

BacDive ID: 14706

Type strain: Yes

Species: Lactococcus plantarum

Strain Designation: 5L

Strain history: CIP <- 1986, NCFB <- 1966, J.J. Cavett: strain 5L, Streptococcus cremoris

NCBI tax ID(s): 1348632 (strain), 1365 (species)

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

@ref: 9008

BacDive-ID: 14706

DSM-Number: 20686

keywords: genome sequence, 16S sequence, Bacteria, facultative anaerobe, mesophilic

description: Lactococcus plantarum 5L is a facultative anaerobe, mesophilic bacterium that was isolated from frozen peas.

NCBI tax id

NCBI tax idMatching level
1348632strain
1365species

strain history

@refhistory
9008<- NCDO <- J.J. Cavett, 5L
67770CIP 102506 <-- NCFB <-- J. J. Cavett 5L.
121864CIP <- 1986, NCFB <- 1966, J.J. Cavett: strain 5L, Streptococcus cremoris

doi: 10.13145/bacdive14706.20230509.8.1

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 plantarum
  • full scientific name: Lactococcus plantarum (Collins et al. 1984) Schleifer et al. 1986
  • synonyms

    • @ref: 20215
    • synonym: Streptococcus plantarum

@ref: 9008

domain: Bacteria

phylum: Firmicutes

class: Bacilli

order: Lactobacillales

family: Streptococcaceae

genus: Lactococcus

species: Lactococcus plantarum

full scientific name: Lactococcus plantarum (Collins et al. 1984) Schleifer et al. 1986

strain designation: 5L

type strain: yes

Morphology

cell morphology

@refmotilityconfidencegram staincell shape
69480no97.688
69480100positive
121864nopositivecoccus-shaped

colony morphology

  • @ref: 121864

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
9008TRYPTICASE 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
38973MEDIUM 29- Brain heart agaryesDistilled water make up to (1000.000 ml);Brain heart infusion agar (52.000 g)
121864CIP Medium 72yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=72
121864CIP Medium 29yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=29

culture temp

@refgrowthtypetemperaturerange
9008positivegrowth30mesophilic
38973positivegrowth30mesophilic
54687positivegrowth30mesophilic
67770positivegrowth30mesophilic
121864positivegrowth10-37
121864nogrowth41thermophilic
121864nogrowth45thermophilic

Physiology and metabolism

oxygen tolerance

  • @ref: 121864
  • oxygen tolerance: facultative anaerobe

spore formation

@refspore formationconfidence
69481no100
69480no99.999

halophily

  • @ref: 121864
  • salt: NaCl
  • growth: positive
  • tested relation: growth
  • concentration: 6.5 %

murein

  • @ref: 9008
  • murein short key: A11.18
  • type: A3alpha L-Lys-L-Ser-L-Ala

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
68371xylitol-builds acid from17151
68371glycogen-builds acid from28087
68371starch-builds acid from28017
68371raffinose-builds acid from16634
68371melezitose+builds acid from6731
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
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
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
121864hippurate+hydrolysis606565
121864nitrate-reduction17632
121864nitrite-reduction16301

metabolite tests

  • @ref: 121864
  • Chebi-ID: 15688
  • metabolite: acetoin
  • voges-proskauer-test: +

enzymes

@refvalueactivityec
121864oxidase-
121864beta-galactosidase-3.2.1.23
121864alcohol dehydrogenase-1.1.1.1
121864catalase-1.11.1.6
121864gamma-glutamyltransferase-2.3.2.2
121864lysine decarboxylase-4.1.1.18
121864ornithine 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

API zym

@refControlAlkaline phosphataseEsteraseEsterase LipaseLipaseLeucine arylamidaseValine arylamidaseCystine arylamidaseTrypsinalpha- ChymotrypsinAcid phosphataseNaphthol-AS-BI-phosphohydrolasealpha- Galactosidasebeta- Galactosidasebeta- Glucuronidasealpha- Glucosidasebeta- GlucosidaseN-acetyl-beta- glucosaminidasealpha- Mannosidasealpha- Fucosidase
121864-+++-+----++---++---

API 50CHac

@refQGLYERYDARALARARIBDXYLLXYLADOMDXGALGLUFRUMNESBERHADULINOMANSORMDMMDGNAGAMYARBESCSALCELMALLACMELSACTREINUMLZRAFAMDGLYGXLTGENTURLYXTAGDFUCLFUCDARLLARLGNT2KG5KG
9008----------++++----++-++++++++--++-+----+/-+---------
121864+/----------+++----++-+++/-+++++--++++----++--------+

Isolation, sampling and environmental information

isolation

@refsample type
9008frozen peas
54687Frozen peas
67770Frozen peas
121864Food, Frozen peas

isolation source categories

Cat1Cat2Cat3
#Engineered#Food production#Food
#Host#Plants#Herbaceous plants (Grass,Crops)
#Host Body-Site#Plant#Fruit (Seed)
#Condition#Psychrophilic (<10°C)

taxonmaps

  • @ref: 69479
  • File name: preview.99_5260.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_58;96_1605;97_1917;98_3922;99_5260&stattab=map
  • Last taxonomy: Lactococcus plantarum subclade
  • 16S sequence: LC145561
  • Sequence Identity:
  • Total samples: 8909
  • soil counts: 1086
  • aquatic counts: 1614
  • animal counts: 5833
  • plant counts: 376

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
90081Risk group (German classification)
1218641Risk group (French classification)

Sequence information

16S sequences

@refdescriptionaccessionlengthdatabaseNCBI tax ID
20218Lactococcus plantarum strain DSM 20686 16S ribosomal RNA gene, partial sequenceEF6940291433ena1365
20218Lactococcus plantarum strain DSM 20686 16S ribosomal RNA gene, partial sequence; 16S-23S ribosomal RNA intergenic spacer, complete sequence; and 23S ribosomal RNA gene, partial sequenceHM241919575ena1365
20218Lactococcus plantarum strain NIZO2426T 16S ribosomal RNA gene, partial sequenceEU091464646ena1365
20218Lactococcus plantarum gene for 16S rRNA, partial sequence, strain: NBRC 100936AB6812971474ena1365
20218Lactococcus plantarum 16S ribosomal RNAX542591473ena1365
67770Lactococcus plantarum gene for 16S ribosomal RNA, partial sequence, strain: JCM 11056LC1455611488ena1365

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Lactococcus plantarum NBRC 1009361348632.3wgspatric1348632
66792Lactococcus plantarum strain DSM 206861365.4wgspatric1365
66792Lactococcus plantarum DSM 206862903266210draftimg1365
66792Lactococcus plantarum NBRC 1009362731957665draftimg1348632
67770Lactococcus plantarum NBRC 100936GCA_001591745contigncbi1348632
67770Lactococcus plantarum DSM 20686GCA_002441715contigncbi1365

GC content

  • @ref: 9008
  • GC-content: 36.9

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno100no
motileno96.74no
gram-positiveyes96.065no
anaerobicno93.436no
halophileyes84.213no
spore-formingno96.202no
thermophileno99.796yes
glucose-utilyes88.204no
aerobicno97.679no
flagellatedno97.99no
glucose-fermentyes90.009no

External links

@ref: 9008

culture collection no.: DSM 20686, ATCC 43199, NCDO 1869, CCUG 39180, JCM 11056, CCM 4542, CIP 102506, HAMBI 1593, KCTC 3645, LMG 8517, NBRC 100936, NCIMB 11945, VTT E-90411

straininfo link

  • @ref: 83825
  • straininfo: 3459

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny6663283Streptococcus garvieae sp. nov. and Streptococcus plantarum sp. nov.Collins MD, Farrow JA, Phillips BA, Kandler OJ Gen Microbiol10.1099/00221287-129-11-34271983Animals, Carbohydrates/analysis, Cattle, Fabaceae/microbiology, Fatty Acids/analysis, Female, Mastitis, Bovine/microbiology, Plants, Medicinal, Species Specificity, Streptococcus/*classification/isolation & purification/metabolismEnzymology
Phylogeny32614762Lactococcus insecticola sp. nov. and Lactococcus hodotermopsidis sp. nov., isolated from the gut of the wood-feeding lower termite Hodotermopsis sjostedti.Noda S, Koyama F, Aihara C, Ikeyama N, Yuki M, Ohkuma M, Sakamoto MInt J Syst Evol Microbiol10.1099/ijsem.0.0043092020Animals, Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, Fatty Acids/chemistry, Gastrointestinal Tract/*microbiology, Genes, Bacterial, Isoptera/*microbiology, Lactococcus/*classification/isolation & purification, Nucleic Acid Hybridization, Peptidoglycan/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, WoodTranscriptome

Reference

@idauthorscataloguedoi/urltitlejournalpubmed
9008Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 20686)https://www.dsmz.de/collection/catalogue/details/culture/DSM-20686
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
38973Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/14199
54687Curators of the CCUGCulture Collection University of Gothenburg (CCUG) (CCUG 39180)https://www.ccug.se/strain?id=39180
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
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
83825Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID3459.1StrainInfo: A central database for resolving microbial strain identifiers
121864Curators of the CIPCollection of Institut Pasteur (CIP 102506)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20102506