Strain identifier

BacDive ID: 14707

Type strain: Yes

Species: Lactococcus raffinolactis

Strain Designation: 23.C.5

Strain history: CIP <- 1986, NCFB <- 1949, E.J. Garvie: strain 23 C5, Streptococcus sp. group N

NCBI tax ID(s): 1348633 (strain), 1366 (species)

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General

@ref: 8815

BacDive-ID: 14707

DSM-Number: 20443

keywords: genome sequence, 16S sequence, Bacteria, anaerobe, mesophilic, Gram-positive, rod-shaped

description: Lactococcus raffinolactis 23.C.5 is an anaerobe, mesophilic, Gram-positive bacterium that was isolated from raw milk.

NCBI tax id

NCBI tax idMatching level
1348633strain
1366species

strain history

@refhistory
8815<- NCDO <- E.I. Garvie, 23.C.5
67770DSM 20443 <-- NCDO 617 <-- E. I. Garvie 23.C.5.
122131CIP <- 1986, NCFB <- 1949, E.J. Garvie: strain 23 C5, Streptococcus sp. group N

doi: 10.13145/bacdive14707.20230509.8.1

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 raffinolactis
  • full scientific name: Lactococcus raffinolactis (Orla-Jensen and Hansen 1932) Schleifer et al. 1988

  • synonyms

    • @ref: 20215
    • synonym: Streptococcus raffinolactis

@ref: 8815

domain: Bacteria

phylum: Firmicutes

class: Bacilli

order: Lactobacillales

family: Streptococcaceae

genus: Lactococcus

species: Lactococcus raffinolactis

full scientific name: Lactococcus raffinolactis (Orla-Jensen and Hansen 1932) Schleifer et al. 1988

strain designation: 23.C.5

type strain: yes

Morphology

cell morphology

  • @ref: 122131
  • gram stain: positive
  • cell shape: rod-shaped
  • motility: no

colony morphology

  • @ref: 50899
  • incubation period: 3 days

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
8815TRYPTICASE 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
38094MEDIUM 29- Brain heart agaryesDistilled water make up to (1000.000 ml);Brain heart infusion agar (52.000 g)
122131CIP Medium 29yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=29

culture temp

@refgrowthtypetemperaturerange
8815positivegrowth30mesophilic
38094positivegrowth30mesophilic
50899positivegrowth30mesophilic
67770positivegrowth30mesophilic

Physiology and metabolism

oxygen tolerance

  • @ref: 50899
  • oxygen tolerance: anaerobe

murein

  • @ref: 8815
  • murein short key: A11.25
  • type: A3alpha L-Lys-L-Thr-L-Ala

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
6838129016arginine-hydrolysis
6838116988D-ribose-builds acid from
6838116899D-mannitol-builds acid from
6838130911sorbitol-builds acid from
6838117716lactose-builds acid from
6838127082trehalose+builds acid from
6838116634raffinose+builds acid from
6838117992sucrose+builds acid from
6838130849L-arabinose-builds acid from
6838118333D-arabitol-builds acid from
6838140585alpha-cyclodextrin+builds acid from
68381606565hippurate-hydrolysis
6838128087glycogen-builds acid from
6838127941pullulan-builds acid from
6838117306maltose+builds acid from
6838128053melibiose+builds acid from
683816731melezitose-builds acid from
68381320055methyl beta-D-glucopyranoside-builds acid from
6838116443D-tagatose-builds acid from
6838116199urea-hydrolysis

metabolite production

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

metabolite tests

  • @ref: 68381
  • Chebi-ID: 15688
  • metabolite: acetoin
  • voges-proskauer-test: +

enzymes

@refvalueactivityec
68381urease-3.5.1.5
68381beta-mannosidase-3.2.1.25
68381glycyl tryptophan arylamidase-
68381N-acetyl-beta-glucosaminidase-3.2.1.52
68381pyrrolidonyl arylamidase-3.4.19.3
68381beta-galactosidase-3.2.1.23
68381alpha-galactosidase+3.2.1.22
68381beta-glucuronidase-3.2.1.31
68381beta-glucosidase+3.2.1.21
68381arginine dihydrolase-3.5.3.6

API rID32STR

@refADH Argbeta GLUbeta GARbeta GURalpha GALPALRIBMANSORLACTRERAFSACLARADARLCDEXVPAPPAbeta GALPyrAbeta NAGGTAHIPGLYGPULMALMELMLZMbeta DGTAGbeta MANURE
8815-+--+-----+++--++--------++-----
8815-+--++----+++--+++-------++-----

Isolation, sampling and environmental information

isolation

@refsample type
8815raw milk
50899Raw milk
67770Raw milk
122131Food, Raw milk

isolation source categories

Cat1Cat2Cat3
#Host Body Product#Fluids#Milk
#Host#Mammals

taxonmaps

  • @ref: 69479
  • File name: preview.99_7003.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_58;96_1605;97_3793;98_5143;99_7003&stattab=map
  • Last taxonomy: Lactococcus raffinolactis subclade
  • 16S sequence: LC071827
  • Sequence Identity:
  • Total samples: 75110
  • soil counts: 7093
  • aquatic counts: 17312
  • animal counts: 48624
  • plant counts: 2081

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
88151Risk group (German classification)
1221311Risk group (French classification)

Sequence information

16S sequences

@refdescriptionaccessionlengthdatabaseNCBI tax ID
20218Lactococcus raffinolactis strain DSM20443T 16S-23S ribosomal RNA intergenic spacer region and tRNA-Ala gene, complete sequenceAF284219366ena1366
20218Lactococcus raffinolactis strain DSM 20443 16S ribosomal RNA gene, partial sequenceEF6940301440ena1366
20218Lactococcus raffinolactis strain KCTC 3982 16S ribosomal RNA gene, partial sequence; 16S-23S ribosomal RNA intergenic spacer, complete sequence; and 23S ribosomal RNA gene, partial sequenceHM241918572ena1366
20218Lactococcus raffinolactis strain NIZO2429T 16S ribosomal RNA gene, partial sequenceEU091467645ena1366
20218Lactococcus raffinolactis gene for 16S rRNA, partial sequence, strain: NBRC 100932AB6812941482ena1366
20218Lactococcus raffinolactis 16S ribosomal RNAX542611479ena1366
67770Lactococcus raffinolactis gene for 16S ribosomal RNA, partial sequence, strain: JCM 5706LC0718271447ena1366

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Lactococcus raffinolactis KACC 13441GCA_010669245completencbi1366
66792Lactococcus raffinolactis ATCC 43920GCA_002441745contigncbi1366
66792Lactococcus raffinolactis NBRC 100932GCA_001591765contigncbi1348633
66792Lactococcus raffinolactis NBRC 1009321348633.3wgspatric1348633
66792Lactococcus raffinolactis strain ATCC 439201366.7wgspatric1366
66792Lactococcus raffinolactis strain KACC 134411366.23completepatric1366
66792Lactococcus raffinolactis ATCC 439202874262289draftimg1366
66792Lactococcus raffinolactis NBRC 1009322731957666draftimg1348633

GC content

@refGC-contentmethod
881541.5
6777041.5thermal denaturation, midpoint method (Tm)

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
flagellatedno97.714no
gram-positiveyes96.147no
anaerobicno88.036yes
aerobicno98.367no
halophileyes78.107no
spore-formingno94.79no
thermophileno99.794no
glucose-utilyes87.503no
motileno94.781no
glucose-fermentyes89.619no

External links

@ref: 8815

culture collection no.: CCUG 32209, DSM 20443, ATCC 43920, NCDO 617, JCM 5706, BCRC 14039, CCM 4543, CECT 988, CGMCC 1.1935, CIP 102300, HAMBI 1589, KACC 13441, KCTC 3509, KCTC 3982, LMG 13095, LMG 9463, NBRC 100932, NCIMB 13197, NRIC 1781, VTT E-91453

straininfo link

  • @ref: 83826
  • straininfo: 92334

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Biotechnology12450840Novel food-grade plasmid vector based on melibiose fermentation for the genetic engineering of Lactococcus lactis.Boucher I, Parrot M, Gaudreau H, Champagne CP, Vadeboncoeur C, Moineau SAppl Environ Microbiol10.1128/AEM.68.12.6152-6161.20022002Base Sequence, Cloning, Molecular, *Fermentation, Food Industry, *Genetic Engineering, Genetic Vectors/*genetics, *Industrial Microbiology, Lactococcus/genetics, Lactococcus lactis/*genetics/growth & development, Melibiose/*metabolism, Molecular Sequence Data, alpha-Galactosidase/genetics/metabolismEnzymology
Metabolism12839781Characterization of genes involved in the metabolism of alpha-galactosides by Lactococcus raffinolactis.Boucher I, Vadeboncoeur C, Moineau SAppl Environ Microbiol10.1128/AEM.69.7.4049-4056.20032003Amino Acid Sequence, Bacterial Proteins/*genetics/metabolism, Base Sequence, Galactosides/*metabolism, Gene Expression Regulation, Bacterial, Lactococcus/*enzymology/genetics, Molecular Sequence Data, Operon, Sequence Analysis, DNA, alpha-Galactosidase/*genetics/metabolismGenetics
Enzymology15956297Use of an alpha-galactosidase gene as a food-grade selection marker for Streptococcus thermophilus.Labrie S, Bart C, Vadeboncoeur C, Moineau SJ Dairy Sci10.3168/jds.S0022-0302(05)72912-X2005Dairy Products/*microbiology/standards, Enzyme Stability, Fermentation, Gene Expression/drug effects, Genetic Markers, Hot Temperature, Lactic Acid/biosynthesis, Lactococcus/enzymology, Lactose/pharmacology, Melibiose/metabolism, Phenotype, Plasmids/genetics, RNA, Messenger/analysis, Recombinant Proteins, Selection, Genetic, Streptococcus thermophilus/enzymology/*genetics/growth & development, Transcription, Genetic/drug effects, Transformation, Bacterial, alpha-Galactosidase/*genetics/metabolismPathogenicity
Enzymology26142864Alcohol dehydrogenase activity in Lactococcus chungangensis: application in cream cheese to moderate alcohol uptake.Konkit M, Choi WJ, Kim WJ Dairy Sci10.3168/jds.2015-96972015Alcohol Dehydrogenase/genetics/*metabolism, Animals, Cell Line, Tumor, Cell Survival/drug effects, Cheese/*microbiology, Culture Media/chemistry, Ethanol/metabolism, Food Handling, L-Lactate Dehydrogenase/metabolism, Lactococcus/*enzymology, Mice, Mice, Inbred ICRMetabolism
Metabolism26723119Aldehyde dehydrogenase activity in Lactococcus chungangensis: Application in cream cheese to reduce aldehyde in alcohol metabolism.Konkit M, Choi WJ, Kim WJ Dairy Sci10.3168/jds.2015-105492015Acetaldehyde/blood/metabolism, Acetates/metabolism, Aldehyde Dehydrogenase/genetics/*metabolism, Animals, Bacterial Proteins/metabolism, Cheese/*microbiology, Ethanol/*metabolism, Female, Humans, Lactococcus lactis/*enzymology, Male, Mice, Species SpecificityEnzymology
Phylogeny29300157Lactococcus reticulitermitis sp. nov., isolated from the gut of the subterranean termite Reticulitermes speratus.Yuki M, Sakamoto M, Nishimura Y, Ohkuma MInt J Syst Evol Microbiol10.1099/ijsem.0.0025492018Animals, Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, Fatty Acids/chemistry, Gastrointestinal Tract/*microbiology, Isoptera/*microbiology, Lactococcus/*classification/genetics/isolation & purification, *Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNATranscriptome

Reference

@idauthorscataloguedoi/urltitlejournalpubmed
8815Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 20443)https://www.dsmz.de/collection/catalogue/details/culture/DSM-20443
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
38094Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/13971
50899Curators of the CCUGCulture Collection University of Gothenburg (CCUG) (CCUG 32209)https://www.ccug.se/strain?id=32209
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/
68381Automatically annotated from API rID32STR
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
83826Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID92334.1StrainInfo: A central database for resolving microbial strain identifiers
122131Curators of the CIPCollection of Institut Pasteur (CIP 102300)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20102300