Strain identifier

BacDive ID: 6626

Type strain: Yes

Species: Lactiplantibacillus argentoratensis

Strain history: CIP <- 2004, F. Bringel, CNRS-Univ. Louis Pasteur of Strasbourg, France: strain DKO22 <- D.K. Olukoya, Lagos, Nigeria

NCBI tax ID(s): 1590 (species)

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

@ref: 6403

BacDive-ID: 6626

DSM-Number: 16365

keywords: genome sequence, 16S sequence, Bacteria, microaerophile, mesophilic, human pathogen

description: Lactiplantibacillus argentoratensis DSM 16365 is a microaerophile, mesophilic human pathogen that was isolated from fermented cassava roots .

NCBI tax id

  • NCBI tax id: 1590
  • Matching level: species

strain history

@refhistory
6403<- F. Bringel <- D.K. Olukoya, DKO 22, Lagos, Nigeria
67770CIP 108320 <-- F. Bringel DKO 22 <-- D. K. Olukoya DKO 22.
116494CIP <- 2004, F. Bringel, CNRS-Univ. Louis Pasteur of Strasbourg, France: strain DKO22 <- D.K. Olukoya, Lagos, Nigeria

doi: 10.13145/bacdive6626.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/bacillota
  • domain: Bacteria
  • phylum: Bacillota
  • class: Bacilli
  • order: Lactobacillales
  • family: Lactobacillaceae
  • genus: Lactiplantibacillus
  • species: Lactiplantibacillus argentoratensis
  • full scientific name: Lactiplantibacillus argentoratensis (Bringel et al. 2005) Liu and Gu 2020
  • synonyms

    @refsynonym
    20215Lactiplantibacillus plantarum subsp. argentoratensis
    20215Lactobacillus argentoratensis
    20215Lactobacillus plantarum subsp. argentoratensis

@ref: 6403

domain: Bacteria

phylum: Firmicutes

class: Bacilli

order: Lactobacillales

family: Lactobacillaceae

genus: Lactiplantibacillus

species: Lactiplantibacillus argentoratensis

full scientific name: Lactiplantibacillus argentoratensis (Bringel et al. 2005) Liu and Gu 2020

type strain: yes

Morphology

cell morphology

@refmotilityconfidencegram staincell shape
69480no97.538
69480100positive
116494nopositiverod-shaped

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
6403MRS MEDIUM (DSMZ Medium 11)yeshttps://mediadive.dsmz.de/medium/11Name: MRS MEDIUM (DSMZ Medium 11) Composition: Glucose 20.0 g/l Casein peptone 10.0 g/l Meat extract 10.0 g/l Na-acetate 5.0 g/l Yeast extract 5.0 g/l (NH4)3 citrate 2.0 g/l K2HPO4 2.0 g/l Tween 80 1.0 g/l MgSO4 x 7 H2O 0.2 g/l MnSO4 x H2O 0.05 g/l Distilled water
38269MEDIUM 40- for Lactobacillus and LeuconostocyesDistilled water make up to (1000.000 ml);Man Rogosa Sharp agar (68.000 g)
116494CIP Medium 40yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=40

culture temp

@refgrowthtypetemperaturerange
6403positivegrowth30mesophilic
38269positivegrowth30mesophilic
58997positivegrowth37mesophilic
67770positivegrowth30mesophilic
116494positivegrowth15-37
116494nogrowth10psychrophilic
116494nogrowth45thermophilic

Physiology and metabolism

oxygen tolerance

@refoxygen tolerance
6403microaerophile
58997anaerobe
116494facultative anaerobe

spore formation

@refspore formationconfidence
69481no100
69480no99.991

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
116494nitrate-reduction17632
116494nitrite-reduction16301
116494nitrate+respiration17632

antibiotic resistance

  • @ref: 116494
  • metabolite: 0129 (2,4-Diamino-6,7-di-iso-propylpteridine phosphate)
  • is antibiotic: yes
  • is sensitive: yes
  • is resistant: no

metabolite tests

  • @ref: 116494
  • Chebi-ID: 15688
  • metabolite: acetoin
  • voges-proskauer-test: +

enzymes

@refvalueactivityec
68382alpha-fucosidase-3.2.1.51
68382alpha-mannosidase-3.2.1.24
68382N-acetyl-beta-glucosaminidase+3.2.1.52
68382beta-glucosidase+3.2.1.21
68382alpha-glucosidase+3.2.1.20
68382beta-glucuronidase-3.2.1.31
68382beta-galactosidase+3.2.1.23
68382alpha-galactosidase+3.2.1.22
68382naphthol-AS-BI-phosphohydrolase+
68382acid phosphatase+3.1.3.2
68382alpha-chymotrypsin-3.4.21.1
68382trypsin-3.4.21.4
68382cystine arylamidase-3.4.11.3
68382valine arylamidase-
68382leucine arylamidase+3.4.11.1
68382lipase (C 14)-
68382esterase lipase (C 8)-
68382esterase (C 4)-
68382alkaline phosphatase-3.1.3.1
116494oxidase-
116494alcohol dehydrogenase-1.1.1.1
116494catalase-1.11.1.6
116494lysine decarboxylase-4.1.1.18
116494ornithine decarboxylase-4.1.1.17

API zym

@refControlAlkaline phosphataseEsteraseEsterase LipaseLipaseLeucine arylamidaseValine arylamidaseCystine arylamidaseTrypsinalpha- ChymotrypsinAcid phosphataseNaphthol-AS-BI-phosphohydrolasealpha- Galactosidasebeta- Galactosidasebeta- Glucuronidasealpha- Glucosidasebeta- GlucosidaseN-acetyl-beta- glucosaminidasealpha- Mannosidasealpha- Fucosidase
116494-----+----++++-+++--

API 50CHac

@refQGLYERYDARALARARIBDXYLLXYLADOMDXGALGLUFRUMNESBERHADULINOMANSORMDMMDGNAGAMYARBESCSALCELMALLACMELSACTREINUMLZRAFAMDGLYGXLTGENTURLYXTAGDFUCLFUCDARLLARLGNT2KG5KG
6403-----+----++++----++--+++++++++++--+---+-------+--
6403-----+----++++----++--+++++++++++--+---+-------+--
116494----+----++++----++--+++++++++++--+---+-------+--

Isolation, sampling and environmental information

isolation

@refsample typecountryorigin.countrycontinentgeographic locationisolation date
6403fermented cassava roots (fufu)NigeriaNGAAfrica
58997Sour cassava (fufu)NigeriaNGAAfrica
67770Vegetable matrices
116494Plant, Root of fermented maniocNigeriaNGAAfricaLagos1992

isolation source categories

Cat1Cat2Cat3
#Engineered#Food production
#Host#Plants#Shrub (Scrub)
#Host Body-Site#Plant#Root (Rhizome)

taxonmaps

  • @ref: 69479
  • File name: preview.99_195.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_45;96_140;97_151;98_168;99_195&stattab=map
  • Last taxonomy: Lactobacillaceae
  • 16S sequence: LC258153
  • Sequence Identity:
  • Total samples: 38637
  • soil counts: 2696
  • aquatic counts: 4479
  • animal counts: 29069
  • plant counts: 2393

Safety information

risk assessment

@refpathogenicity humanbiosafety levelbiosafety level comment
6403yes, in single cases1Risk group (German classification)
1164941Risk group (French classification)

Sequence information

16S sequences

@refdescriptionaccessionlengthdatabaseNCBI tax ID
6403Lactobacillus plantarum subsp. argentoratensis partial 16S rRNA gene, type strain DK0 22TAJ6400781517ena271881
67770Lactobacillus plantarum subsp. argentoratensis gene for 16S ribosomal RNA, partial sequence, strain: JCM 16169LC2581531432ena271881

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Lactiplantibacillus argentoratensis DSM 16365GCA_003641165completencbi271881
66792Lactobacillus plantarum subsp. argentoratensis DSM 163651423831.3wgspatric1423831
66792Lactobacillus plantarum subsp. argentoratensis strain DSM 16365271881.5completepatric271881
66792Lactobacillus plantarum subsp. argentoratensis strain NBRC 106468271881.7wgspatric271881
66792Lactiplantibacillus plantarum argentoratensis DSM 163652700989149draftimg1423831
66792Lactiplantibacillus plantarum argentoratensis DSM 163652902495512completeimg1423831
67770Lactiplantibacillus argentoratensis DSM 16365GCA_001435215scaffoldncbi1423831
66792Lactiplantibacillus argentoratensis NBRC 106468GCA_007991855contigncbi271881

GC content

  • @ref: 67770
  • GC-content: 45.3
  • method: genome sequence analysis

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno100no
motileno95.437no
flagellatedno96.844no
gram-positiveyes97no
anaerobicno83.485no
aerobicno97.34yes
halophileyes82.652no
spore-formingno93.447no
glucose-utilyes90.267no
thermophileno99.892no
glucose-fermentyes87.797no

External links

@ref: 6403

culture collection no.: DSM 16365, CIP 108320, CCUG 50787, DKO 22, JCM 16169, BCRC 17638, NBRC 106468, NRIC 0653

straininfo link

  • @ref: 76100
  • straininfo: 3348

literature

  • topic: Phylogeny
  • Pubmed-ID: 32250238
  • title: Proposal of Lactobacillus kosoi Chiou et al. 2018 as a later heterotypic synonym of Lactobacillus micheneri McFrederick et al. 2018, elevation of Lactobacillus plantarum subsp. argentoratensis to the species level as Lactobacillus argentoratensis sp. nov., and Lactobacillus zhaodongensis sp. nov., isolated from traditional Chinese pickle and the intestinal tract of a honey bee (Apis mellifera).
  • authors: Li TT, Liu DD, Fu ML, Gu CT
  • journal: Int J Syst Evol Microbiol
  • DOI: 10.1099/ijsem.0.004141
  • year: 2020
  • mesh: Animals, Bacterial Typing Techniques, Base Composition, Bees/*microbiology, DNA, Bacterial/genetics, Fatty Acids/chemistry, Fermented Foods/*microbiology, *Food Microbiology, Gastrointestinal Tract/microbiology, Genes, Bacterial, Lactobacillus/*classification/isolation & purification, Lactobacillus plantarum/classification, Nucleic Acid Hybridization, *Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA
  • topic2: Biotechnology

Reference

@idauthorscataloguedoi/urltitle
6403Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 16365)https://www.dsmz.de/collection/catalogue/details/culture/DSM-16365
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
38269Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/5930
58997Curators of the CCUGCulture Collection University of Gothenburg (CCUG) (CCUG 50787)https://www.ccug.se/strain?id=50787
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
76100Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID3348.1StrainInfo: A central database for resolving microbial strain identifiers
116494Curators of the CIPCollection of Institut Pasteur (CIP 108320)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20108320