Strain identifier

BacDive ID: 6591

Type strain: Yes

Species: Lentilactobacillus diolivorans

Strain Designation: JKD6

Strain history: CIP <- 2002, DSMZ <- LMG <- M. Vancanneyt <- J. Krooneman: strain JKD6

NCBI tax ID(s): 1423739 (strain), 179838 (species)

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General

@ref: 5345

BacDive-ID: 6591

DSM-Number: 14421

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

description: Lentilactobacillus diolivorans JKD6 is a facultative anaerobe, mesophilic bacterium that was isolated from maize silage.

NCBI tax id

NCBI tax idMatching level
179838species
1423739strain

strain history

@refhistory
5345<- LMG <- M. Vancanneyt <- J. Krooneman; JKD6
67770LMG 19667 <-- M. Vancanneyt R-6806 <-- J. Krooneman JKD6.
118939CIP <- 2002, DSMZ <- LMG <- M. Vancanneyt <- J. Krooneman: strain JKD6

doi: 10.13145/bacdive6591.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/bacillota
  • domain: Bacteria
  • phylum: Bacillota
  • class: Bacilli
  • order: Lactobacillales
  • family: Lactobacillaceae
  • genus: Lentilactobacillus
  • species: Lentilactobacillus diolivorans
  • full scientific name: Lentilactobacillus diolivorans (Krooneman et al. 2002) Zheng et al. 2020

  • synonyms

    • @ref: 20215
    • synonym: Lactobacillus diolivorans

@ref: 5345

domain: Bacteria

phylum: Firmicutes

class: Bacilli

order: Lactobacillales

family: Lactobacillaceae

genus: Lentilactobacillus

species: Lentilactobacillus diolivorans

full scientific name: Lentilactobacillus diolivorans (Krooneman et al. 2002) Zheng et al. 2020

strain designation: JKD6

type strain: yes

Morphology

cell morphology

@refmotilityconfidencegram staincell shape
69480no94.91
69480100positive
118939nopositiverod-shaped

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
5345MRS 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
33809MEDIUM 40- for Lactobacillus and LeuconostocyesDistilled water make up to (1000.000 ml);Man Rogosa Sharp agar (68.000 g)
118939CIP Medium 40yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=40

culture temp

@refgrowthtypetemperaturerange
5345positivegrowth30mesophilic
33809positivegrowth37mesophilic
67770positivegrowth30mesophilic
118939positivegrowth22-37
118939nogrowth10psychrophilic
118939nogrowth15psychrophilic
118939nogrowth45thermophilic

Physiology and metabolism

oxygen tolerance

  • @ref: 118939
  • oxygen tolerance: facultative anaerobe

spore formation

@refspore formationconfidence
69481no100
69480no99.997

murein

  • @ref: 5345
  • murein short key: A11.31
  • type: A4alpha L-Lys-D-Asp

metabolite utilization

@refmetaboliteutilization activitykind of utilization testedChebi-ID
68371Potassium 2-ketogluconate-builds acid from
68371L-arabitol-builds acid from18403
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
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
68371arbutin-builds acid from18305
68371amygdalin-builds acid from27613
68371N-acetylglucosamine-builds acid from59640
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
118939nitrate-reduction17632
118939nitrite-reduction16301
118939nitrate+respiration17632

metabolite tests

  • @ref: 118939
  • 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
118939oxidase-
118939alcohol dehydrogenase+1.1.1.1
118939catalase-1.11.1.6
118939lysine decarboxylase+4.1.1.18
118939ornithine 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
118939-+++-++++-+++++++---

API 50CHac

@refQGLYERYDARALARARIBDXYLLXYLADOMDXGALGLUFRUMNESBERHADULINOMANSORMDMMDGNAGAMYARBESCSALCELMALLACMELSACTREINUMLZRAFAMDGLYGXLTGENTURLYXTAGDFUCLFUCDARLLARLGNT2KG5KG
5345----+++--++++---------------+-+--------------+----
5345----+++--++++--------+/----+--+-+----+/----------+/--+/--+/-

Isolation, sampling and environmental information

isolation

@refsample typecountryorigin.countrycontinent
5345maize silageNetherlandsNLDEurope
67770Maize silageNetherlandsNLDEurope
118939Maize silageNetherlandsNLDEurope

isolation source categories

Cat1Cat2Cat3
#Engineered#Agriculture
#Host#Plants#Herbaceous plants (Grass,Crops)

taxonmaps

  • @ref: 69479
  • File name: preview.99_6846.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_45;96_367;97_831;98_967;99_6846&stattab=map
  • Last taxonomy: Lactobacillaceae
  • 16S sequence: LC311745
  • Sequence Identity:
  • Total samples: 5642
  • soil counts: 317
  • aquatic counts: 383
  • animal counts: 4598
  • plant counts: 344

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
53451Risk group (German classification)
1189391Risk group (French classification)

Sequence information

16S sequences

@refdescriptionaccessionlengthdatabaseNCBI tax ID
5345Lactobacillus sp. JKD6 16S ribosomal RNA gene, complete sequenceAF2647011491ena179838
67770Lactobacillus diolivorans gene for 16S ribosomal RNA, partial sequence, strain: JCM 12183LC3117451511ena179838

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Lactobacillus diolivorans DSM 144211423739.3wgspatric1423739
66792Lactobacillus diolivorans strain NBRC 107869179838.8wgspatric179838
66792Lentilactobacillus diolivorans DSM 144212657245078draftimg1423739
67770Lentilactobacillus diolivorans DSM 14421GCA_001434255scaffoldncbi1423739
67770Lentilactobacillus diolivorans NBRC 107869GCA_007992335contigncbi179838

GC content

@refGC-contentmethod
534539.6high performance liquid chromatography (HPLC)
6777040high performance liquid chromatography (HPLC)

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno100no
motileno93.818no
gram-positiveyes96.658no
anaerobicno88.786no
halophileyes82.873no
spore-formingno91.031no
thermophileno99.492no
glucose-utilyes89.526no
aerobicno91.284no
flagellatedno98.152no
glucose-fermentyes87.499no

External links

@ref: 5345

culture collection no.: DSM 14421, LMG 19667, JCM 12183, CIP 107499, KCTC 13927, NBRC 107869

straininfo link

  • @ref: 76065
  • straininfo: 14634

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny11931178Lactobacillus diolivorans sp. nov., a 1,2-propanediol-degrading bacterium isolated from aerobically stable maize silage.Krooneman J, Faber F, Alderkamp AC, Elferink SJHWO, Driehuis F, Cleenwerck I, Swings J, Gottschal JC, Vancanneyt MInt J Syst Evol Microbiol10.1099/00207713-52-2-63920021-Propanol/analysis, Anaerobiosis, Biodegradation, Environmental, DNA, Bacterial/chemistry, Lactobacillus/*classification/isolation & purification/physiology, Molecular Sequence Data, Nucleic Acid Hybridization, Phylogeny, Propionates/analysis, Propylene Glycol/metabolism, RNA, Ribosomal, 16S/chemistry, Silage/*microbiology, Zea mays/*microbiologyGenetics
Phylogeny23223818Lactobacillus curieae sp. nov., isolated from stinky tofu brine.Lei X, Sun G, Xie J, Wei DInt J Syst Evol Microbiol10.1099/ijs.0.041830-02012Bacterial Typing Techniques, Base Composition, China, DNA, Bacterial/genetics, *Food Microbiology, Genes, Bacterial, Lactobacillus/*classification/genetics/isolation & purification, Molecular Sequence Data, Peptidoglycan/analysis, *Phylogeny, RNA, Ribosomal, 16S/genetics, Salts, Sequence Analysis, DNA, Soy Foods/*microbiologyBiotechnology

Reference

@idauthorscataloguedoi/urltitle
5345Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 14421)https://www.dsmz.de/collection/catalogue/details/culture/DSM-14421
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
33809Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/4941
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
76065Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID14634.1StrainInfo: A central database for resolving microbial strain identifiers
118939Curators of the CIPCollection of Institut Pasteur (CIP 107499)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20107499