Strain identifier

BacDive ID: 6534

Type strain: Yes

Species: Lapidilactobacillus dextrinicus

Strain Designation: L95

Strain history: CIP <- 1990, DSM, Pediococcus dextrinicus <- NCDO <- E. Coster, Pediococcus cerevisiae subsp. dextrinicus <- H.L. Günter: strain L95

NCBI tax ID(s): 1423738 (strain), 51664 (species)

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General

@ref: 8726

BacDive-ID: 6534

DSM-Number: 20335

keywords: genome sequence, 16S sequence, Bacteria, microaerophile, mesophilic, Gram-positive, coccus-shaped

description: Lapidilactobacillus dextrinicus L95 is a microaerophile, mesophilic, Gram-positive bacterium that was isolated from silage.

NCBI tax id

NCBI tax idMatching level
1423738strain
51664species

strain history

@refhistory
8726<- NCDO <- E. Coster (Pediococcus cerevisiae var. dextrinicus) <- H.L. Günther, L95
67770ATCC 33087 <-- W. Back <-- NCDO 1561 <-- E. Coster ("Pediococcus cerevisiae subsp. dextrinicus") <-- H. L. Günther L 95.
118926CIP <- 1990, DSM, Pediococcus dextrinicus <- NCDO <- E. Coster, Pediococcus cerevisiae subsp. dextrinicus <- H.L. Günter: strain L95

doi: 10.13145/bacdive6534.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/bacillota
  • domain: Bacteria
  • phylum: Bacillota
  • class: Bacilli
  • order: Lactobacillales
  • family: Lactobacillaceae
  • genus: Lapidilactobacillus
  • species: Lapidilactobacillus dextrinicus
  • full scientific name: Lapidilactobacillus dextrinicus (Coster and White 1964) Zheng et al. 2020

  • synonyms

    @refsynonym
    20215Lactobacillus dextrinicus
    20215Pediococcus dextrinicus

@ref: 8726

domain: Bacteria

phylum: Firmicutes

class: Bacilli

order: Lactobacillales

family: Lactobacillaceae

genus: Lapidilactobacillus

species: Lapidilactobacillus dextrinicus

full scientific name: Lapidilactobacillus dextrinicus (Coster and White 1964) Zheng et al. 2020

strain designation: L95

type strain: yes

Morphology

cell morphology

  • @ref: 118926
  • gram stain: positive
  • cell shape: coccus-shaped
  • motility: no

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
8726MRS 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
40629MEDIUM 40- for Lactobacillus and LeuconostocyesDistilled water make up to (1000.000 ml);Man Rogosa Sharp agar (68.000 g)
118926CIP Medium 41yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=41
118926CIP Medium 40yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=40

culture temp

@refgrowthtypetemperaturerange
8726positivegrowth30mesophilic
40629positivegrowth30mesophilic
46907positivegrowth25-35mesophilic
67770positivegrowth26mesophilic
118926positivegrowth15-37
118926nogrowth45thermophilic

Physiology and metabolism

oxygen tolerance

@refoxygen tolerance
46907microaerophile
118926facultative anaerobe

murein

  • @ref: 8726
  • murein short key: A11.31
  • type: A4alpha L-Lys-D-Asp

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
68371melibiose-builds acid from28053
68371esculin+builds acid from4853
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-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
118926nitrate-reduction17632
118926nitrite-reduction16301
118926nitrate+respiration17632

metabolite tests

  • @ref: 118926
  • 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
118926oxidase-
118926alcohol dehydrogenase-1.1.1.1
118926catalase-1.11.1.6
118926lysine decarboxylase-4.1.1.18
118926ornithine 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
118926-+---+----++---+++--

API 50CHac

@refQGLYERYDARALARARIBDXYLLXYLADOMDXGALGLUFRUMNESBERHADULINOMANSORMDMMDGNAGAMYARBESCSALCELMALLACMELSACTREINUMLZRAFAMDGLYGXLTGENTURLYXTAGDFUCLFUCDARLLARLGNT2KG5KG
8726-----------+++-------+/-++-+-----++---+--+-------+--
118926----------+++/---------++/-++++++/--+/-+---+--+-------+--

Isolation, sampling and environmental information

isolation

@refsample type
8726silage
46907Silage
67770Silage
118926Other, Silage

isolation source categories

Cat1Cat2Cat3
#Engineered#Food production#Animal feed
#Engineered#Biodegradation#Composting
#Host#Plants#Herbaceous plants (Grass,Crops)

taxonmaps

  • @ref: 69479
  • File name: preview.99_8167.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_45;96_1782;97_2132;98_5943;99_8167&stattab=map
  • Last taxonomy: Lapidilactobacillus
  • 16S sequence: LC071836
  • Sequence Identity:
  • Total samples: 4384
  • soil counts: 578
  • aquatic counts: 506
  • animal counts: 3156
  • plant counts: 144

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
87261Risk group (German classification)
1189261Risk group (French classification)

Sequence information

16S sequences

@refdescriptionaccessionlengthdatabaseNCBI tax ID
20218Pediococcus dextrinicus clone P17 16S ribosomal RNA gene, partial sequenceAF404726548ena51664
20218Pediococcus dextrinicus clone P17 16S ribosomal RNA gene, partial sequence; 16S-23S ribosomal RNA intergenic spacer, complete sequence; and 23S ribosomal RNA gene, partial sequenceAF405370546ena51664
8726Lactobacillus dextrinicus gene for 16S rRNA, partial sequenceD876791464ena51664
67770Lactobacillus dextrinicus gene for 16S ribosomal RNA, partial sequence, strain: JCM 5887LC0718361470ena51664

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Lactobacillus dextrinicus DSM 203351423738.3wgspatric1423738
66792Lactobacillus dextrinicus DSM 203352663762931draftimg1423738
67770Lapidilactobacillus dextrinicus DSM 20335GCA_001436095scaffoldncbi1423738

GC content

@refGC-contentmethod
872640.6
6777038.5thermal denaturation, midpoint method (Tm)
6777038.1genome sequence analysis

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
motileno94.958no
gram-positiveyes95.19no
anaerobicno92.431no
halophileyes92.804no
spore-formingno95.127no
thermophileno99.295yes
glucose-utilyes90.464no
aerobicno98.474yes
flagellatedno98.36no
glucose-fermentyes80.858no

External links

@ref: 8726

culture collection no.: DSM 20335, ATCC 33087, CIP 103407, JCM 5887, LMG 11485, NCDO 1561, CCUG 18834, CCM 3457, BCRC 12842, CECT 4791, CGMCC 1.2693, KCTC 3506, LMG 10649, NCIMB 701561, VKM B-1603, VTT E-93494

straininfo link

  • @ref: 76006
  • straininfo: 3819

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny16166732Lactobacillus concavus sp. nov., isolated from the walls of a distilled spirit fermenting cellar in China.Tong H, Dong XInt J Syst Evol Microbiol10.1099/ijs.0.63509-02005Base Composition, China, DNA, Bacterial/analysis, DNA, Ribosomal/analysis, Fermentation, Genes, rRNA, Genotype, Geologic Sediments/*microbiology, Lactic Acid/*metabolism, Lactobacillus/classification/genetics/isolation & purification, Molecular Sequence Data, Nucleic Acid Hybridization, Phenotype, Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Wine/*microbiologyGenetics
Phylogeny19244449Reclassification of Pediococcus dextrinicus (Coster and White 1964) back 1978 (Approved Lists 1980) as Lactobacillus dextrinicus comb. nov., and emended description of the genus Lactobacillus.Haakensen M, Dobson CM, Hill JE, Ziola BInt J Syst Evol Microbiol10.1099/ijs.0.65779-02009Bacterial Proteins/*genetics, Bacterial Typing Techniques, DNA, Bacterial/analysis, Genes, rRNA, Lactobacillus/*classification/genetics, Molecular Sequence Data, Pediococcus/*classification/genetics, Phylogeny, RNA, Ribosomal, 16S/*genetics, *Sequence Analysis, DNA, Species Specificity, *Terminology as TopicGenetics

Reference

@idauthorscataloguedoi/urltitlejournalpubmed
8726Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 20335)https://www.dsmz.de/collection/catalogue/details/culture/DSM-20335
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
40629Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/15202
46907Curators of the CCUGCulture Collection University of Gothenburg (CCUG) (CCUG 18834)https://www.ccug.se/strain?id=18834
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)
66794Antje Chang, Lisa Jeske, Sandra Ulbrich, Julia Hofmann, Julia Koblitz, Ida Schomburg, Meina Neumann-Schaal, Dieter Jahn, Dietmar Schomburg10.1093/nar/gkaa1025BRENDA, the ELIXIR core data resource in 2021: new developments and updatesNucleic Acids Res. 49: D498-D508 202033211880
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
76006Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID3819.1StrainInfo: A central database for resolving microbial strain identifiers
118926Curators of the CIPCollection of Institut Pasteur (CIP 103407)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20103407