Strain identifier

BacDive ID: 131552

Type strain: Yes

Species: Lactiplantibacillus herbarum

Strain Designation: TCF032-E4

Strain history: <- Y. Mao, DuPont Nutrition and Health, Shanghai, China; TCF032-E4

NCBI tax ID(s): 1670446 (species)

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General

@ref: 22779

BacDive-ID: 131552

DSM-Number: 100358

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

description: Lactiplantibacillus herbarum TCF032-E4 is an anaerobe, mesophilic bacterium that was isolated from traditional Chinese fermented radish.

NCBI tax id

  • NCBI tax id: 1670446
  • Matching level: species

strain history

  • @ref: 22779
  • history: <- Y. Mao, DuPont Nutrition and Health, Shanghai, China; TCF032-E4

doi: 10.13145/bacdive131552.20230509.8.1

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 herbarum
  • full scientific name: Lactiplantibacillus herbarum (Mao et al. 2015) Zheng et al. 2020

  • synonyms

    • @ref: 20215
    • synonym: Lactobacillus herbarum

@ref: 22779

domain: Bacteria

phylum: Firmicutes

class: Bacilli

order: Lactobacillales

family: Lactobacillaceae

genus: Lactiplantibacillus

species: Lactiplantibacillus herbarum

full scientific name: Lactiplantibacillus herbarum (Mao et al. 2015) Zheng et al. 2020

strain designation: TCF032-E4

type strain: yes

Morphology

cell morphology

@refmotilityconfidencegram stain
69480no95.547
69480100positive

Culture and growth conditions

culture medium

  • @ref: 22779
  • name: MRS MEDIUM (DSMZ Medium 11)
  • growth: yes
  • link: https://mediadive.dsmz.de/medium/11
  • composition: Name: 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

culture temp

  • @ref: 22779
  • growth: positive
  • type: growth
  • temperature: 30
  • range: mesophilic

Physiology and metabolism

oxygen tolerance

@refoxygen tolerance
22779anaerobe
22779microaerophile

spore formation

@refspore formationconfidence
69481no100
69480no99.999

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
68380urea-hydrolysis16199
68380arginine-hydrolysis29016
68380D-mannose+fermentation16024
68380raffinose+fermentation16634
68380L-glutamate-degradation29985
68380nitrate+reduction17632
68380tryptophan-energy source27897

metabolite production

  • @ref: 68380
  • Chebi-ID: 35581
  • metabolite: indole
  • production: no

metabolite tests

  • @ref: 68380
  • Chebi-ID: 35581
  • metabolite: indole
  • indole test: -

enzymes

@refvalueactivityec
68380serine arylamidase-
68380glutamyl-glutamate arylamidase-
68380histidine arylamidase-
68380glycin arylamidase-
68380alanine arylamidase-3.4.11.2
68380tyrosine arylamidase+
68380pyrrolidonyl arylamidase-3.4.19.3
68380leucine arylamidase+3.4.11.1
68380phenylalanine arylamidase+
68380leucyl glycin arylamidase-3.4.11.1
68380proline-arylamidase+3.4.11.5
68380alkaline phosphatase-3.1.3.1
68380tryptophan deaminase-4.1.99.1
68380alpha-fucosidase-3.2.1.51
68380glutamate decarboxylase-4.1.1.15
68380N-acetyl-beta-glucosaminidase-3.2.1.52
68380beta-glucuronidase-3.2.1.31
68380alpha-arabinosidase-3.2.1.55
68380beta-glucosidase+3.2.1.21
68380alpha-glucosidase+3.2.1.20
68380beta-Galactosidase 6-phosphate-
68380beta-galactosidase+3.2.1.23
68380alpha-galactosidase+3.2.1.22
68380arginine dihydrolase-3.5.3.6
68380urease-3.5.1.5

API 50CHac

@refQGLYERYDARALARARIBDXYLLXYLADOMDXGALGLUFRUMNESBERHADULINOMANSORMDMMDGNAGAMYARBESCSALCELMALLACMELSACTREINUMLZRAFAMDGLYGXLTGENTURLYXTAGDFUCLFUCDARLLARLGNT2KG5KG
22779-----+----++++----+---+++++++++-+------+----------

API rID32A

@refUREADH Argalpha GALbeta GALbeta GPalpha GLUbeta GLUalpha ARAbeta GURbeta NAGMNERAFGDCalpha FUCNITINDPALArgAProALGAPheALeuAPyrATyrAAlaAGlyAHisAGGASerA
22779--++-++---++--+--+/-+-++-+-----

Isolation, sampling and environmental information

isolation

  • @ref: 22779
  • sample type: traditional Chinese fermented radish
  • geographic location: Guilin, Guangxi province
  • country: China
  • origin.country: CHN
  • continent: Asia

isolation source categories

Cat1Cat2Cat3
#Engineered#Food production#Vegetable (incl. Grains)
#Engineered#Food production#Fermented

Safety information

risk assessment

  • @ref: 22779
  • biosafety level: 1
  • biosafety level comment: Risk group (German classification)

Sequence information

16S sequences

  • @ref: 22779
  • description: Lactobacillus herbarum strain TCF032-E4 16S ribosomal RNA gene, partial sequence
  • accession: KR706503
  • length: 1372
  • database: ena
  • NCBI tax ID: 1670446

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Lactiplantibacillus herbarum TCF032-E4GCA_001039045scaffoldncbi1670446
66792Lactiplantibacillus herbarum TCF032-E42630968393draftimg1670446

GC content

  • @ref: 22779
  • GC-content: 43.5
  • method: sequence analysis

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno100no
motileno94.136no
flagellatedno97.354no
gram-positiveyes95.844no
anaerobicno89.803no
aerobicno98.23yes
halophileyes88.293no
spore-formingno95.31no
glucose-utilyes91.671no
thermophileno99.908yes
glucose-fermentyes86.617no

External links

@ref: 22779

culture collection no.: DSM 100358, CCTCC AB 2015090

straininfo link

  • @ref: 89966
  • straininfo: 405953

literature

  • topic: Phylogeny
  • Pubmed-ID: 26410554
  • title: Lactobacillus herbarum sp. nov., a species related to Lactobacillus plantarum.
  • authors: Mao Y, Chen M, Horvath P
  • journal: Int J Syst Evol Microbiol
  • DOI: 10.1099/ijsem.0.000636
  • year: 2015
  • mesh: Bacterial Typing Techniques, Base Composition, China, DNA, Bacterial/genetics, Fermentation, *Food Microbiology, Genes, Bacterial, Lactobacillus/*classification/genetics/isolation & purification, Molecular Sequence Data, *Phylogeny, RNA, Ribosomal, 16S/genetics, Raphanus/*microbiology, Sequence Analysis, DNA
  • topic2: Biotechnology

Reference

@idauthorstitledoi/urlcatalogue
20215Parte, A.C., Sardà Carbasse, J., Meier-Kolthoff, J.P., Reimer, L.C. and Göker, M.List of Prokaryotic names with Standing in Nomenclature (LPSN) moves to the DSMZ10.1099/ijsem.0.004332
22779Curators of the DSMZhttps://www.dsmz.de/collection/catalogue/details/culture/DSM-100358Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 100358)
66792Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg OvermannAutomatically annotated for the DiASPora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information)https://diaspora-project.de/progress.html#genomes
68371Automatically annotated from API 50CH acid
68380Automatically annotated from API rID32A
69480Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg OvermannPredictions based on genome sequence made in the Diaspora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information)https://diaspora-project.de/progress.html#genomes
69481Xiao-Yin To, René Mreches, Martin Binder, Alice C. McHardy, Philipp C. MünchPredictions based on the model GenomeNet Sporulation v. 110.21203/rs.3.rs-2527258/v1
89966Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.StrainInfo: A central database for resolving microbial strain identifiers10.60712/SI-ID405953.1