Strain identifier

BacDive ID: 24127

Type strain: Yes

Species: Ligilactobacillus pobuzihii

Strain Designation: E100301

Strain history: CIP <- 2011, KCTC

NCBI tax ID(s): 449659 (species)

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

@ref: 20987

BacDive-ID: 24127

DSM-Number: 28122

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

description: Ligilactobacillus pobuzihii E100301 is a microaerophile, mesophilic, Gram-positive bacterium that was isolated from fermented cummingcordia .

NCBI tax id

  • NCBI tax id: 449659
  • Matching level: species

strain history

@refhistory
379692011, KCTC
20987<- NBRC; NBRC 103219 <- Y.-S. Chen, Yamanashi Univerity; RIFY 6501
67770KCTC 13174 <-- Y.-S. Chen E100301.
67771<- Y Chen, Yamanashi Univ., Japan
121918CIP <- 2011, KCTC

doi: 10.13145/bacdive24127.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/bacillota
  • domain: Bacteria
  • phylum: Bacillota
  • class: Bacilli
  • order: Lactobacillales
  • family: Lactobacillaceae
  • genus: Ligilactobacillus
  • species: Ligilactobacillus pobuzihii
  • full scientific name: Ligilactobacillus pobuzihii (Chen et al. 2010) Zheng et al. 2020
  • synonyms

    • @ref: 20215
    • synonym: Lactobacillus pobuzihii

@ref: 20987

domain: Bacteria

phylum: Firmicutes

class: Bacilli

order: Lactobacillales

family: Lactobacillaceae

genus: Ligilactobacillus

species: Ligilactobacillus pobuzihii

full scientific name: Ligilactobacillus pobuzihii (Chen et al. 2010) Zheng et al. 2020

strain designation: E100301

type strain: yes

Morphology

cell morphology

@refgram staincell lengthcell widthcell shapemotility
29607positive2.2-3.9 µm0.5 µmrod-shaped
67771rod-shaped
67771positive
121918positiverod-shapedno

pigmentation

  • @ref: 29607
  • production: yes

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
20987MRS MEDIUM (DSMZ Medium 11)yeshttps://mediadive.dsmz.de/medium/11Name: MRS MEDIUM (DSMZ Medium 11; with strain-specific modifications) Composition: NaCl 50.0 g/l Glucose 20.0 g/l Meat extract 10.0 g/l Casein peptone 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
37969MEDIUM 40- for Lactobacillus and LeuconostocyesDistilled water make up to (1000.000 ml);Man Rogosa Sharp agar (68.000 g)
121918CIP Medium 40yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=40

culture temp

@refgrowthtypetemperaturerange
20987positivegrowth37mesophilic
29607positivegrowth30-37mesophilic
29607positiveoptimum37mesophilic
37969positivegrowth37mesophilic
67770positivegrowth37mesophilic
67771positivegrowth37mesophilic

culture pH

@refabilitytypepH
29607positivegrowth7
29607positiveoptimum7

Physiology and metabolism

oxygen tolerance

@refoxygen tolerance
20987microaerophile
29607facultative anaerobe
67771facultative anaerobe
121918facultative anaerobe

halophily

@refsaltgrowthtested relationconcentration
29607NaClpositivegrowth10 %
29607NaClpositiveoptimum10 %

observation

  • @ref: 29607
  • observation: aggregates in chains

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
29607581435-dehydro-D-gluconate+carbon source
2960722599arabinose+carbon source
2960728757fructose+carbon source
2960717234glucose+carbon source
2960717716lactose+carbon source
2960717306maltose+carbon source
2960726546rhamnose+carbon source
2960733942ribose+carbon source
2960727082trehalose+carbon source
68371Potassium 5-ketogluconate-builds acid from
68371Potassium 2-ketogluconate-builds acid from
6837124265gluconate-builds acid from
6837118403L-arabitol-builds acid from
6837118333D-arabitol-builds acid from
6837118287L-fucose-builds acid from
6837128847D-fucose-builds acid from
6837116443D-tagatose+builds acid from
6837162318D-lyxose-builds acid from
6837132528turanose-builds acid from
6837128066gentiobiose+builds acid from
6837117151xylitol-builds acid from
6837128087glycogen-builds acid from
6837128017starch-builds acid from
6837116634raffinose-builds acid from
683716731melezitose-builds acid from
6837115443inulin-builds acid from
6837127082trehalose+builds acid from
6837117992sucrose-builds acid from
6837128053melibiose-builds acid from
6837117716lactose+builds acid from
6837117306maltose-builds acid from
6837117057cellobiose+builds acid from
6837117814salicin-builds acid from
683714853esculin+builds acid from
6837118305arbutin-builds acid from
6837127613amygdalin-builds acid from
6837159640N-acetylglucosamine+builds acid from
68371320061methyl alpha-D-glucopyranoside-builds acid from
6837143943methyl alpha-D-mannoside-builds acid from
6837117924D-sorbitol-builds acid from
6837116899D-mannitol-builds acid from
6837117268myo-inositol-builds acid from
6837116813galactitol-builds acid from
6837162345L-rhamnose-builds acid from
6837117266L-sorbose-builds acid from
6837116024D-mannose+builds acid from
6837115824D-fructose+builds acid from
6837117634D-glucose+builds acid from
6837112936D-galactose+builds acid from
6837174863methyl beta-D-xylopyranoside-builds acid from
6837115963ribitol-builds acid from
6837165328L-xylose-builds acid from
6837165327D-xylose-builds acid from
6837116988D-ribose+builds acid from
6837130849L-arabinose+builds acid from
6837117108D-arabinose-builds acid from
6837117113erythritol-builds acid from
6837117754glycerol-builds acid from
12191817632nitrate-reduction
12191816301nitrite-reduction

metabolite production

  • @ref: 121918
  • Chebi-ID: 35581
  • metabolite: indole
  • production: no

enzymes

@refvalueactivityec
121918oxidase-
121918catalase-1.11.1.6
121918urease-3.5.1.5
68382alkaline phosphatase-3.1.3.1
68382esterase (C 4)-
68382esterase lipase (C 8)-
68382lipase (C 14)-
68382leucine arylamidase+3.4.11.1
68382valine arylamidase+
68382cystine arylamidase-3.4.11.3
68382trypsin-3.4.21.4
68382alpha-chymotrypsin-3.4.21.1
68382acid phosphatase-3.1.3.2
68382naphthol-AS-BI-phosphohydrolase+
68382alpha-galactosidase-3.2.1.22
68382beta-galactosidase-3.2.1.23
68382beta-glucuronidase-3.2.1.31
68382alpha-glucosidase+3.2.1.20
68382beta-glucosidase-3.2.1.21
68382N-acetyl-beta-glucosaminidase-3.2.1.52
68382alpha-mannosidase-3.2.1.24
68382alpha-fucosidase-3.2.1.51

API zym

@refControlAlkaline phosphataseEsteraseEsterase LipaseLipaseLeucine arylamidaseValine arylamidaseCystine arylamidaseTrypsinalpha- ChymotrypsinAcid phosphataseNaphthol-AS-BI-phosphohydrolasealpha- Galactosidasebeta- Galactosidasebeta- Glucuronidasealpha- Glucosidasebeta- GlucosidaseN-acetyl-beta- glucosaminidasealpha- Mannosidasealpha- Fucosidase
121918-----++----+---+----

API 50CHac

@refQGLYERYDARALARARIBDXYLLXYLADOMDXGALGLUFRUMNESBERHADULINOMANSORMDMMDGNAGAMYARBESCSALCELMALLACMELSACTREINUMLZRAFAMDGLYGXLTGENTURLYXTAGDFUCLFUCDARLLARLGNT2KG5KG
20987----++----++++--------+--+-+-+--+------+--+-------

Isolation, sampling and environmental information

isolation

@refsample typecountryorigin.countrycontinentgeographic location
20987fermented cummingcordia (pobuzihi)TaiwanTWNAsia
67770Fermented cummingcordia (pobuzihi)TaiwanTWNAsia
67771From pobuzih, fermented cummingcordiaTaiwanTWNAsiaTaichung city
121918Food, Fermented cummingcordia, foodTaiwanTWNAsia

isolation source categories

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

taxonmaps

  • @ref: 69479
  • File name: preview.99_7875.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_45;96_937;97_1090;98_1300;99_7875&stattab=map
  • Last taxonomy: Ligilactobacillus pobuzihii
  • 16S sequence: LC521982
  • Sequence Identity:
  • Total samples: 2466
  • soil counts: 81
  • aquatic counts: 41
  • animal counts: 2303
  • plant counts: 41

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
209871Risk group (German classification)
1219181Risk group (French classification)

Sequence information

16S sequences

@refdescriptionaccessionlengthdatabaseNCBI tax ID
20987Lactobacillus pobuzihii gene for 16S rRNA, partial sequence, strain: NBRC 103219AB3263581489ena1242253
67770Lactobacillus pobuzihii JCM 18084 gene for 16S rRNA, partial sequenceLC5219821500ena449659

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Ligilactobacillus pobuzihii NBRC 103219GCA_007991295contigncbi449659
66792Lactobacillus pobuzihii E100301 = KCTC 131741242253.4wgspatric1242253
66792Lactobacillus pobuzihii strain NBRC 103219449659.4wgspatric449659
66792Lactobacillus pobuzihii strain NBRC 103219449659.10wgspatric449659
66792Ligilactobacillus pobuzihii E1003012554235039draftimg1242253
66792Ligilactobacillus pobuzihii NBRC 1032192667528017draftimg449659
66792Ligilactobacillus pobuzihii E1003012700989127draftimg1242253
67770Ligilactobacillus pobuzihii NBRC 103219GCA_001438865scaffoldncbi449659
67771Ligilactobacillus pobuzihii E100301 = KCTC 13174GCA_000349725scaffoldncbi1242253
67771Ligilactobacillus pobuzihii E100301 = KCTC 13174GCA_001433815contigncbi1242253

GC content

@refGC-contentmethod
2098737.2
6777037.7genome sequence analysis
6777137.2high performance liquid chromatography (HPLC)

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
motileno93.882no
gram-positiveyes96.858no
anaerobicno90.807yes
aerobicno95.934no
halophileyes95.166no
spore-formingno95.639no
glucose-utilyes91.656yes
flagellatedno97.789no
thermophileno99.518yes
glucose-fermentyes90.299no

External links

@ref: 20987

culture collection no.: DSM 28122, KCTC 13174, NBRC 103219, RIFY 6501, JCM 18084, CIP 110289

straininfo link

  • @ref: 88086
  • straininfo: 370396

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny19783610Lactobacillus pobuzihii sp. nov., isolated from pobuzihi (fermented cummingcordia).Chen YS, Miyashita M, Suzuki KI, Sato H, Hsu JS, Yanagida FInt J Syst Evol Microbiol10.1099/ijs.0.016873-02009Carbohydrate Metabolism, Cordia/metabolism/*microbiology, DNA, Bacterial/genetics, DNA, Ribosomal/genetics, Fermentation, Lactobacillus/*classification/genetics/*isolation & purification/metabolism, Molecular Sequence Data, Phylogeny, RNA, Ribosomal, 16S/geneticsMetabolism
Genetics23661478Draft Genome Sequence of Lactobacillus pobuzihii E100301T.Chiu CM, Chang CH, Pan SF, Wu HC, Li SW, Chang CH, Lee YS, Chiang CM, Chen YSGenome Announc10.1128/genomeA.00185-132013
Phylogeny30628884Lactobacillus salitolerans sp. nov., a novel lactic acid bacterium isolated from spent mushroom substrates.Tohno M, Tanizawa Y, Kojima Y, Sakamoto M, Nakamura Y, Ohkuma M, Kobayashi HInt J Syst Evol Microbiol10.1099/ijsem.0.0032242019*Agaricales, Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, Fatty Acids/chemistry, Japan, Lactobacillus/*classification/isolation & purification, Multilocus Sequence Typing, *Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNATranscriptome

Reference

@idauthorstitledoi/urlcatalogueID_cross_referencepubmed
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
20987Curators of the DSMZhttps://www.dsmz.de/collection/catalogue/details/culture/DSM-28122Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 28122)
29607Barberan A, Caceres Velazquez H, Jones S, Fierer N.Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information10.1128/mSphere.00237-172599728776041
37969Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/8132
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
67770Curators of the JCMhttps://jcm.brc.riken.jp/en/
67771Curators of the KCTChttps://kctc.kribb.re.kr/En/Kctc
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.MicrobeAtlas 1.0 betahttps://microbeatlas.org/
88086Reimer, 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-ID370396.1
121918Curators of the CIPhttps://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20110289Collection of Institut Pasteur (CIP 110289)