Strain identifier

BacDive ID: 159797

Type strain: Yes

Species: Lactobacillus paragasseri

Strain Designation: 5

Strain history: ATCC 4963 (Lactobacillus sp.) <-- L. F. Rettger 5 ("Lactobacillus bifidus").

NCBI tax ID(s): 2107999 (species)

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General

@ref: 66734

BacDive-ID: 159797

keywords: genome sequence, 16S sequence, Bacteria, facultative anaerobe, Gram-positive, rod-shaped, colony-forming

description: Lactobacillus paragasseri 5 is a facultative anaerobe, Gram-positive, rod-shaped bacterium that forms circular colonies and was isolated from human faeces.

NCBI tax id

  • NCBI tax id: 2107999
  • Matching level: species

strain history

@refhistory
67771<- JCM <- ATCC 4963, `Lactobacillus` sp. <- LF Rettger, 5, `"Lactobacillus bifidus"`
67770ATCC 4963 (Lactobacillus sp.) <-- L. F. Rettger 5 ("Lactobacillus bifidus").

doi: 10.13145/bacdive159797.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/bacillota
  • domain: Bacteria
  • phylum: Bacillota
  • class: Bacilli
  • order: Lactobacillales
  • family: Lactobacillaceae
  • genus: Lactobacillus
  • species: Lactobacillus paragasseri
  • full scientific name: Lactobacillus paragasseri Tanizawa et al. 2018

@ref: 66734

domain: Bacteria

phylum: Firmicutes

class: Bacilli

order: Lactobacillales

family: Lactobacillaceae

genus: Lactobacillus

species: Lactobacillus paragasseri

strain designation: 5

type strain: yes

Morphology

cell morphology

@refgram staincell lengthcell widthcell shapemotility
66734positive1.5-5.0 µm0.5 µmrod-shapedno
67771rod-shapedno
67771positive

colony morphology

  • @ref: 66734
  • colony size: 1-2 mm
  • colony color: grey-white
  • colony shape: circular
  • incubation period: 3 days
  • medium used: MRS agar

Culture and growth conditions

culture medium

  • @ref: 66734
  • name: MRS agar
  • growth: yes

culture temp

@refgrowthtypetemperaturerange
66734positivegrowth25-45
67770positivegrowth37mesophilic
67771positivegrowth37mesophilic

culture pH

  • @ref: 66734
  • ability: positive
  • type: growth
  • pH: 4-8.5
  • PH range: alkaliphile

Physiology and metabolism

oxygen tolerance

@refoxygen tolerance
66734facultative anaerobe
67771facultative anaerobe

spore formation

@refspore formation
66734no
67771no

halophily

@refsaltgrowthtested relationconcentration
66734NaClpositivegrowth2 %(w/v)
66734NaClnogrowth4.5 %(w/v)

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
667346731melezitose-builds acid from
6673415443inulin-builds acid from
6673415963ribitol-builds acid from
6673416634raffinose-builds acid from
6673416813galactitol-builds acid from
6673416899D-mannitol-builds acid from
6673416988D-ribose-builds acid from
6673417113erythritol-builds acid from
6673417151xylitol-builds acid from
6673417266L-sorbose-builds acid from
6673417268myo-inositol-builds acid from
6673417754glycerol-builds acid from
6673417924D-sorbitol-builds acid from
6673418222xylose-builds acid from
6673418287L-fucose-builds acid from
6673422599arabinose-builds acid from
6673422605arabinitol-builds acid from
6673424265gluconate-builds acid from
6673428053melibiose-builds acid from
6673428087glycogen-builds acid from
6673428847D-fucose-builds acid from
6673462318D-lyxose-builds acid from
6673462345L-rhamnose-builds acid from
6673474863methyl beta-D-xylopyranoside-builds acid from
667344853esculin+builds acid from
6673412936D-galactose+builds acid from
6673415824D-fructose+builds acid from
6673416024D-mannose+builds acid from
6673416443D-tagatose+builds acid from
6673417057cellobiose+builds acid from
6673417306maltose+builds acid from
6673417634D-glucose+builds acid from
6673417716lactose+builds acid from
6673417814salicin+builds acid from
6673417992sucrose+builds acid from
6673418305arbutin+builds acid from
6673427082trehalose+builds acid from
6673427613amygdalin+builds acid from
6673428017starch+builds acid from
6673428066gentiobiose+builds acid from
6673459640N-acetylglucosamine+builds acid from
66734320061methyl alpha-D-glucopyranoside+builds acid from
66734esculin ferric citrate+builds acid from
6673432528turanose+/-builds acid from
6673417234glucose-builds gas from
667344853esculin+hydrolysis

enzymes

@refvalueactivityec
66734alkaline phosphatase-3.1.3.1
66734alpha-fucosidase-3.2.1.51
66734alpha-mannosidase-3.2.1.24
66734catalase-1.11.1.6
66734chymotrypsin-3.4.4.5
66734lipase (C 14)-
66734trypsin-3.4.21.4
66734acid phosphatase+3.1.3.2
66734beta-glucosidase+3.2.1.21
66734cystine aminopeptidase+3.4.11.3
66734esterase (C 4)+
66734leucine aminopeptidase+3.4.1.1
66734N-acetyl-beta-glucosaminidase+3.2.1.52
66734naphthol-AS-BI-phosphohydrolase+
66734valine aminopeptidase+

Isolation, sampling and environmental information

isolation

@refsample typesampling datecountryorigin.countrycontinentenrichment cultureenrichment culture temperatureisolation procedure
66734human faeces1934JapanJPNAsiade Man, Rogosa and Sharpe medium (MRS; Difco)37were obtained from the Japanese Collection of Microorganisms (JCM)/enrichment under anaerobic conditions
67771From human faeces

isolation source categories

Cat1Cat2Cat3
#Host#Human
#Host Body Product#Gastrointestinal tract#Feces (Stool)

taxonmaps

  • @ref: 69479
  • File name: preview.99_840.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_46;96_506;97_581;98_668;99_840&stattab=map
  • Last taxonomy: Lactobacillus
  • 16S sequence: LC374363
  • Sequence Identity:
  • Total samples: 185237
  • soil counts: 4782
  • aquatic counts: 5652
  • animal counts: 173268
  • plant counts: 1535

Sequence information

16S sequences

  • @ref: 67770
  • description: Lactobacillus paragasseri gene for 16S ribosomal RNA, partial sequence
  • accession: LC374363
  • length: 1495
  • database: ena
  • NCBI tax ID: 2107999

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Lactobacillus paragasseri JCM 5343GCA_003584685completencbi2107999
66792Lactobacillus gasseri strain JCM 53431596.87wgspatric1596
66792Lactobacillus paragasseri strain JCM 53432107999.3completepatric2107999
66792Lactobacillus gasseri JCM 53432916510943completeimg2107999
67770Lactobacillus paragasseri JCM 5343GCA_003307275contigncbi2107999
66792Lactobacillus paragasseri LMG 11478GCA_029823055contigncbi2107999

GC content

@refGC-contentmethod
6777134.9genome sequence analysis
6777134.0thermal denaturation, midpoint method (Tm)
6777034thermal denaturation, midpoint method (Tm)

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
motileno96.336no
flagellatedno97.922yes
gram-positiveyes96.206no
anaerobicno59.926no
aerobicno97.599yes
halophileyes87.849no
spore-formingno95.739no
thermophileno99.249yes
glucose-utilyes93.831no
glucose-fermentyes90.677no

External links

@ref: 66734

culture collection no.: ATCC 4963, LMG 11478, NCFB 1375, KCTC 3172, NCIMB 8931, VPI 0334, JCM 5343

straininfo link

  • @ref: 112171
  • straininfo: 3300

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny30226464Lactobacillus paragasseri sp. nov., a sister taxon of Lactobacillus gasseri, based on whole-genome sequence analyses.Tanizawa Y, Tada I, Kobayashi H, Endo A, Maeno S, Toyoda A, Arita M, Nakamura Y, Sakamoto M, Ohkuma M, Tohno MInt J Syst Evol Microbiol10.1099/ijsem.0.0030202018Bacterial Typing Techniques, DNA, Bacterial/genetics, DNA-Directed RNA Polymerases/genetics, Fatty Acids/chemistry, *Genome, Bacterial, Lactobacillus/*classification/genetics, Lactobacillus gasseri, Nucleic Acid Hybridization, *Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNAGenetics
Phylogeny35250928Isolation of a Highly Thermostable Bile Salt Hydrolase With Broad Substrate Specificity From Lactobacillus paragasseri.Kusada H, Arita M, Tohno M, Tamaki HFront Microbiol10.3389/fmicb.2022.8108722022
Pathogenicity35733973Bile Salt Hydrolase Degrades beta-Lactam Antibiotics and Confers Antibiotic Resistance on Lactobacillus paragasseri.Kusada H, Arita M, Tohno M, Tamaki HFront Microbiol10.3389/fmicb.2022.8582632022

Reference

@idauthorstitledoi/urljournalpubmed
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
66734Yasuhiro Tanizawa, Ipputa Tada, Hisami Kobayashi, Akihito Endo, Shintaro Maeno, Atsushi Toyoda, Masanori Arita, Yasukazu Nakamura, Mitsuo Sakamoto, Moriya Ohkuma and Masanori TohnoLactobacillus paragasseri sp. nov., a sister taxon of Lactobacillus gasseri, based on whole-genome sequence analyses10.1099/ijsem.0.003020IJSEM 68: 3512-3517 201830226464
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
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/
112171Reimer, 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-ID3300.1