Strain identifier

BacDive ID: 6702

Type strain: Yes

Species: Lentilactobacillus senioris

Strain history: K. Oki YIT 12364.

NCBI tax ID(s): 931534 (species)

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General

@ref: 17627

BacDive-ID: 6702

DSM-Number: 24302

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

description: Lentilactobacillus senioris DSM 24302 is a microaerophile, mesophilic, Gram-positive bacterium that was isolated from feces of a healthy 100-year-old Japanese female.

NCBI tax id

  • NCBI tax id: 931534
  • Matching level: species

strain history

@refhistory
17627<- K. Oki, Yakult Central Inst. Microbiol. Res., Kunitachi, Japan; YIT 12364 <- K. Watanabe
67770K. Oki YIT 12364.

doi: 10.13145/bacdive6702.20250331.9.3

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 senioris
  • full scientific name: Lentilactobacillus senioris (Oki et al. 2012) Zheng et al. 2020

  • synonyms

    • @ref: 20215
    • synonym: Lactobacillus senioris

@ref: 17627

domain: Bacteria

phylum: Firmicutes

class: Bacilli

order: Lactobacillales

family: Lactobacillaceae

genus: Lentilactobacillus

species: Lentilactobacillus senioris

full scientific name: Lentilactobacillus senioris (Oki et al. 2012) Zheng et al. 2020

type strain: yes

Morphology

cell morphology

@refgram staincell lengthcell widthcell shapemotilityconfidence
30248positive01-10 µm0.7 µmrod-shapedno
125438no90.5
125438positive93.683

pigmentation

  • @ref: 30248
  • production: yes

Culture and growth conditions

culture medium

  • @ref: 17627
  • 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

@refgrowthtypetemperature
17627positivegrowth37
67770positivegrowth37

Physiology and metabolism

oxygen tolerance

@refoxygen toleranceconfidence
17627microaerophile
30248facultative anaerobe
125439obligate aerobe99.5

spore formation

@refspore formationconfidence
30248no
125438no91.953

murein

  • @ref: 17627
  • murein short key: A11.31
  • type: A4alpha L-Lys-D-Asp

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
3024828757fructose+carbon source
3024824265gluconate+carbon source
30248506227N-acetylglucosamine+carbon source
68371Potassium 5-ketogluconate-builds acid from
68371320061methyl alpha-D-glucopyranoside-builds acid from
68371Potassium 2-ketogluconate-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
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
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

API 50CHac

@refQGLYERYDARALARARIBDXYLLXYLADOMDXGALGLUFRUMNESBERHADULINOMANSORMDMMDGNAGAMYARBESCSALCELMALLACMELSACTREINUMLZRAFAMDGLYGXLTGENTURLYXTAGDFUCLFUCDARLLARLGNT2KG5KG
17627----+++----+++/---------+/-------------------------+/---

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinent
17627feces of a healthy 100-year-old Japanese femaleOkinawaJapanJPNAsia
67770Feces of a 100-year-old Japanese

isolation source categories

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

taxonmaps

  • @ref: 69479
  • File name: preview.99_7636.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_45;96_367;97_414;98_5590;99_7636&stattab=map
  • Last taxonomy: Lentilactobacillus senioris subclade
  • 16S sequence: LC519995
  • Sequence Identity:
  • Total samples: 904
  • soil counts: 17
  • aquatic counts: 115
  • animal counts: 717
  • plant counts: 55

Safety information

risk assessment

  • @ref: 17627
  • biosafety level: 1
  • biosafety level comment: Risk group (German classification)

Sequence information

16S sequences

@refdescriptionaccessionlengthdatabaseNCBI tax ID
17627Lactobacillus senioris gene for 16S rRNA, partial sequenceAB6025701562nuccore1423802
67770Lactobacillus senioris JCM 17472 gene for 16S rRNA, partial sequenceLC5199951501nuccore931534

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Lactobacillus senioris DSM 24302 = JCM 174721423802.4wgspatric1423802
66792Lactobacillus senioris DSM 24302 = JCM 174721423802.3wgspatric1423802
66792Lentilactobacillus senioris JCM 174722728369707draftimg1423802
66792Lentilactobacillus senioris DSM 243022660237942draftimg1423802
67770Lentilactobacillus senioris DSM 24302 = JCM 17472GCA_001436555scaffoldncbi1423802
67770Lentilactobacillus senioris DSM 24302 = JCM 17472GCA_001312065contigncbi1423802

GC content

@refGC-contentmethod
1762737.9high performance liquid chromatography (HPLC)
3024839.8
6777039.9genome sequence analysis

Genome-based predictions

predictions

@refmodeltraitdescriptionpredictionconfidencetraining_data
125438gram-positivegram-positivePositive reaction to Gram-stainingyes93.683yes
125438anaerobicanaerobicAbility to grow under anoxygenic conditions (including facultative anaerobes)no85.84yes
125438spore-formingspore-formingAbility to form endo- or exosporesno91.953yes
125438aerobicaerobicAbility to grow under oxygenic conditions (including facultative aerobes)no96.665yes
125438thermophilethermophilicAbility to grow at temperatures above or equal to 45°Cno95.5yes
125438motile2+flagellatedAbility to perform flagellated movementno90.5yes
125439BacteriaNetspore_formationAbility to form endo- or exosporesyes62.8
125439BacteriaNetmotilityAbility to perform movementyes70
125439BacteriaNetgram_stainReaction to gram-stainingpositive73.5
125439BacteriaNetoxygen_toleranceOxygenic conditions needed for growthobligate aerobe99.5

External links

@ref: 17627

culture collection no.: DSM 24302, JCM 17472, YIT 12364

straininfo link

  • @ref: 76176
  • straininfo: 405210

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny21515698Lactobacillus saniviri sp. nov. and Lactobacillus senioris sp. nov., isolated from human faeces.Oki K, Kudo Y, Watanabe KInt J Syst Evol Microbiol10.1099/ijs.0.031658-02011Aerobiosis, Anaerobiosis, Bacterial Typing Techniques, Base Composition, Catalase/metabolism, Cluster Analysis, DNA, Bacterial/chemistry/genetics, DNA, Ribosomal/chemistry/genetics, DNA-Directed RNA Polymerases/genetics, Feces/*microbiology, Humans, Lactobacillus/*classification/genetics/*isolation & purification/physiology, Locomotion, Molecular Sequence Data, Phenylalanine-tRNA Ligase/genetics, Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNAPathogenicity
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
Phylogeny33174826Lentilactobacillus kribbianus sp. nov., isolated from the small intestine of a mini pig.Bai L, Paek J, Shin Y, Park HY, Chang YHInt J Syst Evol Microbiol10.1099/ijsem.0.0045602020Animals, Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, Fatty Acids/chemistry, Intestine, Small/*microbiology, Lactobacillaceae/*classification/isolation & purification, Nucleic Acid Hybridization, *Phylogeny, RNA, Ribosomal, 16S/genetics, Republic of Korea, Sequence Analysis, DNA, Swine, Swine, Miniature/*microbiologyTranscriptome
Phylogeny35576246Lentilactobacillus laojiaonis sp. nov., isolated from the mud in a fermentation cellar for the production of Chinese liquor.Zhao Q, Yang S, Bao G, Wang W, Miao L, Wang S, Shen C, Li YInt J Syst Evol Microbiol10.1099/ijsem.0.0053492022Bacterial Typing Techniques, Base Composition, China, DNA, Bacterial/genetics, Ethanol, *Fatty Acids/chemistry, Fermentation, Humans, *Lactobacillaceae, Phospholipids/chemistry, Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNAPathogenicity

Reference

@idauthorscataloguedoi/urltitleID_cross_referencepubmedjournal
17627Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 24302)https://www.dsmz.de/collection/catalogue/details/culture/DSM-24302
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
30248Barberan A, Caceres Velazquez H, Jones S, Fierer N.10.1128/mSphere.00237-17Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information2659028776041
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 updates33211880Nucleic Acids Res. 49: D498-D508 2020
67770Curators of the JCMhttps://jcm.brc.riken.jp/en/
68371Automatically annotated from API 50CH acid
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
76176Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID405210.1StrainInfo: A central database for resolving microbial strain identifiers
125438Julia Koblitz, Lorenz Christian Reimer, Rüdiger Pukall, Jörg Overmann10.1101/2024.08.12.607695Predicting bacterial phenotypic traits through improved machine learning using high-quality, curated datasets
125439Philipp Münch, René Mreches, Martin Binder, Hüseyin Anil Gündüz, Xiao-Yin To, Alice McHardyhttps://github.com/GenomeNet/deepGdeepG: Deep Learning for Genome Sequence Data. R package version 0.3.1