Strain identifier

BacDive ID: 6562

Type strain: Yes

Species: Limosilactobacillus pontis

Strain history: CIP <- 1994, P. Stolz, Inst. für Lebensmitteltechnol., Germany: strain LTH 2587 <- Hohenheim Univ., Germany

NCBI tax ID(s): 1423794 (strain), 35787 (species)

« back to strain detail view
For citation purpose refer to the digital object identifier (doi) of the current version.
Archive
version 9.3 (current version):
version 9.2:
version 9.1:
version 9:
version 8.1:
version 8:
version 7.1:
version 7:
version 6:
version 5:
version 4.1:
version 4:
version 3:
version 2.1:
version 2:
version 1:
version 9.3 (current version)

General

@ref: 3288

BacDive-ID: 6562

DSM-Number: 8475

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

description: Limosilactobacillus pontis DSM 8475 is an anaerobe, mesophilic, Gram-positive bacterium that was isolated from rye sourdough.

NCBI tax id

NCBI tax idMatching level
35787species
1423794strain

strain history

@refhistory
3288<- P. Stolz <- G. Böcker, LTH 2587
67770DSM 8475 <-- P. Stolz <-- G. Böcker LTH 2587.
121939CIP <- 1994, P. Stolz, Inst. für Lebensmitteltechnol., Germany: strain LTH 2587 <- Hohenheim Univ., Germany

doi: 10.13145/bacdive6562.20250331.9.3

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/bacillota
  • domain: Bacteria
  • phylum: Bacillota
  • class: Bacilli
  • order: Lactobacillales
  • family: Lactobacillaceae
  • genus: Limosilactobacillus
  • species: Limosilactobacillus pontis
  • full scientific name: Limosilactobacillus pontis (Vogel et al. 1994) Zheng et al. 2020

  • synonyms

    • @ref: 20215
    • synonym: Lactobacillus pontis

@ref: 3288

domain: Bacteria

phylum: Firmicutes

class: Bacilli

order: Lactobacillales

family: Lactobacillaceae

genus: Limosilactobacillus

species: Limosilactobacillus pontis

full scientific name: Limosilactobacillus pontis (Vogel et al. 1994) Zheng et al. 2020

type strain: yes

Morphology

cell morphology

@refgram staincell shapemotilityconfidence
121939positiverod-shapedno
125438no90.5
125438positive94.388

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
3288LACTOBACILLUS MEDIUM III (DSMZ Medium 638)yeshttps://mediadive.dsmz.de/medium/638Name: LACTOBACILLUS MEDIUM III (DSMZ Medium 638) Composition: Tryptone 10.0 g/l Glucose 7.0 g/l Maltose 7.0 g/l Fructose 7.0 g/l Na-acetate x 3 H2O 5.0 g/l Yeast extract 5.0 g/l Meat extract 5.0 g/l K2HPO4 x 3 H2O 2.6 g/l (NH4)2 citrate 2.0 g/l Na-gluconate 2.0 g/l L-Cysteine HCl x H2O 0.5 g/l MgSO4 x 7 H2O 0.1 g/l MnSO4 x 4 H2O 0.05 g/l Tween 80 Distilled water
38168MEDIUM 42 - for Lactobacillus pontisyesDistilled water make up to (1000.000 ml);Man Rogosa Sharp broth (55.000 g);Lactobacillus pontis solution - M0209 (18.000 ml)
121939CIP Medium 42yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=42

culture temp

@refgrowthtypetemperature
3288positivegrowth30
38168positivegrowth30
51530positivegrowth37
67770positivegrowth30
121939positivegrowth15-45

Physiology and metabolism

oxygen tolerance

@refoxygen toleranceconfidence
51530anaerobe
121939facultative anaerobe
125439anaerobe98.4

spore formation

  • @ref: 125438
  • spore formation: no
  • confidence: 91.675

murein

  • @ref: 3288
  • murein short key: A21.04
  • type: A4ß L-Orn-D-Asp

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
12193917632nitrate-reduction
12193916301nitrite-reduction
12193917632nitrate+respiration
68371Potassium 5-ketogluconate-builds acid from
6837118305arbutin-builds acid from
6837127613amygdalin-builds acid from
68371320061methyl alpha-D-glucopyranoside-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
6837117634D-glucose-builds acid from
6837112936D-galactose-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
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
6837159640N-acetylglucosamine-builds acid from
6837143943methyl alpha-D-mannoside-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

metabolite tests

  • @ref: 121939
  • Chebi-ID: 15688
  • metabolite: acetoin
  • voges-proskauer-test: -

enzymes

@refvalueactivityec
121939oxidase-
121939alcohol dehydrogenase+1.1.1.1
121939catalase-1.11.1.6
121939lysine decarboxylase-4.1.1.18
121939ornithine decarboxylase-4.1.1.17

API 50CHac

@refQGLYERYDARALARARIBDXYLLXYLADOMDXGALGLUFRUMNESBERHADULINOMANSORMDMMDGNAGAMYARBESCSALCELMALLACMELSACTREINUMLZRAFAMDGLYGXLTGENTURLYXTAGDFUCLFUCDARLLARLGNT2KG5KG
3288-----+----------------------+--+------------------
121939----+------+---------------+--+---+/------------+/---

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinentisolation date
3288rye sourdoughGermany, StuttgartGermanyDEUEurope
51530Sour doughStuttgartGermanyDEUEurope
67770Sourdough
121939Rye sourdoughGermanyDEUEurope1988

isolation source categories

Cat1Cat2Cat3
#Engineered#Food production#Food
#Host#Plants#Herbaceous plants (Grass,Crops)

taxonmaps

  • @ref: 69479
  • File name: preview.99_8168.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_45;96_369;97_416;98_5944;99_8168&stattab=map
  • Last taxonomy: Limosilactobacillus
  • 16S sequence: LC145562
  • Sequence Identity:
  • Total samples: 38681
  • soil counts: 1269
  • aquatic counts: 1526
  • animal counts: 35132
  • plant counts: 754

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
32881Risk group (German classification)
1219391Risk group (French classification)

Sequence information

16S sequences

@refdescriptionaccessionlengthdatabaseNCBI tax ID
20218Lactobacillus pontis gene for 16S rRNA, partial sequence, strain: JCM 11051AB289267731nuccore35787
20218Lactobacillus pontis 16S rRNA gene, type strain LMG 14187AJ4220321480nuccore35787
3288L.pontis (LTH 2587) 16S rRNA geneX763291570nuccore35787
67770Lactobacillus pontis gene for 16S ribosomal RNA, partial sequence, strain: JCM 11051LC1455621458nuccore35787
124043Lactobacillus pontis partial 23S rRNA gene and 16S-23S IGS, strain DSM 8475AJ616013696nuccore35787
124043Lactobacillus pontis strain DSM 8475 16S-23S ribosomal RNA large intergenic spacer, tRNA-Ile, and tRNA-Ala genes, complete sequence.AY839302403nuccore35787
124043Lactobacillus pontis strain DSM 8475 16S-23S ribosomal RNA small intergenic spacer, complete sequence.AY839303207nuccore35787

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Lactobacillus pontis DSM 84751423794.3wgspatric1423794
66792Limosilactobacillus pontis DSM 84752700989158draftimg1423794
67770Limosilactobacillus pontis DSM 8475GCA_001435345scaffoldncbi1423794

GC content

@refGC-contentmethod
328853high performance liquid chromatography (HPLC)
6777053.3high performance liquid chromatography (HPLC)

Genome-based predictions

predictions

@refmodeltraitdescriptionpredictionconfidencetraining_data
125438gram-positivegram-positivePositive reaction to Gram-stainingyes94.388no
125438anaerobicanaerobicAbility to grow under anoxygenic conditions (including facultative anaerobes)no84.514no
125438spore-formingspore-formingAbility to form endo- or exosporesno91.675no
125438aerobicaerobicAbility to grow under oxygenic conditions (including facultative aerobes)no94.248no
125438thermophilethermophilicAbility to grow at temperatures above or equal to 45°Cno97no
125438motile2+flagellatedAbility to perform flagellated movementno90.5no
125439BacteriaNetspore_formationAbility to form endo- or exosporesno84.8
125439BacteriaNetmotilityAbility to perform movementno67.4
125439BacteriaNetgram_stainReaction to gram-stainingpositive74.7
125439BacteriaNetoxygen_toleranceOxygenic conditions needed for growthanaerobe98.4

External links

@ref: 3288

culture collection no.: DSM 8475, ATCC 51518, JCM 11051, LMG 14187, CCUG 33456, LTH 2587, CIP 104232

straininfo link

  • @ref: 76034
  • straininfo: 8943

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny8186088Identification of lactobacilli from sourdough and description of Lactobacillus pontis sp. nov.Vogel RF, Bocker G, Stolz P, Ehrmann M, Fanta D, Ludwig W, Pot B, Kersters K, Schleifer KH, Hammes WPInt J Syst Bacteriol10.1099/00207713-44-2-2231994Bacterial Proteins/analysis, Base Sequence, Bread/*microbiology, *Food Microbiology, Lactobacillus/*classification/cytology/isolation & purification/ultrastructure, Molecular Sequence Data, Nucleic Acid Hybridization, Oligonucleotide Probes, RNA, Ribosomal, 16S/genetics, Sequence Analysis, RNABiotechnology
Metabolism17496130Glutathione reductase from Lactobacillus sanfranciscensis DSM20451T: contribution to oxygen tolerance and thiol exchange reactions in wheat sourdoughs.Jansch A, Korakli M, Vogel RF, Ganzle MGAppl Environ Microbiol10.1128/AEM.02322-062007Aerobiosis, Anaerobiosis, Anti-Bacterial Agents/metabolism/pharmacology, Biological Transport, Cysteine/metabolism, Cystine/metabolism, DNA, Bacterial/chemistry/genetics, Fermentation, Flour/analysis/*microbiology, Glutathione Reductase/*genetics/*physiology, Lactobacillus/*enzymology/growth & development/*physiology, Molecular Sequence Data, Mutagenesis, Insertional, Oxygen/*metabolism/pharmacology, Paraquat/pharmacology, Sequence Analysis, DNA, Sulfhydryl Compounds/*metabolism, *Triticum/metabolismEnzymology

Reference

@idauthorscataloguedoi/urltitlejournalpubmed
3288Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 8475)https://www.dsmz.de/collection/catalogue/details/culture/DSM-8475
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
38168Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/16118
51530Curators of the CCUGCulture Collection University of Gothenburg (CCUG) (CCUG 33456)https://www.ccug.se/strain?id=33456
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)
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
76034Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID8943.1StrainInfo: A central database for resolving microbial strain identifiers
121939Curators of the CIPCollection of Institut Pasteur (CIP 104232)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20104232
124043Isabel Schober, Julia KoblitzData extracted from sequence databases, automatically matched based on designation and taxonomy
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