Strain identifier

BacDive ID: 6669

Type strain: Yes

Species: Limosilactobacillus secaliphilus

Strain history: CIP <- 2007, CCUG <- 2006, M. Ehrmann, Munich Univ., Freising, Germany: strain TMW 1.1309

NCBI tax ID(s): 396268 (species)

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General

@ref: 7230

BacDive-ID: 6669

DSM-Number: 17896

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

description: Limosilactobacillus secaliphilus DSM 17896 is a microaerophile, Gram-positive, rod-shaped bacterium that was isolated from sour dough.

NCBI tax id

  • NCBI tax id: 396268
  • Matching level: species

strain history

@refhistory
7230<- M.A. Ehrmann <- M. Brandt <- Ernst Böcker GmbH, strain WP/5
67770CCUG 53218 <-- M. Ehrmann TMW 1.1309.
122530CIP <- 2007, CCUG <- 2006, M. Ehrmann, Munich Univ., Freising, Germany: strain TMW 1.1309

doi: 10.13145/bacdive6669.20240916.9.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/bacillota
  • domain: Bacteria
  • phylum: Bacillota
  • class: Bacilli
  • order: Lactobacillales
  • family: Lactobacillaceae
  • genus: Limosilactobacillus
  • species: Limosilactobacillus secaliphilus
  • full scientific name: Limosilactobacillus secaliphilus (Ehrmann et al. 2007) Zheng et al. 2020

  • synonyms

    • @ref: 20215
    • synonym: Lactobacillus secaliphilus

@ref: 7230

domain: Bacteria

phylum: Firmicutes

class: Bacilli

order: Lactobacillales

family: Lactobacillaceae

genus: Limosilactobacillus

species: Limosilactobacillus secaliphilus

full scientific name: Limosilactobacillus secaliphilus (Ehrmann et al. 2007) Zheng et al. 2020

type strain: yes

Morphology

cell morphology

@refgram staincell lengthcell widthcell shapemotilityconfidence
31950positive02-04 µm0.5-1 µmrod-shapedno
122530positiverod-shapedno
69480positive94.102
69480no91

pigmentation

  • @ref: 31950
  • production: no

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
7230LACTOBACILLUS 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
37765MEDIUM 40- for Lactobacillus and LeuconostocyesDistilled water make up to (1000.000 ml);Man Rogosa Sharp agar (68.000 g)
122530CIP Medium 40yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=40

culture temp

@refgrowthtypetemperature
7230positivegrowth37
31950positivegrowth35-45
31950positiveoptimum40
37765positivegrowth37
59833positivegrowth37
67770positivegrowth37

Physiology and metabolism

oxygen tolerance

@refoxygen tolerance
7230microaerophile
31950facultative anaerobe
59833microaerophile
122530facultative anaerobe

spore formation

@refspore formationconfidence
31950no
69480no90.352
69481no100

halophily

  • @ref: 31950
  • salt: NaCl
  • growth: positive
  • tested relation: optimum
  • concentration: 3 %

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
3195033942ribose+carbon source
3195017992sucrose+carbon source
12253017632nitrate+reduction
12253016301nitrite-reduction

metabolite production

  • @ref: 122530
  • Chebi-ID: 35581
  • metabolite: indole
  • production: yes

enzymes

@refvalueactivityec
68382alpha-fucosidase-3.2.1.51
68382alpha-mannosidase-3.2.1.24
68382N-acetyl-beta-glucosaminidase-3.2.1.52
68382beta-glucosidase-3.2.1.21
68382alpha-glucosidase-3.2.1.20
68382beta-glucuronidase-3.2.1.31
68382beta-galactosidase-3.2.1.23
68382alpha-galactosidase-3.2.1.22
68382naphthol-AS-BI-phosphohydrolase-
68382acid phosphatase-3.1.3.2
68382alpha-chymotrypsin-3.4.21.1
68382trypsin+3.4.21.4
68382cystine arylamidase-3.4.11.3
68382valine arylamidase-
68382leucine arylamidase-3.4.11.1
68382lipase (C 14)-
68382esterase lipase (C 8)-
68382esterase (C 4)-
68382alkaline phosphatase-3.1.3.1
122530oxidase-
122530catalase-1.11.1.6
122530urease+3.5.1.5

API zym

@refControlAlkaline phosphataseEsteraseEsterase LipaseLipaseLeucine arylamidaseValine arylamidaseCystine arylamidaseTrypsinalpha- ChymotrypsinAcid phosphataseNaphthol-AS-BI-phosphohydrolasealpha- Galactosidasebeta- Galactosidasebeta- Glucuronidasealpha- Glucosidasebeta- GlucosidaseN-acetyl-beta- glucosaminidasealpha- Mannosidasealpha- Fucosidase
122530--------+-----------

Isolation, sampling and environmental information

isolation

@refsample typecountryorigin.countrycontinentgeographic location
7230sour doughGermanyDEUEurope
59833Rye sourdoughGermanyDEUEuropeMinden
67770Type II sourdough fermentation
122530Rye sourdoughGermanyDEUEuropeMinden

isolation source categories

  • Cat1: #Engineered
  • Cat2: #Food production
  • Cat3: #Fermented

taxonmaps

  • @ref: 69479
  • File name: preview.99_7134.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_45;96_1124;97_4102;98_5248;99_7134&stattab=map
  • Last taxonomy: Limosilactobacillus secaliphilus subclade
  • 16S sequence: AM279150
  • Sequence Identity:
  • Total samples: 11439
  • soil counts: 217
  • aquatic counts: 287
  • animal counts: 10646
  • plant counts: 289

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
72301Risk group (German classification)
1225301Risk group (French classification)

Sequence information

16S sequences

@refdescriptionaccessionlengthdatabaseNCBI tax ID
7230Lactobacillus secaliphilus 16S rRNA gene, type strain TMW 1.1309TAM2791501551nuccore396268
67770Lactobacillus secaliphilus JCM 15613 gene for 16S ribosomal RNA, partial sequenceLC4808081514nuccore396268

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Lactobacillus secaliphilus strain DSM 17896396268.3wgspatric396268
66792Limosilactobacillus secaliphilus DSM 178962671180593draftimg396268
67770Limosilactobacillus secaliphilus DSM 17896GCA_001437055scaffoldncbi396268

GC content

@refGC-content
723048.0
3195048
6777047.7

Genome-based predictions

predictions

@reftraitmodeldescriptionpredictionconfidencetraining_data
69481spore-formingspore-formingAbility to form endo- or exosporesno100no
69480gram-positivegram-positivePositive reaction to Gram-stainingyes94.102no
69480anaerobicanaerobicAbility to grow under anoxygenic conditions (including facultative anaerobes)no84.755yes
69480spore-formingspore-formingAbility to form endo- or exosporesno90.352yes
69480aerobicaerobicAbility to grow under oxygenic conditions (including facultative aerobes)no93.151yes
69480thermophilicthermophileAbility to grow at temperatures above or equal to 45°Cno95.5yes
69480flagellatedmotile2+Ability to perform flagellated movementno91yes

External links

@ref: 7230

culture collection no.: DSM 17896, CCUG 53218, TMW 1.1309, CIP 109557, JCM 15613

straininfo link

  • @ref: 76143
  • straininfo: 302644

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny17392199Lactobacillus secaliphilus sp. nov., isolated from type II sourdough fermentation.Ehrmann MA, Brandt M, Stolz P, Vogel RF, Korakli MInt J Syst Evol Microbiol10.1099/ijs.0.64700-02007Bread/*microbiology, DNA, Bacterial, DNA, Ribosomal/genetics, Fermentation, Lactobacillus/*classification/genetics/isolation & purification/metabolism, Molecular Sequence Data, Phylogeny, RNA, Ribosomal, 16S/genetics, Random Amplified Polymorphic DNA TechniqueGenetics
Phylogeny22092683Lactobacillus alvi sp. nov., isolated from the intestinal tract of chicken.Kim HJ, Eom SJ, Park SJ, Cha CJ, Kim GBFEMS Microbiol Lett10.1111/j.1574-6968.2011.02361.x2011Aerobiosis, Anaerobiosis, Animals, Catalase/metabolism, Chickens, Cluster Analysis, DNA, Bacterial/chemistry/genetics, DNA, Ribosomal/chemistry/genetics, Fatty Acids/analysis, Gastrointestinal Tract/*microbiology, Lactobacillus/*classification/genetics/*isolation & purification/physiology, Locomotion, Molecular Sequence Data, Nucleic Acid Hybridization, Phospholipids/analysis, Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, TemperatureGenetics

Reference

@idauthorscataloguedoi/urltitleID_cross_referencepubmedjournal
7230Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 17896)https://www.dsmz.de/collection/catalogue/details/culture/DSM-17896
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
31950Barberan A, Caceres Velazquez H, Jones S, Fierer N.10.1128/mSphere.00237-17Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information2820628776041
37765Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/7313
59833Curators of the CCUGCulture Collection University of Gothenburg (CCUG) (CCUG 53218)https://www.ccug.se/strain?id=53218
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/
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.https://microbeatlas.org/MicrobeAtlas 1.0 beta
69480Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmannhttps://diaspora-project.de/progress.html#genomesPredictions based on genome sequence made in the Diaspora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information)
69481Xiao-Yin To, René Mreches, Martin Binder, Alice C. McHardy, Philipp C. Münch10.21203/rs.3.rs-2527258/v1Predictions based on the model GenomeNet Sporulation v. 1
76143Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID302644.1StrainInfo: A central database for resolving microbial strain identifiers
122530Curators of the CIPCollection of Institut Pasteur (CIP 109557)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20109557