Strain identifier

BacDive ID: 6576

Type strain: Yes

Species: Limosilactobacillus frumenti

Strain history: CIP <- 2001, M. Ehrmann, Munich Univ., Munich, Germany: strain TMW 1.666

NCBI tax ID(s): 1423746 (strain), 104955 (species)

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General

@ref: 4921

BacDive-ID: 6576

DSM-Number: 13145

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

description: Limosilactobacillus frumenti CCUG 56446 is an anaerobe, thermophilic, Gram-positive bacterium that was isolated from rye-bran sourdough.

NCBI tax id

NCBI tax idMatching level
1423746strain
104955species

strain history

@refhistory
4921<- M. Müller; TMW 1.666
341262001, M. Ehrmann, Univ. München, Germany, strain TMW 1.666
67770M. A. Ehrmann TMW 1.666.
119472CIP <- 2001, M. Ehrmann, Munich Univ., Munich, Germany: strain TMW 1.666

doi: 10.13145/bacdive6576.20250331.9.3

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 frumenti
  • full scientific name: Limosilactobacillus frumenti (Müller et al. 2000) Zheng et al. 2020

  • synonyms

    • @ref: 20215
    • synonym: Lactobacillus frumenti

@ref: 4921

domain: Bacteria

phylum: Firmicutes

class: Bacilli

order: Lactobacillales

family: Lactobacillaceae

genus: Limosilactobacillus

species: Limosilactobacillus frumenti

full scientific name: Limosilactobacillus frumenti (Müller et al. 2000) Zheng et al. 2020

type strain: yes

Morphology

cell morphology

@refgram staincell shapemotilityconfidence
119472positiverod-shapedno
125438positive95.085
125439positive90.3

colony morphology

  • @ref: 60961
  • incubation period: 2 days

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
4921LACTOBACILLUS 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
34126MEDIUM 40- for Lactobacillus and LeuconostocyesDistilled water make up to (1000.000 ml);Man Rogosa Sharp agar (68.000 g)
119472CIP Medium 40yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=40

culture temp

@refgrowthtypetemperature
4921positivegrowth40
34126positivegrowth37
60961positivegrowth37
67770positivegrowth40
119472positivegrowth22-45
119472nogrowth10
119472nogrowth15

Physiology and metabolism

oxygen tolerance

@refoxygen toleranceconfidence
60961anaerobe
119472facultative anaerobe
125439microaerophile95.2

spore formation

@refspore formationconfidence
125438no92.007
125439no96.1

murein

  • @ref: 4921
  • murein short key: A11.31
  • type: A4alpha L-Lys-D-Asp

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
11947217632nitrate-reduction
11947216301nitrite-reduction
11947217632nitrate+respiration
68371Potassium 5-ketogluconate-builds acid from
6837118305arbutin-builds acid from
6837127613amygdalin-builds acid from
68371320061methyl alpha-D-glucopyranoside-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
683716731melezitose-builds acid from
6837115443inulin-builds acid from
6837127082trehalose-builds acid from
6837117992sucrose+builds acid from
6837117306maltose+builds acid from
6837117814salicin-builds acid from
6837159640N-acetylglucosamine-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
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

antibiotic resistance

  • @ref: 119472
  • metabolite: 0129 (2,4-Diamino-6,7-di-iso-propylpteridine phosphate)
  • is antibiotic: yes
  • is sensitive: no
  • is resistant: yes

metabolite tests

  • @ref: 119472
  • Chebi-ID: 15688
  • metabolite: acetoin
  • voges-proskauer-test: -

enzymes

@refvalueactivityec
68382alpha-fucosidase-3.2.1.51
68382alpha-mannosidase-3.2.1.24
68382N-acetyl-beta-glucosaminidase-3.2.1.52
68382alpha-glucosidase-3.2.1.20
68382beta-galactosidase+3.2.1.23
68382beta-glucuronidase-3.2.1.31
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
68382leucine arylamidase+3.4.11.1
68382valine arylamidase-
68382lipase (C 14)-
68382esterase lipase (C 8)+
68382esterase (C 4)+
68382alkaline phosphatase-3.1.3.1
119472oxidase-
119472alcohol dehydrogenase+1.1.1.1
119472catalase-1.11.1.6
119472lysine decarboxylase-4.1.1.18
119472ornithine decarboxylase-4.1.1.17
68382beta-glucosidase-3.2.1.21

API zym

@refControlAlkaline phosphataseEsteraseEsterase LipaseLipaseLeucine arylamidaseValine arylamidaseCystine arylamidaseTrypsinalpha- ChymotrypsinAcid phosphataseNaphthol-AS-BI-phosphohydrolasealpha- Galactosidasebeta- Galactosidasebeta- Glucuronidasealpha- Glucosidasebeta- GlucosidaseN-acetyl-beta- glucosaminidasealpha- Mannosidasealpha- Fucosidase
119472--++-+----++++------

API 50CHac

@refQGLYERYDARALARARIBDXYLLXYLADOMDXGALGLUFRUMNESBERHADULINOMANSORMDMMDGNAGAMYARBESCSALCELMALLACMELSACTREINUMLZRAFAMDGLYGXLTGENTURLYXTAGDFUCLFUCDARLLARLGNT2KG5KG
4921-----------+/-----------------+--+---+/---------------
4921-+---------+---------------+++++------------------
119472---------+/-+++-----------+/---++++---+--------------

Isolation, sampling and environmental information

isolation

@refsample typecountryorigin.countrycontinent
4921rye-bran sourdoughGermanyDEUEurope
60961Rye-bran sourdoughGermanyDEUEurope
67770Rye-bran sourdough
119472Rye-bran sourdoughGermanyDEUEurope

isolation source categories

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

taxonmaps

  • @ref: 69479
  • File name: preview.99_7135.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_45;96_369;97_416;98_5249;99_7135&stattab=map
  • Last taxonomy: Limosilactobacillus frumenti subclade
  • 16S sequence: LC480798
  • Sequence Identity:
  • Total samples: 15405
  • soil counts: 360
  • aquatic counts: 192
  • animal counts: 14742
  • plant counts: 111

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
49211Risk group (German classification)
1194721Risk group (French classification)

Sequence information

16S sequences

@refdescriptionaccessionlengthdatabaseNCBI tax ID
20218Lactobacillus frumenti partial 23S rRNA gene and 16S-23S IGS, strain DSM 13145AJ616011689nuccore104955
20218Lactobacillus frumenti 16S ribosomal RNA gene, partial sequence; tRNA-Ala and tRNA-Ile genes, and 16S-23S ribosomal RNA intergenic spacer region, complete sequence; and 23S ribosomal RNA gene, partialAY2754331069nuccore104955
20218Lactobacillus frumenti strain DSM 13145 16S-23S ribosomal RNA large intergenic spacer, tRNA-Ile, and tRNA-Ala genes, complete sequenceAY839304397nuccore104955
20218Lactobacillus frumenti strain DSM 13145 16S-23S ribosomal RNA small intergenic spacer, complete sequenceAY839305204nuccore104955
4921Lactobacillus sp. TMW 1.666 16S rRNA gene, strain TMW 1.666AJ2500741561nuccore104955
67770Lactobacillus frumenti JCM 11122 gene for 16S ribosomal RNA, partial sequenceLC4807981512nuccore104955
124043Lactobacillus frumenti gene for 16S rRNA, partial sequence, strain: JCM 11122.AB289119653nuccore104955

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Lactobacillus frumenti DSM 131451423746.3wgspatric1423746
66792Limosilactobacillus frumenti DSM 131452667528021draftimg1423746
67770Limosilactobacillus frumenti DSM 13145GCA_001436045scaffoldncbi1423746

GC content

@refGC-contentmethod
492143.3
6777042.6genome sequence analysis
6777044.4high performance liquid chromatography (HPLC)

Genome-based predictions

predictions

@refmodeltraitdescriptionpredictionconfidencetraining_data
125438gram-positivegram-positivePositive reaction to Gram-stainingyes95.085no
125438anaerobicanaerobicAbility to grow under anoxygenic conditions (including facultative anaerobes)no78.752no
125438spore-formingspore-formingAbility to form endo- or exosporesno92.007no
125438aerobicaerobicAbility to grow under oxygenic conditions (including facultative aerobes)no93.441no
125438thermophilethermophilicAbility to grow at temperatures above or equal to 45°Cno96.375yes
125438motile2+flagellatedAbility to perform flagellated movementno88.5no
125439BacteriaNetspore_formationAbility to form endo- or exosporesno96.1
125439BacteriaNetmotilityAbility to perform movementno80.3
125439BacteriaNetgram_stainReaction to gram-stainingpositive90.3
125439BacteriaNetoxygen_toleranceOxygenic conditions needed for growthmicroaerophile95.2

External links

@ref: 4921

culture collection no.: CCUG 56446, CIP 106922, JCM 11122, DSM 13145, LMG 19473, TMW 1.666

straininfo link

  • @ref: 76050
  • straininfo: 13507

literature

  • topic: Phylogeny
  • Pubmed-ID: 11155988
  • title: Lactobacillus frumenti sp. nov., a new lactic acid bacterium isolated from rye-bran fermentations with a long fermentation period.
  • authors: Muller MR, Ehrmann MA, Vogel RF
  • journal: Int J Syst Evol Microbiol
  • DOI: 10.1099/00207713-50-6-2127
  • year: 2000
  • mesh: Bread/*microbiology, DNA, Ribosomal/analysis, Dietary Fiber/*microbiology, Electrophoresis, Polyacrylamide Gel/methods, Fermentation, Lactobacillus/chemistry/*classification/genetics/*physiology, Molecular Sequence Data, Nucleic Acid Hybridization, Phylogeny, RNA, Ribosomal, 16S/genetics, Secale/*microbiology, Sequence Analysis, DNA
  • topic2: Enzymology

Reference

@idauthorscataloguedoi/urltitlejournalpubmed
4921Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 13145)https://www.dsmz.de/collection/catalogue/details/culture/DSM-13145
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
34126Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/19106
60961Curators of the CCUGCulture Collection University of Gothenburg (CCUG) (CCUG 56446)https://www.ccug.se/strain?id=56446
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 updatesNucleic Acids Res. 49: D498-D508 202033211880
67770Curators of the JCMhttps://jcm.brc.riken.jp/en/
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.https://microbeatlas.org/MicrobeAtlas 1.0 beta
76050Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID13507.1StrainInfo: A central database for resolving microbial strain identifiers
119472Curators of the CIPCollection of Institut Pasteur (CIP 106922)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20106922
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