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, Gram-positive

description: Limosilactobacillus frumenti CCUG 56446 is an anaerobe, 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/bacdive6576.20240916.9.1

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 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
69480positive95.085

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 tolerance
60961anaerobe
119472facultative anaerobe

spore formation

  • @ref: 69480
  • spore formation: no
  • confidence: 92.007

murein

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

metabolite utilization

@refmetaboliteutilization activitykind of utilization testedChebi-ID
68371Potassium 5-ketogluconate-builds acid from
68371Potassium 2-ketogluconate-builds acid from
68371gluconate-builds acid from24265
68371L-arabitol-builds acid from18403
68371D-arabitol-builds acid from18333
68371L-fucose-builds acid from18287
68371D-fucose-builds acid from28847
68371D-tagatose-builds acid from16443
68371D-lyxose-builds acid from62318
68371turanose-builds acid from32528
68371gentiobiose-builds acid from28066
68371xylitol-builds acid from17151
68371glycogen-builds acid from28087
68371starch-builds acid from28017
68371melezitose-builds acid from6731
68371inulin-builds acid from15443
68371trehalose-builds acid from27082
68371sucrose+builds acid from17992
68371maltose+builds acid from17306
68371salicin-builds acid from17814
68371arbutin-builds acid from18305
68371amygdalin-builds acid from27613
68371N-acetylglucosamine-builds acid from59640
68371methyl alpha-D-glucopyranoside-builds acid from320061
68371methyl alpha-D-mannoside-builds acid from43943
68371D-sorbitol-builds acid from17924
68371D-mannitol-builds acid from16899
68371myo-inositol-builds acid from17268
68371galactitol-builds acid from16813
68371L-rhamnose-builds acid from62345
68371L-sorbose-builds acid from17266
68371methyl beta-D-xylopyranoside-builds acid from74863
68371ribitol-builds acid from15963
68371L-xylose-builds acid from65328
68371D-xylose-builds acid from65327
68371D-ribose-builds acid from16988
68371L-arabinose-builds acid from30849
68371D-arabinose-builds acid from17108
68371erythritol-builds acid from17113
119472nitrate-reduction17632
119472nitrite-reduction16301
119472nitrate+respiration17632

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
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
119472oxidase-
119472alcohol dehydrogenase+1.1.1.1
119472catalase-1.11.1.6
119472lysine decarboxylase-4.1.1.18
119472ornithine decarboxylase-4.1.1.17

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

@reftraitmodeldescriptionpredictionconfidencetraining_data
69480gram-positivegram-positivePositive reaction to Gram-stainingyes95.085no
69480anaerobicanaerobicAbility to grow under anoxygenic conditions (including facultative anaerobes)no78.752no
69480spore-formingspore-formingAbility to form endo- or exosporesno92.007no
69480aerobicaerobicAbility to grow under oxygenic conditions (including facultative aerobes)no93.441no
69480thermophilicthermophileAbility to grow at temperatures above or equal to 45°Cno96.375yes
69480flagellatedmotile2+Ability to perform flagellated movementno88.5no

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
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)
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
124043Dr. Isabel Schober, Dr. Julia KoblitzData extracted from sequence databases, automatically matched based on designation and taxonomy