Strain identifier

BacDive ID: 6458

Type strain: Yes

Species: Limosilactobacillus fermentum

Strain Designation: 28, Bb28

Strain history: CIP <- 1987, NCFB <- 1964, M.E. Sharpe, Reading, UK <- S. Orla-Jensen : strain 28, Betabacterium longum

NCBI tax ID(s): 525325 (strain), 1613 (species)

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General

@ref: 8455

BacDive-ID: 6458

DSM-Number: 20052

keywords: genome sequence, 16S sequence, Bacteria, anaerobe, mesophilic, human pathogen

description: Limosilactobacillus fermentum 28 is an anaerobe, mesophilic human pathogen that was isolated from fermented beets.

NCBI tax id

NCBI tax idMatching level
1613species
525325strain

strain history

@refhistory
8455<- ATCC <- P.A. Hansen, Bb28 <- Roy. Techn. Coll., Copenhagen <- S. Orla-Jensen, 28 (Betabacterium longum)
67770ATCC 14931 <-- P. A. Hansen Bl 28 <-- R. Tech. Coll., Copenhagen <-- S. Orla-Jensen 28 ("Betabacterium longum").
119329CIP <- 1987, NCFB <- 1964, M.E. Sharpe, Reading, UK <- S. Orla-Jensen : strain 28, Betabacterium longum

doi: 10.13145/bacdive6458.20230509.8.1

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 fermentum
  • full scientific name: Limosilactobacillus fermentum (Beijerinck 1901) Zheng et al. 2020

  • synonyms

    @refsynonym
    20215Lactobacillus cellobiosus
    20215Lactobacillus fermentum

@ref: 8455

domain: Bacteria

phylum: Firmicutes

class: Bacilli

order: Lactobacillales

family: Lactobacillaceae

genus: Limosilactobacillus

species: Limosilactobacillus fermentum

full scientific name: Limosilactobacillus fermentum (Beijerinck 1901) Zheng et al. 2020

strain designation: 28, Bb28

type strain: yes

Morphology

cell morphology

@refmotilityconfidencegram staincell shape
69480no97.056
69480100positive
119329nopositiverod-shaped

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
8455MRS MEDIUM (DSMZ Medium 11)yeshttps://mediadive.dsmz.de/medium/11Name: 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
38114MEDIUM 40- for Lactobacillus and LeuconostocyesDistilled water make up to (1000.000 ml);Man Rogosa Sharp agar (68.000 g)
119329CIP Medium 40yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=40
119329CIP Medium 41yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=41

culture temp

@refgrowthtypetemperaturerange
8455positivegrowth37mesophilic
38114positivegrowth37mesophilic
49932positivegrowth37mesophilic
67770positivegrowth37mesophilic
119329positivegrowth15-45
119329nogrowth10psychrophilic

Physiology and metabolism

oxygen tolerance

@refoxygen tolerance
49932anaerobe
119329facultative anaerobe

spore formation

  • @ref: 69480
  • spore formation: no
  • confidence: 99.991

murein

  • @ref: 8455
  • murein short key: A21.04
  • type: A4ß L-Orn-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-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
68371lactose+builds acid from17716
68371maltose+builds acid from17306
68371cellobiose-builds acid from17057
68371salicin-builds acid from17814
68371esculin-builds acid from4853
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
68371D-mannose-builds acid from16024
68371D-fructose+builds acid from15824
68371D-glucose+builds acid from17634
68371D-galactose+builds acid from12936
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
68371glycerol-builds acid from17754
119329nitrate-reduction17632
119329nitrite-reduction16301
119329nitrate+respiration17632

metabolite tests

  • @ref: 119329
  • 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
119329oxidase-
119329alcohol dehydrogenase+1.1.1.1
119329catalase-1.11.1.6
119329lysine decarboxylase-4.1.1.18
119329ornithine 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
119329-----+----++-+------

API 50CHac

@refQGLYERYDARALARARIBDXYLLXYLADOMDXGALGLUFRUMNESBERHADULINOMANSORMDMMDGNAGAMYARBESCSALCELMALLACMELSACTREINUMLZRAFAMDGLYGXLTGENTURLYXTAGDFUCLFUCDARLLARLGNT2KG5KG
8455-----+----+++---------------++-+------------------
8455-----+----+++---------------++-+------------------
8455-----+----+++---------------++-+------------------
8455-----+----+++---------------++--------------------
119329----+----+++---------------++++---+/-------+-------

Isolation, sampling and environmental information

isolation

@refsample type
8455fermented beets
49932Fermented beets (Beta vulgaris)
67770Fermented beets
119329Food, Fermented beets

isolation source categories

  • Cat1: #Engineered
  • Cat2: #Food production

taxonmaps

  • @ref: 69479
  • File name: preview.99_145.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_45;96_107;97_114;98_126;99_145&stattab=map
  • Last taxonomy: Limosilactobacillus fermentum subclade
  • 16S sequence: LC065036
  • Sequence Identity:
  • Total samples: 63221
  • soil counts: 1466
  • aquatic counts: 4660
  • animal counts: 55710
  • plant counts: 1385

Safety information

risk assessment

@refpathogenicity humanbiosafety levelbiosafety level comment
8455yes, in single cases1Risk group (German classification)
1193291Risk group (French classification)

Sequence information

16S sequences

@refdescriptionaccessionlengthdatabaseNCBI tax ID
20218Lactobacillus fermentum gene for 16S rRNA, partial sequence, strain: ATCC 14931AB017345501ena1613
20218Lactobacillus fermentum 16S ribosomal RNA gene, partial sequence; 16S-23S ribosomal RNA intergenic spacer region, complete sequence; and 23S ribosomal RNA gene, partial sequenceAF080099518ena1613
20218Lactobacillus fermentum ATCC 14931 16S ribosomal RNA gene, partial sequenceAF429506515ena1613
20218Lactobacillus fermentum strain ATCC 14931 16S ribosomal RNA gene, partial sequence; 16S-23S intergenic spacer, complete sequence; and 23S ribosomal RNA gene, partial sequenceAF429593523ena1613
20218Lactobacillus fermentum gene for 16S ribosomal RNA, partial sequenceD31689159ena1613
20218Lactobacillus fermentum 16S ribosomal RNAM588191580ena1613
20218Lactobacillus fermentum strain CIP 102980 16S ribosomal RNA gene, complete sequenceJN1753311502ena1613
20218Lactobacillus fermentum gene for 16S rRNA, partial sequence, strain: JCM 1137AB289104677ena1613
20218Lactobacillus fermentum gene for 16S rRNA, partial sequence, strain: JCM 1173AB289105672ena1613
20218Lactobacillus fermentum 16S ribosomal RNA, partial sequence; 16S/23S intergenic spacer region, complete sequence; and 23S ribosomal RNA partial sequenceAF182720665ena1613
20218Lactobacillus fermentum gene for 16S rRNA, partial sequence, strain: JCM 12530AB289114689ena1613
20218Lactobacillus fermentum strain LMG 9846 16S-23S ribosomal RNA intergenic spacer and 23S ribosomal RNA gene, partial sequenceEU161600785ena1613
20218Lactobacillus fermentum gene for 16S rRNA, partial sequence, strain: NBRC 15885AB6260521501ena1613
20218L.fermentum 16S rRNA geneX611421381ena1613
67770Lactobacillus fermentum gene for 16S ribosomal RNA, partial sequence, strain: JCM 1173LC0650361477ena1613

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Limosilactobacillus fermentum DSM 20052GCA_013394085chromosomencbi1613
66792Limosilactobacillus fermentum ATCC 14931 SRR9217392-mag-bin.15GCA_905371965contigncbi525325
66792Lactobacillus fermentum ATCC 14931525325.3wgspatric525325
66792Lactobacillus fermentum ATCC 14931 strain SRR9217392-mag-bin.15525325.50wgspatric525325
66792Lactobacillus fermentum strain B1 281613.432completepatric1613
66792Lactobacillus fermentum strain DSM 200521613.547completepatric1613
66792Limosilactobacillus fermentum ATCC 14931643886061draftimg525325
67770Limosilactobacillus fermentum ATCC 14931GCA_000159215scaffoldncbi525325
66792Limosilactobacillus fermentum LMG 6902GCA_029823225contigncbi1613

GC content

@refGC-contentmethod
845553.4
6777050thermal denaturation, midpoint method (Tm)
6777052.4genome sequence analysis
6777053.4thermal denaturation, midpoint method (Tm)

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno84no
motileno96.026no
gram-positiveyes97.361no
anaerobicno85.541yes
aerobicno96.361yes
halophileyes94.887no
spore-formingno97.531no
thermophileno98.665yes
glucose-utilyes88.181no
flagellatedno98.824no
glucose-fermentyes88.224no

External links

@ref: 8455

culture collection no.: DSM 20052, ATCC 14931, NCDO 1750, CCUG 30138, LMG 6902, JCM 1173, BCRC 12190, CECT 4007, CIP 102980, IFO 15885, KCTC 3112, NBRC 15885, NCIMB 11840, NRIC 1752, NRRL B-4524, VTT E-93489

straininfo link

  • @ref: 75931
  • straininfo: 3285

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Pathogenicity9241587Digoxigenin-labeled deoxyribonucleic acid probes for the enumeration of bifidobacteria in fecal samples.Kaneko T, Kurihara HJ Dairy Sci10.3168/jds.S0022-0302(97)76054-51997Adult, Bifidobacterium/genetics/*growth & development, Colony Count, Microbial, *DNA Probes, DNA, Bacterial/*analysis, *Digoxigenin, Feces/*microbiology, Humans, Middle Aged, Nucleic Acid HybridizationPhylogeny
Metabolism11549028Evaluation of nitric oxide production by lactobacilli.Xu J, Verstraete WAppl Microbiol Biotechnol10.1007/s0025301006162001Arginine/metabolism, Culture Media, Lactobacillus/enzymology/growth & development/*metabolism, Nitrates/metabolism, Nitric Oxide/*biosynthesis, Nitric Oxide Synthase/metabolism, Nitrite Reductases/metabolism, Oxidation-ReductionCultivation
14618783[Influence lactobacilli on the functional activity of macrophages and delayed hypersensitivity reaction in mice].Ielyns'ka NO, Kur'iata NV, Filippova TO, Ivanytsia VOMikrobiol Z2003Animals, Hypersensitivity, Delayed/*immunology, Lactobacillus/immunology/*physiology, Macrophages, Peritoneal/*immunology/microbiology, Mice, Phagocytosis, *Probiotics
Phylogeny16085805Development and assessment of a real-time pcr assay for rapid and sensitive detection of a novel thermotolerant bacterium, Lactobacillus thermotolerans, in chicken feces.Selim AS, Boonkumklao P, Sone T, Assavanig A, Wada M, Yokota AAppl Environ Microbiol10.1128/AEM.71.8.4214-4219.20052005Animals, Chickens/*microbiology, Colony Count, Microbial, DNA Primers, DNA, Bacterial/analysis, Feces/*microbiology, *Hot Temperature, Lactobacillus/classification/genetics/*growth & development/*isolation & purification, Polymerase Chain Reaction/*methods, Species Specificity, Time FactorsStress
Metabolism21036038Effects of ensilage on storage and enzymatic degradability of sugar beet pulp.Zheng Y, Yu C, Cheng YS, Zhang R, Jenkins B, VanderGheynst JSBioresour Technol10.1016/j.biortech.2010.09.1052010Bacteria/metabolism, Beta vulgaris/*metabolism, Cellulase/*metabolism, Hydrogen-Ion Concentration, Lactic Acid/metabolism, Silage/*analysis, Waste Products/*analysis
Enzymology23064454Stable integration and expression of heterologous genes in several lactobacilli using an integration vector constructed from the integrase and attP sequences of phage PhiAT3 isolated from Lactobacillus casei ATCC 393.Lin CF, Lo TC, Kuo YC, Lin THAppl Microbiol Biotechnol10.1007/s00253-012-4393-52012*Attachment Sites, Microbiological, Bacteriophages/enzymology/genetics, *Genetic Vectors, Genetics, Microbial/*methods, Genomic Instability, Integrases/*genetics, Lactobacillus/*genetics/virology, Lactobacillus fermentum, Lactobacillus rhamnosus, Lactococcus lactis, Molecular Biology/*methods, Promoter Regions, Genetic
Phylogeny25240022Lactobacillus gorillae sp. nov., isolated from the faeces of captive and wild western lowland gorillas (Gorilla gorilla gorilla).Tsuchida S, Kitahara M, Nguema PPM, Norimitsu S, Fujita S, Yamagiwa J, Ngomanda A, Ohkuma M, Ushida KInt J Syst Evol Microbiol10.1099/ijs.0.068429-02014Animals, Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, Fatty Acids/chemistry, Feces/microbiology, Female, Gabon, Gorilla gorilla/*microbiology, Japan, Lactobacillus/*classification/genetics/isolation & purification, Male, Molecular Sequence Data, Nucleic Acid Hybridization, Peptidoglycan/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNAGenetics
Phylogeny28935567Lactobacillus fermentum FTDC 8312 combats hypercholesterolemia via alteration of gut microbiota.Lye HS, Kato T, Low WY, Taylor TD, Prakash T, Lew LC, Ohno H, Liong MTJ Biotechnol10.1016/j.jbiotec.2017.09.0072017Animals, *Anticholesteremic Agents, Apolipoprotein A-I, Bacteria/classification/genetics, Bile Acids and Salts/analysis, Body Weight, Cholesterol/blood, Cholesterol, Dietary/adverse effects, DNA, Bacterial/genetics, Diet, Feces/chemistry, *Gastrointestinal Microbiome/genetics, Genes, Bacterial/genetics, Hypercholesterolemia/*drug therapy, *Lactobacillus fermentum/genetics, Lipid Metabolism/*drug effects, Lipids/blood, Lipoproteins/blood, Lipoproteins, HDL/blood, Lipoproteins, LDL/blood, Male, Mice, Mice, Inbred BALB C, Phospholipids/blood, Probiotics/*therapeutic use, RNA, Ribosomal, 16S/genetics, Sterols/analysis, Triglycerides/blood, Whole Genome SequencingPathogenicity
Metabolism30456749Effect of Lyophilized, Encapsulated Lactobacillus fermentum and Lactulose Feeding on Growth Performance, Heavy Metals, and Trace Element Residues in Rainbow Trout (Oncorhynchus mykiss) Tissues.Madreseh S, Ghaisari HR, Hosseinzadeh SProbiotics Antimicrob Proteins10.1007/s12602-018-9487-72019Animal Feed/analysis/microbiology, Animals, Drug Compounding, Gills/chemistry/metabolism, Lactobacillus fermentum/chemistry/physiology, Lactulose/*metabolism, Liver/chemistry/metabolism, Metals, Heavy/analysis/*metabolism, Muscle, Skeletal/chemistry/metabolism, Oncorhynchus mykiss/*growth & development/*metabolism/microbiology, Probiotics/*administration & dosage/chemistry, Trace Elements/analysis/*metabolism
Genetics32349666Genomic characterization of Lactobacillus fermentum DSM 20052.Brandt K, Nethery MA, O'Flaherty S, Barrangou RBMC Genomics10.1186/s12864-020-6740-82020CRISPR-Cas Systems/genetics, Genetic Variation, *Genome, Bacterial, Genomic Islands, Genomics, Interspersed Repetitive Sequences, Lactobacillus fermentum/classification/*genetics, PhylogenyPhylogeny
Phylogeny34721319Comparison of 16S rRNA Gene Based Microbial Profiling Using Five Next-Generation Sequencers and Various Primers.Park C, Kim SB, Choi SH, Kim SFront Microbiol10.3389/fmicb.2021.7155002021
36305089Changes in nutrient consumption patterns of Lactobacillus fermentum mediated by sodium lactate.Zhang K, Zhang Z, Guo X, Guo R, Zhu L, Qiu X, Yu X, Chai J, Gu C, Feng ZJ Sci Food Agric10.1002/jsfa.122952022
36359959Use of Selected Lactic Acid Bacteria for the Fermentation of Legume-Based Water Extracts.Demarinis C, Verni M, Pinto L, Rizzello CG, Baruzzi FFoods10.3390/foods112133462022

Reference

@idauthorscataloguedoi/urltitlejournalpubmed
8455Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 20052)https://www.dsmz.de/collection/catalogue/details/culture/DSM-20052
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
38114Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/14726
49932Curators of the CCUGCulture Collection University of Gothenburg (CCUG) (CCUG 30138)https://www.ccug.se/strain?id=30138
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)
75931Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID3285.1StrainInfo: A central database for resolving microbial strain identifiers
119329Curators of the CIPCollection of Institut Pasteur (CIP 102980)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20102980