Identification of Antimicrobial Peptides from Novel Lactobacillus fermentum Strain


Antimicrobial peptides (AMPs) are natural antagonistic tools of many bacteria and are considered as attractive antimicrobial agents for the treatment of bacteria with multidrug resistance. Lactic acid bacteria from the gastrointestinal tract of animals and human produce various AMPs inhibiting the growth of pathogens. Here we report the isolation and identification of novel Lactobacillus fermentum strain HF-D1 from the human gut producing AMPs which prevents the growth of P. aeruginosa and S. marcescens. The active fraction of peptides was obtained from the culture liquid by precipitation at 80% saturation of ammonium sulphate. For peptides identification, the precipitate was treated with guanidine hydrochloride to desorb from proteins, separated with ultrafiltration on spin columns with 10,000 MWCO, desalted with a reversed-phase chromatography and subjected to LC–MS/MS analysis. The in silico analysis of the identified 1111 peptides by using ADAM, CAMPR3 and AMPA prediction servers led to identification of the linear peptide with highly probable antimicrobial activity and further investigation of its antibacterial activity mechanism is promising. By using the dereplication algorithm, the peptide highly similar to non-ribosomal cyclic AMPs originally isolated from Staphylococcus epidermidis has been identified. This indicates that L. fermentum HF-D1 represents a novel strain producing antimicrobial peptides targeting P. aeruginosa and S. marcescens.

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Fig. 1
Fig. 2
Fig. 3



A database of anti-microbial peptides


Antimicrobial peptide


Basic local alignment search tool


Bacteriocin like peptide


Collection of anti-microbial peptides


Formic acid


False discovery rate




High performance liquid chromatography


Isoelectric point calculator




Lactic acid bacteria




Liquid chromatography–mass spectrometry and liquid chromatography–tandem mass spectrometry


Matrix assisted laser desorption ionization-time of fight


Modular approach to software construction operation and test


Mascot generic format


Man, Rogosa, Sharpe


Mass spectrometry


Molecular weight cut-off


National center for biotechnology information


Non-ribosomal peptide


Phosphate-buffered saline


Peptidic natural products


Ribosomally synthesized and posttranslationally modified peptides


Trifluoroacetic acid


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Pavlova, A.S., Ozhegov, G.D., Arapidi, G.P. et al. Identification of Antimicrobial Peptides from Novel Lactobacillus fermentum Strain. Protein J (2020).

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  • Antimicrobial peptides
  • Lactobacillus fermentum
  • Mass-spectrometry
  • Cyclic peptides