Identification of Antimicrobial Peptides from Novel Lactobacillus fermentum Strain

Pavlova, Anna S; Arapidi, Georgij; Butenko, Ivan; Fomin, E. S.; Alemasov, N. A.; Afonnikov, D. A.; Yarullina, D. R.; Иванов, В. Т.; Govorun, Vadim M.; Kayumov, Airat R.

doi:10.1007/s10930-019-09879-8

Cited by 16 publications

(17 citation statements)

References 58 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…From left to right are shown in order: peptide contig, AVP motif model results, alignment model results, composition model results, the physio-chemical model results, the overall results for the antiviral prediction, antifungal score and prediction result for the antifungal activity. www.nature.com/scientificreports/ the approach we reported is based on the use of several softwares, previously employed to perform similar analyses [49][50][51] , that exploit different algorithms for the determination of a score that predicts the biological activity of unknown peptides. We demonstrated that a similar approach can provide reliable indications about the potential biological activities of candidate AMPs, as confirmed by our preliminary tests on the antimicrobial activity of four identified AMPs ( Supplementary Fig.…”

Section: Discussionmentioning

confidence: 99%

A bioinformatic study of antimicrobial peptides identified in the Black Soldier Fly (BSF) Hermetia illucens (Diptera: Stratiomyidae)

Moretta

Salvia

Scieuzo

et al. 2020

Sci Rep

115

View full text Add to dashboard Cite

Antimicrobial peptides (AMPs) play a key role in the innate immunity, the first line of defense against bacteria, fungi, and viruses. AMPs are small molecules, ranging from 10 to 100 amino acid residues produced by all living organisms. Because of their wide biodiversity, insects are among the richest and most innovative sources for AMPs. In particular, the insect Hermetia illucens (Diptera: Stratiomyidae) shows an extraordinary ability to live in hostile environments, as it feeds on decaying substrates, which are rich in microbial colonies, and is one of the most promising sources for AMPs. The larvae and the combined adult male and female H. illucens transcriptomes were examined, and all the sequences, putatively encoding AMPs, were analysed with different machine learning-algorithms, such as the Support Vector Machine, the Discriminant Analysis, the Artificial Neural Network, and the Random Forest available on the CAMP database, in order to predict their antimicrobial activity. Moreover, the iACP tool, the AVPpred, and the Antifp servers were used to predict the anticancer, the antiviral, and the antifungal activities, respectively. The related physicochemical properties were evaluated with the Antimicrobial Peptide Database Calculator and Predictor. These analyses allowed to identify 57 putatively active peptides suitable for subsequent experimental validation studies.

show abstract

Section: Discussionmentioning

confidence: 99%

A bioinformatic study of antimicrobial peptides identified in the Black Soldier Fly (BSF) Hermetia illucens (Diptera: Stratiomyidae)

Moretta

Salvia

Scieuzo

et al. 2020

Sci Rep

115

View full text Add to dashboard Cite

show abstract

“…Colonies on MRS agar were small (approximately 1 mm in diameter), round, convex, smooth, with entire margins, and white. Identification of the strain was completed by MALDI-TOF mass spectrometry (MALDI Biotyper system, Bruker Daltonik, Germany) [1] and genotyping. For further cultivation of the isolate, MRS broth (HiMedia, India) was used.…”

Section: Experimental Design Materials and Methodsmentioning

confidence: 99%

“…Antibacterial peptides were predicted by using AMPA ( http://tcoffee.crg.cat/apps/ampa/do ) [11] , ADAM ( http://bioinformatics.cs.ntou.edu.tw/ADAM/ ) [12] , CAMPR3 ( http://www.camp3.bicnirrh.res.in/ ) [13] . The following thresholds were selected for positive decision regarding putative antimicrobial activity: >0.2 in AMPA, >0 in ADAM and >0.5 in CAMPR3 [1] .…”

Section: Experimental Design Materials and Methodsmentioning

confidence: 99%

“…Lactobacilli were isolated from the feces of healthy woman. From 40 randomly selected colonies, an isolate producing antibacterial compounds capable of suppressing the growth of P. aeruginosa and S. marcescens was chosen [1] . Initial identification of the bacterial isolate by MALDI-TOF mass spectrometry on Brucker Biotyper and 16S rRNA sequencing revealed that the studied isolate is a representive of the species Lactobacillus fermentum (score 2.007 according to Brucker Biotyper and 99.9% identity with 16S rRNA gene of L. fermentum strain YL-11 , GenBank: CP034193.1).…”

Section: Data Descriptionmentioning

confidence: 99%

“…L. fermentum HFD1 produces antibacterial compounds of peptide nature [1] . The analysis of ORFs encoding for putative small peptides and proteins with unknown function by using AMPA, ADAM and CAMPR3 algorithms [ 11 , 12 , 13 ] in order to predict their potential antimicrobial activities allowed revealing of 4 proteins as putative antimicrobial peptides ( Table 2 ).…”

Section: Data Descriptionmentioning

confidence: 99%

See 2 more Smart Citations

Whole genome sequence data of Lactobacillus fermentum HFD1, the producer of antibacterial peptides

et al. 2020

Self Cite

View full text Add to dashboard Cite

Here we report the whole genome sequence of Lactobacillus fermentum HFD1 strain, the producer of antibacterial peptides. The genome consists of one circular chromosome with 2101878 bp in length and GC-content of 51.8%, and includes linear DNA with 5386 bp in length with 100% identity to bacteriophage phiX174. The analysis of the genome has revealed 2049 genes encoding for proteins including 867 proteins without known function and 70 genes encoding for RNAs (10 rRNAs, 59 tRNAs and 1 tmRNA). Putative genes responsible for the biosynthesis of 4 antimicrobial peptides were identified. The NCBI Bioproject has been deposited at NCBI under the accession number PRJNA615901 ( https://www.ncbi.nlm.nih.gov/bioproject/PRJNA615901/ ) and consist of full annotated genome and raw sequence data.

show abstract

Whole-genome sequencing and antimicrobial potential of bacteria isolated from Polish honey

Hafeez,

Pełka,

Buzun

et al. 2023

Appl Microbiol Biotechnol

View full text Add to dashboard Cite

The aim of this study was the whole-genome analysis and assessment of the antimicrobial potential of bacterial isolates from honey harvested in one geographical location—the north of Poland. In total, 132 strains were derived from three honey samples, and the antimicrobial activity of CFAM (cell-free after-culture medium) was used as a criterion for strain selection and detailed genomic investigation. Two of the tested isolates (SZA14 and SZA16) were classified as Bacillus paralicheniformis, and one isolate (SZB3) as Bacillus subtilis based on their ANI and phylogenetic analysis relatedness. The isolates SZA14 and SZA16 were harvested from the same honey sample with a nucleotide identity of 98.96%. All three isolates have been found to be potential producers of different antimicrobial compounds. The secondary metabolite genome mining pipeline (antiSMASH) identified 14 gene cluster coding for non-ribosomal peptide synthetases (NRPs), polyketide synthases (PKSs), and ribosomally synthesized and post-translationally modified peptides (RiPPs) that are potential sources of novel antibacterials. The BAGEL4 analysis revealed the presence of nine putative gene clusters of interest in the isolates SZA14 and SZA16 (including the presence of six similar clusters present in both isolates, coding for the production of enterocin Nkr-5-3B, haloduracin-alpha, sonorensin, bottromycin, comX2, and lasso peptide), and four in B. subtilis isolate SZB3 (competence factor, sporulation-killing factor, subtilosin A, and sactipeptides). The outcomes of this study confirm that honey-derived Bacillus spp. strains can be considered potential producers of a broad spectrum of antimicrobial agents. Key points • Bacteria of the genus Bacillus are an important component of honey microbiota. • Honey-derived Bacillus spp. strains are potential producers of new antimicrobials.

show abstract

Identification of Antimicrobial Peptides from Novel Lactobacillus fermentum Strain

Cited by 16 publications

References 58 publications

A bioinformatic study of antimicrobial peptides identified in the Black Soldier Fly (BSF) Hermetia illucens (Diptera: Stratiomyidae)

A bioinformatic study of antimicrobial peptides identified in the Black Soldier Fly (BSF) Hermetia illucens (Diptera: Stratiomyidae)

Whole genome sequence data of Lactobacillus fermentum HFD1, the producer of antibacterial peptides

Whole-genome sequencing and antimicrobial potential of bacteria isolated from Polish honey

Contact Info

Product

Resources

About