In Silico Identification of Antimicrobial Peptides in the Proteomes of Goat and Sheep Milk and Feta Cheese

Abstract

Milk and dairy products are a major functional food group of growing scientific and commercial interest due to their nutritional value and bioactive “load”. A major fraction of the latter is attributed to milk’s rich protein content and its biofunctional peptides that occur naturally during digestion. On the basis of the identified proteome datasets of milk whey from sheep and goat breeds in Greece and feta cheese obtained during previous work, we applied an in silico workflow to predict and characterise the antimicrobial peptide content of these proteomes. We utilised existing tools for predicting peptide sequences with antimicrobial traits complemented by in silico protein cleavage modelling to identify frequently occurring antimicrobial peptides (AMPs) in the gastrointestinal (GI) tract in humans. The peptides of interest were finally assessed for their stability with respect to their susceptibility to cleavage by endogenous proteases expressed along the intestinal part of the GI tract and ranked with respect to both their antimicrobial and stability scores.

FoodOmicsGR_RI: A Consortium for Comprehensive Molecular Characterisation of Food Products

“…Specifically, high-resolution-mass spectrometry (HRMS) nano-LC MS/MS Orbitrap Elite is used for the proteomic and peptidomic analysis of Greek dairy products including local cheeses such as feta, graviera, etc. Proteome and peptidome are very important information for the characterization of the uniqueness of Greek cheese [ 77 ]. The analysis is targeted at the detailed identification of the proteome and peptidome content of the major Greek cheeses.…”

Proteomics Analysis in Dairy Products: Cheese, a Review

“…As previously discussed, these peptides are well protected in the protein matrix of milk, requiring proteolytic enzymes, originating from various sources, such as natural rennet or starter bacteria, for their release. A growing body of evidence indicates that milk and dairy products have unique metabolic, signaling and antimicrobial effects, apart from their high nutritional content [102][103][104][105]. Such peptides are involved in many physiological activities, including regulation of inflammatory and immune response, signaling and metabolic process, antihypertensive, antioxidant and antimicrobial properties [105].…”

“…The milk and dairy products from different animal breeds and species have unique compositions of bioactive peptides offering a broad range of sequences to screen for peptides with functional traits of medical and scientific interest [109]. Tomazou et al [102] focused on the potential antimicrobial properties of Feta cheese, to probe for AMPs following an assessment of their stability in an intestine-like environment and they characterized the antimicrobial "load" of the proteomes of interest. Protein sequences from Feta cheese were screened using the publicly available tool AMPA [110,111] to find sequence stretches with predicted high antimicrobial potential (i.e., low AMPA propensity).…”

Proteomic profiling of ovine milk after grading up

“…Some proteomic studies of bovine milk have characterized its bioactive profile and verified various biological functions (Lönnerdal, 2014; Reznikov et al ., 2014). Also, there are some studies that described the difference between ovine and other species milk (Anagnostopoulos et al ., 2016; Chen et al ., 2016; Greco et al ., 2018; Tomazou et al ., 2019). However, few studies focused on cross breeding effects on milk proteomics.…”