Metataxonomic identification of the microbial diversity of fermented foods; Evaluation of bacterial strains for antimicrobial activity

Kamilari, Eleni

Metataxonomic identification of the microbial diversity of fermented foods; Evaluation of bacterial strains for antimicrobial activity

cbn

Date

2025

Authors

Kamilari, Eleni

Publisher

University College Cork

Abstract

Microbial contamination that deteriorates food quality continues to pose a significant challenge for the food industry. Estimates indicate that nearly 300 million tons of food suitable for human consumption, approximately one-third of global production, are lost annually. In parallel, foodborne illnesses affect an estimated 600 million individuals each year, resulting in approximately 420,000 deaths worldwide. These statistics highlight the pressing need for preservation strategies that are not only effective and sustainable but also safe for consumers. Increasing public concern over the health risks associated with synthetic preservatives has further generated the demand for natural alternatives. In this context, the use of natural biopreservatives, such as microorganisms with a long-standing record of safe use or microbially derived antimicrobial peptides, emerges as a promising solution to help mitigate this global problem. The present thesis aims to address this global challenge by identifying microbial strains with Generally Recognized as Safe (GRAS) or Qualified Presumption of Safety (QPS) status, and novel antimicrobial peptides, such as bacteriocins, with the potential to be applied as biocontrol agents in food products. Drawing from current scientific literature, Chapter 1 aims to highlight the potential for replacing synthetic preservatives with natural, consumer-safe biopreservatives, including QPS and GRAS status microbial strains, and clean-label antimicrobial peptides (AMPs), thereby contributing to the global effort to reduce food waste. In light of the growing concern surrounding foodborne pathogens harboring antibiotic resistance genes, particular attention is given to the application of bacteriocins, a specific category of AMPs, for the selective inhibition of specific harmful microorganisms in food systems. The chapter also explores strategies to enhance the antimicrobial effectiveness of bacteriocins against both Gram-negative and Gram-positive bacteria. Chapter 2 examines the biotechnological significance of the filamentous yeast-like fungus Geotrichum candidum, a widespread species widely recognized for its role as a starter culture in the dairy industry. Beyond its conventional applications in dairy and brewing, our analysis highlights its use as a probiotic nutritional supplement in aquaculture, and its industrial importance associated with the production of diverse range of industrially relevant enzymes, including cellulases, β-glucanases, xylanases, lipases, proteases, and α-amylases. Additionally, certain strains have demonstrated antimicrobial activity and bioremediation potential. The findings presented in this review underscore the relevance of G. candidum to both the agrifood and bio-industrial sectors and shed light on its prospective applications in emerging biotechnological fields. Fermented dairy products, such as cheeses, play a vital role in supporting local economies and serve as rich reservoirs of beneficial microorganisms, particularly lactic acid bacteria (LAB). The objective of Chapter 3 was to investigate the microbial diversity of cheeses from distinct geographical regions, focusing specifically on Irish and Eastern Mediterranean varieties—namely Greek and Cypriot cheeses—using amplicon sequencing. This comparative analysis aimed to identify microbial patterns linked to regional production practices in ripened cheeses. Furthermore, the construction of microbial interaction networks was employed to elucidate potential relationships and interactions within the microbial communities. Similarly, chapter 4 aimed to characterize the microbial biodiversity of fermented sausages originating from the Eastern Mediterranean islands of Cyprus and Mytilini through amplicon sequencing. An additional objective was to compare the microbial communities present in traditionally versus industrially produced Cypriot sausages, in order to assess the impact of production methods on microbial composition. Moreover, microbial interaction networks were constructed to uncover potential associations and interactions within these microbial ecosystems. Chapter 5 presents the findings of an industrial project performed in collaboration with Kraft Heinz company, aimed at identifying natural, safe, and effective microbial strains and novel AMPs for use as biopreservatives targeting specific food spoilage microorganisms, with the goal of extending product shelf life. As part of this initiative, a comprehensive screening of 3,415 microbial isolates from 36 varied sources was conducted. From this collection, 24 strains exhibiting QPS status and strong antimicrobial activity against major foodborne pathogens and spoilage organisms were selected for whole-genome sequencing (WGS). Subsequent genome mining revealed multiple biosynthetic gene clusters (BGCs), including 13 clusters potentially encoding novel bacteriocins and other bioactive secondary metabolites. Taken together, the broad-spectrum antimicrobial properties exhibited by the detected microbial strains underscore their strong potential as effective agents for the biological management of microbial communities within food systems. Chapter 6 highlights the potential of Bacillus safensis APC 4099 as a promising biopreservative candidate for food applications. Antimicrobial screening demonstrated its broad-spectrum inhibitory activity, targeting both Gram-positive pathogenic bacteria and food spoilage fungi. This efficacy is attributed to the production of multiple antimicrobial peptides, including the novel circular bacteriocin safencin E. Collectively, this strain and its bioactive compounds represent a valuable strategy for mitigating food spoilage and, consequently, reducing food waste on a global scale. Fungal contamination of food presents significant economic challenges and health hazards, particularly due to the production of mycotoxins. Chapter 7 investigates the potential of the antifungal lipopeptides herbicolin A and B, derived from Pantoea agglomerans APC 4211, as biocontrol agents against spoilage fungi in dairy products. The chapter outlines the purification process of the lipopeptides, determination of their minimum inhibitory concentration (MIC) required to suppress fungal growth, assessment of their thermal stability and protease resistance, comparison with five commercially available antifungal agents, and evaluation of cytotoxicity on S9 epithelial cell lines. Notably, application of herbicolins in 10% skim milk demonstrated that a concentration of 5 μg/ml effectively inhibited Aspergillus niger and Penicillium notatum after three days of fermentation, outlining the importance of herbicolins A and B as possible biopreservatives in food matrices. Overall, this work highlights the potential of utilizing natural, consumer-safe microbial strains and clean-label AMPs as effective biopreservatives against spoilage and pathogenic microorganisms, thereby contributing to global efforts to reduce food waste. Additionally, it provides insights into how to regional production practices may influence the composition and dynamics of microbial communities in fermented products, specifically cheeses and sausages.

Description

Controlled Access

Keywords

Natural biopreservatives , Antimicrobial peptides , Bacteriocins , Food biopreservation , Antimicrobial resistance , High throughput sequencing , Microbial diversity , Metataxonomic sequencing , Mature cheeses , Fermented sausages

Citation

Kamilari, E. 2025. Metataxonomic identification of the microbial diversity of fermented foods; Evaluation of bacterial strains for antimicrobial activity. PhD Thesis, University College Cork.