The increasing complexity of food safety concerns, driven by the rising risks of contamination from pathogens, chemical hazards, and environmental influences, has highlighted the need for more effective detection and prevention strategies. Metagenomics, a powerful molecular tool, is transforming the food industry by providing a comprehensive understanding of the microbial communities in fresh produce, poultry, and meat. Advances in microbial detection techniques, such as shotgun sequencing, metabarcoding, and long-read sequencing technologies, have led to faster and more accurate pathogen detection, reducing the risk of outbreaks and ensuring public health protection. Despite its promise, several challenges remain in implementing metagenomics on a broader scale, including the high cost of sequencing technologies, the complexity of analyzing large datasets, and the lack of standardized procedures across platforms. These limitations hinder its adoption, particularly for smaller operations or in regions with fewer resources. This review examines the applications of metagenomics in food safety, focusing on its impact on meat, poultry, and fresh produce, while discussing the obstacles to its widespread use and potential solutions to overcome these barriers.

Rice husk (RH), a major byproduct of rice production, represents a significant environmental burden due to its high volume and common disposal through open burning. This study explores the potential of alkali-extracted lignin from Dominican rice husk (RHL) as a value-added bioproduct, with a focus on its characterization and antibacterial properties. Lignin was extracted using alkaline digestion from two rice varieties (Juma 69-20 and Prosequisa 4), and characterized via UV-Vis and FTIR spectroscopy. Extraction yields ranged from 18–23%, with no significant differences among varieties. Further optimization using Juma 69-20 showed that higher temperature (100°C) and smaller particle size (850–425 µm) significantly enhanced lignin recovery, with a maximum yield of 37.6%. Pretreatment had no significant effect. Spectroscopic analysis confirmed the presence of key lignin functional groups, although high oxidation levels and a predominance of ether bonds were noted. Despite literature reports of antimicrobial activity in lignin, RHL showed no inhibitory effects against ten bacterial strains. This may be due to unfavorable structural traits or particle size heterogeneity. Future work should focus on alternative extraction techniques and improved control over lignin structure to enhance its functional potential. This research supports the valorization of RH as a sustainable resource in biotechnological applications.

Metagenomics has revolutionized the study of microbial communities, enabling researchers to explore the complex and diverse ecosystems present in various environments, including food products. This review provides an overview of the recent advancements in metagenomic techniques applied to food analysis, highlighting their potential for enhancing food safety, quality, and understanding of food microbiomes. The use of metagenomics in food analysis has significantly expanded our knowledge of the microbial diversity and functional potential of edible products, shedding light on the interactions between food components and the microbiota. This review highlights the growing importance of metagenomic approaches in food analysis and emphasizes the potential implications for food safety, quality, and preservation. It also showcases the wide range of studies that have utilized metagenomics to unravel the hidden microbial world of edible products. However, the field of metagenomics in food analysis is continuously evolving, and future research is expected to bring even more exciting discoveries and applications to the food industry. Challenges and perspectives of this novel approach are also considered.