Advances in Foodborne Pathogenic Bacteria Microcosm Mapping and Its Interrelation Within the Food Production Setting

A special issue of Applied Microbiology (ISSN 2673-8007).

Deadline for manuscript submissions: 31 October 2025 | Viewed by 1045

Special Issue Editors


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Guest Editor

Special Issue Information

Dear Colleagues,

The occurrence of foodborne pathogenic bacteria is a major concern. Each year, hundreds of thousands of incidences are reported, resulting in thousands of hospitalizations and deaths, which are accompanied by significant economic losses. Therefore, their subsistence in the food production chain has been under intensive scientific scrutiny. Their prevalence from farm to fork, the sources of contamination and the effect of the interventions employed, as well as their physiology both outside and inside the host have been thoroughly assessed in recent decades. The application of next-generation sequencing-based techniques has led to the generation of data that improved our understanding regarding the aforementioned issues and allowed us to gain valuable insights in an effort to efficiently mitigate the effect that these pathogens have on human health and enhance food safety. At the same time, the utilization of this approach to reduce the time needed for foodborne pathogenic bacteria detection and to study emerging issues, such as antimicrobial resistance, is gaining scientific interest. The aim of this Special Issue is to create a collection of high-quality articles that facilitate understanding, update current knowledge, and identify research gaps regarding foodborne pathogenic bacteria persistence within the food processing environment and across the food production chain.

You may choose our Joint Special Issue in Microorganisms.

Dr. Marios Mataragas
Dr. Nikolaos D. Andritsos
Dr. Spiros Paramithiotis
Guest Editors

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Keywords

  • foodborne pathogenic bacteria
  • food processing
  • next-generation

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Published Papers (1 paper)

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Review

25 pages, 739 KiB  
Review
Unlocking the Hidden Microbiome of Food: The Role of Metagenomics in Analyzing Fresh Produce, Poultry, and Meat
by Tania Isabel Muñoz-Martinez, Bianca Rodríguez-Hernández, Milagros Rodríguez-Montaño, Jessica Alfau, Claudia Reyes, Yumeris Fernandez, Rommel T. Ramos, Edian F. Franco De Los Santos and Luis Orlando Maroto-Martín
Appl. Microbiol. 2025, 5(1), 26; https://doi.org/10.3390/applmicrobiol5010026 - 27 Feb 2025
Viewed by 741
Abstract
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 [...] Read more.
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. Full article
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