Soil-to-Shelf Microbiome Dynamics: Systems Approaches for Food Quality and Safety Assurance             (Microbiome and Food Safety: From Soil to Shelf)

Food safety challenges continue to escalate due to climate change, evolving agricultural practices, soil degradation, pesticide use, and complex supply chains. In this context, the microbiome has emerged as a critical determinant of food quality and safety at every stage of crop production and postharvest handling. Yet, the soil, plant, postharvest, and processing-related microbiomes are rarely studied holistically, despite their interdependence. Recent research demonstrates that Soil microbiota directly influences plant immunity, pathogen suppression, and nutrient availability. Endophytic communities modulate mycotoxin production, both inhibiting and enhancing fungal metabolite accumulation. Postharvest microbiome dynamics regulate spoilage, pathogen growth, and shelf-life outcomes. The scientific community urgently needs an integrated platform that consolidates advances from soil ecology, plant microbiology, postharvest biology, and food safety. Launching this Special Issue will meet this need by providing a comprehensive and multidisciplinary forum focused on microbiome-driven solutions to food safety challenges.

Keywords: Soil microbiome, Endophytes, Mycotoxins, Postharvest microbiome, Food safety, Microbiome engineering, Metagenomics, Predictive microbial modeling, Shelf-life extension, Biocontrol agents

 

Scope of the Special Issue

This Special Issue will highlight cutting-edge research and reviews in the following areas:

Soil Microbiome and Crop Safety

Microbial biodiversity and pathogen suppression

Soil health indicators linked to crop contamination risk

Microbiome responses to fertilizers, pesticides, and climate stress

Horizontal gene transfer and antimicrobial resistance (AMR) emergence in soil

Endophytes and Mycotoxin Regulation

Beneficial vs. pathogenic endophytes in toxin-producing crops

Mechanisms of Aspergillus, Fusarium, and Penicillium metabolite regulation

Microbial interactions affecting aflatoxin, fumonisin, DON, and OTA levels

Biocontrol endophytes for toxin reduction

Postharvest Microbiome Dynamics

Fungal and bacterial population shifts during storage

Cold chain microbiome evolution

Predictive modeling of spoilage or contamination

Microbiome-based postharvest interventions (biocontrol, natural antimicrobials)

Emerging Technologies

Metagenomics, metatranscriptomics, metabolomics

AI-driven microbiome analysis for food safety prediction

Microbial fingerprinting for crop authentication

Microbiome engineering strategies

Soil-to-Shelf Microbiome Perspective

Integrative studies linking field, harvest, storage, and retail microbiomes

Environmental drivers of microbial contamination pathways

Microbiome-informed risk assessment models

Timelines:

Submission of manuscript opens:                                                           January 1, 2026

Deadline for manuscript submission:                                                     July 30, 2026

 

Submission guidelines:

• The journal's Guide for Authors on how to prepare a paper is available at:

 https://qascf.com/index.php/qas/guidelines

• Papers must be submitted electronically via https://mc03.manuscriptcentral.com/qascf
• To ensure that all manuscripts are correctly identified for inclusion in the special issue, it is important to select the Section “Microbiome and Food Safety”.

 

Any inquiries regarding the content of papers should be submitted to:

Guest Editor

Professor Dr Lin Lin

School of Food Science and Biology Engineering, Jiangsu University, Zhenjiang, China

Email: [email protected]