Protocols
Standardized methodologies for food microbiome research and analysis
Sample Collection
Implementation of harmonized protocols for microbial sampling, metadata capture, and high-throughput DNA extraction across food types and locations.
Reference:
Barcenilla, C., Cobo-Díaz, J.F., De Filippis, F. et al. Improved sampling and DNA extraction procedures for microbiome analysis in food-processing environments. Nat Protoc 19, 1291–1310 (2024). https://doi.org/10.1038/s41596-023-00949-x
Data Integration
Comprehensive metagenomic sequencing followed by taxonomic profiling, functional annotation, and contextual analysis to reveal patterns across food categories, geography, and processing.
Reference:
Bai, Defeng, Tong Chen, Jiani Xun, Chuang Ma, Hao Luo, Haifei Yang, Chen Cao, et al. 2025. "EasyMetagenome: A user-friendly and flexible pipeline for shotgun metagenomic analysis in microbiome research." iMeta 4: e70001. https://doi.org/10.1002/imt2.70001
- User-friendly shotgun metagenomic analysis
- Flexible pipeline for microbiome research
- Comprehensive taxonomic profiling
- Functional annotation and analysis
- Cross-food category pattern analysis
- Geographical distribution studies
- Processing method impact assessment
- Contextual data integration
