Towards standardization in pig microbiome research based on a comprehensive twenty-year review

The pig microbiome plays a crucial role in animal health, productivity, and meat quality. This comprehensive review analyzed 438 publications on pig microbiome studies from 2003 to 2023, focusing on experimental methodologies, bioinformatic tools, sequencing approaches, and metadata reporting practices. It critically analyzes the variability introduced by different DNA extraction methods, sequencing platforms, and bioinformatics pipelines, emphasizing their impacts on reproducibility and data comparability. We identify critical gaps in metadata reporting, particularly in DNA extraction protocols and bioinformatic workflows. To address these issues, we propose a standardized metadata template for pig microbiome studies, integrating Genomic Standards Consortium guidelines with project-specific criteria. This review provides a framework for developing standardized protocols in pig microbiome research, aiming to improve reproducibility and facilitate cross-study comparisons.