Importance of methods selected for microbiome studies: State of the science and challenges

The microbiota has impact on virtually every aspect of poultry production, including performance, health, and food safety. It is therefore not surprising that considerable promise exists for the application of microbiota science in addressing current and future challenges faced across the poultry industry. Yet, methodological variation among poultry microbiota studies has had negative impact on reproducibility of findings, thereby slowing the application of effective microbiota-based solutions in a production setting. The experimental workflow in microbiota research involves many steps, ranging from sample collection to bioinformatic processing. Likewise, at each experimental stage there exists a vast methodological toolbox available to poultry microbiota researchers. As the technical decisions made at each experimental stage have demonstrable impact on each downstream step, outcomes in microbiota research are largely dependent on the methodologies employed. In order to improve translatability and reproducibility between different methodological pipelines, it is essential that a best practice framework be adopted in poultry science regarding microbiota research. The present review seeks to briefly encapsulate our symposium on microbiome methodology in poultry research. This symposium discussed the need for a robust set of evidence-based guidelines that streamline microbiota research in poultry. Attention was given to each major stage of a typical poultry microbiota study, including sample collection, storage, extraction, library preparation, sequencing, bioinformatic and data analyses, as well as data reporting and repositories. The use of positive and negative controls, improved reporting of raw data, and other tangible aspects that improve consistency and reproducibility across poultry microbiota study designs were highlighted. Ultimately, it was the goal of this symposium not to advocate a single methodology, but instead to demonstrate the need for robust practices at each experimental stage that enable cross-study comparisons of findings in poultry microbiota research.