Best Practice in Microbiome Research

📒 Link to the book (Open Access)

The human gut microbiome is one of the most active areas in biomedical research. Thousands of studies link it to health and disease, yet the field still faces a major problem: poor reproducibility. Different studies often use different methods, making results hard to compare and slowing progress towards clinical applications.

One of the main reasons is the lack of widely accepted standards. Variations in sample collection, storage, sequencing, and data analysis can all strongly affect results. Without shared best practices, even large datasets can lose much of their value.

At the Quadram Institute, reproducibility is a core principle of microbiome research. To support this, Quadram has developed and shared a set of standardised protocols covering the entire workflow, from study design and sample handling to sequencing, bioinformatics, and statistics. These are not theoretical guidelines, but methods tested and used across real research projects.

These protocols are collected in the open-access book Best Practice in Microbiome Research, edited by Simon R. Carding. The book includes step-by-step methods, practical advice, and protocols for bacterial, viral, and fungal microbiomes, as well as dedicated chapters on reproducible bioinformatics.

All protocols are released under a Creative Commons license, meaning they can be freely used and adapted with proper attribution. While the field continues to evolve, these methods provide a clear and reliable benchmark for robust, comparable microbiome research.