Quadram Institute Best Practice in Microbiome Research

The human microbiome and in particular the gut microbiome, is at the leading edge of scientific research. Despite the publication of more than 50,000 research articles since 2000 (Web of Science) implicating the gut microbiome in health and disease, there is a staggering lack of reproducibility amongst the majority of these studies; this has hampered the translation of microbiome research to the clinic [1-2].

In particular, the application of different methodologies and techniques to different microbiome studies limits their usefulness and validation, and the ability to compare data across different studies. Few widely accepted standards or reference reagents exist for conducting gut microbiome research [3]. Establishing standard operating procedures (SOPs) for sample collection and analysis is a prerequisite for the establishment of biospecimen repositories and large databases, and for validating and comparing results from different studies.

To help achieve this the Quadram Institute (QI) is providing protocols that have been developed, optimised and applied to microbiome studies across the Institute. It is to be noted that some protocols, particularly those involving automation and informatics, are constantly evolving and being improved.

While it is our intention to keep these protocols up to date, users are reminded that this is a rapidly evolving field and they should monitor the latest literature. Nevertheless, these protocols highlight critical concepts and key features, and so serve as a valuable benchmark.

We have made the protocols available under a Creative Commons Attribution-ShareAlike 4.0 International License. You can use share and adapt them as long as you give appropriate credit, using the citation on each protocol.

Contents

• 1. Study Design Considerations
• 2. Sample Size for a Microbiome Experiment
• 3. Sample Collection and Initial Processing of Faecal Samples
• 4. DNA Extraction and Quality Control
• 5. 16S Illumina Library Preparation
• 6. Shotgun Metagenomic Illumina Library Preparation
• 7. Microbiome Informatics
• 8. Statistical Analysis of Microbiome Data
• 9. Virome-Specific Protocols
• 10. Mycobiome-Specific Protocols

Lectures, seminars and videos 

• MRC NuTrioM ‘Best Practice in Microbiome Research’ Workshop (QI June 2021).

Contact

If you have any questions, comments or queries, please contact info@quadram.ac.uk

References

1. Falony G, Vandeputte D, Caenepeel C, Vieira-Silva S, Daryoush T, Vermeire S, Raes J.(2019) The human microbiome in health and disease: hype or hope, Acta Clin Belg 74:2, 53-64, doi: 1080/17843286.2019.1583782

2. Li D, Gao C, Zhang F, Yang R, Lan C, Ma Y, Wang J. (2020) Seven facts and five initiatives for gut microbiome research. Protein Cell 11:391-400. doi: 10.1007/s13238-020-00697-8. PMID: 32172500; PMCID: PMC7251010.

3. Amos GCA, Logan A, Anwar S, Fritzsche M, Mate R, Bleazard T, Rijpkema S. (2020)Developing standards for the microbiome field. Microbiome 8: doi: 10.1186/s40168-020-00856-3