Microbiome research best practice website launched

27th June 2021

Microbiome scientists from the Quadram Institute on the Norwich Research Park have combined their expertise to produce a Best Practice in Microbiome Research website.

The website contains freely accessible protocols developed and optimised for microbiome studies, and these will be updated to keep pace with the rapidly evolving field of 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 implicating the gut microbiome in health and disease, there is a staggering lack of reproducibility amongst the majority of these studies hampering the translation of microbiome research to the clinic.

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. 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. Nevertheless, these protocols highlight critical concepts and key features, and so serve as a valuable benchmark.

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.

Where can I find protocols for microbiome research?


What do the microbiome protocols cover?

  • Study Design Considerations
  • Sample Size for a Microbiome Experiment
  • Sample Collection and Initial Processing of Faecal Samples
  • DNA Extraction and Quality Control
  • 16S Illumina Library Preparation
  • Shotgun Metagenomic Illumina Library Preparation
  • Microbiome Informatics
  • Statistical Analysis of Microbiome Data
  • Virome-Specific Protocols
  • Mycobiome-Specific Protocols

How do I use, modify, share or cite the protocols?

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.

Who created these protocols?

Quadram Institute researchers who are regularly planning, designing, carrying out and analysing microbiome research contributed their expertise to this, as listed in each protocol. Meet the team below.

Related Targets

Targeting the understanding of the microbiome

Understanding the Microbiome

Related Research Groups

Evelien Adriaenssens

Falk Hildebrand

Carding group

Simon Carding

Related Research Areas