Collection and sequencing of fecal material as a proxy of gut microbial content is becoming more and more frequent for clinical and/or research studies. However, there are still no universally accepted guidelines and it is consequently often difficult to choose appropriate methodologies for those who are not familiar with the field. This review evaluates the different options available for conducting such studies. We give an overview of sampling methods and important points to take into account for DNA extraction. Sequencing strategies including 16S-based taxonomic repertoire and random shotgun sequencing are explained, including an extensive comparison of the pros and cons of these two different analyses that are often grouped under the term “metagenomics”. The review also includes a specific section on quality controls and validation methods that can be applied to the full process.
Vincent Thomas Vincent has a broad range of experience in microbial ecology, including environmental and clinical microbiology. He worked for 10 years at the interface between academics and private companies, succeeding in conducting strategic research projects and publishing more than 35 peer-reviewed papers.