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.
Thomas V et al. (2015) Fecal microbiota analysis: an overview of sample collection methods and sequencing strategies. Future Microbiology 10(9) pp. 1485-1504 doi:10.2217/fmb.15.87