Fecal microbiota analysis: an overview of sample collection methods and sequencing strategies.
Despite huge interest, there are still no universally accepted standards to conduct clinical studies in the field of gut microbiota analysis. Stool material is frequently used as a proxy of gut microbiota, but many different protocols can be used for collection and DNA extraction. Whereas 16S rRNA encoding gene amplification and sequencing has been widely used to study the composition of bacterial populations, it is now being challenged by the random, shotgun approach that brings far more information, although at a higher cost. In this review we give an overview of existing methods and important points to consider when conducting gut microbiota studies, with the objective to provide recommendations to those who would like to conduct such research.
Enterome Biosciences, 94-96 Avenue Ledru Rollin, 75011 Paris, France.
Vincent
V
Thomas
Enterome Biosciences, 94-96 Avenue Ledru Rollin, 75011 Paris, France.
James
J
Clark
INRA, MetaGenoPolis & Micalis Research Units 1319 & 1367, Jouy-en-Josas, France.
Joël
J
Doré
D035843:Biomedical Research; D004269:DNA, Bacterial / Q000235:genetics; D005243:Feces / Q000382:microbiology*; D000069196:Gastrointestinal Microbiome; D006801:Humans; D056186:Metagenomics / Q000379:methods; D010802:Phylogeny; D012336:RNA, Ribosomal, 16S / Q000235:genetics; D017422:Sequence Analysis, DNA; D013048:Specimen Handling
D004269:DNA, Bacterial; D012336:RNA, Ribosomal, 16S
16S; DNA extraction; clinical trials; fecal; gut microbiota; metagenomics; quality control; sequencing; stool