Interrogating the microbiome: experimental and computational considerations in support of study reproducibility

•Growing evidence indicates that the microbiome plays an important role in health and disease.•Reliable and meaningful scientific conclusions from microbiome studies rely on accurate analysis of microbial communities.•Current experimental and computational recommendations for the conduct of a microbiome study are summarized here.•However, standardized procedures and guidelines are necessary to ensure reproducibility and comparability across microbiome studies.•The review also highlights international synergies in the metagenomics community to establish standards and robust methods.