Interrogating the microbiome: experimental and computational considerations in support of study reproducibility. Issue 9 (September 2018)

• Record Type: Journal Article
• Authors: Poussin, Carine; Sierro, Nicolas; Boué, Stéphanie; Battey, James; Scotti, Elena; Belcastro, Vincenzo; Peitsch, Manuel C.; Ivanov, Nikolai V.; Hoeng, Julia
• Is Part Of: Drug discovery today. Volume 23:Issue 9(2018)
• Page Start: 1644
• Page End: 1657
• Publication Date: 2018-09
• Subjects: Drugs -- Design -- Periodicals; Drugs -- Research -- Periodicals; 615.1
• DOI: 10.1016/j.drudis.2018.06.005
• Languages: English
• ISSNs: 1359-6446

Abstract

Graphical abstract: Highlights: 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. Abstract : The microbiome is an important factor in human health and disease and is investigated to develop novel therapeutics. Metagenomics leverages advances in sequencing technologies and computational analysis to identify and quantify the microorganisms present in a sample. This field has, however, not yet reached maturity and the international metagenomics community, aware of the current limitations and of the necessity for standardization, has started investigating sources of variability in experimental and computational workflows. The first studies have already resulted in the identification of crucial steps and factors affecting metagenomics data quality, quantification and interpretation. This review summarizes experimental and computational considerations for interrogating the microbiome and establishing reproducible and robust analysis workflows.