Reproducible, interactive, scalable and extensible microbiome data science using QIIME 2

E Bolyen, JR Rideout, MR Dillon, NA Bokulich… - Nature …, 2019 - nature.com
Nature biotechnology, 2019nature.com
To the Editor—Rapid advances in DNA-sequencing and bioinformatics technologies in the
past two decades have substantially improved understanding of the microbial world. This
growing understanding relates to the vast diversity of microorganisms; how microbiota and
microbiomes affect disease 1 and medical treatment 2; how microorganisms affect the health
of the planet 3; and the nascent exploration of the medical 4, forensic 5, environmental 6 and
agricultural 7 applications of microbiome biotechnology. Much of this work has been driven …
To the Editor—Rapid advances in DNA-sequencing and bioinformatics technologies in the past two decades have substantially improved understanding of the microbial world. This growing understanding relates to the vast diversity of microorganisms; how microbiota and microbiomes affect disease 1 and medical treatment 2; how microorganisms affect the health of the planet 3; and the nascent exploration of the medical 4, forensic 5, environmental 6 and agricultural 7 applications of microbiome biotechnology. Much of this work has been driven by marker-gene surveys (for example, bacterial/archaeal 16S rRNA genes, fungal internal-transcribed-spacer regions and eukaryotic 18S rRNA genes), which profile microbiota with varying degrees of taxonomic specificity and phylogenetic information. The field is now transitioning to integrate other data types, such as metabolite 8, metaproteome 9 or metatranscriptome 9, 10 profiles.
The QIIME 1 microbiome bioinformatics platform has supported many microbiome studies and gained a broad user and developer community. Interactions with QIIME 1 users in our online support forum, our workshops and direct collaborations have shown the platform’s potential to serve an increasingly diverse array of microbiome researchers in academia, government and industry. Here, we present QIIME 2, a completely reengineered and rewritten system that is expected to facilitate reproducible and modular analysis of microbiome data to enable the next generation of microbiome science.
nature.com