QIIME

QIIME 2 is a software tool that has been completely reengineered and rewritten to enable the next generation of microbiome science. It was developed based on a plugin architecture that allows third parties to contribute functionality. It is a powerful and versatile data science platform that can be rapidly adapted to analyze diverse microbiome features.

QIIME 2 provides new interactive visualization tools that facilitate exploratory analyses and result reporting. Moreover, it includes a unique and secure service called QIIME 2 View, which allows users to share and interact with results without installing QIIME 2. The QIIME 2 visualizations presented in Fig. 1 are provided in Supplementary File 1 to allow readers to interact with QIIME 2 View.

In the past two decades, rapid advances in DNA-sequencing and bioinformatics technologies have substantially improved our understanding of the microbial world. This growing understanding relates to the vast diversity of microorganisms, including how microbiota and microbiomes affect disease and medical treatment, how microorganisms affect the planet's health, and the nascent exploration of the medical, forensic, environmental, and agricultural applications of microbiome biotechnology.

Marker-gene surveys have driven much of this work, profiling microbiota with varying degrees of taxonomic specificity and phylogenetic information. However, the field is now transitioning to integrate other data types, such as metabolite, metaproteome, or metatranscriptome profiles. QIIME 2 has been developed to support multidimensional and powerful data science analysis of diverse microbiome features to meet this challenge.