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We demonstrate the ways in which automatic, integrated, decentralized provenance tracking in QIIME 2, a leading microbiome bioinformatics platform, enables reproducible microbiome science. We use sample data from a recent study of arid soil microbiomes (Significant Impacts of Increasing Aridity on the Arid Soil Microbiome; Neilson et al, 2017[2]), to illustrate specific analyses that QIIME 2 supports, and to frame our discussion of the QIIME 2 platform. QIIME 2 actions yield as outputs Artifacts integrating the requested data or visualization with comprehensive data provenance that describes the computational history of that data or visualization, including all methods and parameters involved in its creation. This approach gives users, reviewers, and readers powerful tools for understanding, reproducing, and extending studies. The benefits this approach provides to both the researcher and the scientific community are significant, and provide a useful model for research software developers across disciplines.