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In this tutorial, we analyze a subset of the Early Childhood Antibiotics and the Microbiome (ECAM) study, which tracked the microbiome composition and development of 43 infants in the United States from birth to 2 years of age, identifying microbiome associations with antibiotic exposure, delivery mode, and diet. For more information about QIIME 2, see https//qiime2.org. To troubleshoot or ask questions about QIIME 2 and microbiome analysis, join the active community at https//forum.qiime2.org. © 2020 The Authors. Basic Protocol Using Q