Joint Genome Institute 1 article published in JoVE Biology Purifying the Impure: Sequencing Metagenomes and Metatranscriptomes from Complex Animal-associated Samples Yan Wei Lim1, Matthew Haynes2, Mike Furlan1, Charles E. Robertson3, J. Kirk Harris4, Forest Rohwer1 1Department of Biology, San Diego State University, 2DOE Joint Genome Institute, 3Department of Molecular, Cellular and Developmental Biology, University of Colorado, 4Department of Pediatrics, School of Medicine, University of Colorado Using the cystic fibrosis airway as an example, the manuscript presents a comprehensive workflow comprising a combination of metagenomic and metatranscriptomic approaches to characterize the microbial and viral communities in animal-associated samples.