TY - JOUR T1 - PICRUSt2: An improved and extensible approach for metagenome inference JF - bioRxiv DO - 10.1101/672295 SP - 672295 AU - Gavin M. Douglas AU - Vincent J. Maffei AU - Jesse Zaneveld AU - Svetlana N. Yurgel AU - James R. Brown AU - Christopher M. Taylor AU - Curtis Huttenhower AU - Morgan G. I. Langille Y1 - 2019/01/01 UR - http://biorxiv.org/content/early/2019/06/15/672295.abstract N2 - One major limitation of microbial community marker gene sequencing is that it does not provide direct information on the functional composition of sampled communities. Here, we present PICRUSt2, which expands the capabilities of the original PICRUSt method to predict approximate functional potential of a community based on marker gene sequencing profiles. This updated method and implementation includes several improvements over the previous algorithm: an expanded database of gene families and reference genomes, a new approach now compatible with any OTU-picking or denoising algorithm, novel phenotype predictions, and novel fungal reference databases that enable predictions from 18S rRNA gene and internal transcribed spacer amplicon data. Upon evaluation, PICRUSt2 was more accurate than PICRUSt1 and other current approaches and also more flexible to allow the addition of custom reference databases. Last, we demonstrate the utility of PICRUSt2 by identifying potential disease-associated microbial functional signatures based on 16S rRNA gene sequencing of ileal biopsies collected from a cohort of human subjects with inflammatory bowel disease. PICRUSt2 is freely available at: https://github.com/picrust/picrust2. ER -