Assessing microbiome engraftment extent following fecal microbiota transplant with q2-fmt

Abstract

We present q2-fmt, a QIIME 2 plugin that provides diverse methods for assessing the extent of microbiome engraftment following fecal microbiota transplant. The methods implemented here were informed by a recent literature review on approaches for assessing FMT engraftment, and cover aspects of engraftment including Chimeric Asymmetric Community Coalescence, Donated Microbiome Indicator Features, and Temporal Stability. q2-fmt is free for all use, and detailed documentation illustrating worked examples on a real-world data set are provided in the project's documentation.