  Fecal Microbiota Transplant (FMT) is an FDA approved treatment for recurrent
Clostridium difficile infections, and is being explored for other clinical
applications, from alleviating digestive and neurological disorders, to priming
the microbiome for cancer treatment, and restoring microbiomes impacted by
cancer treatment.
  Quantifying the extent of engraftment following an FMT is important in
determining if a recipient didn't respond because the engrafted microbiome
didn't produce the desired outcomes (a successful FMT, but negative treatment
outcome), or the microbiome didn't engraft (an unsuccessful FMT and negative
treatment outcome). The lack of a consistent methodology for quantifying FMT
engraftment extent hinders the assessment of FMT success and its relation to
clinical outcomes, and presents challenges for comparing FMT results and
protocols across studies.
  Here we review 46 studies of FMT in humans and model organisms and group
their approaches for assessing the extent to which an FMT engrafts into three
criteria: 1) Chimeric Asymmetric Community Coalescence investigates microbiome
shifts following FMT engraftment. 2) Donated Microbiome Indicator Features
tracks donated microbiome features as a signal of engraftment with methods such
as differential abundance testing based on the current sample collection, or
tracking changes in feature abundances that have been previously identified. 3)
Temporal Stability examines how resistant post-FMT recipient's microbiomes are
to reverting back to their baseline microbiome. Investigated together, these
criteria provide a clear assessment of microbiome engraftment.
  We discuss the pros and cons of each of these criteria, providing
illustrative examples of their application. We also introduce key terminology
and recommendations on how FMT studies can be analyzed for rigorous engraftment
extent assessment.
