DOI: 10.1101/19000307Sep 26, 2019Paper

Framework for rational donor selection in fecal microbiota transplant clinical trials

MedRxiv : the Preprint Server for Health Sciences
Claire DuvalletEric J Alm

Abstract

Early clinical successes are driving enthusiasm for fecal microbiota transplantation (FMT), the transfer of healthy gut bacteria through whole stool, as emerging research is linking the microbiome to many different diseases. However, preliminary trials have yielded mixed results and suggest that heterogeneity in donor stool may play a role in patient response. Thus, clinical trials may fail because an ineffective donor was chosen rather than because FMT is not appropriate for the indication. Here, we describe a conceptual framework to guide rational donor selection to increase the likelihood that FMT clinical trials will succeed. We argue that the mechanism by which the microbiome is hypothesized to be associated with a given indication should inform how donors are selected for FMT trials, categorizing these mechanisms into four disease models and presenting associated donor selection strategies. We next walk through examples based on previously published FMT trials and ongoing investigations to illustrate how donor selection might occur in practice. Finally, we show that typical FMT trials are not powered to discover individual taxa mediating patient responses, suggesting that clinicians should develop targeted hypotheses for ...Continue Reading

Datasets Mentioned

BETA
PRJNA388210

Methods Mentioned

BETA
amplicon sequencing

Software Mentioned

Python
scipy
QIIME
OpenBiome
statsmodels
MicrobiomeHD
stats
Metabolomics Workbench

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