Understanding the factors underlying colonization of donor microbes in recipients of fecal microbiota transplantation is a necessary first step to develop directed approaches to couple colonization to clinical outcomes. FMT
. We found that limits to gut microbiome resilience at community, species and strain level can be defined by a relatively small set of measurable variables that point to distinct underlying processes. The interplay between propagule pressure and residual species abundance provided a neutral baseline for colonization although, again, recipient effects outweighed donor effects.
By design, our study is predominantly descriptive and only probes potential mechanisms underlying our observations to the extent of interpreting them in an ecological context. Moreover, our study focuses on the bacterial and archaeal microbiota and is limited by the relatively small available sample size for some disease indications in our dataset, by the technical, procedural and physiological heterogeneity between cohorts and by the inherent detection limits of metagenomic strain calls.
Our results indicate that microbiome dynamics following FMT are impacted by defined parameters that are tunable in clinical practice, thus supporting the notion that predictable and efficacious microbiome modulation using personalized probiotic mixtures, rather than entire complex fecal samples, is possible and may profit from an ecological perspective.
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