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mSystems
2017 ; 2
(1
): ? Nephropedia Template TP
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Uncovering the Horseshoe Effect in Microbial Analyses
#MMPMID28251186
Morton JT
; Toran L
; Edlund A
; Metcalf JL
; Lauber C
; Knight R
mSystems
2017[Jan]; 2
(1
): ? PMID28251186
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The horseshoe effect is a phenomenon that has long intrigued ecologists. The
effect was commonly thought to be an artifact of dimensionality reduction, and
multiple techniques were developed to unravel this phenomenon and simplify
interpretation. Here, we provide evidence that horseshoes arise as a consequence
of distance metrics that saturate-a familiar concept in other fields but new to
microbial ecology. This saturation property loses information about community
dissimilarity, simply because it cannot discriminate between samples that do not
share any common features. The phenomenon illuminates niche differentiation in
microbial communities and indicates species turnover along environmental
gradients. Here we propose a rationale for the observed horseshoe effect from
multiple dimensionality reduction techniques applied to simulations, soil
samples, and samples from postmortem mice. An in-depth understanding of this
phenomenon allows targeting of niche differentiation patterns from high-level
ordination plots, which can guide conventional statistical tools to pinpoint
microbial niches along environmental gradients. IMPORTANCE The horseshoe effect
is often considered an artifact of dimensionality reduction. We show that this is
not true in the case for microbiome data and that, in fact, horseshoes can help
analysts discover microbial niches across environments.
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