Uncovering the Horseshoe Effect in Microbial Analyses

ABSTRACT 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 ar...

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Autores principales:	James T. Morton, Liam Toran, Anna Edlund, Jessica L. Metcalf, Christian Lauber, Rob Knight
Formato:	article
Lenguaje:	EN
Publicado:	American Society for Microbiology 2017
Materias:	decomposition horseshoe microbial ecology pH soil Microbiology QR1-502
Acceso en línea:	https://doaj.org/article/50b9099cd7e94228ad0ed0893576c690
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spelling	oai:doaj.org-article:50b9099cd7e94228ad0ed0893576c6902021-12-02T19:47:35ZUncovering the Horseshoe Effect in Microbial Analyses10.1128/mSystems.00166-162379-5077https://doaj.org/article/50b9099cd7e94228ad0ed0893576c6902017-02-01T00:00:00Zhttps://journals.asm.org/doi/10.1128/mSystems.00166-16https://doaj.org/toc/2379-5077ABSTRACT 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.James T. MortonLiam ToranAnna EdlundJessica L. MetcalfChristian LauberRob KnightAmerican Society for Microbiologyarticledecompositionhorseshoemicrobial ecologypHsoilMicrobiologyQR1-502ENmSystems, Vol 2, Iss 1 (2017)
institution	DOAJ
collection	DOAJ
language	EN
topic	decomposition horseshoe microbial ecology pH soil Microbiology QR1-502
spellingShingle	decomposition horseshoe microbial ecology pH soil Microbiology QR1-502 James T. Morton Liam Toran Anna Edlund Jessica L. Metcalf Christian Lauber Rob Knight Uncovering the Horseshoe Effect in Microbial Analyses
description	ABSTRACT 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.
format	article
author	James T. Morton Liam Toran Anna Edlund Jessica L. Metcalf Christian Lauber Rob Knight
author_facet	James T. Morton Liam Toran Anna Edlund Jessica L. Metcalf Christian Lauber Rob Knight
author_sort	James T. Morton
title	Uncovering the Horseshoe Effect in Microbial Analyses
title_short	Uncovering the Horseshoe Effect in Microbial Analyses
title_full	Uncovering the Horseshoe Effect in Microbial Analyses
title_fullStr	Uncovering the Horseshoe Effect in Microbial Analyses
title_full_unstemmed	Uncovering the Horseshoe Effect in Microbial Analyses
title_sort	uncovering the horseshoe effect in microbial analyses
publisher	American Society for Microbiology
publishDate	2017
url	https://doaj.org/article/50b9099cd7e94228ad0ed0893576c690
work_keys_str_mv	AT jamestmorton uncoveringthehorseshoeeffectinmicrobialanalyses AT liamtoran uncoveringthehorseshoeeffectinmicrobialanalyses AT annaedlund uncoveringthehorseshoeeffectinmicrobialanalyses AT jessicalmetcalf uncoveringthehorseshoeeffectinmicrobialanalyses AT christianlauber uncoveringthehorseshoeeffectinmicrobialanalyses AT robknight uncoveringthehorseshoeeffectinmicrobialanalyses
_version_	1718375959974903808

Uncovering the Horseshoe Effect in Microbial Analyses

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