The Divergence as a Diversity Measure. Application to Gut Microbiome Analysis

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  • Entropy measures of probability distributions are widely used measures in ecology, biology, genetics, and in other fields, to quantify species diversity of a community. Unfortunately, entropy–based diversity indices, or diversity indices for short, suffer from three problems. First, when computing the diversity for samples withdrawn from communities with different structures, diversity indices can easily yield non-comparable and hard to interpret results. Second, diversity indices impose weighting schemes on the species distributions that unnecessarily emphasize low abundant rare species, or erroneously identified ones. Third, diversity indices do not allow for comparing distributions against each other, which is necessary when a community has a wellknown species’ distribution. In this paper we propose a new methodology based on divergence measures to quantify the species diversity of a community. Our two–step approach naturally overcomes the previous mentioned problems, and can be used as an efficient biomarker for health risks. We validate our proposed approach in the diversity analysis of infants’ gut microbiota according to mode of delivery and diet. Unlike entropy–based indices, divergence–based measures yield sharp and significantly different diversity results between the groups of each mode, which is consistent with recently reported taxa profiles for these cases. | TRID-ID TR13-05

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    Attribution-NonCommercial 3.0 International