Stochastic neutral modelling of the Gut Microbiota’s relative species abundance from next generation sequencing data

BMC Bioinformatics

Research

Paolo Garagnani¹  Silvia Vitali²  Daniel Remondini²  Gastone Castellani²  Claudia Sala²  Enrico Giampieri²  Ìtalo Faria do Valle³  Luciano Milanesi⁴  Ettore Mosca⁴  Matteo Bersanelli⁴ 

[1] Department of Experimental, Diagnostic and Specialty Medicine, University of Bologna, 40138, Bologna, Italy;Department of Physics and Astronomy, University of Bologna, 40127, Bologna, Italy;Department of Physics and Astronomy, University of Bologna, 40127, Bologna, Italy;CAPES Foundation, Ministry of Education of Brazil, 70040-020, Brasìlia, DF, Brazil;Institute of Biomedical Technologies, National Research Council, 20090, Milan, Segrate, Italy;

关键词: Microbiota;    16S RNA;    OTU;    RSA;    Biodiversity;    Ecological modelling;   

DOI  :  10.1186/s12859-015-0858-8

来源: Springer

【 摘 要 】

BackgroundInterest in understanding the mechanisms that lead to a particular composition of the Gut Microbiota is highly increasing, due to the relationship between this ecosystem and the host health state. Particularly relevant is the study of the Relative Species Abundance (RSA) distribution, that is a component of biodiversity and measures the number of species having a given number of individuals. It is the universal behaviour of RSA that induced many ecologists to look for theoretical explanations. In particular, a simple stochastic neutral model was proposed by Volkov et al. relying on population dynamics and was proved to fit the coral-reefs and rain forests RSA. Our aim is to ascertain if this model also describes the Microbiota RSA and if it can help in explaining the Microbiota plasticity.ResultsWe analyzed 16S rRNA sequencing data sampled from the Microbiota of three different animal species by Jeraldo et al. Through a clustering procedure (UCLUST), we built the Operational Taxonomic Units. These correspond to bacterial species considered at a given phylogenetic level defined by the similarity threshold used in the clustering procedure. The RSAs, plotted in the form of Preston plot, were fitted with Volkov’s model. The model fits well the Microbiota RSA, except in the tail region, that shows a deviation from the neutrality assumption. Looking at the model parameters we were able to discriminate between different animal species, giving also a biological explanation. Moreover, the biodiversity estimator obtained by Volkov’s model also differentiates the animal species and is in good agreement with the first and second order Hill’s numbers, that are common evenness indexes simply based on the fraction of individuals per species.ConclusionsWe conclude that the neutrality assumption is a good approximation for the Microbiota dynamics and the observation that Volkov’s model works for this ecosystem is a further proof of the RSA universality. Moreover, the ability to separate different animals with the model parameters and biodiversity number are promising results if we think about future applications on human data, in which the Microbiota composition and biodiversity are in close relationships with a variety of diseases and life-styles.

【 授权许可】

CC BY   
© Sala et al. 2016