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

BMC Bioinformatics
Claudia SalaGastone Castellani

Abstract

Interest 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. We 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 we...Continue Reading

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Citations

Dec 31, 2016·Environmental Microbiology·Fátima C Pereira, David Berry
Jun 20, 2019·PLoS Biology·Michael SieberArne Traulsen
Mar 24, 2017·FEMS Microbiology Letters·Richard A Stein, David E Katz
Nov 3, 2020·PLoS Computational Biology·Román Zapién-CamposArne Traulsen

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Methods Mentioned

BETA
RSA
RSAs

Software Mentioned

RDP
GUT
Metagenomics
Silva
USEARCH
Greengenes
UCLUST

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