title: Stochastic neutral modelling of the Gut Microbiota's relative species abundance from next generation sequencing data.
abstract: BACKGROUND
  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.
  
  
  RESULTS
  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 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.
  
  
  CONCLUSIONS
  We 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.
authors.affiliation: Department of Physics and Astronomy, University of Bologna, Bologna, 40127, Italy. claudia.sala3@unibo.it.
authors.forename: Claudia
authors.initials: C
authors.lastname: Sala
authors.affiliation: Department of Physics and Astronomy, University of Bologna, Bologna, 40127, Italy.
authors.forename: Silvia
authors.initials: S
authors.lastname: Vitali
authors.affiliation: Department of Physics and Astronomy, University of Bologna, Bologna, 40127, Italy.
authors.forename: Enrico
authors.initials: E
authors.lastname: Giampieri
authors.affiliation: Department of Physics and Astronomy, University of Bologna, Bologna, 40127, Italy.|CAPES Foundation, Ministry of Education of Brazil, Brasìlia, DF, 70040-020, Brazil.
authors.forename: Ìtalo Faria
authors.initials: ÌF
authors.lastname: do Valle
authors.affiliation: Department of Physics and Astronomy, University of Bologna, Bologna, 40127, Italy.
authors.forename: Daniel
authors.initials: D
authors.lastname: Remondini
authors.affiliation: Department of Experimental, Diagnostic and Specialty Medicine, University of Bologna, Bologna, 40138, Italy.
authors.forename: Paolo
authors.initials: P
authors.lastname: Garagnani
authors.affiliation: Institute of Biomedical Technologies, National Research Council, Milan, 20090, Segrate, Italy.
authors.forename: Matteo
authors.initials: M
authors.lastname: Bersanelli
authors.affiliation: Institute of Biomedical Technologies, National Research Council, Milan, 20090, Segrate, Italy.
authors.forename: Ettore
authors.initials: E
authors.lastname: Mosca
authors.affiliation: Institute of Biomedical Technologies, National Research Council, Milan, 20090, Segrate, Italy.
authors.forename: Luciano
authors.initials: L
authors.lastname: Milanesi
authors.affiliation: Department of Physics and Astronomy, University of Bologna, Bologna, 40127, Italy.
authors.forename: Gastone
authors.initials: G
authors.lastname: Castellani
mesh_terms: D000818:Animals; D001419:Bacteria / Q000145:classification* / Q000235:genetics / Q000302:isolation & purification*; D044822:Biodiversity; D002417:Cattle / Q000382:microbiology*; D002645:Chickens / Q000382:microbiology*; D000069196:Gastrointestinal Microbiome; D059014:High-Throughput Nucleotide Sequencing; D006801:Humans; D010802:Phylogeny; D012329:RNA, Bacterial / Q000235:genetics; D012336:RNA, Ribosomal, 16S / Q000235:genetics; D017423:Sequence Analysis, RNA; D034421:Sus scrofa / Q000382:microbiology*
chemical_list: D012329:RNA, Bacterial; D012336:RNA, Ribosomal, 16S
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