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Stochastic neutral modelling of the Gut Microbiota's relative species abundance from next generation sequencing data
- Source :
- BMC bioinformatics (2016). doi:10.1186/s12859-015-0858-8, info:cnr-pdr/source/autori:Sala C.; Vitali S.; Giampieri E.; do Valle I.F.; Remondini D.; Garagnani P.; Bersanelli M.; Mosca E.; Milanesi L.; Castellani G./titolo:Stochastic neutral modelling of the Gut Microbiota's relative species abundance from next generation sequencing data/doi:10.1186%2Fs12859-015-0858-8/rivista:BMC bioinformatics/anno:2016/pagina_da:/pagina_a:/intervallo_pagine:/volume, BMC Bioinformatics
- Publication Year :
- 2016
- Publisher :
- BioMed Central, [London] , Regno Unito, 2016.
-
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.
- Subjects :
- 0301 basic medicine
OTU
Sus scrofa
030106 microbiology
Population
Biodiversity
Biology
Biochemistry
03 medical and health sciences
RSA
Structural Biology
RNA, Ribosomal, 16S
Animals
Humans
Ecosystem
education
Cluster analysis
Molecular Biology
Relative species abundance
Phylogeny
Ecological modelling
16S RNA
education.field_of_study
Bacteria
Phylogenetic tree
Sequence Analysis, RNA
Ecology
Research
Applied Mathematics
Microbiota
High-Throughput Nucleotide Sequencing
Computer Science Applications1707 Computer Vision and Pattern Recognition
15. Life on land
Gastrointestinal Microbiome
Computer Science Applications
Applied Mathematic
RNA, Bacterial
030104 developmental biology
Evolutionary biology
Species evenness
Cattle
Chickens
Global biodiversity
Subjects
Details
- Language :
- English
- Database :
- OpenAIRE
- Journal :
- BMC bioinformatics (2016). doi:10.1186/s12859-015-0858-8, info:cnr-pdr/source/autori:Sala C.; Vitali S.; Giampieri E.; do Valle I.F.; Remondini D.; Garagnani P.; Bersanelli M.; Mosca E.; Milanesi L.; Castellani G./titolo:Stochastic neutral modelling of the Gut Microbiota's relative species abundance from next generation sequencing data/doi:10.1186%2Fs12859-015-0858-8/rivista:BMC bioinformatics/anno:2016/pagina_da:/pagina_a:/intervallo_pagine:/volume, BMC Bioinformatics
- Accession number :
- edsair.doi.dedup.....e1d40781ad86cb43a7284f4c962bbe3d
- Full Text :
- https://doi.org/10.1186/s12859-015-0858-8