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Identifier

000397223

Title

Inferring positive selection and demography in the human gut microbiota

Alternative Title

Ανίχνευση θετικής επιλογής και δημογραφίας στο ανθρώπινο εντερικό μικροβίωμα

Author

Ζιούτης, Χρήστος Α.

Thesis advisor

Παυλίδης, Παύλος

Reviewer

Νικολάου, Χριστόφορος
Ηλιόπουλος, Αριστείδης

Abstract

The animal gut is considered to be one of the most densely populated by microorganisms ecosystem. All this microbial weight, vital for host's health and homeostasis, has been co-evolving along with the gut structure, for millions years now. Recent studies on human gut microbiome have already demonstrated the genetic repertoire of this community and highlighted its genetic variation among individuals, not only in health states but also in various disease conditions. However, the evolutionary processes that drive the genetic diversity of the gut microbiome have not been thoroughly investigated. Here, we use metagenomic datasets from stool samples of 39 healthy US individuals to construct the genomic variation landscape of the most abundant bacterial species in the human gut. Our main goals are, the detection of events of strong positive selection, based on the site frequency spectrum (SFS) and the inference of a demographic model for each one of the bacterial species comprising the metagenomic sample. To infer the demographic scenarios we use an approximate computation bayesian technique based on coalescent simulations, taking into account the SFS. We find that the abundance or even presence of previously reported as highly abundant gut species varies among the individuals in our cohort. We report the most possible demographic scenarios for each bacterial strains, which, for most of the bacteria, comprises a recent, sharp population size decline. Furthermore, we report our findings on the detection of strong positive selection. Finally,, we report a plethora of difficulties in the estimation of SFS from metagenomic samples, such as the method for estimating allele frequencies from datasets with missing observations.

Language

English

Subject

Microbiome

SNP

Sweep

Issue date

2015-11-20

Collection

School/Department--School of Sciences and Engineering--Department of Biology--Post-graduate theses

Type of Work--Post-graduate theses

Views

236

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