title: Integrating metatranscriptomes and metagenomes for deconvolution of composition and expression in human gut and artificial communities
creator: Alves, Renato
subject: ddc-570
subject: 570 Life sciences
description: Over the last 15 years the human microbiome has received increasing attention.During this time, many studies have contributed to shed light on the complex network of interactions both between the microorganisms and their host, and within microbial communities themselves.  While traditionally aiming at assessing composition, recent studies have broadened this scope to multi-dimensional aspects, using multi-omics approaches.By integrating information about genomes, transcripts, proteins and metabolites, a holistic understanding of the microbiome is now within reach.However progressive, these studies generally suffer from a lack of closure, as interpretation and integration of this data is all but straightforward.  In the particular case of metatranscriptomes, species abundance and gene expression are coupled into a single readout.Consequently, normalization of this data is a crucial but poorly understood and unresolved problem. Here I present different approaches to normalise metatranscriptomes and highlight procedural concerns when obtaining this type of data.  Results show that better normalization strategies are necessary when integrating multi-omics data and that controlled pilot experiments are required for a better understanding of the intricate dynamics and interactions between members of these communities. This work further exposes concerns about the interpretation of functional aspects of microbial populations, primarily driven by the many uncontrolled sources of variation herein discussed.  As these new data types become more widespread, methods will certainly evolve towards better standardization and controlled procedures. This will help the microbiome field to move beyond its descriptive state into one able to provide a more detailed and mechanistic understanding.
date: 2020
type: Dissertation
type: info:eu-repo/semantics/doctoralThesis
type: NonPeerReviewed
format: application/pdf
identifier: https://archiv.ub.uni-heidelberg.de/volltextserverhttps://archiv.ub.uni-heidelberg.de/volltextserver/27471/1/RenatoAlves-PhDthesis.pdf
identifier: DOI:10.11588/heidok.00027471
identifier: urn:nbn:de:bsz:16-heidok-274710
identifier:   Alves, Renato  (2020) Integrating metatranscriptomes and metagenomes for deconvolution of composition and expression in human gut and artificial communities.  [Dissertation]     
relation: https://archiv.ub.uni-heidelberg.de/volltextserver/27471/
rights: info:eu-repo/semantics/openAccess
rights: http://archiv.ub.uni-heidelberg.de/volltextserver/help/license_urhg.html
language: eng