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From Sept of 2010 to January 2014, I have been a postdoctoral fellow in Prof. Janet K. Jansson’s laboratory at Lawrence Berkeley National Laboratory. I received my PhD in December 2009 from the Ecole Centrale de Lyon, University of Lyon, France, with Prof. T.M. Vogel. I now work at Stanford University and study the impact of the gut microbiome on the brain using crowdsourced trinical trials, with Dennis Wall.
My expertise is in microbilogy, bioinformatics and biochemistry, and more specifically in molecular biology, utilizing metagenomics, metatranscriptomics and metaproteomics to understand microbial community functions in the environment. My grad-school work focused on the bacterial adaptation to chlorinated compounds, at the genome level (evolution mechanisms) and community (bioremediation). My research is now looking at the impact of climate change such as altered precipitation on the carbon cycle in soil.
Meta-"Omics" Analysis of Microbial Carbon Cycling Responses to Altered Rainfall Inputs in Native Prairie Soils
In this project we are exploring the impact of climate change on the carbon cycle of native prairie soil in the US. Our goal is to harness the power of multiple omics tools to understand the functioning of whole-soil microbial communities and their role in C cycling. => more about this project
I addressed several tasks within that project.
First, I worked on improving the database needed to apply the omics methods chosen in this project. The Kansas prairie soil presents a very high biomass and important diversity of microorganisms, which makes it difficult to study. Indeed, if the latest technology of sequencing allowed to produce a deep sequencing of that soil, only a few % could be assembled to be used as a database in order to map the metatranscriptome and perform proteomic searches. I am working on significantly reducing the diversity of this complex ecosystem by labeling active microbes.
In addition, I did the analysis and the annotation of the metagenome and transcriptome data by building a comprehensive database where specific-to-soil functions of proteins have been manually selected and organized. In addition we turned each KEGG KO set of sequences into Markov models. This work is performed in collaboration with Kostas Mavrommatis at JGI.
In order to optimize the DNA, RNA and protein extractions protocols and to practice the
integration of those data, we used the gfp (green fluorescent protein)-tagged soil microbe Arthrobacter chlorophenolicus. We aimed to study which A. chlorophenolicus genes are specifically transcribed and expressed in soil amended with different substrates and in the rhizosphere. This eco-systems biology approach enabled us to compare the activity and expression of this microorganism in different environmental samples and to determine what functions were important for survival in the different conditions and environments tested. This work is performed in collaboration with Steve Lindow laboratory, UC Berkeley.
Finally, I will use the methods optimized during three first tasks to perform the integration of the field and meta-Omics data with the help of the partners of the project.