An eco-systems view of complex natural microbiomes

Samuel Chaffron (Universite Nantes)
Thursday, June 15, 2017 - 10:30
Room Aurigny
Talk abstract: 

Microbial communities play crucial ecological roles on our planet, impacting all ecosystems at various levels. Notably, they sustain Earth’s biogeochemical cycles in the oceans, protect plants from pathogens, and also influence host nutrition, immunity and development in humans. Next-Generation Sequencing (NGS) and functional genomics technologies (so called omics approaches) are revolutionizing the field of environmental microbiology and are reshaping our view on microbial ecosystems. These approaches enable the study of ecological systems at the molecular scale and are revealing the under-explored diversity and complexity of microbial ecosystems. Yet our ability to understand and predict the structures and functions of these complex and dynamic microbial communities is very limited. Notwithstanding, the genomic content of naturally co-occurring microbes can now be investigated in situ, and their metabolic networks can be reconstructed and integrated to gain insights into their physiology (from an environmental genotype to its phenotype). Past and on-going work presented here will ultimately lead to the design of integrative models through a microbial metabolic modeling platform integrating omics data, ecological information and metabolic networks reconstruction to further understand and predict microbial communities and ecosystems in and around us. This Microbial Systems Ecology (ECOSYSMIC) platform will enable to go beyond the simple description of natural microbial communities by building computational models to gain a predictive understanding of community function and dynamics, and acquire a mechanistic understanding of microbial species interactions and ecosystem functioning.