Metabolite and Species Dynamics in Microbial Communities

Metabolite and Species Dynamics in Microbial Communities is organized by European Molecular Biology Laboratory (EMBL) and will be held from Oct 13 - 18, 2024 at EMBL Advanced Training Centre (ATC), Heidelberg, Baden-Wurttemberg, Germany.

Note:
This is a two-hub course taking place in parallel at both EMBL Heidelberg, Germany and the Bangalore Life Science Cluster (BLiSC) Campus in Bangalore, India

Course overview:
Metagenomics studies are rapidly uncovering the compositional richness of microbial communities in diverse habitats ranging from the oceans to the human gut. While their fundamental role in our health and environment is undeniable, there is an urgent need for unravelling molecular mechanisms underlying the dynamics of these communities. This requires a combined experimental and computational approach. Recent studies (including those from the organisers’ and speakers’ labs) have underlined the success of such integrative approaches. For example, emergence of cell subpopulations (Varahan et al. eLife 2019, 2020), and long-term stability (Blasche, Kim et al. Nat Microbiol. 2021) through metabolic cross-feeding.

As researchers world-wide map species dynamics in the ecosystems of their interest, this course will provide the necessary overview and tools for moving from cataloguing to identifying key interaction agents, especially metabolites. This will include integrating species and metabolite dynamics data, as well as leveraging the power of genome-scale metabolic models to predict community interactions.

Modules/Resources:

• Experimental design and kefir culture set-up and sampling
• 16S analysis of kefir communities using Nanopore sequencing technology
• Metabolite changes during kefir fermentation using Metabolomics
• Interaction mapping plating experiment
• Computational analysis introduction using R-studio/Python
• 16S and metabolomics data analysis (computational)
• Metabolic modelling of community interactions (computational)

Learning outcomes:
The main goal of the course is to equip the participants with the state-of-the-art concepts in microbial ecosystems and introduce them to the key tools towards gaining mechanistic insights in community dynamics. The central learning objective is that the participants will be able to apply these concepts and tools in their own research. Further, we also aim at enabling scientific networking among the participants (including speakers and trainers) and foster dialogue between scientists from different areas (microbiology, metabolomics, modelling, ecology).