Metabolite and species dynamics in microbial communities

Overview

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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.

Audience

This course is aimed at PhD students and post-doctoral researchers who would apply the methods covered in the course. Applicants are requested to send a motivation letter summarizing their current research and their need for the methods addressed in this course. Furthermore, there is a specific questionnaire to query the background and access to the relevant methods. We aim for a broad geographical distribution of participants to identify needs for applying the methods in different countries, this includes newer EU member states. To ensure optimal tutoring during the practicals, we
target for 20 participants (10 each site). The course will bring together participants from various disciplines (microbiology, metabolomics, modelling, ecology) and ensure a distribution on both sites.

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).

What past participants say about the course

“The two hub course organized by EMBL was a great success where participants like me notonly learnt wet lab techniques like LC-MS but also learnt data visualisation using R and pythonwhich will be a great help while analysing our own data.” – Nidhi Yadav, ICGEB, New Delhi, India

“This EMBO course was very well-organized and provided me essential tools and newapproaches that I will apply in my research to study metabolic interactions within microbialcommunities. The combination of wet- and dry-lab techniques, as well as the involvement oftwo hubs in Germany and India, made the course very complete and enriching.” – Laura Camus, IMIT – University of Tübingen, Germany

Please see EMBL’s COVID-19 safety policy for testing and other requirements to attend this on-site course.

Sponsors

Media partners

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