Unlocking the Gut Microbial Functional Diversity – Typas Group

EMBL Workshop

Unlocking the Gut Microbial Functional Diversity

The event has been postponed, new dates to be confirmed.

Workshop overview

The human gut microbiome is a complex microbial ecosystem with well-established links to human health and disease. As a “genuine human organ” with many more genes than the rest of our body and far-reaching interactions, from the immune system to the brain, the gut microbiota offers unprecedented opportunities for controlled modulation in personalized health efforts. Such applications heavily rely on our ability to map causal effects, and on discovering the underlying molecular players (genes, proteins, metabolites) and mechanisms.

In the past two decades, data-driven research has revealed a remarkable stability, diversity, genomic richness and individuality for the human gut microbiome. Yet, our current view on its functional capacities and its interplay with the host remains mostly descriptive, often lacking molecular understanding. As the field is now striving for causality and mechanistic insights towards a deeper understanding of the microbiome-human health links, these efforts are hindered by the lack of model gut microorganisms and foundational functional knowledge. Our current knowledge of bacterial gene functions, pathways and cellular architecture stems from very few model bacteria, which fail to capture the phylogenetic and genetic diversity of the gut microbiota. As a consequence, the vast majority of genes in the gut microbiome remain “dark matter” with respect to function, that is of elusive or completely unknown function.

This workshop aims at fostering discussion and charting a framework on how we can systematically tackle this vast dark genetic matter in the human gut microbiome by selecting and establishing new model microbes. What tools and approaches are needed? What knowledge will propel microbiome research and help to dissect correlative from causal links, reveal underlying molecular mechanisms and ultimately, to progress to health applications? A targeted group of participants has been invited to discuss and plan initiatives that can help creating this foundational knowledge towards transforming the field and providing a roadmap for targeting other microbial ecosystems.

Session Topics

  • Data-driven functional discovery
  • Genetic tools for mapping gene function and interactions
  • Multi-omics for mapping gene function and cellular organization
  • Visualizing functional units
  • Gene function in ecological context (communities, host, phages)
  • Looking outward & forward – links to other microbiomes


Day 1
12:00 – 13:30Registration and lunch
Operon Registration Desk, ATC Foyer
13:30 – 14:00Opening remarksLarge Operon
14:00 – 15:30Session 1: Data-driven functional discovery

Peer Bork, Pedro Beltrao, Ami Bhatt, Nicola Segata
Panel: Eran Segal, Jeroen Raes, Isabel Gordo, Thomas Lemberger
Large Operon
15:30 – 16:00Coffee breakOperon Foyer
16:00 – 17:30Session 2: HT Reverse Genetics & Genetic tools for Gene Function

Laurie Comstock, David Bikard, Adam Deutschbauer, Csaba Pal
Panel: Nassos Typas, Carol Gross, Victor Sourjik, Nonia Pariente
Large Operon
117:30 – 18:00Coffee breakOperon Foyer
18:00 – 19:30Session 3: Multi-Omics for Gene Function

Jörg Vogel, Mikhail Savitski, Michael Zimmermann, Markus Ralser
Panel: Uwe Sauer, Paul Wilmes, Caroline Ash
Large Operon
20:00 – 23:00Dinner in Schloss

Day 2
09:00 – 10:30Session 4: Visualising Functional Units

KC Huang, David Berry, Martin Pilhofer, Julia Mahamid
Panel: Orsolya Barabas, Mathias Wilmanns, Tâm Mignot, Sri Narasimhan
Large Operon
10:30 – 11:00Coffee break
Operon Foyer
11:00 – 12:30Session 5: Gene function in ecological context

Kevin Foster, Karina Xavier, Bärbel Stecher, Colin Hill
Panel: Kiran Raosaheb Patil, Pascale Cossart, Rotem Sorek, Lakshmi Goyal
Large Operon
12:30 – 13:45Lunch & discussions
ATC Foyer
13:45 – 15:30Session 6: Looking forward & outward

Melanie Blokesh, Rob Finn, Funding Agency, Funding Agency
Panel: Jan Van der Meer, Eric Pamer, Edith Heard, Dirk Heinz
Large Operon
15:30 – 15:45Closing remarks
Large Operon

Participants and organisers

Scientific organisers

Conference organiser


Caroline Ash

Science, UK

photo of Lakshmi Goyal

Lakshmi Goyal

Cell Host & Microbe, USA

photo of Thomas Lemberger

Thomas Lemberger

EMBO Press, Germany

photo of Sri Narasimhan

Sri Narasimhan

Cell, USA

photo of Csaba Pal

Csaba Pal

Biological Research Center, Szeged, Hungary

photo of Christina Tobin

Christina Tobin

Kåhrström Nature, UK


Location: EMBL Heidelberg


  • Peer Bork
    EMBL Heidelberg, Germany