Workshop A

Morning "Coffee Room" Networking

09:30 - 10:00 EDT

Using Next-Generation Sequencing, Artificial Intelligence & the Human Microbiome to Address Precision Medicine & Antimicrobial Resistance

10:00 - 12:00 EDT

As the current pandemic as well as the ongoing spread of infectious diseases and increase in AMR continues, nextgeneration
sequencing (NGS) tools powered by artificial intelligence have emerged as robust tools to discover, diagnose and monitor the spread of infectious diseases while helping to guide precision treatment.
This workshop will outline how NGS and new bioinformatic tools can be used to enable personalized, data-driven pathogen discovery and diagnostics from the individual to the community.

Workshop Outline

  • Harness microbial information to understand how microbes evolve and spread
  • Understand how new bioinformatics tools can be used to provide new insights on AMR pathogens
  • Learn how artificial intelligence can better predict patterns to guide patient treatment in infectious diseases and other chronic disorders
  • Leverage insights gathered from the microbiome to fight infectious disease through the development of precision diagnostics
  • Further the understanding and treatment women’s health through the microbiome

You should attend this workshop if you:

  • Work in the field of infectious diseases
  • Utilize metagenomic data in academic or clinical settings
  • Would like to leverage insights how metagenomic data can evolve in the clinical diagnostic field of infectious diseases with its challenges

Workshop Leader:

Dora Nagy-Szakal

Dorottya Nagy- Szakal
Chief Medical Officer

Mara Couto-Rodriguez

Mara Couto-Rodriguez
Director of R&D

Workshop B

Lunch "Coffee Room" Networking

13:00 - 13:30 EDT

A Deep-Dive into Microbe-Centric Metabolic Modelling

13:30 - 15:30 EDT

The first few years of life are essential in shaping the human gut microbiota and priming the host immune system. They establish our highly personalized gut microbiome which will interact with the host throughout the entire lifespan. However, the exact causal role the gut microbiome plays in health and disease remains elusive. Metagenome-scale metabolic modelling provides a detailed strategy to study microbial metabolism in a single individual and predict the effects of potential interventions.

This workshop will outline the opportunities and limitations of metabolic models and provide hands-on experience in simulating microbial metabolism in the human gut.


Workshop Outline

What is metabolic Modelling?

  • Metabolic fluxes

  • The steady-state assumption

  • Flux Balance Analysis

  • Environmental conditions

Genome-scale metabolic network reconstructions for gut microbes

  • Draft reconstructions (CarveMe, ModelSEED, gapseq)

  • Standardized model databases (AGORA)

  • Assessing model quality and manual curation (MEMOTE, minimal media)

  • Limitations and pitfalls

Metagenome-scale Metabolic Modelling

  • Reducing the flux space with the cooperative tradeoff method

  • Simulating microbial community models with MICOM

  • Identifying growth niches

  • Simulating personalized interventions


You should attend this workshop if you:

  • Use systems biology approaches in your research or product development portfolio

  • Would like to understand the potential impact and limitations of genome-scale metabolic models applied to the microbiome

  • Would like to identify optimal intervention strategies for the gut microbiome

Workshop Leader:


Christian Diener
Research Scientist
Institute for Systems Biology