Microbial Systems Bioinformatics

Vision

The Microbial Systems Bioinformatics group envision an interdisciplinary Systems Biology approach where Microbial Ecology, Modeling, Microbial Physiology and Bioinformatics meet to create out of the box thinking towards prediction microbial interactions in complex systems.

Mission

Environmental health regulates the conditions life is sustained on Earth. A clear definition of environmental health is necessary to allow the implementation of practices that guarantee sustainable exploration of our limited natural resources. The Microbial Systems Bioinformatics group works to define environmental health by exploring microbial interactions. We want to achieve our mission by developing concepts and theories to expand modeling of microbial communities to the vast diversity found in natural ecosystems with focus on the fate of chemicals in the environment.


Research Topics

Our group strives to assess environmental health of terrestrials and man made environments by predicting how resilient/stable a microbial community is to specific disturbances. A special emphasis is put on the development of concepts and theories to scale microbial interactions to the real diversity found in nature.

The key research topics of the Microbial Systems Bioinformatics group are based on genetic potential of microbial communities and integration of multi-omics analysis. Currently these topics cover:

  1. Use of (in silico) mock microbial communities to test microbial ecology theories: (i) Elucidation of factors influencing the recovery of genomes from metagenomes, (ii) Development of neutral and niche theories to study microbial interactions using multi-omics data.
  2. From microbial 'Big Data' to novel ecological concepts and theories: Use of public available 'omics' databases to elucidate long-time assumptions in microbiology.
  3. Scaling modeling of microbial interactions to the diversity found in natural ecosystems: Definition of concepts and theories to use partial genome-scale metabolic modeling as a tool to explore microbial community interactions. 

The many faces of the Bioavailability Group
Microbial Systems Bioinformatics team in December 2017. From left to right, Rodolfo, Ulisses, João and Felipe.

  • Interdisciplinary approach to understand microbial interactions in highly complex system.
  • Genomics of microbial species using genomes metagenome-assembled genomes.
  • Metabolic modeling of microbial systems where links between genes, reactions and metabolites are available.
  • Development of concepts and theories to scale modeling of the molecular mechanisms of inter-species interactions to the diversity found in natural ecosystems.

"If you want to go fast, go alone. If you want to go far, go together." (unkown origin)

  • Open discussion with team members and collaborators to set goals and deadlines as well as to analyze progress of the work
  • Each member of the team is responsible for a different set of skills and for connecting them to the different partners within team members of collaborators
  • Out of the box thinking is stimulated
  • Establishment of collaborations within UFZ, the Helmholtz family, German and international universities and research groups.