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Department of Plant and Microbial Biology

Microbial Evogenomics Lab (MiEL)

General Description

The Microbial Evogenomics Lab (MiEL) at the University of Zurich, led by Dr. Adrian-Stefan Andrei, is a dynamic group combining computational biology with environmental microbiome research. Our lab leverages cutting-edge omics technologies and advanced bioinformatics to study the evolutionary and ecological aspects shaping microbial diversity. Using environmentally-derived sequencing data, we aim to unravel the intricate eco-evolutionary dynamics influencing microbial diversity in aquatic ecosystems.

Areas of competence

  1. Ecogenomics: Applying large-scale metagenomics to elucidate lifestyle strategies and processes shaping prokaryotic genomic architecture.
  2. Microbial ecology: Utilizing cultivation-independent methods to explore the interplay between microbial communities and their surrounding biogeochemical milieu.
  3. Evogenomics: Employing advanced phylogenomics to retrace the evolutionary history of life.


Our lab's expertise encompasses computational microbiome analyses, genome-resolved metagenomics, metaproteomics, phylogenomics, genome-inferred metabolic reconstructions, and bioinformatics.

Current Projects

SERI Leading House Asia Grant No. RPG 072023_2: "Exploring the Resilience and Adaptation of Aquatic Microbiomes to Global Warming" (Duration: 01.02.2024 - 31.12.2024).

SNSF Ambizione Grant No. 193240: "Retracing the Evolutionary History of Mitochondria Through Environmental Evogenomics" (Duration: 01.01.2021 - 31.12.2024).

Group Members

Lucas Serra Moncadas, Ph.D. Candidate

Intrigued by eco-evolutionary biology, my interest lies in unravelling the many different processes responsible for genome reduction in aquatic bacteria as well as retracing the mitochondrial evolutionary history and diversification. To address these questions, I employ genome-resolved metagenomics techniques, allowing a detailed exploration of microbial communities and the dynamics of their genomic architectures.

Cyrill Hofer, Ph.D. Candidate (Co-supervised with Prof. Jakob Pernthaler)

In my current research, I am dedicated to generating and analyzing extensive sequencing datasets which are obtained through sequencing of DNA and proteins derived from Lake Zurich microbiomes. The primary objective of my study is to explore the functional characteristics of elusive, yet uncultured bacteria, during lake blooming events. I aim to develop an integrative multi-omics workflow, designed to correlate the genomic potential of these bacteria with their physiological attributes over varying temporal dimensions. This endeavor involves generating environmentally-derived high-quality genomes through the usage of advanced hybrid metagenomics approaches. My goal is to construct sample and species-specific proteomics databases to associate distinct bacteria with their respective in situ functionalities.

Alisa Shakurova, Ph.D. Candidate (Co-supervised with Prof. Jakob Pernthaler)

Dale Hager, Master's Candidate