Social Systems Microbiology
We are particularly interested in the role of horizontal gene transfer, which is the sharing of genes between bacteria, and how this affects their interactions. A major concern is the rise in antibiotic resistance among harmful bacteria, which is a frightening result of this rampant gene-sharing process. Genes are usually shared via mobile genetic elements like plasmids and bacteriophages. We study how these elements interact with each other and with the host, as well as how these interactions influence the social behavior of the host bacteria.
To test our hypotheses, we develop advanced molecular tools and engineer bacteria using:
- Genome Engineering (e.g., CRISPR-Cas)
- Synthetic Biology
- Fluorescence Reporter Gene Technologies
- Flow cytometry and Cell Sorting
- Confocal Microscopy
- High-Throughput Sequencing
- Single Cell Transcriptomics
- Advanced Microbiology Methods
These methods allow us to study bacteria at the single-cell level, revealing that even genetically identical bacteria, plasmids, and phages can exhibit complex social behaviors like cooperation, altruism, division of labor, and bet-hedging.
If you're a student looking for an exciting research or thesis project (BSc or MSc), we invite you to contact PI Jonas Stenløkke Madsen. Here are some of the fascinating topics you could explore with us:
- Cooperative antibiotic resistance
- Division of labor and bet-hedging in clonal populations
- Phage therapy and evolutionary medicine
- Phage and plasmid manipulation of their hosts via intracellular signaling
- Plasmid-host crosstalk and transfer of antibiotic resistance genes
- Bioinformatic analysis (e.g. of single-cell transcriptomics/genomics)
Exploiting evolution: Designing microbial interactions for industrial scenarios.
This project will address the use of microbial communities to maintain increased food and energy production in an environmentally friendly and sustainable way.
We are planning to isolate and identify microbial communities (bacteria or fungi) to construct synthetic microbial consortia to help in bio-industrial processes and support Europe’s developing bio-economy.
A project may include:
- Microcosms enrichment
- Fluorescent activated cell sorting
- Classic culturing
- Enzymes activities
- PCR and qPCR analysis
- Metagenome and metatranscriptome
- Sequencing
- Bioinformatic analysis
Keywords: Next generation, sequencing, bioinformatics, bio-industry
Supervisor: Søren Sørensen
Email: sjs@bio.ku.dk
Horizontal gene transfer - Spread of antibiotic resistance
Increased antibiotic resistance in a wide range of human pathogens is a growing public health threat. This rapid spread of antibiotic resistance genes is mediated by mobile genetic elements like plasmids, which can be rapidly transferred between microorganisms.
We study plasmid transfer in various natural environments such as wastewater, soil and animal model systems.
A project may include:
- Microcosms / Animal model systems
- Genetically engineering
- Fluorescent activated cell sorting
- Metagenome sequencing
- Bioinformatic analysis
Supervisor: Søren Sørensen, sjs@bio.ku.dk