Projects for Master Students
Understanding Clostridioides difficile ecology
We are currently interested in exploring the ecology and evolution of Clostridioides difficile. For this purpose, we offer several interesting research projects for Master Students.
- A comparative genomics approach to understanding the genetic diversity of Clostridioides difficile
Clostridioides difficile harbors a fascinating diversity, with closely related strains exhibiting distinct metabolic and phenotypic characteristics. Recent genomic studies (Knight et al. 2021, Williamson et al. 2022) have identified several distinct clades within C. difficile. We are particularly interested in understanding how these clades evolved such diverse metabolic capabilities.
This project delves into the fascinating interplay between ecology and evolution to explain the remarkable diversification within C. diff. Your role will be to perform comparative genomic analyses on a massive dataset of 30,000 C. diff genomes. Through this analysis, we aim to identify genes and metabolic pathways that contribute to the unique characteristics of each clade.
This project is ideal for a highly motivated individual with:
Excellent computational skills in bioinformatics tools relevant to comparative genomics.
In-depth knowledge of bacterial metabolism and its underlying genetic basis.
A strong passion for bacterial genomics and unraveling the secrets of microbial evolution.
If you possess these skills and are eager to contribute to this exciting research, we encourage you to apply to nejc.stopnisek(at)nlzoh.si. Briefly describe the relevant skills and research interests that fuel your passion for this project.
2. Phenotypic characterization of C. difficile strains
The genomics era has brought unprecedented advancements to microbiology. However, traditional bacteriological techniques remain crucial for validating these insights.
Our in-house C. difficile strain collection consists of nearly 700 strains isolated from diverse environments and characterized genotypically. We're investigating how this genetic diversity relates to the strains' phenotypes, particularly antibiotic resistance, toxin production (focusing on TcdA and TcdB), and growth potential on different substrates relevant to human gut colonization.
If you are passionate about laboratory work and have a strong background in bacterial physiology, we encourage you to apply to nejc.stopnisek(at)nlzoh.si. Briefly describe the relevant skills and research interests that motivate you to participate in this project.
3. Development of a PCR method to detect Cdiff activity
4. Growth of Cdiff in non-host environment
Wheat microbiome
We recently launched a 3-year project, WHEATSHIELD, focused on exploring the wheat microbiome and its potential to enhance drought tolerance in this globally important crop. This project offers multiple opportunities for master’s students from diverse academic backgrounds to contribute and develop their theses. Here are a few examples:
- Defining drought-tolerant wheat lines (if you are interested in agronomy, plant biology, or similar)
- Quantifying drought effects on wheat (if you are interested in agronomy, plant biology, biology, or similar)
- Investigating microbe-wheat interactions (if you are interested in microbiology, plant biology, ecology, or similar)
If you are interested in any of these topics or would like to propose a project aligned with our research, feel free to contact us!