Modeling and Microbial Communities
We publish internships via the Biosb-interns mailing list server. If you subscribe to this mailing server you will obtain emails with internship projects in the fields of Bioinformatics and Systems Biology. You can also browse the archive of earlier mails.
You can also contact the team leader Douwe Molenaar directly with questions about opportunities for internships: d.molenaar@vu.nl
For additional internships, see the table below or contact Matti Gralka.
| Project title | Type of research | Supervisor(s) |
|---|---|---|
| Marine Bacteriophage Isolation and Characterization | Experimental (Bachelor) | Sarah Flickinger (s.f.flickinger[at]vu.nl) |
| Motivation: Bacteriophage are the most abundant biological entity in the ocean and lyse up to 20% of marine bacteria daily. Thus, they hypothetically have large impacts on marine bacterial abundance, diversity, and function. However, attempts to quantitatively measure the impact of marine bacteriophage have shown mixed results so far. To gain a quantitative understanding of how individual bacteriophage-host interactions contribute to community impacts, a library of characterized bacteriophage is necessary. We hypothesize that bacteriophage may have the greatest impact in spatially structured environments, with dense host abundances, and high nutrients. Phytoplankton blooms are one such example of an environment with both spatial structuring and high host concentration in which phage impacts may be greater. Aim of Project: In this project, you will isolate and characterize bacteriophages that infect phytoplankton bloom-associated bacteria. Natural seawater samples will be enriched with nutrients to induce phytoplankton growth and both bacteria and bacteriophages will be isolated from these samples. The physiology and growth of several phage-host pairs will be investigated, using parameters including growth rates, host range, collapse time, and 16S sequencing. Methods and techniques: Aseptic technique, bacterial culturing, bacteriophage isolation, bacteriophage amplification, bacteriophage purification, quantitative microbial physiology (growth rates, yields) Impact: During this project, you will become proficient in many standard microbiology methods which are widely used in academic, hospital, and industry labs. In addition, you will learn quantitative skills including growth curve analysis. |
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| Investigating nitrogen preference and novel nitrogen storage in marine bacteria | Experimental (Master) | Sarah Flickinger (s.f.flickinger[at]vu.nl) |
| Motivation: Marine bacteria species are critical to global biogeochemical cycles of carbon, nitrogen, and other nutrients. These microbes exist in an environment with a huge diversity in nitrogen sources, both inorganic and organic, yet little is currently understood about the rules governing nitrogen source preferences among bacteria. Furthermore, vast areas of the global ocean are known to be nitrogen-limited for microbial growth. Recent work in our lab has indicated that i) bacterial strains grow on a diverse array of nitrogen sources and nitrogen source preferences may correlate with taxonomy and ii) several strains of marine heterotrophic bacteria are capable of growing in media without nitrogen sources for several generations, indicating that the bacteria may be storing nitrogen when grown in replete nitrogen conditions, which can then be used when nitrogen is limited. Bacterial strains with this novel mechanism may therefore have an advantage in dynamic marine environments. Aim of Project: The goal of this project is to i) explore genomic explanations for nitrogen source preference among marine bacteria and ii) explore conditions for which marine bacterial strains can grow without nitrogen. You will analyze existing genomic data to uncover statistical patterns of gene pathways correlated with nitrogen source utilization. This work will improve our ability to predict nitrogen source utilization from bacterial genomes. In the lab, you will use high throughput techniques to explore conditions for which marine bacterial strains can grow without nitrogen. The putative nitrogen storage compound will be investigated through elemental analysis. Methods and techniques: Quantitative microbial physiology (growth rates, yield), high throughput culturing of bacteria, elemental analysis, statistical analysis of biological data sets, genomics |
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| Modeling of phage-bacteria interactions | Computational (Bachelor/Master) | Matti Gralka (m.gralka@vu.nl) |
| Phages play key roles in microbial communities in all ecosystems, from the oceans to the human gut, by infecting vast numbers of bacteria every day. Phages are thought to dramatically impact microbial community dynamics and function in the environment, but they also hold clinical promise as they can eradicate bacterial infections – even those resistant to antibiotics. In this project, you will explore mathematical models of phage-bacteria interactions in communities of increasing complexity. First, you will study classical models of phage-bacteria pairs in isolation, before modeling adding environmental complexity by explicitly modeling environmental parameters like resources, temperature, etc. We will also computationally explore the effects of additional species on phage-host interactions. In this internship, you will learn about the biological processes underlying phage-bacteria interactions and numerical techniques for modeling their dynamics. You will develop and numerically solve complex differential equations and analyze the results across parameter range to gain fundamental insights into the expected dynamics in various scenarios. These insights will interface with phage-bacteria experiments performed in the lab, giving your work immediate scientific impact. |
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| Design of a simplified water kefir-based consortium in a chemically defined medium | Experimental (Master) | Sabine Michielsen (s.michielsen[at]vu.nl) |
| Microbes occupy most natural niches. They are typically in close proximity to one another and often form interactions ranging from antagonistic to commensal and even mutualistic. As evolution often works on the level of individual benefit, the onset of antagonistic reactions is relatively easy to explain. Microbes may, for example, scavenge nutrients from the exometabolome of nearby species. While mutualistic interactions often increase growth of both interaction partners through division of labour and specialisation, the downside is that the interaction partners become dependent on one another for nutrient production. For this to happen organisms need to have access to each other for an extended period. Due to this, mutualistic interactions may form more readily in a spatially structured environment. An example of a microbial community grown in a spatially structured environment is the water kefir community. A community typically used to ferment a mixture of tap water and table sugar supplemented with a piece of fruit into water kefir. In its original state, the water kefir community contains approximately 30 species, which makes it difficult to uncover underlying interactions. One way to study interactions in water kefir is by simplifying the community and establish which community members are essential. The aim of this project is to design a simplified spatially-structured water kefir consortium, which will be used to study interactions between consortium members. During this project you will: - Characterize potentially interesting strains (based on genome and metagenome data) isolated from the water kefir community. - Look for interactions and exopolysaccharide production in co-cultures - Design a simplified water kefir consortium and follow stability and aggregation over time using flowcytometry and microscopy |
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