The work of our group has characterized the colonization of the infant microbiome using several different data layers. These data layers include: (1) sequencing of the bacterial and viral microbiome throughout the infant’s first year of life; (2) characterization of the oligosaccharide content of breast milk, a potential ecological driver of selection for the infant’s microbiome; (3) and the metabolic profile of the infant’s blood plasma, which contains signatures of the interplay between host and microbiome. Important findings of these surveys indicate that particular species, such as Bifidobacterium spp. and Bacteroides spp., may serve as keystone species that promote the diversity and colonization of the microbiome. Other species, such as Staphylococcus spp., appear to be selected by oligosaccharides found in the mother’s milk. The aim of this PhD project is to study the role of such key species by culturing them from stool samples, characterizing their function via wet and dry lab approaches, and creating synthetic microbial communities from these isolates to test ecological and evolutionary theories of ecological succession and colonization. The focus of this project is therefore primarily lab based, although statistical and analytical experience is important to interpret results. Bioinformatic experience or an interest in learning the bioinformatic analyses is also a plus.
Information about our team and work:
Our team's
website.
Links to recent papers from our team:
Paper: Environmental factors shaping the gut microbiome in a Dutch population
Paper: Host genetic regulation of human gut microbial structural variation
PhD student working on this project will be expected to:
- Perform microbiological analyses such as isolating and culturing isolates in both anaerobic and aerobic conditions.
- Perform molecular microbiology tasks such as DNA extraction and PCR.
- Set up and execute culture-based experiments.
- Process and analyze data from experiments.
- Summarize and report key analytical findings in both oral and written form at work meetings, at international scientific conferences and in scientific publications.