Microorganisms fulfill crucial roles in all aspects of life, ranging from global biochemical nutrient cycling to human health and disease. Recent advances in sequencing, bioinformatic tools and databases make it possible to better investigate uncultured microbes, which make up the majority of bacterial diversity.
It is therefore important to know where these microbes are found, how they interact and how they may react to changing conditions, such as climate change. To achieve this, we have to investigate the forces governing microbial community structure. In this thesis, I examine several aspects influencing microbial community composition and dynamics across different scales. I show how a small ribozyme can influence the bacterial composition by likely regulating the timing of lysis in their respective phages. I furthermore investigate how Escherichia coli is able to locate and occupy specific niches in the gut of mice, and how it can gain a competitive advantage with a single nucleotide change in the start codon of sugar utilization regulator genes.
Next, I discuss how microbiomes could be investigated by strategically adding or removing individual microbes. Lastly, I leverage a database with millions of samples and hundreds of thousands of pairs of microbial taxa to investigate an underappreciated consequence of evolution: community conservatism. Here, I show that closely related taxa also tend to share similar communities, and propose a way to integrate community conservatism in an alternative way to generate "species-level" clusters in microbes
