Jakob Russel:
Interactions in Microbial Community Assembly from Patterns to Processes and Back

Date: 20-11-2018    Supervisor: Mette Burmølle & Søren J. Sørensen

Microbes are invisible to the naked eye, yet almost unimaginably impactful. Microbial communities affect human health for the better and the worse, they ensure the global turnover of chemical substances, and they are the essential workforce in many industrial settings, just to mention a few examples. Still, how these communities come together and the fundamental question of why some microbes coexist, while others do not, is to a large degree unknown. This thesis explores this question through four studies, each incrementing the complexity compared to the former.

In Manuscript I we showed that soil bacteria had a propensity to inhibit the growth of evolutionary related species, and we further linked this to their metabolic similarity; that is, bacteria were more likely to inhibit the growth of bacteria using the same nutrients as it. Furthermore, the inhibitors were able to grow on a wider array of nutrient sources, thereby linking an inhibitory with a generalist strategy.

In Manuscript II we sought to predict the assembly of a relatively complex community of 32 bacterial species. Intriguingly, we found that the higher the growth rate and growth yield the species had in isolation, the higher abundance they had in the community. Their coexistence was, surprisingly, not associated with their pairwise interactions.

In Manuscript III we studied small self-assembled communities called ‘pink berries’. Here we found that some of the geographical variation in the composition of these pink berries could be explained by the metabolic potential of the constituent species. We further found that genetic variation within species was to some extent linked to the community composition.

In Manuscript IV we explored whether the gut microbiome early in life, at 1 week and 1 month of age, could impact the composition of the gut microbiome at 1 year of age in a cohort of 700 Danish children. Despite the transition in diet and immune development of the human host, we did see associations between the early and late gut microbiome. Especially, one group of bacteria, the Bacteroidetes, were notably stable over time, but this was still overshadowed by an overall convergence of the gut microbiomes through development.