Evolution in the microbiome

Laboratory evolution experiments with micro-organisms have shown that micro-organisms can evolve meaningful changes on short timescales. That leads to the question: Do the plentiful micro-organisms in our body evolve in ways that affect our interaction with them?

We can distinguish three processes that change the microbiome (the genes present in the microbiota):
    (1) changes in the population structure,
    (2) replacement of species by species and strains from the environment, and

    (3) evolutionary changes by mutations and horizontal gene transfers.

Current studies characterize the microbiome at the species level, and therefore only focus on the population structure and species replacement in the microbiome. While these studies have shown that species profiles are linked with disease, species changes are only part of the story, and evolutionary changes within species will complete our understanding of the microbiome. This project focusses on the strain replacement part of process two and on process three. The aim is to elucidate how common evolutionary changes are, in which species they happen, how often it happens, what type of genetic changes occur and how important the evolutionary changes are for the shaping of the microbiome. This projects studies of the evolution in the gut microbiome during arguably the most important time for our health, the “first 1000 days”, using metagenome sequencing of a Norwegian cohort of 12 infant, studied during the first year of life.

Scientists involved in this project

Meike Wortel
Roel van der Ploeg
Stanley Brul
Anna Heintz Buschart
Shijia Li
Johan Westerhuis
Tim de Meij (Amsterdam UMC)
Remko Kort (VU)


  1. Towards evolutionary predictions: Current promises and challenges.

    Wortel, M. T., Agashe, D., Bailey, S. F., Bank, C., Bisschop, K., Blankers, T., Cairns, J., Colizzi, E. S., Cusseddu, D., Desai, M. M., van Dijk, B., Egas, M., Ellers, J., Groot, A. T., Heckel, D. G., Johnson, M. L., Kraaijeveld, K., Krug, J., Laan, L. … Pennings, P. S. (2022). Evolutionary Applications, 00, 1– 19. https://doi.org/10.1111/eva.13513