Combinatorial ecology in the fruit fly gut microbiome

Will Ludington
Department for Embryology, Carnegie Institution for Science, Baltimore, USA

ludington@carnegiescience.edu

The gut microbiome is an ecosystem within an animal host that impacts health and disease in mysterious ways. Complex interactions between individual species produce unexpected results, often involving feedbacks with the host physiology. Discovering general principles of microbiome-host systems can benefit human health and also teach us about how groups of interacting organisms behave differently from their separate parts. To deconstruct this complexity, my lab develops the fruit fly gut microbiome as a model with its natural set of just five stably colonizing gut bacteria. We reconstruct this system combinatorially to ask how bacteria influence each other’s ability to colonize the gut and how these interactions influence physiology of the fly. We find that colonization ability of new species is strongly influenced by previous colonizers due both to spatial and metabolic interactions, which an example of a priority effect. These interactions also shape host fitness, altering the lifespan and reproduction of flies in a tradeoff, where shorter-lived individuals reproduce more. Overall, we find that the fly gut serves as an effective combinatorial model to dissect the gut microbiome-host complexity.

Recent publications:

·       Eble, H., Joswig, M., Lamberti, L., & Ludington, W. B. (2019). Cluster partitions and fitness landscapes of the Drosophila fly microbiome. Journal of Mathematical Biology, 1–39. http://doi.org/10.1007/s00285-019-01381-0

·       Aranda-Díaz, A., Obadia, B., Thomsen, T., Hallberg, Z. F., Guvener, Z. T., Huang, K. C., & Ludington, W. B. (2019). Bacterial interspecies interactions modulate pH-mediated antibiotic tolerance in a model gut microbiota: Supplemental Information. bioRxiv, 1–66. http://doi.org/10.1101/538132

·       Gould, A. L., Zhang, V., Lamberti, L., Jones, E. W., Obadia, B., Korasidis, N., et al. (2018). Microbiome interactions shape host fitness. Proceedings of the National Academy of Sciences, 6, 201809349. http://doi.org/10.1073/pnas.1809349115

·       Obadia, B., Güvener, Z. T., Zhang, V., Ceja-Navarro, J. A., Brodie, E. L., Ja, W. W., & Ludington, W. B. (2017). Probabilistic Invasion Underlies Natural Gut Microbiome Stability. Current Biology : CB, 27(13), 1999–2006.e8. http://doi.org/10.1016/j.cub.2017.05.034