Systematically dissecting the lifestyle of human gut microbes
Our body provides an ideal ecosystem for microbial communities. The most complex and dense one, the gut microbiome, resides mainly in our lower intestine, and plays a fundamental role in host physiology and pathology. Recently, medication has arisen as one of the most impactful factors on the gut microbiota composition [1, 2] and we identified a generalized effect of non-antibiotics on gut microbes (24% of the tested FDA-approved human-targeted drugs) . For the vast majority of these drug-microbe interactions, we do not know the underlying drug targets in microbes and do not understand whether they have beneficial (required for the drug to work) or detrimental (side) effects for humans. In our group, we want to further investigate questions at the drug-microbiome-host interface. Specifically, we aim at assessing the stability of these microbial communities, their resistance to intruders and ability to silence pathogenic members of the community, and understand how drugs can impact communities and whether one could use drugs to restore a healthy balance.
To this end, we focus on a set of representative species for the healthy human microbiome , characterize them using automated high-throughput platforms (video) and develop novel experimental set-ups to systematically study the drug-microbiome interface. As the host tightly influences the microbiome composition, we will also investigate the impact of the host on drug-microbiome interactions and anticipate following up a handful of strong findings in vivo.
1. Falony, G., et al., Population-level analysis of gut microbiome variation. Science, 2016. 352(6285): p. 560-4.
2. Jackson, M.A., et al., Gut microbiota associations with common diseases and prescription medications in a population-based cohort. Nat Commun, 2018. 9(1): p. 2655.
3. Maier, L., et al., Extensive impact of non-antibiotic drugs on human gut bacteria. Nature, 2018. 555(7698): p. 623-628.
4. Tramontano, M., et al., Nutritional preferences of human gut bacteria reveal their metabolic idiosyncrasies. Nat Microbiol, 2018. 3(4): p. 514-522.