Lubrano, P.; Magnan, M.; Steiner, C.; Birgy, A.; Chassaing, B.; Deschasaux-Tanguy, M.; Gutierrez, A.; Barreto, H. C.; Hobson, C.; Magreault, S.; Jullien, V.; Lescat, M.; Tenaillon, O.

The gut microbiota plays key roles in human health by providing essential services such as nutrient degradation, essential metabolite synthesis and pathogen protection. However, it is also at the forefront of antibiotic treatments, as many require oral administration. As a result, antibiotic can perturb the equilibrium of the gut microbiota, which leads to dysbiosis and potential selection of antibiotic resistance. To date, studies using murine models and human patients have shown differential patterns of gut microbiota dysbiosis and antibiotic resistance spread, hinting for a role of the gut microbiota in determining treatments outcomes. However, the implication of confounding host factors does not permit to fully investigate this role. Here, we use a robust in vitro system to evaluate the impact of the widely used beta-lactam amoxicillin (AMX) on 16 human gut microbiotas from the NutriNet Sante cohort. Using 16S amplicon sequencing to follow community composition shifts upon treatment, we observed a wide range of perturbation profiles amongst the 16 microbiotas, confirming their strong influence on AMX-mediated perturbation irrespective of host-specific factors. Combining the beta-lactamase inhibitor clavulanic acid and dynamic quantification of AMX with mass spectrometry, we further highlight that the key factor determining robustness to perturbation is the capacity of communities to deplete amoxicillin during treatment and protect their most sensitive members. Additionally, we highlight that amoxicillin robustness could substantially limit the spread of antibiotic resistance to resident Enterobacteriaceae.