Collective protection drives human gut microbiota response to amoxicillin treatment

The gut microbiota is central to human health, contributing to nutrient processing, metabolite production and protection against pathogens. Yet it is also an unintended target of antibiotic treatments, particularly after oral administration. Antibiotic exposure can therefore disrupt community structure, leading to dysbiosis and promoting the selection of resistant bacteria. Although studies in patients and animal models have shown that these effects vary markedly between individuals, host-related factors have made it difficult to isolate the specific contribution of the microbiota itself. Here, we used a controlled in vitro gut model (MBRA) to examine how 16 human gut microbiotas from the NutriNet-Santé cohort respond to the widely prescribed β-lactam amoxicillin (AMX). By combining dense temporal sampling, 16S amplicon sequencing and mass spectrometry, we observed highly heterogeneous response trajectories, ranging from near-stable communities to strong but reversible disruptions. These differences were not only reflected in the final magnitude of perturbation, but also in the timing, pace and recovery of microbiota change during treatment. Initial community composition partly structured these responses, as Lachnospiraceae / Bacteroidaceae ratio strongly correlated with perturbation. Dynamic quantification of AMX further showed that microbiotas differed in their capacity to deplete the drug over time, thereby altering the duration of exposure above critical concentration thresholds. Supplementation with clavulanic acid that inhibits β-lactamases confirmed that this process was largely mediated by β-lactamase activity. Finally, microbiotas displaying rapid AMX depletion showed reduced selection of resistant Enterobacteriaceae . Together, our results indicate that both initial community composition and the temporal dynamics of antibiotic inactivation jointly determine microbiota resilience and resistance selection.