Description
Microbial communities perform essential ecosystem functions, from driving biogeochemical cycles to aiding digestion in the gut. Their metabolic diversity creates both redundancy and complementarity. Over time, some microbes discard costly biosynthetic pathways (as described by the Black Queen Hypothesis), becoming auxotrophs reliant on cross-feeding nutrients from neighbours. In turn, cross-feeding of metabolites like amino acids becomes critical for community stability. Widespread antibiotic use perturbs these communities and promotes resistance, yet its effects on interspecies metabolic interactions remain poorly understood.
We investigated how antibiotics influence nutrient sharing using a microfluidic co-culture platform on family machine chips. Prototrophic E. coli capable of synthesising all essential amino acids were paired with different single-gene knockout auxotroph strains, each requiring a specific amino acid. These cocultures were grown on-chip under sub-minimum inhibitory concentration (MIC) gradients of a ribosome–inhibiting antibiotic to impose sub-MIC stress. The microfluidic device enabled precise control of antibiotic levels and real-time observation of cell growth. We continuously monitored growth dynamics and amino acid exchange between strains under various antibiotic conditions. We hypothesised that antibiotic stress would disrupt internal metabolic processes, reducing amino acid synthesis from prototrophs and thus weakening cross-feeding.
Expectedly, without antibiotics, prototroph–auxotroph pairs stably coexisted via mutualistic cross-feeding of leaked amino acids (allowing auxotroph growth without external supplementation). However, contrary to expectation, introducing moderate antibiotic stress actually enhanced metabolic exchange. Under sub-MIC antibiotic concentrations, auxotrophs grew more robustly likely due to increased amino acid leakage from prototrophs. Inhibiting protein synthesis in prototrophs likely caused intracellular amino acid buildup, leading to greater release of these metabolites into the environment. This heightened nutrient release strengthened cross-feeding interactions and supported auxotroph proliferation despite the stress.
Our findings reveal a counterintuitive consequence of antibiotic exposure; the reinforcement of metabolic dependencies within microbial communities. Rather than simply suppressing growth, sub-MIC antibiotics can tighten cooperative links by amplifying nutrient sharing. This insight suggests that antibiotics may paradoxically stabilise certain community interactions even as they inhibit individual cells. Such effects highlight the complexity of antibiotic impacts beyond resistance, potentially shaping host-associated microbiomes by helping pathogens or commensals survive therapeutic stress or even invade stable microbiome communities. Overall, our study underscores the importance of accounting for community-level responses when evaluating antibiotic strategies or microbiome interventions.