Antimicrobials Shape the Gut Microbiome Structure and Digestive Profile of Invertebrates

The gut microbiome is crucial for host well-being but is vulnerable to external stressors, such as antimicrobials. This study examined how an antibiotic, a fungicide, and their mixture affect the prokaryotic and fungal gut microbiome in Gammarus fossarum via dietary, waterborne, and combined exposure. Antimicrobial exposure altered the relative abundance of bacterial classes, including Verrucomicrobiae, Alphaproteobacteria, Betaproteobacteria, and Gammaproteobacteria, with effect directions depending on the antimicrobial. These structural shifts were predicted to enhance lipid and energy metabolism, particularly under dietary and combined exposure, potentially influencing host physiology. Previous studies on the same species reported up to 25% higher biomass gain under these exposure routes, whereas waterborne exposure had negligible effects. As this study primarily relies on predictive models linking microbiome shifts to physiological changes, experimental validation is required to substantiate these findings. Likewise, several fungal classes were affected, but limited knowledge of the mycobiome hinders functional interpretation. Overall, dietary uptake emerged as a key driver of gut microbiome changes, while waterborne exposure played a minor role in the metabolic and physiological responses. Future research should investigate the mycobiome alongside its prokaryotic counterpart for a more comprehensive understanding of the gut digestive profile of invertebrates as a whole and its role in host health.