A new study examining the effects of an antibiotic, a fungicide, and their mixture on the gut microbiome of Gammarus fossarum found that the antimicrobial exposure altered the relative abundance of bacterial classes within the gut microbiome, with effect directions depending on the type of antimicrobial used.

We took a closer look at the balance of the gut microbiome and its vulnerability to external stressors, such as antimicrobials. Our recent study examined the effects of an antibiotic, a fungicide, and their mixture on the gut microbiome of Gammarus fossarum, a small crustacean found in local streams. By exposing these organisms to antimicrobials through their diet, water, and a combination of both, we gained valuable insights into the complex relationships between the gut microbiome, antimicrobials, and host physiology.

The results showed that antimicrobial exposure altered the relative abundance of several bacterial classes within the gut microbiome, with the direction of these effects depending on the type of antimicrobial used. We predicted that these structural shifts would enhance lipid and energy metabolism, particularly when antimicrobials were introduced through the diet or a combination of diet and water. This, in turn, could have had significant implications for host physiology. Consistently, previous studies reported up to 25% higher biomass gain in Gammarus fossarum under dietary and combined exposure routes.

While our study provided valuable insights into the prokaryotic gut microbiome, we recognized the need for further research into the mycobiome, the fungal component of the gut microbiome. Limited knowledge of the mycobiome hindered our ability to interpret the functional implications of changes to the fungal composition. Therefore, future research is needed to investigate the mycobiome alongside its prokaryotic counterpart, in order to gain a more comprehensive understanding of the gut digestive profile of invertebrates and its in host health.

The Study

The publication “Antimicrobials shape the gut microbiome structure and digestive profile of invertebrates” by Alexander Feckler, Eric Bollinger, Sven Katzenmeier, Ondrej Adamovsky, Hana Vespalcova, Eva Budinska, Thorsten Stoeck, and Mirco Bundschuh was published on 12 September 2025 in the Volume 59 Issue 37 Environmental Science & Technology journal

Feckler, A., Bollinger, E., Katzenmeier, S., Adamovsky, O., Vespalcova, H., Budinska, E., Stoeck, T., & Bundschuh, M. (2025). Antimicrobials shape the gut microbiome structure and digestive profile of invertebrates. PubMed. https://doi.org/10.1021/acs.est.5c04159