Dataset from: Petitjean et al. (Submitted) Experimental metal contamination reduces gut microbiota diversity and alters its composition and function in wild-caught fish.

Wild organisms face multiple environmental stressors that can interact and affect their health in unexpected ways. In this context, a growing body of evidence suggests that some responses to environmental stressors might be mediated by changes in gut microbiome with cascading effects on host health. However, the combined effects of multiple stressors on host microbiota and health are still overlooked. Here, we investigated the single and interactive effects of a realistic metal pollution and an immune challenge mimicking a parasite attack on the gut microbiome of wild fish while taking into account the intraspecific variability among populations. We tested the effects of experimental exposure to trace metal elements (i.e., mixture of Cd, Cu, Zn) and of an injection of antigens on the taxonomic and functional diversity and composition of gut microbiota among several wild freshwater fish (Gobio occitaniae) populations sampled along gradients of contamination in streams. We found that gut microbial community was strongly altered by the experimental metal contamination, with no interaction with the immune secondary stressor. Indeed, metal contamination reduced both taxonomic and functional gut microbial diversity, affecting the microbial community's taxonomic and functional composition, with predicted consequences for their functional role in fish. We found that metal contamination reduced microbial function related to molecule biosyntheses (e.g., cell structure and amino acid precursors) while increasing functions associated with energy production (e.g., anaerobic respiration). In addition, populations sampled along a gradient of pollution in the wild did not differ in their response, suggesting a consistent impact of contaminants irrespective of the host’s past exposure to pollution. Although the long-term implications for fitness remain to be determined, our results shed light on the alterations induced by realistic levels of metal contamination on fish gut microbiome with potential consequences on fish's ability to cope with environmental stressors.