In ecotoxicology, sentinel species, such as the freshwater amphipod Gammarus fossarum, are used to assess the quality of the environment based on responsive biomarkers for physiological effects caused by bioavailable pollutants. Recently, interest for microbiota is growing as the gut microbiota plays a key role in fate and transformation of contaminants as well as in toxicity-related responses in host organisms. Our long-term aim is to describe the dynamics of the gut microbiota and the health status of the host organism, G. fossarum, upon different exposure conditions. Here, we characterize the gut microbial community and how it functions in normal conditions (contaminant-free) by testing different diets (alder leaf, carrot, spinach and marketed granules) during 9 days. This metaproteomics study benefits from extensive data obtained for this sentinel species for which no annotated genome is yet established. The interpretation relies on annotated genomes and RNA-seq derived proteogenomics information, as no reference metagenomics data is yet available. The microbial communities highlighted in the gut microbiota include 37 bacteria genera and 5 fungi genera that have been identified at the genera level in at least one diet condition. The relative biomass of the main phyla includes 38% Proteobacteria, 25% Actinobacteria, 12% Firmicutes and 9% Bacteroidetes. We show in this study an effect of diet on the taxonomic composition of the gut microbiota with, for instance, the presence of taxa specific to a diet or a change in the abundance of taxa. The effect on the microbial communities in these detritivorous animals induced by food is mainly explained by the ingestion of microorganisms present in the food. We also observe a core microbiota common to all the individuals whatever the diet. This core microbiota comprises 8 bacteria genera and 1 fungi genera, most but not all of these genera being found in other amphipods. The functional analysis of such a core microbiota should provide interesting information regarding its key physiological role for the host. That a core microbiota is not significantly affected by fluctuations in environmental factors (e.g. food) is an important point to consider in future ecotoxicological studies.