Vertebrates harbour diverse communities of symbiotic gut microbes. Host diet is known to alter microbiota composition, implying that dietary treatments might alleviate diseases arising from altered microbial composition (‘dysbiosis’). However, it remains unclear whether diet effects are general or depend on host genotype. Here we show that gut microbiota composition depends on interactions between host diet and sex within populations of wild and laboratory fish, laboratory mice and humans. Within each of two natural fish populations (threespine stickleback and Eurasian perch), among-individual diet variation is correlated with individual differences in gut microbiota. However, these diet–microbiota associations are sex dependent. We document similar sex-specific diet–microbiota correlations in humans. Experimental diet manipulations in laboratory stickleback and mice confirmed that diet affects microbiota differently in males versus females. The prevalence of such genotype by environment (sex by diet) interactions implies that therapies to treat dysbiosis might have sex-specific effects.

Vertebrates' diets profoundly influence the composition of symbiotic gut microbial communities. Studies documenting diet-microbiota associations typically focus on univariate or categorical diet variables. However, in nature individuals often consume diverse combinations of foods. If diet components act independently, each providing distinct microbial colonists or nutrients, we expect a positive relationship between diet diversity and microbial diversity. We tested this prediction within each of two fish species (stickleback and perch), in which individuals vary in their propensity to eat littoral or pelagic invertebrates or mixtures of both prey. Unexpectedly, in most cases individuals with more generalised diets had less diverse microbiota than dietary specialists, in both natural and laboratory populations. This negative association between diet diversity and microbial diversity was small but significant, and most apparent after accounting for complex interactions between sex, size and diet. Our results suggest that multiple diet components can interact non-additively to influence gut microbial diversity.

Research on the uptake and effects of bioplastics by aquatic organisms is still in its infancy. Here, we aim to advance the field by comparing uptake and effects of microplastic particles (MPP) of a biodegradable bioMPP (polyhydroxybutyrate (PHB)) and petroleum-based MPP (polymethylmethacrylate (PMMA)) in the freshwater amphipod Gammarus fossarum. Ingestion of both MPP in different particle sizes (32–250 µm) occurred after 24 h, with highest ingestion of particles in the range 32–63 µm and almost complete egestion after 64 h. A four-week effect-experiment showed a significant decrease of the assimilation efficiency in amphipods exposed to the petroleum-based MPP from week two onwards. The petroleum-based PMMA affected assimilation efficiency significantly in contrast to the biodegradable PHB, but overall differences in direct comparison of MPP types were small. Both MPP types led to a significantly lower wet weight gain relative to the control treatments. After four weeks, differences between both MPP types and silica, used as a natural particle control, were detected. In summary, these results suggest that both MPP types provoke digestive constraints on the amphipods, which go beyond those of natural non-palatable particles. This highlights the need for more detailed research comparing environmental effects of biodegradable and petroleum-based MPP and testing those against naturally occurring particle loads.