Dietary fibre combinations modulate gut microbiome composition and metabolic responses in zebrafish, with lasting effects on intestinal barrier gene expression

Abstract

Food sources provide a complex mixture of dietary fibres, not a single type. Consuming a diverse range of these dietary fibre-containing foods is associated with health benefits. However, how the effects of combining dietary fibres translate across different biological levels remains poorly characterised. This study uses an integrated microbiome-metabolome analytical approach that combines 16S rRNA gene sequencing with metabolomic profiling of the intestine, brain and liver. Specifically, we examined the combined effects of apple pectin (AP) and cellulose (C) within the same diet, compared with their isolated effects, in adult female and male zebrafish (Danio rerio). Notably, the combined apple pectin and cellulose diet (APC) produced a microbiome composition that could not be predicted by simply adding the changes observed with each dietary fibre individually, indicating a significant non-additive interaction between the two dietary components, specifically a less-than-additive response in gut microbiome composition. The resulting community composition under the combined diet also more closely resembled that induced by apple pectin. We found that predicted microbial functional capabilities did not translate directly into quantified intestinal and brain short-chain fatty acid (SCFA) concentrations, nor did intestinal SCFA levels directly mirror those observed in the brain. Moreover, we used targeted qPCR gene expression analysis to assess responses to a subsequent saponin challenge after dietary fibre cessation, revealing a potentially protective effect on the intestinal barrier. Collectively, we show that dietary fibres within the same diet interact to shape the gut microbiome and do not act in isolation, leading to non-linear health ramifications for the host that may persist even after active consumption ends.