How Complex Dietary Fibers Can Be Used to Shape the Human Gut Microbiome Toward Reduced Inflammatory Potential: A Pilot Study

Abstract

Microbiome-linked pathologies in humans have significantly increased over recent decades, suggesting that lifestyle changes, particularly those related to diet, have contributed to the disruption of beneficial microbial composition and functions. Specifically, modern processed diets that are low in dietary fiber and high in fat and sugar can lead to the depletion of bacterial taxa over generations and contribute to chronic inflammatory diseases. These pathologies can potentially be prevented by increasing fiber intake, making the promotion of dietary fiber crucial for human health. Despite the recognized importance of fiber integration, there remains a significant gap in the understanding of the use of multiple dietary fibers in food to promote microbiota diversity, as well as which dietary fibers promote specific microbial taxa to restore symbiosis. To address this gap, we conducted an in vitro fermentation study using fecal samples from two individuals. We tested three types of dietary fibers of varying complexity: inulin, pectin, and dextran in a β-glucan–based medium. Samples were collected over a 48 h fermentation period (0–4–8–24–32–48 h) to evaluate temporal shifts in microbial composition and short-chain fatty acid (SCFA) production. Through 16S rRNA gene amplicon sequencing, we found that the introduction of different fibers steered the microbiota of both individuals toward a convergent trajectory by 24–48 h. This result indicated that fiber complexity can reduce inter-individual variation in microbial community structure. Distinct levels of polysaccharide complexity between fiber types modulated specific bacterial taxa, supporting the concept that consuming a diversity of dietary fiber acts on complementary microbial niches. Notably, the observed shifts toward butyrate-associated taxa and reduction of pro-inflammatory lineages with dextran/β-glucan are relevant for pathologies characterized by dysbiosis, such as inflammatory bowel disease (IBD). Together, these results underscore the value of incorporating multiple fibers into food production, including fermented foods, to enhance prebiotic properties, stimulate the growth of fiber-fermenting bacteria, and promote microbial diversity. While these observations derive from a controlled in vitro pilot setting, they support the concept that multi-fiber dietary strategies based on complementary fermentable fibers with prebiotic properties may help shift the microbiome away from a pro-inflammatory state. Accordingly, dietary guidelines and public health approaches aimed at reducing chronic disease risk may benefit from emphasizing the inclusion of composite fiber blends rather than relying solely on single-fiber supplementation.