Perspective: Leveraging the Gut Microbiota to Predict Personalized Responses to Dietary, Prebiotic, and Probiotic Interventions

Abstract

Humans often show variable responses to dietary, prebiotic, and probiotic interventions. Emerging evidence indicates that the gut microbiota is a key determinant for this population heterogeneity. Here, we provide an overview of some of the major computational and experimental tools being applied to critical questions of microbiota-mediated personalized nutrition and health. First, we discuss the latest advances in in silico modeling of the microbiota-nutrition-health axis, including the application of statistical, mechanistic, and hybrid artificial intelligence models. Second, we address high-throughput in vitro techniques for assessing inter-individual heterogeneity, from ex vivo batch culturing of stool and continuous culturing in anaerobic bioreactors, to more sophisticated organ-on-a-chip models that integrate both host and microbial compartments. Third, we explore in vivo approaches for better understanding personalized, microbiota-mediated responses to diet, prebiotics, and probiotics, from non-human animal models and human observational studies, to human feeding trials and crossover interventions. We highlight examples of existing, consumer-facing precision nutrition platforms that are currently leveraging the gut microbiota. Furthermore, we discuss how the integration of a broader set of the tools and techniques described in this piece can generate the data necessary to support a greater diversity of precision nutrition strategies. Finally, we present a vision of a precision nutrition and healthcare future, which leverages the gut microbiota to design effective, individual-specific interventions.

Early life exposure to broccoli sprouts confers stronger protection against enterocolitis development in an immunological mouse model of inflammatory bowel disease

“…Diet can play an important, economical, and accessible role in the prevention and/or management of IBD as a source of anti-inflammatory metabolites (8,9), and broadly as a tool for influencing the robustness of gut microbiomes (10)(11)(12). How IBD affects gut microbial ecology (13,14), how gut microbiota mediate disease (15) or response to diet (16,17), and how dietary components and microbial metabolites improve symptoms are still poorly understood (18,19). Moreover, the delicate health status in CD patients requires a thorough understanding of host-microbe-diet interactions before suggesting therapeutic strategies.…”

Probiotics: Bridging the interplay of a healthy gut and psychoneurological well‐being

“…Exploring an individual's distinctive microbiome and specific health needs presents significant promise in healthcare and nutrition, particularly with the emergence of innovative food engineering techniques in biotics preparation. However, the effective implementation of these personalized approaches encounters substantial challenges (Gibbons et al, 2022). Tailoring interventions based on an individual's microbiome composition and nutritional requirements, incorporating emerging food engineering techniques for biotics preparation, holds the potential to optimize health outcomes by enhancing the efficacy of treatments and preventive measures (Zmora et al, 2018).…”

Advances in Lactobacillus Restoration for β-Lactam Antibiotic-Induced Dysbiosis: A System Review in Intestinal Microbiota and Immune Homeostasis

“…In recent decades, the intake of Lactobacillus strains and other probiotics has applied in the therapy or intervention of antibiotic-induced dysbiosis [ 63 ], and these studies using Lactobacillus have investigated the mechanisms leading to the amelioration of antibiotic-induced dysbiosis in humans and animals ( Table 2 ). The dose of oral Lactobacillus strains was varied from 10 8 to 10 11 CFU, and 10 10 CFU were applied for administration in most studies.…”