Precision Nutrition Initiative: Toward Personalized Diet Recommendations for Patients With Inflammatory Bowel Diseases

Predicting metabolite response to dietary intervention using deep learning

Due to highly personalized biological and lifestyle characteristics, different individuals may have different metabolite responses to specific foods and nutrients. In particular, the gut microbiota, a collection of trillions of microorganisms living in the gastrointestinal tract, is highly personalized and plays a key role in the metabolite responses to foods and nutrients. Accurately predicting metabolite responses to dietary interventions based on individuals' gut microbial compositions holds great promise for precision nutrition. Existing prediction methods are typically limited to traditional machine learning models. Deep learning methods dedicated to such tasks are still lacking. Here we develop a method McMLP (Metabolite response predictor using coupled Multilayer Perceptrons) to fill in this gap. We provide clear evidence that McMLP outperforms existing methods on both synthetic data generated by the microbial consumer-resource model and real data obtained from six dietary intervention studies. Furthermore, we perform sensitivity analysis of McMLP to infer the tripartite food-microbe-metabolite interactions, which are then validated using the ground-truth (or literature evidence) for synthetic (or real) data, respectively. The presented tool has the potential to inform the design of microbiota-based personalized dietary strategies to achieve precision nutrition.

What is the link between the dietary inflammatory index and the gut microbiome? A systematic review

PURPOSE

One highlighted pathogenesis mechanism of diseases is the negative impact of pro-inflammatory diets (PD) on the gut microbiome. This systematic review aimed to study the link between dietary inflammatory index (DII), as an indicator of PD, and gut microbiome.

METHODS

A systematic search was done in PubMed and Scopus, adhering to the guidelines of Preferred Reporting Items for Systematic Reviews and Meta-Analysis. The assessment of the included studies' quality was performed using the critical appraisal checklist from the Joanna Briggs Institute.

RESULTS

Ten articles were included eight cross-sectional, one case-control, and, one cohort study. Seven and three included articles reported a weak and moderate relationship between gut microbiome and DII scores, respectively. DII scores were linked to variety in microbiome composition and diversity/richness. More importantly, anti-inflammatory diets as measured by lower DII scores were linked to a more desirable gut microbiome profile. Prevotella stercorea, Veillonella rogosae, Morganella morganii, Ruminococcus torques, Eubacterium nodatum, Alistipes intestine, Clostridium leptum, Morganellaceae family, Enterobacteriaceae family, and, Bacteroides thetaiotaomicron were related to higher DII scores. While, Butyrate-producing bacteria such as Ruminococcaceae and Lachnospiraceae families, Faecalibacterium prausnitzii, and Akkermansia muciniphila were related to lower DII scores.

CONCLUSION

An anti-inflammatory diet, as measured by a lower DII score, might be linked to variations in the composition and variety of the microbiome. Therefore, the DII score could be useful in microbiota research, however, this possibility needs to be investigated more precisely in future studies.

Diet-Microbiota Interactions in Inflammatory Bowel Disease

Inflammatory bowel disease (IBD) is a chronic inflammatory disease of the gastrointestinal tract. Although the precise etiology of IBD is largely unknown, it is widely thought that diet contributes to the development of IBD. Diet shapes the composition of the gut microbiota, which plays critical roles in intestinal homeostasis. In contrast, intestinal inflammation induces gut dysbiosis and may affect the use of dietary nutrients by host cells and the gut microbiota. The interaction of diet and the gut microbiota is perturbed in patients with IBD. Herein, we review the current knowledge of diet and gut microbiota interaction in intestinal homeostasis. We also discuss alterations of diet and gut microbiota interaction that influence the outcome and the nutritional treatment of IBD. Understanding the complex relationships between diet and the gut microbiota provides crucial insight into the pathogenesis of IBD and advances the development of new therapeutic approaches.