Current dietary recommendations are often generalized, conflicting, and highly subjective, depending on the source biases. This results in confusion, skepticism, and frustration in the general population. As an alternative, we propose an objective, integrated, automated, algorithmic approach to diet and supplement recommendations that is powered by artificial intelligence that analyzes individualized molecular data from the gut microbiome, the human host, and their interactions. This platform enables precise, personalized, and data-driven nutritional recommendations that consist of foods and supplements, based on the individual molecular data, to support healthy homeostasis. We describe the application of this precision technology platform to populations with depression, anxiety, irritable bowel syndrome (IBS), and type 2 diabetes (T2D). We show that our precision nutritional recommendations resulted in improvements in clinical outcomes by 36% in severe cases of depression, 40% in severe cases of anxiety, 38% in severe cases of IBS, and more than 30% in the T2D risk score which was validated against clinical measurement of HbA1c. Our data support the integration of precision food and supplements into the standard of care for these chronic conditions.
Background Current dietary recommendations are often generalized, conflicting, and highly subjective, depending on the source biases. This results in confusion, skepticism, and frustration in the general population. Methods We have developed an objective, integrated, automated, algorithmic approach to diet and supplement recommendations that is powered by artificial intelligence that analyzes individualized molecular data from the gut microbiome, the human host, and their interactions. This platform enables precise, personalized, and data-driven nutritional recommendations that consist of foods and supplements, based on the individual molecular data, to establish and maintain healthy homeostasis. Results We describe the application of our precision nutrition technology platform to populations with depression, anxiety, irritable bowel syndrome (IBS), and type 2 diabetes (T2D). In a blinded interventional study, we provided the study participants with precision nutritional recommendations and observed improvements in clinical outcomes by 36% in severe cases of depression, 40% in severe cases of anxiety, 38% in severe cases of IBS, and more than 30% in the T2D risk score that was validated against clinical measurements of HbA1c. Conclusion Our AI-driven precision nutrition program achieved statistically significant improvements in clinical outcomes of depression, anxiety, IBS, and type 2 diabetes. These data support the integration of precision food and supplements into the standard of care for these chronic conditions.
Recognizing and treating the early stages of type 2 diabetes (T2D) is the most cost effective way to decrease prevalence, before heart disease, renal disease, blindness, and limb amputation become inevitable. In this study, we employ high resolution gut microbiome metatranscriptomic analysis of stool samples from 53,970 individuals to identify predictive biomarkers of type 2 diabetes progression and potential for diagnosis and treatment response. The richness of the metatranscriptomic data enabled us to develop a T2D risk model to delineate individuals with glycemic dysregulation from those within normal glucose levels, with ROC-AUC of 0.83+/-0.04. This risk score can predict the probability of having insulin dysregulation before detecting high glycated hemoglobin (HbA1c), the standard-of-care marker for prediabetes and diabetes. Additionally, a machine learning model was able to distinguish novel metatranscriptomic features that segregate patients who receive metformin and are able to control their HbA1c from those who do not. These discoveries set the stage for developing multiple therapeutic avenues for prevention and treatment of T2D.
The study of microbial communities and their interactions has attracted the interest of the scientific community, because of their potential for applications in biotechnology, ecology and medicine. The complexity of interspecies interactions, which are key for the macroscopic behavior of microbial communities, cannot be studied easily experimentally. For this reason, the modeling of microbial communities has begun to leverage the knowledge of established constraint-based methods, which have long been used for studying and analyzing the microbial metabolism of individual species based on genome-scale metabolic reconstructions of microorganisms. A main problem of genome-scale metabolic reconstructions is that they usually contain metabolic gaps due to genome misannotations and unknown enzyme functions. This problem is traditionally solved by using gap-filling algorithms that add biochemical reactions from external databases to the metabolic reconstruction, in order to restore model growth. However, gap-filling algorithms could evolve by taking into account metabolic interactions among species that coexist in microbial communities. In this work, a gap-filling method that resolves metabolic gaps at the community level was developed. The efficacy of the algorithm was tested by analyzing its ability to resolve metabolic gaps on a synthetic community of auxotrophic Escherichia coli strains. Subsequently, the algorithm was applied to resolve metabolic gaps and predict metabolic interactions in a community of Bifidobacterium adolescentis and Faecalibacterium prausnitzii, two species present in the human gut microbiota, and in an experimentally studied community of Dehalobacter and Bacteroidales species of the ACT-3 community. The community gap-filling method can facilitate the improvement of metabolic models and the identification of metabolic interactions that are difficult to identify experimentally in microbial communities.
The study of microbial communities and their interactions has attracted the interest of the scientific community, because of their potential for applications in biotechnology, ecology and medicine. The complexity of interspecies interactions, which are key for the macroscopic behavior of microbial communities, cannot be studied easily experimentally. For this reason, the modeling of microbial communities has begun to leverage the knowledge of established constraint-based methods, which have long been used for studying and analyzing the microbial metabolism of individual species based on genome-scale metabolic reconstructions of microorganisms. A main problem of genome-scale metabolic reconstructions is that they usually contain metabolic gaps due to genome misannotations and unknown enzyme functions. This problem is traditionally solved by using gap-filling algorithms that add biochemical reactions from external databases to the metabolic reconstruction, in order to restore model growth. However, gap-filling algorithms could evolve by taking into account metabolic interactions among species that coexist in microbial communities. In this work, a gap-filling method that resolves metabolic gaps at the community level was developed. The efficacy of the algorithm was tested by analyzing its ability to resolve metabolic gaps on a synthetic community of auxotrophic Escherichia coli strains. Subsequently, the algorithm was applied to resolve metabolic gaps and predict metabolic interactions in a community of Bifidobacterium adolescentis and Faecalibacterium prausnitzii, two species present in the human gut microbiota, and in an experimentally studied community of Dehalobacter and Bacteroidales species of the ACT-3 community. The community gap-filling method can facilitate the improvement of metabolic models and the identification of metabolic interactions that are difficult to identify experimentally in microbial communities.
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