Abstract
Food and human health are inextricably linked. As such, revolutionary impacts on health have been derived from advances in the production and distribution of food relating to food safety and fortification with micronutrients. During the past two decades, it has become apparent that the human microbiome has the potential to modulate health, including in ways that may be related to diet and the composition of specific foods. Despite the excitement and potential surrounding this area, the complexity of the gut microbiome, the chemical composition of food, and their interplay in situ remains a daunting task to fully understand. However, recent advances in high-throughput sequencing, metabolomics profiling, compositional analysis of food, and the emergence of electronic health records provide new sources of data that can contribute to addressing this challenge. Computational science will play an essential role in this effort as it will provide the foundation to integrate these data layers and derive insights capable of revealing and understanding the complex interactions between diet, gut microbiome, and health. Here, we review the current knowledge on diet-health-gut microbiota, relevant data sources, bioinformatics tools, machine learning capabilities, as well as the intellectual property and legislative regulatory landscape. We provide guidance on employing machine learning and data analytics, identify gaps in current methods, and describe new scenarios to be unlocked in the next few years in the context of current knowledge.
Highlights
During the past two decades, the human microbiome has emerged as a biological system with the potential to significantly influence health and disease (Shreiner et al, 2015)
Significant advances in microbiology, genomics, analytical chemistry, computational science, bioinformatics, and other critical disciplines have begun to converge such that it is possible to foresee a new era of health and nutrition research enabling the design of food products capable of optimizing health via predictable interactions with the gut microbiome
Despite the exciting potential in this context demonstrated by pioneering research efforts of many investigators, including those cited in this brief review, the complexity of the microbiome, the chemical composition of food, and their interplay in situ remains a daunting challenge in the context of achieving necessary breakthroughs
Summary
During the past two decades, the human microbiome has emerged as a biological system with the potential to significantly influence health and disease (Shreiner et al, 2015). Advances in genomics and bioinformatics have provided inexpensive tools to acquire biological and clinical data, as well as the tools to Computational Diet, Microbiome and Health translate the data into knowledge (Shoaie et al, 2015; Zeevi et al, 2015; Thaiss et al, 2016a; Korem et al, 2017; Baldini et al, 2018; Bauer and Thiele, 2018; Gilbert et al, 2018; Greenhalgh et al, 2018; Knight et al, 2018) Given these advances, the integration of diet, gut microbiome, and human health (DGMH) data has the potential to drive a paradigm shift in the way wellness states are measured, diseases are treated, products are designed, and health interventions are administered.
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