A Molecular-Level Landscape of Diet-Gut Microbiome Interactions: Toward Dietary Interventions Targeting Bacterial Genes

Could Artificial Intelligence/Machine Learning and Inclusion of Diet-Gut Microbiome Interactions Improve Disease Risk Prediction? Case Study: Coronary Artery Disease

Coronary artery disease (CAD) is the most common cardiovascular disease (CVD) and the main leading cause of morbidity and mortality worldwide, posing a huge socio-economic burden to the society and health systems. Therefore, timely and precise identification of people at high risk of CAD is urgently required. Most current CAD risk prediction approaches are based on a small number of traditional risk factors (age, sex, diabetes, LDL and HDL cholesterol, smoking, systolic blood pressure) and are incompletely predictive across all patient groups, as CAD is a multi-factorial disease with complex etiology, considered to be driven by both genetic, as well as numerous environmental/lifestyle factors. Diet is one of the modifiable factors for improving lifestyle and disease prevention. However, the current rise in obesity, type 2 diabetes (T2D) and CVD/CAD indicates that the “one-size-fits-all” approach may not be efficient, due to significant variation in inter-individual responses. Recently, the gut microbiome has emerged as a potential and previously under-explored contributor to these variations. Hence, efficient integration of dietary and gut microbiome information alongside with genetic variations and clinical data holds a great promise to improve CAD risk prediction. Nevertheless, the highly complex nature of meals combined with the huge inter-individual variability of the gut microbiome poses several Big Data analytics challenges in modeling diet-gut microbiota interactions and integrating these within CAD risk prediction approaches for the development of personalized decision support systems (DSS). In this regard, the recent re-emergence of Artificial Intelligence (AI) / Machine Learning (ML) is opening intriguing perspectives, as these approaches are able to capture large and complex matrices of data, incorporating their interactions and identifying both linear and non-linear relationships. In this Mini-Review, we consider (1) the most used AI/ML approaches and their different use cases for CAD risk prediction (2) modeling of the content, choice and impact of dietary factors on CAD risk; (3) classification of individuals by their gut microbiome composition into CAD cases vs. controls and (4) modeling of the diet-gut microbiome interactions and their impact on CAD risk. Finally, we provide an outlook for putting it all together for improved CAD risk predictions.

Potential of the Microbiome as a Biomarker for Early Diagnosis and Prognosis of Breast Cancer

Breast cancer affects 1 in 8 women globally, and is the leading cause of cancer-related deaths in female patients. The majority of breast cancer cases are of unknown cause; few are linked to genetic predisposition, and some arise sporadically. Finding the cause of these sporadic cases is an important area in cancer research. Investigations into the microbiome show links between microbiome dysbiosis and breast cancer, with possible mechanisms in the association of the microbiome and breast cancer, including estrogen metabolism and the 'oestrobolome,' immune regulation, propensity for obesity, and the regulation of the tumor microenvironment. This paper reviews the literature and discusses the potential implications of links between the microbiome and breast cancer, and concludes that the microbiome may have significant applications as a biomarker for breast cancer diagnosis, prognosis, and management. Further investigation is crucial, since modification of the microbiome can, at the most basic level, be achieved via dietary modification.

To study the intervention mechanism of pediatric massage on intestinal flora and host metabolism in children with anorexia

BACKGROUND

As a common and frequent disease in pediatric patients, pediatric anorexia (PN) poses a serious threat to childhood growth and health. In recent years, societal changes in lifestyle and diet have increased the incidence of this PN, which has attracted extensive attention from both the medical community and parents. It has been shown that massage therapy represents an effective intervention for the treatment of anorexia, but investigation on its mechanism(s) of action remains limited. In this study, we will explore the biological mechanism(s) of PN from the perspective of intestinal flora, to further reveal its site of action and therapeutic mechanism(s).

METHODS

A total of 60 healthy children will be randomly selected for physical examination. According to a random number generated by a computer, children with anorexia who meet the inclusion criteria will be selected. In strict accordance with the time sequence of inclusion, subjects will be randomly assigned to either the massage or control group (n = 60 per group). The blank group will receive no treatment. Children in the massage group will receive a designated massage protocol. The control group will be administered oral Jianweixiaoshi tablets over 4 weeks. Each group will be compared for intestinal flora structure, fecal short chain fatty acids levels, serum trace elements, urine D-xylose-excretion rates, gastric fluid emptying, gastric motility, and hemoglobin levels before and after treatment.

RESULTS

We will review the clinical trial registry in China (http://www.chictr.org.cn/searchprojen.aspx), peer-reviewed journals and academic conferences.

CONCLUSION

This study will verify the intervention mechanism(s) of pediatric massage on intestinal flora and host metabolism in children with anorexia.

TRIAL REGISTRATION NUMBER

ChiCTR2000033274.

The Microbiota and Gut-Related Disorders: Insights from Animal Models

Over the past decade, the scientific committee has called for broadening our horizons in understanding host–microbe interactions and infectious disease progression. Owing to the fact that the human gut harbors trillions of microbes that exhibit various roles including the production of vitamins, absorption of nutrients, pathogen displacement, and development of the host immune system, particular attention has been given to the use of germ-free (GF) animal models in unraveling the effect of the gut microbiota on the physiology and pathophysiology of the host. In this review, we discuss common methods used to generate GF fruit fly, zebrafish, and mice model systems and highlight the use of these GF model organisms in addressing the role of gut-microbiota in gut-related disorders (metabolic diseases, inflammatory bowel disease, and cancer), and in activating host defense mechanisms and amending pathogenic virulence.

Gut/Oral Bacteria Variability May Explain the High Efficacy of Green Tea in Rodent Tumor Inhibition and Its Absence in Humans

Consumption of green tea (GT) and GT polyphenols has prevented a range of cancers in rodents but has had mixed results in humans. Human subjects who drank GT for weeks showed changes in oral microbiome. However, GT-induced changes in RNA in oral epithelium were subject-specific, suggesting GT-induced changes of the oral epithelium occurred but differed across individuals. In contrast, studies in rodents consuming GT polyphenols revealed obvious changes in epithelial gene expression. GT polyphenols are poorly absorbed by digestive tract epithelium. Their metabolism by gut/oral microbial enzymes occurs and can alter absorption and function of these molecules and thus their bioactivity. This might explain the overall lack of consistency in oral epithelium RNA expression changes seen in human subjects who consumed GT. Each human has different gut/oral microbiomes, so they may have different levels of polyphenol-metabolizing bacteria. We speculate the similar gut/oral microbiomes in, for example, mice housed together are responsible for the minimal variance observed in tissue GT responses within a study. The consistency of the tissue response to GT within a rodent study eases the selection of a dose level that affects tumor rates. This leads to the theory that determination of optimal GT doses in a human requires knowledge about the gut/oral microbiome in that human.

Systems Biology Approaches to Understand the Host-Microbiome Interactions in Neurodegenerative Diseases

Neurodegenerative diseases (NDDs) comprise a broad range of progressive neurological disorders with multifactorial etiology contributing to disease pathophysiology. Evidence of the microbiome involvement in the gut-brain axis urges the interest in understanding metabolic interactions between the microbiota and host physiology in NDDs. Systems Biology offers a holistic integrative approach to study the interplay between the different biologic systems as part of a whole, and may elucidate the host–microbiome interactions in NDDs. We reviewed direct and indirect pathways through which the microbiota can modulate the bidirectional communication of the gut-brain axis, and explored the evidence of microbial dysbiosis in Alzheimer’s and Parkinson’s diseases. As the gut microbiota being strongly affected by diet, the potential approaches to targeting the human microbiota through diet for the stimulation of neuroprotective microbial-metabolites secretion were described. We explored the potential of Genome-scale metabolic models (GEMs) to infer microbe-microbe and host-microbe interactions and to identify the microbiome contribution to disease development or prevention. Finally, a systemic approach based on GEMs and ‘omics integration, that would allow the design of sustainable personalized anti-inflammatory diets in NDDs prevention, through the modulation of gut microbiota was described.

Resources and tools for the high-throughput, multi-omic study of intestinal microbiota

The human gut microbiome impacts several aspects of human health and disease, including digestion, drug metabolism and the propensity to develop various inflammatory, autoimmune and metabolic diseases. Many of the molecular processes that play a role in the activity and dynamics of the microbiota go beyond species and genic composition and thus, their understanding requires advanced bioinformatics support. This article aims to provide an up-to-date view of the resources and software tools that are being developed and used in human gut microbiome research, in particular data integration and systems-level analysis efforts. These efforts demonstrate the power of standardized and reproducible computational workflows for integrating and analysing varied omics data and gaining deeper insights into microbe community structure and function as well as host-microbe interactions.

Microbiome Influence in the Pathogenesis of Prion and Alzheimer's Diseases

Misfolded and abnormal β-sheets forms of wild-type proteins, such as cellular prion protein (PrPC) and amyloid beta (Aβ), are believed to be the vectors of neurodegenerative diseases, prion and Alzheimer's disease (AD), respectively. Increasing evidence highlights the "prion-like" seeding of protein aggregates as a mechanism for pathological spread in AD, tauopathy, as well as in other neurodegenerative diseases, such as Parkinson's. Mutations in both PrPC and Aβ precursor protein (APP), have been associated with the pathogenesis of these fatal disorders with clear evidence for their pathogenic significance. In addition, a critical role for the gut microbiota is emerging; indeed, as a consequence of gut-brain axis alterations, the gut microbiota has been involved in the regulation of Aβ production in AD and, through the microglial inflammation, in the amyloid fibril formation, in prion diseases. Here, we aim to review the role of microbiome ("the other human genome") alterations in AD and prion disease pathogenesis.

Gut microbiota in phytopharmacology: A comprehensive overview of concepts, reciprocal interactions, biotransformations and mode of actions

The dynamic and delicate interactions amongst intestinal microbiota, metabolome and metabolism dictates human health and disease. In recent years, our understanding of gut microbial regulation of intestinal immunometabolic and redox homeostasis have evolved mainly out of in vivo studies associated with high-fat feeding induced metabolic diseases. Techniques utilizing fecal transplantation and germ-free mice have been instrumental in reproducibly demonstrating how the gut microbiota affects disease pathogenesis. However, the pillars of modern drug discovery i.e. evidence-based pharmacological studies critically lack focus on intestinal microflora. This is primarily due to targeted in vitro molecular-approaches at cellular-level that largely overlook the etiology of disease pathogenesis from the physiological perspective. Thus, this review aims to provide a comprehensive understanding of the key notions of intestinal microbiota and dysbiosis, and highlight the microbiota-phytochemical bidirectional interactions that affects bioavailability and bioactivity of parent phytochemicals and their metabolites. Potentially by focusing on the three major aspects of gut microbiota i.e. microbial abundance, diversity, and functions, I will discuss phytochemical-microbiota reciprocal interactions, biotransformation of phytochemicals and plant-derived drugs, and pre-clinical and clinical efficacies of herbal medicine on dysbiosis. Additionally, in relation to phytochemical pharmacology, I will briefly discuss the role of dietary-patterns associated with changes in microbial profiles and review pharmacological study models considering possible microbial effects. This review therefore, emphasize on the timely and critically needed evidence-based phytochemical studies focusing on gut microbiota and will provide newer insights for future pre-clinical and clinical phytopharmacological interventions.

The Prenatal Microbiome: A New Player for Human Health

The last few years have featured an increasing interest in the study of the human microbiome and its correlations with health status. Indeed, technological advances have allowed the study of microbial communities to reach a previously unthinkable sensitivity, showing the presence of microbes also in environments usually considered as sterile. In this scenario, microbial communities have been described in the amniotic fluid, the umbilical blood cord, and the placenta, denying a dogma of reproductive medicine that considers the uterus like a sterile womb. This prenatal microbiome may play a role not only in fetal development but also in the predisposition to diseases that may develop later in life, and also in adulthood. Thus, the aim of this review is to report the current knowledge regarding the prenatal microbiome composition, its association with pathological processes, and the future perspectives regarding its manipulation for healthy status promotion and maintenance.

The Science behind Microgreens as an Exciting New Food for the 21st Century

Chronic diseases are a major health problem in the United States. Accumulated data suggest that consumption of vegetables can significantly reduce the risk of many chronic diseases. Dietary guidelines for 2015-2020 from the U.S. Department of Agriculture and the U.S. Department of Health and Human Services recommend 1-4 cups of vegetables per day for males and 1-3 cups of vegetables per day for females, depending on their age. However, the average intake of vegetables is below the recommended levels. Microgreens are young vegetable greens. Although they are small, microgreens have delicate textures, distinctive flavors, and various nutrients. In general, microgreens contain greater amounts of nutrients and health-promoting micronutrients than their mature counterparts. Because microgreens are rich in nutrients, smaller amounts may provide similar nutritional effects compared to larger quantities of mature vegetables. However, literature on microgreens remains limited. In this Review, we discuss chemical compositions, growing conditions, and biological efficacies of microgreens. We seek to stimulate interest in further study of microgreens as a promising dietary component for potential use in diet-based disease prevention.

Functional metagenomics: a tool to gain knowledge for agronomic and veterinary sciences

The increased global demand for food production has motivated agroindustries to increase their own levels of production. Scientific efforts have contributed to improving these production systems, aiding to solve problems and establishing novel conceptual views and sustainable alternatives to cope with the increasing demand. Although microorganisms are key players in biological systems and may drive certain desired responses toward food production, little is known about the microbial communities that constitute the microbiomes associated with agricultural and veterinary activities. Understanding the diversity, structure and in situ interactions of microbes, together with how these interactions occur within microbial communities and with respect to their environments (including hosts), constitutes a major challenge with an enormous relevance for agriculture and biotechnology. The emergence of high-throughput sequencing technologies, together with novel and more accessible bioinformatics tools, has allowed researchers to learn more about the functional potential and functional activity of these microbial communities. These tools constitute a relevant approach for understanding the metabolic processes that can occur or are currently occurring in a given system and for implementing novel strategies focused on solving production problems or improving sustainability. Several 'omics' sciences and their applications in agriculture are discussed in this review, and the usage of functional metagenomics is proposed to achieve substantial advances for food agroindustries and veterinary sciences.

NutriChem 2.0: exploring the effect of plant-based foods on human health and drug efficacy

NutriChem is a database generated by text mining of 21 million MEDLINE abstracts that links plant-based foods with their small molecule components and human health effect. In this new, second release of NutriChem (NutriChem 2.0) we have integrated information on overlapping protein targets between FDA-approved drugs and small compounds in plant-based foods, which may have implications on drug pharmacokinetics and pharmacodynamics. NutriChem 2.0 contains predicted interactions between 428 drugs and 339 foods, supported by 107 jointly targeted proteins. Chemical bioactivity data were integrated, facilitating the comparison of activity concentrations between drugs and phytochemicals. In addition, we have added functionality that allows for user inspection of supporting evidence, the classification of food constituents based on KEGG “Phytochemical Compounds”, phytochemical structure output in SMILES and network output in both static figure and Cytoscape-compatible xgmml format. The current update of NutriChem moves one step further towards a more comprehensive assessment of dietary effects on human health and drug treatment.

Database URL: http://sbb.hku.hk/services/NutriChem-2.0/

Functional Characteristics of the Flying Squirrel's Cecal Microbiota under a Leaf-Based Diet, Based on Multiple Meta-Omic Profiling

Mammalian herbivores rely on microbial activities in an expanded gut chamber to convert plant biomass into absorbable nutrients. Distinct from ruminants, small herbivores typically have a simple stomach but an enlarged cecum to harbor symbiotic microbes; however, knowledge of this specialized gut structure and characteristics of its microbial contents is limited. Here, we used leaf-eating flying squirrels as a model to explore functional characteristics of the cecal microbiota adapted to a high-fiber, toxin-rich diet. Specifically, environmental conditions across gut regions were evaluated by measuring mass, pH, feed particle size, and metabolomes. Then, parallel metagenomes and metatranscriptomes were used to detect microbial functions corresponding to the cecal environment. Based on metabolomic profiles, >600 phytochemical compounds were detected, although many were present only in the foregut and probably degraded or transformed by gut microbes in the hindgut. Based on metagenomic (DNA) and metatranscriptomic (RNA) profiles, taxonomic compositions of the cecal microbiota were dominated by bacteria of the Firmicutes taxa; they contained major gene functions related to degradation and fermentation of leaf-derived compounds. Based on functional compositions, genes related to multidrug exporters were rich in microbial genomes, whereas genes involved in nutrient importers were rich in microbial transcriptomes. In addition, genes encoding chemotaxis-associated components and glycoside hydrolases specific for plant beta-glycosidic linkages were abundant in both DNA and RNA. This exploratory study provides findings which may help to form molecular-based hypotheses regarding functional contributions of symbiotic gut microbiota in small herbivores with folivorous dietary habits.

Structure and function of a CE4 deacetylase isolated from a marine environment

Chitin, a polymer of β(1–4)-linked N-acetylglucosamine found in e.g. arthropods, is a valuable resource that may be used to produce chitosan and chitooligosaccharides, two compounds with considerable industrial and biomedical potential. Deacetylating enzymes may be used to tailor the properties of chitin and its derived products. Here, we describe a novel CE4 enzyme originating from a marine Arthrobacter species (ArCE4A). Crystal structures of this novel deacetylase were determined, with and without bound chitobiose [(GlcNAc)₂], and refined to 2.1 Å and 1.6 Å, respectively. In-depth biochemical characterization showed that ArCE4A has broad substrate specificity, with higher activity against longer oligosaccharides. Mass spectrometry-based sequencing of reaction products generated from a fully acetylated pentamer showed that internal sugars are more prone to deacetylation than the ends. These enzyme properties are discussed in the light of the structure of the enzyme-ligand complex, which adds valuable information to our still rather limited knowledge on enzyme-substrate interactions in the CE4 family.

Designing Dietary Recommendations Using System Level Interactomics Analysis and Network-Based Inference

Background: A range of computational methods that rely on the analysis of genome-wide expression datasets have been developed and successfully used for drug repositioning. The success of these methods is based on the hypothesis that introducing a factor (in this case, a drug molecule) that could reverse the disease gene expression signature will lead to a therapeutic effect. However, it has also been shown that globally reversing the disease expression signature is not a prerequisite for drug activity. On the other hand, the basic idea of significant anti-correlation in expression profiles could have great value for establishing diet-disease associations and could provide new insights into the role of dietary interventions in disease. Methods: We performed an integrated analysis of publicly available gene expression profiles for foods, diseases and drugs, by calculating pairwise similarity scores for diet and disease gene expression signatures and characterizing their topological features in protein-protein interaction networks. Results: We identified 485 diet-disease pairs where diet could positively influence disease development and 472 pairs where specific diets should be avoided in a disease state. Multiple evidence suggests that orange, whey and coconut fat could be beneficial for psoriasis, lung adenocarcinoma and macular degeneration, respectively. On the other hand, fructose-rich diet should be restricted in patients with chronic intermittent hypoxia and ovarian cancer. Since humans normally do not consume foods in isolation, we also applied different algorithms to predict synergism; as a result, 58 food pairs were predicted. Interestingly, the diets identified as anti-correlated with diseases showed a topological proximity to the disease proteins similar to that of the corresponding drugs. Conclusions: In conclusion, we provide a computational framework for establishing diet-disease associations and additional information on the role of diet in disease development. Due to the complexity of analyzing the food composition and eating patterns of individuals our in silico analysis, using large-scale gene expression datasets and network-based topological features, may serve as a proof-of-concept in nutritional systems biology for identifying diet-disease relationships and subsequently designing dietary recommendations.

The prenatal gut microbiome: are we colonized with bacteria in utero?

The colonization of the gut with microbes in early life is critical to the developing newborn immune system, metabolic function and potentially future health. Maternal microbes are transmitted to offspring during childbirth, representing a key step in the colonization of the infant gut. Studies of infant meconium suggest that bacteria are present in the foetal gut prior to birth, meaning that colonization could occur prenatally. Animal studies have shown that prenatal transmission of microbes to the foetus is possible, and physiological changes observed in pregnant mothers indicate that in utero transfer is likely in humans as well. However, direct evidence of in utero transfer of bacteria in humans is lacking. Understanding the timing and mechanisms involved in the first colonization of the human gut is critical to a comprehensive understanding of the early life gut microbiome. This review will discuss the evidence supporting in utero transmission of microbes from mother to infants. We also review sources of transferred bacteria, physiological mechanisms of transfer and modifiers of maternal microbiomes and their potential role in early life infant health. Well-designed longitudinal birth studies that account for established modifiers of the gut microbiome are challenging, but will be necessary to confirm in utero transfer and further our knowledge of the prenatal microbiome.

Exploring the human microbiome from multiple perspectives: factors altering its composition and function

Our microbiota presents peculiarities and characteristics that may be altered by multiple factors. The degree and consequences of these alterations depend on the nature, strength and duration of the perturbations as well as the structure and stability of each microbiota. The aim of this review is to sketch a very broad picture of the factors commonly influencing different body sites, and which have been associated with alterations in the human microbiota in terms of composition and function. To do so, first, a graphical representation of bacterial, fungal and archaeal genera reveals possible associations among genera affected by different factors. Then, the revision of sequence-based predictions provides associations with functions that become part of the active metabolism. Finally, examination of microbial metabolite contents and fluxes reveals whether metabolic alterations are a reflection of the differences observed at the level of population structure, and in the last step, link microorganisms to functions under perturbations that differ in nature and aetiology. The utilisation of complementary technologies and methods, with a special focus on metabolomics research, is thoroughly discussed to obtain a global picture of microbiota composition and microbiome function and to convey the urgent need for the standardisation of protocols.

The interplay between intestinal bacteria and host metabolism in health and disease: lessons from Drosophila melanogaster

All higher organisms negotiate a truce with their commensal microbes and battle pathogenic microbes on a daily basis. Much attention has been given to the role of the innate immune system in controlling intestinal microbes and to the strategies used by intestinal microbes to overcome the host immune response. However, it is becoming increasingly clear that the metabolisms of intestinal microbes and their hosts are linked and that this interaction is equally important for host health and well-being. For instance, an individual's array of commensal microbes can influence their predisposition to chronic metabolic diseases such as diabetes and obesity. A better understanding of host-microbe metabolic interactions is important in defining the molecular bases of these disorders and could potentially lead to new therapeutic avenues. Key advances in this area have been made using Drosophila melanogaster. Here, we review studies that have explored the impact of both commensal and pathogenic intestinal microbes on Drosophila carbohydrate and lipid metabolism. These studies have helped to elucidate the metabolites produced by intestinal microbes, the intestinal receptors that sense these metabolites, and the signaling pathways through which these metabolites manipulate host metabolism. Furthermore, they suggest that targeting microbial metabolism could represent an effective therapeutic strategy for human metabolic diseases and intestinal infection.

Probiotics, gut microbiota, and their influence on host health and disease

The gastrointestinal tract of mammals hosts a high and diverse number of different microorganisms, known as intestinal microbiota. Many probiotics were originally isolated from the gastrointestinal tract, and they were defined by the Food and Agriculture Organization of the United Nations (FAO)/WHO as "live microorganisms which when administered in adequate amounts confer a health benefit on the host." Probiotics exert their beneficial effects on the host through four main mechanisms: interference with potential pathogens, improvement of barrier function, immunomodulation and production of neurotransmitters, and their host targets vary from the resident microbiota to cellular components of the gut-brain axis. However, in spite of the wide array of beneficial mechanisms deployed by probiotic bacteria, relatively few effects have been supported by clinical data. In this regard, different probiotic strains have been effective in antibiotic-associated diarrhea or inflammatory bowel disease for instance. The aim of this review was to compile the molecular mechanisms underlying the beneficial effects of probiotics, mainly through their interaction with the intestinal microbiota and with the intestinal mucosa. The specific benefits discussed in this paper include among others those elicited directly through dietary modulation of the human gut microbiota.

COMAN: a web server for comprehensive metatranscriptomics analysis

Background

Microbiota-oriented studies based on metagenomic or metatranscriptomic sequencing have revolutionised our understanding on microbial ecology and the roles of both clinical and environmental microbes. The analysis of massive metatranscriptomic data requires extensive computational resources, a collection of bioinformatics tools and expertise in programming.

Results

We developed COMAN (Comprehensive Metatranscriptomics Analysis), a web-based tool dedicated to automatically and comprehensively analysing metatranscriptomic data. COMAN pipeline includes quality control of raw reads, removal of reads derived from non-coding RNA, followed by functional annotation, comparative statistical analysis, pathway enrichment analysis, co-expression network analysis and high-quality visualisation. The essential data generated by COMAN are also provided in tabular format for additional analysis and integration with other software. The web server has an easy-to-use interface and detailed instructions, and is freely available at http://sbb.hku.hk/COMAN/

Conclusions

COMAN is an integrated web server dedicated to comprehensive functional analysis of metatranscriptomic data, translating massive amount of reads to data tables and high-standard figures. It is expected to facilitate the researchers with less expertise in bioinformatics in answering microbiota-related biological questions and to increase the accessibility and interpretation of microbiota RNA-Seq data.

Electronic supplementary material

The online version of this article (doi:10.1186/s12864-016-2964-z) contains supplementary material, which is available to authorized users.

Foodomics as part of the host-microbiota-exposome interplay

The functional complexity of human gut microbiota and its relationship with host physiology and environmental modulating factors, offers the opportunity to investigate (i) the host and microbiota role in organism-environment relationship; (ii) the individual functional diversity and response to environmental stimuli (exposome); (iii) the host genome and microbiota metagenomes' modifications by diet-mediated epigenomic controls (nutriepigenomics); and (iv) the genotype-phenotype "trajectories" under physiological and disease constraints. Systems biology-based approaches aim at integrating biological data at cellular, tissue and organ organization levels, using computational modeling to interpret diseases' physiopathological mechanisms (i.e., onset and progression). Proteomics improves the existing gene models by profiling molecular phenotypes at protein abundance level, by analyzing post-translational modifications and protein-protein interactions and providing specific pathway information, hence contributing to functional molecular networks. Transcriptomics and metabolomics may determine host ad microbiota changes induced by food ingredients at molecular level, complementing functional genomics and proteomics data. Since foodomics is an -omic wide methodology may feed back all integrative data to foster the omics-based systems medicine field. Hence, coupled to ecological genomics of gut microbial communities, foodomics may highlight health benefits from nutrients, dissecting diet-induced gut microbiota eubiosis mechanisms and significantly contributing to understand and prevent complex disease phenotypes.

BIOLOGICAL SIGNIFICANCE

Besides transcriptomics and proteomics there is a growing interest in applying metabolic profiling to food science for the development of functional foods. Indeed, one of the biggest challenges of modern nutrition is to propose a healthy diet to populations worldwide, intrinsically respecting the high inter-individual variability, driven by complex host/nutrients/microbiota/environment interactions. Therefore, metabolic profiling can assist at various levels for the development of functional foods, starting from screening for food composition to identification of new biomarkers to trace food intake. This current approach can support diet intervention strategies, epidemiological studies, and controlling of metabolic disorders worldwide spreading, hence ensuring healthy aging. With high-throughput molecular technologies driving foodomics, studying bidirectional interactions of host-microbial co-metabolism, innate immune development, dysfunctional nutrient absorption and processing, complex signaling pathways involved in nutritional metabolism, is now likely. In all cases, as microbiome pipeline efforts continue, it is possible that enhanced standardized protocols can be developed, which may lead to new testable biological and clinical hypotheses. This Review provides a comprehensive update on the current state-of-the-art of the integrated -omics route in food, microbiota and host co-metabolism studies, which may revolutionize the design of new dietary intervention strategies.