A metagenome-wide association study of gut microbiota in type 2 diabetes. Nature. 2012;490:55-60. [PMID: 23023125 DOI: 10.1038/nature11450]

Intestinal microbiota, probiotics and mental health: from Metchnikoff to modern advances: Part II - contemporary contextual research

In recent years there has been a renewed interest concerning the ways in which the gastrointestinal tract – its functional integrity and microbial residents – might influence human mood (e.g. depression) and behavioral disorders. Once a hotbed of scientific interest in the early 20th century, this area lay dormant for decades, in part due to its association with the controversial term ‘autointoxication’. Here we review contemporary findings related to intestinal permeability, small intestinal bacterial overgrowth, lipopolysaccharide endotoxin (LPS) exposure, D-lactic acid, propionic acid, and discuss their relevance to microbiota and mental health. In addition, we include the context of modern dietary habits as they relate to depression, anxiety and their potential interaction with intestinal microbiota.

The role of gut microbiota on insulin resistance

The development of obesity and insulin resistance has been extensively studied in the last decades, but the mechanisms underlying these alterations are still not completely understood. The gut microbiota has been identified as a potential contributor to metabolic diseases. It has been shown that obese individuals present different proportions of bacterial phyla compared with lean individuals, with an increase in Firmicutes and Actinobacteria and a decrease in Bacteroidetes. This alteration seems to interfere with intestinal permeability, increasing the absorption of lipopolysaccharide (LPS), which reaches circulation and initiates activation of Toll-like receptor (TLR) 4 and 2 and LPS receptor CD14, leading to increased activation of inflammatory pathways. With these activations, an impairment of the insulin signaling is observed, with decreased phosphorylation of the insulin receptor, insulin receptor substrate (IRS) and Akt, as well as increased inhibitory serine phosphorylation of IRS-1. Altered proportions of bacterial phyla have also been demonstrated to interfere with host’s biochemical pathways, increasing energy extraction and depot in adipose tissue. Therefore, understanding the mechanisms by which the alteration in the gut microbiota produces different signaling activations and phenotype changes may offer an interesting opportunity for the treatment of obesity and type 2 diabetes.

Structural changes of gut microbiota in a rat non-alcoholic fatty liver disease model treated with a Chinese herbal formula

Accumulating evidence indicates that disruption of the gut microbiota by a high-fat diet (HFD) may play a pivotal role in the progression of metabolic disorders such as non-alcoholic fatty liver disease (NAFLD). In this study, the structural changes of gut microbiota were analyzed in an HFD-induced NAFLD rat model during treatment with an ancient Chinese herbal formula (CHF) used in clinical practice -Qushi Huayu Fang. CHF treatment significantly reduced body weight, alleviated hepatic steatosis, and decreased the content of triglycerides and free fatty acids in the livers of the rats. Gut microbiota of treated and control rats were profiled with polymerase chain reaction-denaturing gradient gel electrophoresis and bar-coded pyrosequencing of the V3 region of 16S rRNA genes. Both analyses indicated that the CHF-treated group harbored significantly different gut microbiota from that of model rats. Partial least squares discriminant analysis and taxonomy-based analysis were further employed to identify key phylotypes responding to HFD and CHF treatment. Most notably, the genera Escherichia/Shigella, containing opportunistic pathogens, were significantly enriched in HFD-fed rats compared to controls fed normal chow (P<0.05) but they decreased to control levels after CHF treatment. Collinsella, a genus with short chain fatty acid producers, was significantly elevated in CHF-treated rats compared to HFD-fed rats (P<0.05). The results revealed that the bacterial profiles of HFD-induced rats could be modulated by the CHF. Elucidation of these differences in microbiota composition provided a basis for further understanding the pharmacological mechanism of the CHF.

Ketone body metabolism and cardiovascular disease

Ketone bodies are metabolized through evolutionarily conserved pathways that support bioenergetic homeostasis, particularly in brain, heart, and skeletal muscle when carbohydrates are in short supply. The metabolism of ketone bodies interfaces with the tricarboxylic acid cycle, β-oxidation of fatty acids, de novo lipogenesis, sterol biosynthesis, glucose metabolism, the mitochondrial electron transport chain, hormonal signaling, intracellular signal transduction pathways, and the microbiome. Here we review the mechanisms through which ketone bodies are metabolized and how their signals are transmitted. We focus on the roles this metabolic pathway may play in cardiovascular disease states, the bioenergetic benefits of myocardial ketone body oxidation, and prospective interactions among ketone body metabolism, obesity, metabolic syndrome, and atherosclerosis. Ketone body metabolism is noninvasively quantifiable in humans and is responsive to nutritional interventions. Therefore, further investigation of this pathway in disease models and in humans may ultimately yield tailored diagnostic strategies and therapies for specific pathological states.

Inter-individual differences in response to dietary intervention: integrating omics platforms towards personalised dietary recommendations

Technologic advances now make it possible to collect large amounts of genetic, epigenetic, metabolomic and gut microbiome data. These data have the potential to transform approaches towards nutrition counselling by allowing us to recognise and embrace the metabolic, physiologic and genetic differences among individuals. The ultimate goal is to be able to integrate these multi-dimensional data so as to characterise the health status and disease risk of an individual and to provide personalised recommendations to maximise health. To this end, accurate and predictive systems-based measures of health are needed that incorporate molecular signatures of genes, transcripts, proteins, metabolites and microbes. Although we are making progress within each of these omics arenas, we have yet to integrate effectively multiple sources of biologic data so as to provide comprehensive phenotypic profiles. Observational studies have provided some insights into associative interactions between genetic or phenotypic variation and diet and their impact on health; however, very few human experimental studies have addressed these relationships. Dietary interventions that test prescribed diets in well-characterised study populations and that monitor system-wide responses (ideally using several omics platforms) are needed to make correlation-causation connections and to characterise phenotypes under controlled conditions. Given the growth in our knowledge, there is the potential to develop personalised dietary recommendations. However, developing these recommendations assumes that an improved understanding of the phenotypic complexities of individuals and their responses to the complexities of their diets will lead to a sustainable, effective approach to promote health and prevent disease - therein lies our challenge.

Understanding the microbiota in the midst of Renaissance architecture and olive groves

Leading scientists working on the microbiome gathered in an October 2012 meeting in Baeza, Spain, to discuss recent advances in the understanding of the role of the microbiota in immunity, pathogen colonization, metabolism and disease.

Fecal transplant: a safe and sustainable clinical therapy for restoring intestinal microbial balance in human disease?

Recent studies have suggested an association between intestinal microbiota composition and human disease, however causality remains to be proven. With hindsight, the application of fecal transplantation (FMT) does indeed suggest a causal relation between interfering with gut microbiota composition and a resultant cure of several disease states. In this review, we aim to show the available evidence regarding the involvement of intestinal microbiota and human (autoimmune) disease. Moreover, we refer to (mostly case report) studies showing beneficial or adverse effects of fecal transplantation on clinical outcomes in some of these disease states. If these findings can be substantiated in larger randomized controlled double blind trials also implementing gut microbiota composition before and after intervention, fecal transplantation might provide us with novel insights into causally related intestinal microbiota, that might be serve as future diagnostic and treatment targets in human disease.

Inflammation-associated enterotypes, host genotype, cage and inter-individual effects drive gut microbiota variation in common laboratory mice

BACKGROUND

Murine models are a crucial component of gut microbiome research. Unfortunately, a multitude of genetic backgrounds and experimental setups, together with inter-individual variation, complicates cross-study comparisons and a global understanding of the mouse microbiota landscape. Here, we investigate the variability of the healthy mouse microbiota of five common lab mouse strains using 16S rDNA pyrosequencing.

RESULTS

We find initial evidence for richness-driven, strain-independent murine enterotypes that show a striking resemblance to those in human, and which associate with calprotectin levels, a marker for intestinal inflammation. After enterotype stratification, we find that genetic, caging and inter-individual variation contribute on average 19%, 31.7% and 45.5%, respectively, to the variance in the murine gut microbiota composition. Genetic distance correlates positively to microbiota distance, so that genetically similar strains have more similar microbiota than genetically distant ones. Specific mouse strains are enriched for specific operational taxonomic units and taxonomic groups, while the 'cage effect' can occur across mouse strain boundaries and is mainly driven by Helicobacter infections.

CONCLUSIONS

The detection of enterotypes suggests a common ecological cause, possibly low-grade inflammation that might drive differences among gut microbiota composition in mammals. Furthermore, the observed environmental and genetic effects have important consequences for experimental design in mouse microbiome research.

Diet-microbiota interactions and their implications for healthy living

It is well established that diet influences the health of an individual and that a diet rich in plant-based foods has many advantages in relation to the health and well-being of an individual. What has been unclear until recently is the large contribution of the gut microbiota to this effect. As well as providing basic nutritional requirements, the long-term diet of an animal modifies its gut microbiota. In adults, diets that have a high proportion of fruit and vegetables and a low consumption of meat are associated with a highly diverse microbiota and are defined by a greater abundance of Prevotella compared to Bacteroides, while the reverse is associated with a diet that contains a low proportion of plant-based foods. Furthermore, it is becoming increasingly clear that the effect of the microbial ecology of the gut goes beyond the local gut immune system and is implicated in immune-related disorders, such as IBS, diabetes and inflamm-ageing. In this review, we investigate the evidence that a balanced diet leads to a balanced, diverse microbiota with significant consequences for healthy ageing by focusing on conditions of interest.

Personal genomes, quantitative dynamic omics and personalized medicine

The rapid technological developments following the Human Genome Project have made possible the availability of personalized genomes. As the focus now shifts from characterizing genomes to making personalized disease associations, in combination with the availability of other omics technologies, the next big push will be not only to obtain a personalized genome, but to quantitatively follow other omics. This will include transcriptomes, proteomes, metabolomes, antibodyomes, and new emerging technologies, enabling the profiling of thousands of molecular components in individuals. Furthermore, omics profiling performed longitudinally can probe the temporal patterns associated with both molecular changes and associated physiological health and disease states. Such data necessitates the development of computational methodology to not only handle and descriptively assess such data, but also construct quantitative biological models. Here we describe the availability of personal genomes and developing omics technologies that can be brought together for personalized implementations and how these novel integrated approaches may effectively provide a precise personalized medicine that focuses on not only characterization and treatment but ultimately the prevention of disease.

Genetic control of obesity and gut microbiota composition in response to high-fat, high-sucrose diet in mice

Obesity is a highly heritable disease driven by complex interactions between genetic and environmental factors. Human genome-wide association studies (GWAS) have identified a number of loci contributing to obesity; however, a major limitation of these studies is the inability to assess environmental interactions common to obesity. Using a systems genetics approach, we measured obesity traits, global gene expression, and gut microbiota composition in response to a high-fat/high-sucrose (HF/HS) diet of more than 100 inbred strains of mice. Here we show that HF/HS feeding promotes robust, strain-specific changes in obesity that are not accounted for by food intake and provide evidence for a genetically determined set point for obesity. GWAS analysis identified 11 genome-wide significant loci associated with obesity traits, several of which overlap with loci identified in human studies. We also show strong relationships between genotype and gut microbiota plasticity during HF/HS feeding and identify gut microbial phylotypes associated with obesity.

Modulating the human gut microbiome as an emerging therapeutic paradigm

The human body is actually a vast and changing ecosystem comprised of billions of microbial organisms, known collectively as the microbiome. Within the last few years, the study of the microbiome and its impact on human health has been a rapidly growing area of biomedical science. The gut intestinal tract microbiome has been a particular focus of research given its potential role in many inflammatory and metabolic diseases as well as drug metabolism. Although a nascent field, the potential for modulating the gut microbiome or human host interactions associated with these microbes offers new therapeutic strategies for many chronic diseases, in particular obesity, diabetes and inflammatory bowel diseases. Here we provide an overview of present knowledge about the gut microbiome, its putative role in metabolic diseases and the potential for microbiome focused treatments from the drug development perspective.

Dietary fiber future directions: integrating new definitions and findings to inform nutrition research and communication

The CODEX Alimentarius definition of dietary fiber includes all nondigestible carbohydrate polymers with a degree of polymerization of 3 or more as dietary fiber with the proviso that they show health benefits. The global definition, if accepted by all authoritative bodies, offers a chance for international harmonization in research, food composition tables, and food labeling. Its nonacceptance highlights problems that may develop when definitions vary by region. The definition requires that the research community agrees upon physiological effects for which there is substantial scientific agreement, e.g., fibers' effects on laxation and gut health, on attenuating blood lipids and blood glucose and insulin, and in promoting fermentation in the large bowel. The definition also necessitates the delineation of research protocols to prove the benefits of various isolated and synthesized fibers. These should emanate from evidence-based reviews that fairly weigh epidemiological data while considering that added fibers are not reflected in many food composition databases. They then should include well-controlled, randomized, control trials and utilize animal studies to determine mechanisms. Agreement on many study variables such as the type of subject and the type of baseline diet that best fits the question under investigation will also be needed. Finally, the definition establishes that all types of fiber can address the severe fiber consumption gap that exists throughout the world by recognizing that the combination of fiber-rich and -fortified foods increases fiber intake while allowing consumers to stay within allowed energy levels.

The intestinal microbiota in chronic liver disease

Recent evidence indicates that the intestinal microflora plays a critical role in physiological and pathological processes; in particular, it is now considered a key determinant of immune pathologies and metabolic syndrome. Receiving the majority of its blood supply from the portal vein, the liver represents the first line of defense against food antigens, toxins, microbial-derived products, and microorganisms. Moreover, the liver is critically positioned to integrate metabolic outcomes with nutrient intake. To accomplish this function, the liver is equipped with a broad array of immune networks. It is now evident that, during pathological processes associated with obesity, alcohol-intake, or autoimmunity, the interaction between these immune cell populations and the intestinal microbiota promotes chronic liver disease progression and therefore they represent a novel therapeutic target. Herein, we highlight recent studies that have shed new light on the relationship between the microbiome, the innate immune system, and chronic liver disease progression.

Probiotics: a potential role in the prevention of gestational diabetes?

The gut microbiome has a complex relationship with host metabolism and immune function. Host health and diet influence the composition of the gut microbiome, and conversely, different microbiome compositions influence host metabolism. Gestational diabetes mellitus is increasingly common and has serious implications for maternal and foetal health both during pregnancy and later in life. To date, clinical trials of exercise and dietary interventions to prevent the onset of gestational diabetes have had heterogeneous results and have proven disappointingly difficult. Alternative prevention strategies of gestational diabetes mellitus need to be considered and trialled in a placebo-controlled manner in combination with dietary and behavioural measures. One such potential preventative therapy is probiotic supplementation, that is, ingestion of specific bacterial strains with beneficial effects on the host. Probiotic supplements have been shown to improve metabolism by increasing host insulin sensitivity, cholesterol metabolism and also have a beneficial effect on the immune system. This discussion paper examines the evidence for the influence of the gut microbiome on host metabolism and the potential metabolic impact of probiotic supplementation, with particular regard for the evidence surrounding a possible use of probiotic supplements for the prevention of gestational diabetes. Probiotics offer the tantalising possibility of a feasible intervention for the prevention of gestational diabetes and improvement of metabolic syndromes, but there is a pressing need for further studies of the mechanisms underlying the apparent metabolic benefits and for the use of randomised controlled trials to allow examination of the effectiveness of probiotic supplementation in this setting.