Diet affects multiple facets of human health and is inextricably linked to chronic metabolic conditions such as obesity, type 2 diabetes, and cardiovascular disease. Dietary nutrients are essential not only for human health but also for the health and survival of the trillions of microbes that reside within the human intestines. Diet is a key component of the relationship between humans and their microbial residents; gut microbes use ingested nutrients for fundamental biological processes, and the metabolic outputs of those processes may have important impacts on human physiology. Studies in humans and animal models are beginning to unravel the underpinnings of this relationship, and increasing evidence suggests that it may underlie some of the broader effects of diet on human health and disease.

Controversy regarding what constitutes a healthful diet has persisted since the advent of nutrition as a scientific discipline and establishment of government nutritional guidelines (1). The emergence of the gut microbiota as a key regulator of health and disease has further complicated this issue. A mutualistic relation exists between diet and the gut microbiota so that dietary factors are among the most potent modulators of microbiota composition and function. Intestinal microbes in turn influence the absorption, metabolism, and storage of ingested nutrients, with potentially profound effects on host physiology.

The human gut microbiota consists of trillions of microbial cells and thousands of bacterial species. The specific compositional features differ among individuals, and although the mature microbiota is fairly resilient, it can be altered within individuals by both internal and external stimuli. Interindividual variability and the plasticity of the gut microbiota have hindered efforts to identify a “healthy” microbiota, although markers of microbial stability, such as richness and diversity, are often used as indicators of gut health because of their inverse association with chronic disease and metabolic dysfunction (2). Microbiota plasticity also creates a distinct opportunity; by manipulating various external factors, the potential exists to reshape the architecture and biological outputs of gut microbes for improved human health.

Diet is an important external factor affecting the gut microbiota, and diet’s ability to alter microbial ecology was first recognized more than a century ago (3). Transient diet-induced alterations occur independently of body weight and adiposity and are detectable in humans within 24 to 48 hours after dietary manipulation (4). The effects of diet on microbial ecology are unsurprising when one considers that gut microbes, like their human hosts, use ingested nutrients as fuel for fundamental biological processes. Thus, changes to host dietary patterns alter bacterial metabolism and favor species most suited to use consumed fuel sources. What was not predicted after the initial observations a century ago, and has only come to light in recent decades, is the important effect that diet-induced changes in microbial structure have on human physiology and disease processes.

Nutrients

Microbiota-accessible carbohydrates When studied in isolation, each of the major macronutrients and numerous micronutrients have been shown to modify the gut microbiome. Among the macronutrients, the effects of dietary carbohydrates (CHO) are best characterized. Simple CHO such as sucrose, both alone and as part of a Western-style high-fat high-sugar diet, cause rapid microbiota remodeling and metabolic dysfunction in experimental animals (5, 6). Complex CHO exhibit a diverse array of monosaccharide linkages, many of which are indigestible by humans. Gut microbes, on the other hand, possess several hundredfold more CHO-degrading enzymes and thus use indigestible CHO as their primary energy source. The term “fiber” is commonly used to describe these indigestible CHO, although this designation is problematic given that some fibers are not used by gut microbes (such as cellulose), whereas other readily fermented CHO fall outside of the definition of fiber (such as resistant starches). Sonnenburg and colleagues (7) recently proposed the term “microbiota-accessible carbohydrate,” or MAC, to describe CHO that are metabolically available to gut microbes, and we use that terminology hereafter. Several lines of evidence indicate that alterations in dietary MACs have important effects on microbiota composition and function. Agronomic and nomadic hunter-gatherer societies that consume high levels of MACs display greater microbial richness and diversity as compared with those of industrialized societies (8, 9). Diets high in MACs alter microbiota composition in humans within days or weeks (10, 11). Mice fed a diet low in MACs experience decreases in numerous taxa, and loss of diversity is compounded over several generations of offspring and not recovered after reintroduction of MACs (7, 9). Reductions in bacterial abundance with low MAC intake are not observed uniformly across all bacterial taxa because certain bacterial species that typically consume dietary glycoproteins can also use glycoproteins of the intestinal mucus layer as an alternative energy source. Over-grazing of the mucus layer by these species may be an important consequence of MAC restriction, as chronic foraging has been shown to compromise barrier integrity and enhance inflammation and pathogen susceptibility in animal studies (12, 13). Another consequence of MAC restriction is a reduction in short chain fatty acid (SCFA) production. SCFAs, the primary end products of bacterial fermentation, represent an excellent example of mutualism between humans and their bacterial symbionts. MACs provide a critical energy source for gut bacteria, and the consequent production of SCFAs benefits the host by serving as both recovered energy from otherwise inaccessible carbohydrates as well as potent regulatory molecules with vast physiological effects (Fig. 1). SCFAs signal via the central nervous system and several G protein–coupled receptors (GPCRs) to modulate a range of physiological processes, including energy homeostasis, lipid and carbohydrate metabolism, and suppression of inflammatory signals (14, 15). Two SCFAs, butyrate and propionate, also act as histone deacetylase inhibitors, suggesting that they can epigenetically influence host gene expression (16). Thus, decreased SCFA production and increased mucus foraging represent two microbiota-dependent consequences of low MAC intake, and it is tempting to speculate that these processes underlie the long-recognized health benefits of high-fiber diets. It should be noted that the extent of mucus foraging in humans, and its importance in human disease processes, have not been directly examined. Furthermore, despite the protective effects of SCFAs observed in preclinical models, obese humans and genetically obese mice display increased fecal and caecal concentrations of SCFA (17), suggesting that they may contribute to enhanced energy harvest. Thus, energy balance status of an individual may determine whether the beneficial effects of SCFA signaling on metabolism outweigh the additional calories harvested (18). Fig. 1 MAC fermentors produce SCFAs that can have multiple interactions with host tissues. Butyrate is taken up by epithelial cells and used as a primary source of energy for these cells. Butyrate (and to a lesser degree, propionate) can block histone deacetylases (HDAC) to regulate gene expression. All of the SCFAs can bind with varying affinities to G protein receptors in the intestines and other cells to regulate energy metabolism, intestinal homeostasis, and immune responses. Acetate and propionate are primarily metabolized in the liver, where propionate is used as a substrate for gluconeogenesis and acetate is used as an energy source and for fatty acid synthesis. It is important to recognize that MACs represent a diverse group of oligo- and polysaccharides with considerable structural heterogeneity and diverse effects on microbial ecology. A specific subset of MACs have been termed “prebiotic,” which originally described a class of oligosaccharides that selectively enhance growth of Bifidobacterium and Lactobacillus (19). These canonical prebiotics, primarily fructo- and galactooligosaccharides of varying chain lengths, have been shown to alter members of the human gut microbiota and modulate inflammation and markers of metabolic syndrome (20, 21). Despite promising data on oligosaccharide use for appetite regulation and obesity-related complications, therapeutic efficacy of these prebiotics in treating gastrointestinal conditions is variable (22). Several studies have shown that restricting oligosaccharides and other fermentable sugars [a low-FODMAPs (fermentable oligosaccharides, disaccharides, monosaccharides, and polyols) diet] alleviates symptoms of irritable bowel syndrome (23). Technological advances that allow for holistic examination of microbial responses to dietary components have led to a recent expansion of the prebiotic concept (24). Although selective use of a dietary substrate by specific microbial populations is still required, the list of potential substrates and microbial targets is more inclusive. For example, candidate prebiotic substrates now include nonpolysaccharide dietary components such as polyunsaturated fats, conjugated linoleic acid, and phytochemicals/phenolics (24, 25). Likewise, prebiotics may be selectively used by bacteria other than Bifidobacterium and Lactobacillus, provided the net effects on host health are beneficial. As a result of these expanded inclusion criteria, studies that characterize distinct host-microbe-substrate interactions are of particular interest.

Dietary fats An increase in dietary fat also substantially alters microbiota composition. Experimental mice fed a high-fat diet (40 to 80% total caloric intake) exhibit decreases at the phyla-level in Bacteroidetes and increases in Firmicutes and Proteobacteria. These changes were observed in mice resistant to weight gain, implying a direct effect of dietary lipids on the microbiota (26, 27). Germ-free (GF) mice are protected from the metabolic consequences of high-fat diets, suggesting that gut microbes may be important mediators of lipid-induced metabolic dysfunction (28). The metabolic protection in GF mice may be due to enhanced fat oxidation or reduced absorption in the small intestine (29). Microbes in the small intestine were recently found to be highly susceptible to fat load and essential for lipid digestion and absorption (17). These data suggest that regional specificity of microbiota composition may have important functional consequences and highlight the need for spatially distinct analyses along the gastrointestinal tract. Importantly, not all studies have found that GF mice are protected from the metabolic consequences of high-fat feeding, and the cholesterol content of the diet may be an important determining factor (30). As with carbohydrates, lipid-mediated effects on the microbiota are dependent on the lipid type and source. For example, mice fed an isocaloric diet rich in long-chain saturated fats derived primarily from meat products displayed greater insulin resistance and adipose tissue inflammation as compared with that of mice fed a high–fish oil diet. These metabolic disturbances were accompanied by reductions in phylogenetic diversity in the saturated fat–fed mice, and receipt of transplanted microbiota from mice fed fish oil abrogated saturated fat–induced inflammation (31). Furthermore, transgenic mice that constitutively produce ω3 polyunsaturated fatty acids possess a microbiome with enhanced phylogenetic diversity that offers protection against the metabolic consequences of a high-saturated-fat, high-sugar diet (32). One mechanism by which gut microbes may mediate the metabolic consequences of high-fat intake is through translocation of lipopolysaccharide (LPS), a cell-wall component of gram-negative bacteria. Increases in circulating LPS have been reported in humans after a high-fat meal, with exacerbated effects in obese individuals (33). Once in circulation, LPS elicits a potent inflammatory response via Toll-like 4 receptor signaling, which has been implicated in the development of cardiovascular and metabolic disease (34). Although existing data that link circulating LPS to cardiometabolic disturbances are compelling, progress in this area has been hindered by the inability of available assays to distinguish between stimulatory and nonstimulatory LPS, as well as by circulating inhibitors that reduce accuracy of LPS quantification (35). Furthermore, although circulating LPS has been reported in obese individuals and correlates with markers of metabolic disease, a direct causal role in human disease has not been examined (36). Primary bile acids are produced in the liver from cholesterol and facilitate the digestion of dietary lipids. Once generated, primary bile acids are secreted into the small intestine, where they facilitate the solubilization and absorption of lipids. Microbial alterations to primary bile acids include hydrolysis of conjugated amino acids, 7α/β-dehydroxylation, and oxidation and epimerization of hydroxyl groups at various positions (Fig. 2) (37). GF mice display increased abundance and reduced diversity of bile acids compared with that of conventional mice (38), and enrichment of specific secondary bile acids has been observed in colorectal cancer cases (39). In addition to their canonical role in aiding lipid digestion, bile acids act as dynamic signaling molecules via the farnesoid X receptor (FXR) and the G protein–coupled bile acid receptor 1 (TGR5). Like SCFAs, bile acids have been shown to regulate energy homeostasis, glucose metabolism, and innate immunity (40). More recent data suggest that gut microbes also have direct effects on FXR and TGR5 expression and signaling (40, 41). Thus, the gut microbiota helps regulate bile acid composition, abundance, and signaling, and this regulation may have important implications not only for lipid digestion and absorption but also for the development and prevention of metabolic disease. Several bile acid–directed therapeutics are currently being examined for obesity-related conditions, and as the clinical utility of these therapeutics is tested, it will be important to consider microbiota composition in determining interindividual efficacy and safety. Fig. 2 Gut bacteria play an important role in bile acid modification. Primary bile acids deposited into the small intestine are deconjugated and dehydroxylated by enzymes from bile-modifying bacteria. These changes influence total bile acid pools available for reabsorption and recycling through enterohepatic circulation. In addition, bile acids can act as regulatory molecules by binding to cell surface or nuclear receptors, influencing host factors such as energy expenditure and lipid metabolism.

Dietary protein Dietary proteins also modulate microbial composition and metabolite production, with amino acids providing gut microbes essential carbon and nitrogen. Amino acid catabolism yields numerous metabolites that affect host physiology (Fig. 3). For example, although SCFAs are derived mainly from MAC fermentation, they are also by-products of bacterial metabolism of amino acids. The relative contribution of amino acid metabolism to total SCFA production is unclear, but total protein and fiber intake are influencing factors. Additional metabolites of amino acid catabolism include branched chain fatty acids, indoles, phenols, ammonia, and amines, all of which can affect human health. For example, phenols, indoles, and amines can combine with nitric oxide to form genotoxic N-nitroso compounds that are associated with gastrointestinal cancers in human populations (42). By contrast, indolepropionic acid, a microbial metabolite of tryptophan, maintains intestinal homeostasis and protects from experimental colitis (43). Indole-3-acetate, another bacterially derived tryptophan metabolite, was recently shown to reduce hepatocyte and macrophage inflammation (44). The source of dietary protein also determines the nature of microbiota-dependent metabolic outputs. This is perhaps best exemplified by production of the compound trimethylamine oxide (TMAO) from the amino acid l-carnitine, which is abundant in animal but not vegetable protein. TMAO is predictive of cardiovascular events in various populations (45) and has been implicated in the development of fatty liver disease (46). A recently developed inhibitor of TMAO production reduced platelet aggregation and thrombus formation in experimental animals, enhancing the potential of TMAO-directed therapies (47). Collectively, these data highlight that the vast effects of microbiota-derived amino acid metabolites on host physiology are only now beginning to emerge and represent an area ripe for future research. Fig. 3 Interactions between amino acids and the gut microbiota. Microbial metabolism of the amino acid carnitine produces trimethylamine (TMA), which is subsequently oxidized in the liver to TMAO in a reaction catalyzed by flavin-containing monooxygenase (FMO). Increased levels of circulating TMAO have been linked to metabolic disease. Gut microbes metabolize the amino acid tryptophan into various substances, including indolepropionic acid (IPA) and indole-3-acetic acid (I3A), both of which can enter the general circulation. The metabolic effects of IPA, I3A, and other microbially derived amino acid metabolites are only now beginning to emerge.

Micronutrients In addition to major macronutrients, the gut microbiota regulates both synthesis and metabolic output of various micronutrients. The B vitamins, for example, can be synthesized by more than 100 bacterial species, and analysis of the synthesis pathways involved suggests that bacteria cooperatively exchange B vitamins to ensure survival (48). The relation between vitamins and the microbiota appears to be bidirectional because several vitamins supplied by the host shape microbial composition and provide critical functions within bacteria. Riboflavin, for example, regulates bacterial extracellular electron transfer and redox status (49), and vitamin D and its receptor help regulate intestinal inflammation, in part by shaping microbial ecology (50). Like vitamins, metals are required cofactors for numerous mammalian and bacterial physiological processes and can dramatically alter the microbiota. Zinc deficiency, which is a strong risk factor for potentially fatal childhood diarrhea in developing countries, enhances populations of pathogenic bacteria (51). Iron is an essential micronutrient for pathogen growth, and restricting iron intake is an effective form of nutritional immunity against pathogen establishment. Human breastmilk transmits lactoferrin, an iron-binding glycoprotein, to protect the undeveloped infant gut from pathogen colonization, and iron supplementation in infants can increase pathogen growth and intestinal inflammation (52). Despite observed bacteriogenic effects of iron, supplementation in experimental mice was recently found to suppress virulence of the rodent enteric pathogen Citrobacter rodentium, essentially converting the pathogen to a commensal microbe (53). High salt intake has been implicated in the cardiovascular consequences of Western diets. Recent data suggest that the hypertensive effects of high-salt diets in experimental animals and humans are mediated by reduced levels of Lactobacillus and subsequent increases in proinflammatory T helper 17 cells (54). Collectively, the interactions identified thus far between the microbiota and micronutrients, as well as the myriad other interactions that undoubtedly await discovery, represent an important avenue of future research. The data also highlight the importance of monitoring micronutrient composition in microbiota-focused dietary intervention studies and beget the need for clinical trials in populations at risk for vitamin and mineral deficiencies.