The Life-Long Role of Nutrition on the Gut Microbiome and Gastrointestinal Disease

INTRODUCTION

The human body is composed of a vast population of microbes, including bacteria, viruses, fungi, and phages, that outnumber human cells 1.3 to 1.0 based on recent calculations and estimates.^1,2 The densest community of these microbes, which are referred to as the human microbiota, resides in the gut. The microbiome refers to the collective genomes of these microbial communities and each niche of the human body has a distinct microbiome responsible for key biologic functions. Since the advent of the US National Institutes of Health Human Microbiome Project, European Metagenomics Human Intestinal Tract project, and multiple worldwide population-based studies more than a decade ago, scientists have cataloged up to 2000 resident gut microbes composed of 100 trillion cells that express a greater number of unique genes than their host’s genome.^3-5 An individual’s microbiome, which is affected by both intrinsic (ie, genetics, age) and extrinsic (ie, diet, medications) factors, is critical for development of mucosal immunity and is a key driver of human health and disease.⁶

Homeostasis of the intestinal microbiota, often referred to as eubiosis, fosters interactions between the gut microbiome and the host that promote effective innate and adaptive immunity, including pathogen recognition, self-tolerance, and identification of beneficial commensals.⁶ Disruptions in the gut microbiome or dysbiosis can lead to misdirected immune responses to environmental or self-antigens that may result in atopic disorders, autoimmune diseases, and inflammatory conditions (Fig. 1). A well-balanced intestinal microbiome is also responsible for harvesting energy from food sources, producing short chain fatty acids (SCFAs) from indigestible carbohydrates, and synthesizing vitamins and amino acids for maintenance of gut barrier function.⁷ Dysbiosis can affect any of these critical processes and increase an individual’s risk of developing chronic diseases, for example, obesity and other metabolic comorbidities.⁸

Fig. 1.

Role of diet on establishing intestinal eubiosis or dysbiosis. Intestinal homeostasis or eubiosis, which is established through a healthy diet including breast milk, foods rich in fiber and low in fat, and prebiotics, imparts health benefits on an individual by promoting normal microbial colonization, a functional intestinal barrier, and a milieu favoring anti-inflammatory cytokines. However, derangements in the gut microbiome, also referred to as a dysbiosis, result from an unhealthy diet composed mainly of commercial formula and foods high in fat and low in fiber. Shifts in bacterial abundance, decreased microbial diversity, increased inflammatory mediators, and increased intestinal permeability are consequences of this type of diet and subsequently increase an individual’s risk for a host of gastrointestinal pathologies.

Diet is recognized as one of the key, modifiable environmental factors and may account for 20% and 50% of microbial structural variations in humans and mice, respectively.^9,10 Recent population-based studies demonstrate that effects of diet on the gut microbiome and long-term health outcomes may dominate over host genetics.¹¹

The purpose of this review is to highlight how diet affects microbial community composition and the development of gastrointestinal (GI) disease from early life to adulthood. We describe how nutrition during pregnancy, including maternal obesity and gestational diabetes, may contribute to adult onset of diseases. We discuss postnatal nutrition (micronutrients, prebiotics, and probiotics) and bacterial colonization, including the role of breast milk on necrotizing enterocolitis. We highlight how diet impacts adult GI diseases, such as gastric pathologies, intestinal disorders (inflammatory bowel disease [IBD], celiac disease [CD], and irritable bowel syndrome [IBS]), obesity, and colorectal cancer (CRC). Finally, we provide a brief overview of how cross-talk between the gut microbiome and other organ systems may drive extraintestinal disorders.

MICROBIOME IN PREGNANCY AND EARLY NUTRITIONAL PROGRAMMING OF THE NEWBORN

Dietary intake is most influential on microbial colonization during the first 2 to 3 years of life when the dynamic and nascent gut microbiome is in its early stages of assembly.² As an infant’s diet expands from breast milk or formula to solid foods, α-diversity (bacterial diversity in one specific region of the body) increases and β-diversity (regional differences in bacterial composition in different parts of the body), which is initially highest at birth, gradually decreases. However, as the gut microbiome stabilizes in adulthood, individuals separate into clusters or “enterotypes,” which are classified based on proportions of major taxa.¹² Environmental factors, including medications, malnutrition, and infections, which can cause large shifts in bacterial composition and the relative abundance of some taxonomic groups.¹³ Although adults are likely to return to their baseline enterotypes, infants may have permanent shifts in their gut flora owing to these acute or chronic perturbations that occur during a critical window of intestinal development.

The microbiome during pregnancy is dynamic, with shifts in both composition and bacterial load unique to each trimester.^14,15 Environmental factors, primarily diet, along with prepregnancy body mass index (BMI) and maternal weight gain during pregnancy, may significantly influence offspring’s gut microbiome and increase their risk of obesity and metabolic syndrome as children and adults.¹⁶ The microbiome of pregnant women was evaluated during the first and second trimester in overweight women (BMI >30) and compared with normal weight individuals (BMI <25). Overweight pregnant women had significantly higher levels of Bacteroides and Staphylococcus compared with controls.¹⁵ Other studies of microbiota shifts during pregnancy in obese women versus controls found a decrease in Bifidobacterium and Bacteroides, findings similar to those in nonpregnant obese individuals.¹⁷

Maternal prepregnancy BMI impacts outcomes for mothers and infants postnatally. Excessive weight gain during pregnancy is a known risk factor for maternal preeclampsia and gestational diabetes, along with an increased risk of diabetes and cardiovascular disease later in life. Infants of mothers who are overweight or obese have a higher likelihood of being macrosomic, whereas infants of mothers who are underweight have a higher likelihood of delivering prematurely and being small for gestational age.¹⁸ Health outcomes of these infants later in life may also be affected. A study of 935 mother-infant dyads found that infants of obese or overweight mothers had a 3-fold increased risk of being obese at 1 year of age.¹⁹

Controversy still exists over whether the fetus develops in a sterile in utero environment or is colonized by microbes during pregnancy. In a number of human and murine studies well-controlled for environmental contaminants, microbial DNA was detected in humans and mice, which most closely resembled maternal microbiomes of the oral cavity.^20,21 These novel studies suggest a role for modulation of maternal diet, including use of prebiotics and probiotics to improve the microbiota of offspring and decrease the risk of adult onset disease. The effect of early life nutritional stimuli, both in utero and postnatally, on infant and adult health is intriguing and evolving areas of research (Fig. 2). Barker’s decades-old hypothesis, now recoined as the developmental origins of health and disease, explores how nutritional programming during fetal development can drive one’s lifelong health status and adult-onset of cardiometabolic disorders.^22,23 Maternal noncommunicable diseases, including obesity, type 2 diabetes, and high cholesterol, can result from malnutrition during pregnancy and result in maternal dysbiosis that perturbs the newborn microbiome. Offspring are also at an increased risk to have noncommunicable diseases as adults if subsequently exposed to postnatal factors (neonatal intensive care unit hospitalization, antibiotic exposure, formula feeds) known to interfere with normal bacterial colonization.²⁴

Fig. 2.

Early life mucosal immune development and microbial colonization. Maternal oral and intestinal microbial flora and bacterial metabolites may be introduced to the growing fetus through the placenta. Mode of delivery (vaginal or caesarean section), diet (breast milk or commercial formula), and environmental factors, including mom’s oral and skin flora, are key contributing factors to the developing infant microbiome and mucosal immune system. Early life influences on infant’s colonization include the infant’s diet and environmental exposures. Introduction of solid foods during this window is associated with the most robust expansion of a child’s microbiome, which will reach a steady state by approximately 3 years of life.

NEWBORN MICROBIOME AND NECROTIZING ENTEROCOLITIS

Normal newborn colonization commences when a healthy bolus of vaginal flora is imparted to the infant during delivery, followed by the introduction of breast milk. Breast milk is rich in nondigestible oligosaccharides that serve as prebiotics to promote the growth of beneficial bacteria, including Lactobacillus acidophilus, Bacteroides fragilis, and Bifidobacterium infantis.²⁵ These commensal bacteria promote the fermentation of oligosaccharides into SCFAs. A symbiotic relationship evolves between the infant and colonizing bacteria as microbes begin to interact with the developing mucosal immune system. Although newborns are also rapidly colonized by a variety of environmental factors (eg, maternal oral and skin flora, household, or hospital organism), the most important environmental factor, much like with adults, is diet whether it be breast milk or formula. Deviations from this normal colonization occur secondary to preterm delivery, cesarean section, antibiotics, and formula feeds. Any of these variables affect the infant microbiome, including sparse and inadequate colonization and the delay of final microbiome assembly until 4 to 6 years of age, increasing these individuals’ susceptibility to infections and immune-mediated diseases.

Necrotizing enterocolitis, the most common GI emergencies in newborn infants, occurs in 1% to 5% of patients admitted to the neonatal intensive care unit.^26,27 The etiology of necrotizing enterocolitis is complex, but is attributed to the triad of an aberrant intestinal microbiome, an immature mucosal immune system, and an exaggerated inflammatory response aggravated by “stressors,” including the introduction of formula-based feeds.²⁸ A single organism or group of organisms responsible for necrotizing enterocolitis remains enigmatic despite a myriad of studies using both traditional and culture-independent techniques.²⁹ However, the majority of studies have been restricted to stool sample analyses, which are collected distal to the ileum, the most common area affected in necrotizing enterocolitis. As such, stool samples may not accurately reflect the microbiota at the actual site of injury. Studies in intestinal tissue samples from patients with necrotizing enterocolitis and from patients with noninfectious intestinal disorders demonstrate a tissue-level gut microbiome unique to each area of the GI tract, suggesting tissue-level bacterial communities as the key drivers of this disease process.²⁰

One of the only dietary strategies that has proven preventative for necrotizing enterocolitis is the use of breast milk.^30,31 The importance of this strategy has led to widespread implementation of donor breast milk programs at institutions for infants at the greatest risk when the optimal choice of expressed maternal milk is unavailable.^26,32 Delivery of breast milk to the newborn infant transfers a host of immunomodulating factors that contribute to a decreased risk of necrotizing enterocolitis, including human milk oligosaccharides, lactoferrin, antimicrobial peptide, and soluble IgA.^33,34 Transmission of bacteria through breast milk is also critical to promote a normal newborn intestinal microbiome, which demonstrates derangements early on secondary to prematurity, exposure to medications, and the intensive care environment itself, including decreased populations of commensal bacteria and increased colonization by potentially pathogenic microorganisms.³⁵ Infants fed directly at the breast have the added benefit of direct contact with the mother’s skin, increasing bacterial diversity of the gut microbiome.³⁶

Mechanisms that might be involved in the protective role of breast milk include indole-3-lactic acid, a metabolite from breast milk tryptophan, which acts as an anti-inflammatory molecule.³⁷ In a recent study, indole-3-lactic acid decreased the inflammatory cytokine IL-8 response after IL-1β stimulus by interacting with the transcription factor aryl hydrocarbon receptor and by preventing transcription of IL-8. Human milk oligosaccharides, the third most abundant component of human milk not present in formula, may also contribute to the lower incidence of necrotizing enterocolitis in infants receiving breast milk.^38,39

INFANCY TO CHILDHOOD: ESTABLISHING AN ADULT-LIKE MICROBIOTA

Over the first 3 years of life, infants transition from an immature gut microbiome to one that can function with the same metabolic capacity as an adult.⁴⁰ One of the major turning points in this maturation is cessation of breast milk with shifts in infant flora to adult microbes, including Bacteroides, Bilophila, Roseburia, Clostridium, and Anaerostipes. Interestingly, in infants who continue consuming breast milk past 12 months, this shift toward adult flora is delayed and colonization with organisms expressed in breast milk, including Bifidobacterium species, persists.⁴¹ During this transition from breast milk or formula to a solid food diet, α-diversity increases dramatically. The final transition to a stable, adult microbiome occurs from 18 to 36 months of age, and diet has a major effect on its composition, including establishing the balance of Bacteroidetes to Firmicutes. SCFAs, especially butyrate levels, increase dramatically, along with functional changes that allow for the breakdown of complex carbohydrates, starch, and xenobiotic degradation, as well as vitamin production.² Although a more adult-like bacterial profile is associated with an increase in stability and a landscape less likely to experience major shifts in composition, significant insults (eg, malnutrition, use of antibiotics, and acute illnesses) can still disrupt the newly laid foundation of the gut microbiome and increase an individual’s risk of adulthood diseases and lifelong health complications, including those discussed elsewhere in this article.

MICROBIOTA OF GASTRIC PATHOLOGIES: ESOPHAGEAL ADENOCARCINOMA, BARRETT’S ESOPHAGUS, AND GASTROESOPHAGEAL REFLUX

Over the last 40 years, a dramatic increase in the incidence of esophageal adenocarcinoma (EAC) has been observed more than with any other malignancy or growth.⁴² Although not all individuals with Barrett’s esophagus (BE) develop EAC, the metaplastic changes of the distal esophageal mucosa observed with BE are often precursors to malignancy.⁴³ Gastroesophageal reflux disease (GERD), which produces inflammation at the gastroesophageal junction, can lead to the transformation of the mucosal lining from squamous to metaplastic columnar epithelial cells. Thus, individuals with GERD are at an increased risk of BE and the development of EAC.

Cross-talk between one’s diet and gastric and esophageal microbiomes drives these malignant transformations. Patients with GERD and BE have lower esophageal tract microbiomes that are high in gram negative organisms, including Proteobacteria, Fusobacteria, and Spirochaetes.⁴⁴ Helicobacter pylori and Escherichia coli are present in BE and EAC, likely secondary to the highly acidic environment generated by GERD.⁴⁵ High-fiber and low-fat diets support a gut microbiome robust with commensals that stimulate normal metabolism, nutrient and vitamin absorption, and elimination of pathogenic bacteria and toxins. Conversely, diets rich in fat and processed foods (simple sugars, animal proteins) are associated with chronic inflammation of the esophagus and a dysbiosis that contributes to BE and EAC.

Dietary differences contributing to perturbations of the microbiota at the gastroesophageal junction and esophageal and gastric pathologies have been observed in rural versus urban populations. Individuals in rural areas, who are more likely to have balanced diets with adequate fiber intake, have microbiomes high in Prevotella, Treponema, and Succinovibrio. These organisms assist with the digestion of fiber-rich foods and polysaccharides. People in urban areas, who are more likely to consume diets high in fat and processed foods, have a gut microbiota with increased levels of Bacteroidetes and decreased amounts of Firmicutes.⁴⁶

MICROBIOTA, DIETARY TRIGGERS, AND THE PATHOGENESIS OF CELIAC DISEASE

CD is a classic example of a diet-sensitive chronic immune disorder that occurs in predisposed individuals in the setting of a microbial imbalance.⁴⁷ The old adage that CD was solely a sequela of a person’s genotype and interactions with environmental triggers was debunked when discordance in the penetrance of CD between monozygotic twins was observed.⁴⁸ In addition, although the introduction of gluten occurs during childhood, disease onset can occur at any point in a person’s lifetime. These observations suggest that other factors could contribute to the pathogenesis of CD, including interactions between the intestinal immune system and the gut microbiota.

One hypothesis behind CD is that an intestinal dysbiosis occurs during critical windows of early life immune development in genetically susceptible individuals.⁴⁹ The integrity of the intestinal epithelium depends on the stimulation of T regulatory cells (Tregs) and activation of intestinal epithelial cells⁵ by the gut microbiota. Tregs stimulation of immune cells by gut bacteria referred to as microbial programming, can be disrupted in certain individuals, and in the setting of defunct immune programming, gut permeability increases even before onset of gluten-induced inflammation.

CD may also be a product of defects in transmembrane proteins and intestinal tight junctions in individuals who have an abnormal gut microbiome and are predisposed to CD. Zonulin is a transmembrane protein responsible for tight junction disassembly that reversibly regulates intestinal permeability to luminal antigens.⁵⁰ Expression of zonulin is upregulated by enteric bacteria and gliadin, a key component of gluten to triggers proinflammatory cytokine release. This process results in increased epithelial permeability and exposure of the submucosa to an even higher antigen load.

The multifactorial nature of CD–microbial imbalance, increased intestinal permeability, and proinflammatory response to gluten exposure makes treatment of this disease more complex than simple adherence to a gluten free diet. Recent studies are evaluating the role of prebiotics, probiotics, and fermentable oligosaccharides, disaccharides, monosaccharides and, polyols (FODMAP) as potential therapies for CD.⁵¹ In CD patients, it is suspected that levels of Bifidobacteria and Lactobacilli are decreased, and probiotics that target these strains might be beneficial.⁵² Other effective strains in patients with CD might be those that produce enzymes capable of degrading gliadin peptides and inducing anti-inflammatory effects.⁵³

INFLAMMATORY BOWEL DISEASES

IBD, including CD and ulcerative colitis, typically occurs during early adulthood and is followed by periods of remission and relapses, which are often responsive to immunomodulatory, immunosuppressive, and dietary interventions.^54-56 In individuals predisposed to IBD, poor nutrition has detrimental effects on the intestinal microbiome, including the production of proinflammatory mediators, disruption of the GI tract’s protective mucus layer, and increased intestinal permeability, making diet a key environmental factor in IBD pathogenesis.^57,58

A Western diet, characterized by excessive consumption of refined sugars, salt, and saturated fat, low consumption of dietary fiber, and limited food diversity, is associated with an increased risk of IBD.⁵⁹ Such a diet promotes the production of bacterial metabolites with adverse effects on the gut microbiota and the intestinal immune system. Conversely, a diet rich in fiber in individuals predisposed to IBD promotes fiber fermentation and stimulates SCFA producing bacteria. SCFAs, notably acetate, propionate, and butyrate, have a variety of anti-inflammatory properties in T cells, specifically Tregs. They can be used as an energy source in intestinal epithelial cells and are vital to maintaining normal intestinal barrier function, including a protective mucus layer.

A swing from breast milk to artificial formula use in the first year of life often accompanies a shift to a Westernized diet.⁶⁰ Breast milk, which is considered to be protective against IBD, contains Lactobacillus rhamnosus, Lactobacillus gasseri, Lactococcus lactic, Leuconostoc mesenteroides, and Bifidobacteria which promote immune tolerance and strengthens the intestinal epithelial barrier. Human milk oligosaccharides contained in breast milk can block adhesion to intestinal epithelial cells by pathogenic organisms, including E coli, Vibrio cholera, and Salmonella fyris.⁶¹ In the absence of human milk oligosaccharides, these pathobionts can adhere to the intestinal epithelium, where they can invade and drive inflammatory cascades.

Commercial formula use and Western diets, more frequently consumed by urban populations and developed countries with easy access to ultraprocessed foods, are also associated with decreased intestinal bacterial diversity.^62,63 Regardless of exposure to a Western diet, individuals with IBD consistently have decreased biodiversity, specifically a decrease in α-diversity and species richness when compared with controls.⁶⁴ Metagenomic studies of patients with IBD have also demonstrated imbalances in other bacterial species related to dietary intake, including a decrease in Clostridium leptum, a member of the Firmicutes phylum, many of whom have anti-inflammatory effects.^65,66

IRRITABLE BOWEL SYNDROME

With approximately 11% of the population diagnosed worldwide, IBS is the most widespread functional gut disorder, characterized by recurrent abdominal pain, bloating, and stool inconsistency.^67,68 Although it is unclear what specific aspects of an affected individual’s gut microbiome are “abnormal” or “unhealthy,” recent studies examining interactions between host and microbial metabolites have informed our design of nutrition therapies for IBS. Bile acids, SCFAs, vitamins, and amino acids are some of the key host- and microbial-derived metabolites that may be effective treatments.^69,70

For example, patients with IBS have aberrant levels of primary bile acids (host metabolites synthesized by the liver from cholesterol) and secondary bile acids (bacterial metabolites produced by colonic microorganisms).⁷¹ Patients with diarrhea-predominant IBS have elevated levels of primary bile acids in feces, which may be consistent with bile acid malabsorption that drives diarrheal symptoms.^72,73 Other variations in primary and secondary bile acid levels are also observed in constipation-predominant IBS. However, in both cases, it is difficult to understand how such alterations in primary and secondary bile acid metabolism drive disease pathogenesis.

OBESITY AND THE GUT MICROBIOME

The interplay between diet and the gut microbiota and its effect on obesity have been a focal area of research since the inception of microbiome research. It is now hypothesized that the microbiota interacts with diet to (1) increase energy extraction from food sources, (2) increase intestinal epithelial permeability resulting in chronic inflammation, and (3) decrease angiopoietin-like protein expression and lipoprotein lipase–mediated fatty acid uptake.⁷⁴ Early studies demonstrated that genetically obese mice, when compared with lean subjects, had lower community diversity along with a 50% decrease in Bacteroidetes and a corresponding increase in Firmicutes.^75,76 Additional studies in which germ-free mice were inoculated with bacteria from obese donors revealed an increased fat mass in recipient mice when compared with those receiving bacteria from lean donors.⁷⁷ These studies suggest that a shift in the Bacteroidetes:-Firmicutes ratio occurs with obesity and that the microbiome alone could drive changes in body.

Although caloric intake is a major driver of obesity, an individual’s gut microbiota and its capacity to harvest energy from food sources are key contributors to an individual’s risk of developing obesity. For example, gut microbiota are capable of fermenting soluble fibers to produce SCFAs, a major energy source for colonocytes, that promote commensal organisms’ growth and limit pathogenic bacteria overgrowth. SCFAs also decrease adipose storage, improve insulin sensitivity, and decrease local and systemic inflammation. Conversely, insoluble fibers that cannot be metabolized will not provide these robust health benefits.⁷⁸

MICROBIOME AND DIETARY ASSOCIATIONS WITH COLORECTAL CANCER

CRC, the third most common cancer and the leading cause of cancer deaths in the United States among men and women is strongly influenced by dietary risk factors that affect the intestinal microbiome.^79,80 In fact, up to 60% of CRC cases are attributable to modifiable risk factors, including BMI, physical activity, and diet.⁸¹ Specific dietary factors, including fiber and red and processed meat, and mechanisms for how they drive inflammation and risk of CRC are discussed elsewhere in this article and reviewed in Fig. 3.

Fig. 3.

Proposed mechanisms of how fiber and red meat modulate the gut microbiota and the risk of colorectal cancer (CRC). Lack of dietary fiber decreases abundance of SCFA-producing bacteria, mainly from the Bacteroidetes and Firmicutes phyla. Decreased SCFAs in the intestinal lumen disrupt signaling of cell surface G-protein coupled receptors (GPCRs) to activate macrophages and increase proinflammatory cytokines, including tumor necrosis factor-α, IL-17, and IL-6. These key cytokines upregulate NF-κB and STAT3 signaling pathways to generate inflammation. A reduction in SCFA-producing bacteria disrupts epithelial barrier integrity by blunting antimicrobial peptide (AMP) synthesis and promoting proliferation of dysplastic intestinal epithelial cells. Extraintestinal effects may also ensue secondary to bacterial and estrogen metabolites produced by increased populations of Clostridia, Enterobacterium, Lactobacillus, Bacteroides, and E coli. Red and processed meat contain choline and carnitine, which are metabolized to trimethylamine (TMA) and TMAO by commensal gut bacteria, which can increase macrophage expression of proatherogenic scavenger receptors, CD36 and SRA, to generate inflammation. TMA and TMAO also increase DNA mutations in proliferating intestinal epithelial cells and decrease barrier function. Meat is also high in sulfur-containing amino acids and processed meats are often packaged with sulfur-containing preservatives. Microbes, including Bilophila wadsworthia, Fusobacterium nucleatum, and Desulfovibrio spp, generate hydrogen sulfide from these compounds, which upregulates Tregs suppression of effector T cells. This impairment of T-cell responses decreased immunity against tumorigenesis. Finally, meat intake increases the risk of colorectal cancer through bacterial fermentation of primary bile acids into secondary bile acids, including deoxycholic acid (DCA), which can cause DNA damage and intestinal dysplasia. Systemic inflammatory mediators generated through all of these pathways may also contribute to extraintestinal diseases.

Studies on the effects of fiber intake on the intestinal microbiome and CRC risk have demonstrated varied results. No linear association was found between fiber intake and CRC risk in a meta-analysis of 21 prospective studies in the United States.⁸² In addition, results from a series of 64 randomized controlled trials summarized in a 2018 meta-analysis where healthy adults received supplementation with fiber or related prebiotics demonstrated how fiber supplementation increased the abundance of Bifidobacterium and Lactobacillus species with no effect on SCFA-producing bacteria.⁸³ Conversely, data from the European Prospective Investigation into Cancer and Nutrition have consistently demonstrated an association between fiber intake and a decreased risk of CRC.^84,85 Differences in the findings between these 2 populations are hypothesized to be due to the dietary sources of fiber, which in the United States is typically whole grains and in Europe is mainly fruits and vegetables, as well as the relatively low amounts of fiber consumed by individuals in US study cohorts.⁸⁶

One of the hypotheses for how fiber affects the intestinal microbiome and reduces CRC risk includes fermentation of fiber by intestinal bacteria into SCFAs. In several studies, SCFAs and SCFA-producing bacteria, including Eubacterium rectale, Roseburia species, and F prausnitzii, were enriched in the feces of individuals with higher fiber intake.^87,88 Individuals who consumed less dietary fiber had decreased abundance of SCFA-producing bacteria (Bacteroidetes, Firmicutes) and bacterial metabolites, including propionate, acetate, butyrate, and lactate which decreased energy metabolism within the intestines and shifted the balance from anti-inflammatory to proinflammatory mediators. Macrophages and other immune cells in the submucosa were then activated to increase IL-6 and tumor necrosis factor-α production. As a result, nuclear factor-κB and STAT-3 signaling were further stimulated, promoting inflammation both within the intestines and in downstream extraintestinal tissue locations.

Red and processed meats may also be implicated in the pathogenesis of CRC. Specifically, the high content of choline and carnitine in red meat can serve as precursors for the production of trimethylamine and trimethylamine N-oxide (TMAO) by the gut microbiota now with pathologic enrichment of gram-negative organisms including Prevotella, Bacteroides, and bacteria from the Teneriticutes and Deferribacteres phyla.⁸⁹ Several meta-analyses of fecal shotgun metagenomic studies supporting the choline–TMAO pathway in the development of CRC have found that CRC patients have higher levels of 2 bacterial genes that regulate TMA synthesis.⁹⁰ One outcome of TMAO synthesis is decreased intestinal epithelial barrier function secondary to DNA mutagenesis and intestinal dysplasia. Macrophage expression of proatherogenic scavenger receptors, CD36, and SRA, is also increased to generate local and systemic inflammation.

Another mechanism through which processed, red meat may increase CRC risk is by the bacterial production of hydrogen sulfide from inorganic sulfur, routinely used as a preservative for red meats. Bacteria driving these hydrogen sulfide–producing pathways, which are known to be increased in metabolomic analyses of fecal samples from CRC patients, include gram-negative Proteobacteria Bilophila wadsworthia and Desulfovibrio spp and Fusobacterium nucleatum, an oral commensal with this surprising link to a GI malignancy. These shifts in bacteria-driven hydrogen sulfide activity trigger increased activity of Tregs and oversuppression of effector T cells, without which tumorigenic activity proceeds unopposed.^91,92

Finally, secondary bile acids produced by bacteria after red meat consumption might also increase CRC risk through a number of downstream pathways that affect antimicrobial peptide expression and the occurrence of intestinal dysplasia. High quantities of fat from red meat enhance the regular activity of colonic organisms, including a cadre of gram-positive bacteria (Clostridium, Enterococcus, Bifidobacterium, and Lactobacillus) that express bile salt hydrolases and are capable of metabolizing primary bile acids to secondary bile acids.⁹³ The significance of this shift in an individual’s bile acid profile is still poorly understood, however, these secondary bile acids are all hypothesized to coalesce on pathways that change interactions with nuclear and G-coupled protein receptors and expression of antimicrobial peptides.⁹⁴ The change in bile acid metabolism also results in DNA mutation and reduced ability to undergo apoptosis to correct these deleterious cellular changes.⁹⁵

Another aspect of microorganisms and mucosal immune system cross-talk, which may be a part of CRC development, involve the 3 major bacteria that populate the colon—E coli, Enterococcus Faecalis, and Bacteroides Fragilis. Although typically symbionts, these species can assume a pathogenic role and induce carcinogenic changes within the colon. For example, E coli can release cell death toxins to cause epithelial proliferation, adenoma formation, and malignant transformation of cells. Enterococcus faecalis can be responsible for DNA destruction via free radical production.⁹⁶ B fragilis carcinogenicity impacts the colon when colonic integrity is disrupted through the release of B fragilis toxin, which cleaves tumor suppressor protein, E-cadherin to incite procarcinogenic effects of E-cadherin Wnt signaling, including colonic epithelial cell proliferation, and epithelial barrier dysfunction.⁹⁷

IMPACT OF DIET AND ABNORMAL MICROBIAL COLONIZATION ON EXTRAINTESTINAL ORGANS

Interestingly, patients with breast cancer have similar alterations in their gut microbiome, including enrichment of Clostridia, Enterobacterium, Lactobacillus, Bacteroides, and E coli.⁹⁸ In a mouse model with commensal bacterial dysbiosis secondary to administration of systemic antibiotics, hormone receptor positive breast cancer cells had increased dissemination to distal sites, including lungs, peripheral blood, and axillary lymph nodes receptor.⁹⁹ The dysbiosis also affected mammary tissue homeostasis with an increased presence of macrophage-derived inflammatory cytokines (granulocyte macrophage colony stimulating factor, CCL2, and CXLC2).¹⁰⁰ Another mechanism for how the microbiome can influence the development of breast cancer is through the regulation of steroid hormone metabolism by GI bacteria. The “estrobolome” or collection of enteric bacterial genes responsible for estrogen metabolism may directly mitigate the pathogenesis of estrogen receptor-positive breast cancer.¹⁰¹ Bacterial expression of β-glucuronidase and β-glucosidase and their subsequent deconjugation of estrogen control circulating levels of this hormone, which is a well-known risk factor for breast cancer. Conversely, the gut microbiome breaks down indigestible dietary phytoestrogens to synthesize estrogen-like compounds, which can act on the estrogen receptor to effect steroid metabolites and reduce circulating estrogen levels, decreasing the risk of breast cancer.¹⁰²

Western diets are identified as a risk factor for developing breast cancer.¹⁰³ Western diets are rich in refined starches, sugar, red and processed meats, and saturated and trans fats, and low in fruits, vegetables, and whole grains. Processed food, which composes one-half of the calories in Western diets, are also correlated with this increased risk.^104,105 Conversely, more plant-based Mediterranean diets, which include soluble fibers and lignans, found in whole grains, soy, fruits, and vegetables, may decrease the risk of breast cancer.^106,107 This risk reduction is attributed to the ability of Mediterranean diets to promote intestinal bacterial diversity and increase the growth of Firmicutes. Products of lignans metabolism by Firmicutes are enterolignans, enterolactone, and enterodiol, which may act as selective modulators of estrogen signaling and may be associated with lowering the risk of breast cancer.¹⁰⁸

More recent research suggests the effects of enteric organisms on the central nervous system, now referred to as the “gut–brain axis,”, ay have a significant role on the pathogenesis of neuropsychiatric disorders, including schizophrenia and autism spectrum disorder.^109,110 Meta-analyses of studies to date in autistic children report dysbiotic profiles when compared with neurotypical children, including an increased abundance of harmful bacteria, specifically the proinflammatory genus Clostridium, and a lesser abundance of protective bacteria such as Bifidobacterium.^111,112 These changes in the gut microbiome can contribute not only to comorbid GI problems observed in the majority of patients with autism spectrum disorder, but also the severity of autistic symptomatology. Higher levels of bacterial metabolites (SCFAs, gamma-aminobutyric acid, serotonin, and catecholamines) accompany this shift in microbial composition and likely contribute to the pathogenesis of autism, which further supports the intricate, bidirectional communication between the gut microbiome and the central nervous system.^113-115 Nutritional interventions have shown some promise in their ability to alter the dysbiosis observed with autism spectrum disorder and to correct imbalances in signaling molecules negatively impacting brain function. Some of these interventions include casein and gluten-free diets, ketogenic diets, and consumption of simple monosaccharides versus complex carbohydrates.^116-118 However, many of these dietary strategies have been more thoroughly researched in patients with IBD, and the effects in patients with autism spectrum disorder have only recently become the subject of further investigations.

ROLE OF DIET AND MICRONUTRIENTS IN MICROBIOME AND DISEASE PREVENTION

Dietary interventions that may modulate the gut microbiome and be protective or therapeutic for GI diseases now include not only macronutrients (fat, carbohydrates, protein), but micronutrients (vitamins, minerals, trace elements) and novel prebiotics and probiotics. All micronutrients and prebiotics and probiotics are unable to be synthesized by the body and are solely derived from the diet, making an individual’s nutritional status critical in the prevention of their deficiencies.¹¹⁹ The goal in modulating the gut microbiome through the ingestion of these dietary components would be to either correct a dysbiosis or generate a healthier gut flora, thus, improving microbiota-driven immune development and function. Micronutrient, prebiotic, and probiotic modulation of the gut microbiome has proven most promising during the first 1000 days of life when nascent communities of microbes are still establishing their niches.¹²⁰

Vitamin D, which can come from diet or from sunlight exposure, is one of the micronutrients recently identified to have a major impact on chronic intestinal inflammation, including IBD.^121,122 Novel studies in intestinal epithelial vitamin D receptor knockout mice demonstrated exaggerated intestinal colitis owing to activation of the nuclear factor-κB pathway and shifts in the gut microbiome toward increased E coli and decreased Lactobacillus and butyrate-producing bacteria.¹²³ Vitamin D receptor knock out mice also had fewer Paneth cells and decreased Paneth cell function, including decreased ileal secretion of antimicrobial peptides, which is a well-recognized mechanism behind IBD. Vitamin D deficiency, common in patients with IBD owing to intestinal malabsorption, was associated with a greater risk of clinical relapse.¹²⁴ In the recent Nurses’ Health Study Cohort which included 72,219 individuals, women with predicted highest vitamin D levels had a significantly lower incidence of Crohn’s disease.¹²⁵

Other fat-soluble vitamins that may have a role in maintaining homeostasis of the gut microbiota include vitamins A and E. In one study, children with infectious diarrhea, who were also found to be vitamin A deficient, had a decrease in butyrate-producing bacteria (E coli, Clostridium butyricum), an increase in opportunistic pathogens (Enterococcus), and an overall decreased bacterial diversity.¹²⁶ Vitamin A may also have a role in modulating the microbiome of children with autism spectrum disorder and in improving behavioral symptoms by restoring Bacteroidetes and Bacteroidales populations and reducing the Firmicutes/Bacteroidetes ratios.¹²⁷ Vitamin E, a well-recognized antioxidant, may have an anti-inflammatory role in the gut microbiome by scavenging for excess free radicals and protecting against mucosal immune damage. These beneficial properties may be attributed to the ability of vitamin E to increase Bacteroidetes, decrease Firmicutes, and increase α-diversity.¹²⁸ Water-soluble vitamins, including vitamin C and the eight B-group vitamins, are likely just as essential in gut microbiota homeostasis. Vitamin C, which is exclusively obtained from dietary sources, has antioxidant properties similar to vitamin E and may support the gut microbiota by increasing intestinal populations of Lactobacillus and Bifidobacterium populations while decreasing E coli.¹²⁹ In contrast, B vitamins, which are essential cofactors for a cadre of cellular reactions, may have multiple effects on bacterial activities including promoting bacterial growth, enhancing bacterial virulence, and engaging in pathogen interactions through modification of the host defense system.¹³⁰

Queuine (q), a precursor of sugaris nucleotide queuosine (Q) and an essential factor for tRNA modification, is a micronutrient with an enigmatic role in the human body and is the subject of several recent studies. Both queuosine and its precursor, queuine, are exclusively obtained from dietary sources and from the gut microbiota in animals and humans.^131,132 A large number of neoplastic tissues and cancer cell lines have decreased Q-modification of tRNA_GUN, exploiting the ability of E coli TGT (transglycosylase) to insert radiolabeled guanine into unmodified TRNA_GUN.^133-138 Specifically, tRNA-guanine transglycosylase is absent in human colonic adenocarcinoma cell lines and Q-deficient tRNA is found in 2 of 13 carcinomas. In this same study, the colon adenocarcinoma-derived cell line had a complete deficiency of Q-modification compared with control cell cultures, attributed to defective queuine-insertase activity.¹³⁹ Proposed etiologies for Q-tRNA deficiencies include decreased uptake of queuine owing to inhibition of transporters or low bioavailability, and deregulation of translation owing to queuine depletion.¹³¹ Because Q is a micronutrient obtained from food and the gut microbiota, the intestinal microbiome plays an important role in Q metabolism, and Q deficiency caused cancer, including CRC. However, the function of Q in mammals, especially in the intestine, remains poorly understood owing to limitations in experimental models.

Trace elements, including zinc and iron, have demonstrated important roles modulating host immune-bacteria interactions and GI disease pathogenesis.¹⁴⁰ Zinc supplementation may promote growth of beneficial bacteria and limit replication of pathogenic organisms. This has been demonstrated best in animal models, including broiler chickens. In chickens infected with Salmonella typhimurium, zinc supplementation increased Lactobacillus growth and decreased pathogenic bacterial populations, including Salmonella. However, human studies on zinc deficiency are limited impairing our ability to provide guidance on appropriate dietary supplementation.¹⁴¹ Iron deficiency is the most common micronutrient deficiency and studies have demonstrated how poor dietary iron during early life assembly of the microbiome has profound and permanent impact on microbial composition, which may be linked with numerous inflammatory diseases.^142,143 One of the mechanisms underlying an iron deficiency dysbiosis may be expansion of pathogenic organisms and diminished colonization by beneficial organisms.¹⁴⁴ For example, one study in colitis-resistant and colitis-susceptible mice highlighted how luminal iron deficiency mediated a reduction of numerous taxa of Firmicutes but an expansion of pathogenic Enterobacteriaceae, including E coli.¹⁴³ Iron supplementation, however, has not proven to be straightforward, and depending on the specific iron formulation, may also be associated with a bloom of Enterobacteriaceae and subsequent intestinal inflammation.¹⁴⁵

PREBIOTIC AND PROBIOTIC MODULATION OF THE MICROBIOME IN DISEASES

Prebiotics are dietary oligosaccharides degraded by intestinal bacteria into byproducts that may support normal gut colonization or restore intestinal homeostasis after specific GI insults.¹⁴⁶ Although health benefits were initially attributed to the ability of prebiotics to stimulate growth of Bifidobacterium, more expansive activities have been identified including SCFA and vitamin production, metabolism of primary to secondary bile salts, regulation of GI transit time, activation stem cells and increased enterocyte regeneration, and neutralization of carcinogens.^147,148 More specific immunomodulatory mechanisms of human milk oligosaccharides contained in breast milk may be protective against necrotizing enterocolitis, including their ability to interfere with pathogen adhesion to the intestinal epithelium and expand anti-inflammatory Th-2 immune responses.¹⁴⁹ A limited number of studies suggest anticarcinogenic properties of prebiotics in the prevention of CRC, including downregulation of cyclo-oxygenase 2, inducible nitric oxide synthase, nuclear factor-κB, and GI glutathione peroxidase.¹⁵⁰

Probiotics, defined as live bacteria beneficial to the host, are promising therapeutics for promoting eubiosis and manipulating the gut microbiome to restore disordered metabolic machinery.¹⁵¹ However, variability in strains that are used in clinical trials has interfered with the broader application of study results to patients. This is particularly the case with probiotics in preterm infants for the prevention of necrotizing enterocolitis. Although many studies, most of which use strains of Bifidobacteria or Lactobacilli, have had promising results, including improvements in feeding intolerance and decreased incidence of necrotizing enterocolitis, studies have not consistently used the same type and number of live bacteria. As such, limited data are available for each strain and, when analyzed collectively, there is insufficient evidence to support the supplementation of neonates with a specific bacterial strain. However, probiotics may have a role in modulating the maternal microbiome during pregnancy or in other disease pathologies, including IBD and CRC. In addition, a larger number of studies have been conducted in these populations who are more likely to be immunocompetent with a decreased risk of sepsis from the probiotic or a contaminated probiotic preparation. Growing interest is in synbiotics, which is a preparation of a prebiotic substrate that selectively favors the probiotic organism. Such a preparation might improve survival of the probiotic as it passes through the highly acidic upper GI tract and provide synergistic benefits to an individual’s health.¹⁵²

SUMMARY AND FUTURE DIRECTIONS

Diet and the gut microbiome have an intricate, mainly symbiotic relationship with the human host that is responsible for a cadre of health outcomes. This relationship starts early in life, perhaps as early as gestation, when maternal nutrition and intestinal flora seed the microbiota of the fetus and stimulate immune cell development in utero. A dysbiosis from early life insults, including malnutrition and infection, establish the basis for chronic GI disorders as described elsewhere in this article. As evidence mounts to support the important role of diet and the gut microbiome on GI disorders, research has shifted to include how these 2 factors affect extraintestinal organs. Systemic effects of the gut microbiome can be mediated by microbiota-derived molecules (endotoxin or lipopolysaccharide) or metabolites (SCFAs, bile acids) that interact with distal organs either directly or through intestinal neural networks or gut-synthesized hormones.^74,153 This bidirectional communication offersexciting opportunities for dietary therapeutics of diseases traditionally not thought to be connected with GI health.

Genetics contributes to the composition of the gut microbiome as evidenced by several inheritable bacterial taxa and associations between single nucleotide polymorphisms and individual bacterial communities and pathways.^154,155 We have contributed to identifying the first human gene Vdr that shape the diversity of gut microbiome.¹⁵⁶ However, the precise role of the human genome in modulating the gut microbiome remains elusive.¹⁵⁷

The complex interplay among nutrients, the microbiome, and mucosal immune function makes the GI tract a major nidus for disease pathogenesis and therapeutic interventions. Over the last 2 decades, studies have mapped the bacterial landscape within the intestines, including identifying dietary substrates for these microorganisms, and are now outlining functional roles of bacteria in both the GI tract and more distal organs. Future studies will need to include other major players in this diverse ecosystem, including viruses and fungi, to fully understand how the gut microbiome processes nutrients, shapes immune development, and impacts human health.

KEY POINTS.

• Diet is a key extrinsic factor that impacts the gut microbiome, particularly during the dynamic colonization process that occurs in the first several years of life.

• An imbalance in the complex gut ecosystem referred to as a dysbiosis can have short- and long-term effects on immune system development and impart life-long health complications on an individual in intestine and extraintestine (eg, breast).

• New research suggests effects of microbiome on the central nervous system. The “gut-brain-microbiome axis” may have a significant role on brain development and the pathogenesis of neuropsychiatric disorders.

• Poor macronutrient and micronutrient intake contribute to a dysbiosis. However, supplementation with specific prebiotics and probiotics might modulate the microbiome and restore host homeostasis.