Like many great political alliances, symbiotic relationships in biology may have started with antagonism, before the two parties reached mutual understanding—at least according to some evolutionary biologists. The often cited example is the mitochondrion, the eukaryotic cell’s energy-supplying organelle, which may have first existed as a prokaryote. As the story goes, this prokaryote was engulfed by a second cell, and the two eventually formed such a close symbiotic alliance that one could not live without the other. This mutual dependence, however, formed over many millennia.

Our own symbionts, the microbes that reside throughout our bodies, primarily in our guts, have a more independent—some might say downright rocky—relationship with us, their hosts.

Although gut bacteria have long been called commensal (in which only one party derives benefit, but neither is harmed), it is now clear that we draw many benefits from their colonization of our body, some of them essential...

Bacteria, inflammation, and cancer

One example of a dangerous gut microbe is Helicobacter pylori—a bacterium that resides in the GI tract of almost two-thirds of the world’s population, and is responsible for stomach ulcers in many people. Gastric MALT (mucosa-associated lymphoid tissue) lymphoma, a cancer that occurs in the stomach, is frequently associated with H. pylori. Not surprisingly, then, the antibiotics that kill this bacterium cause this particular cancer to regress in upwards of 80 percent of these patients, and half are cured. However, this infection is also an important risk factor for gastric cancer, which is much more difficult to treat, as antibiotics provide no cure. But harboring this bacterium does not automatically lead to cancer: the guts of some 4.5 billion people are home to H. pylori, yet stomach cancer occurs in only a fraction of individuals.

Gut microbes are increasingly being linked to medical conditions including obesity, inflammatory bowel disease, diabetes, and cancer.

Another example is a toxin-producing Bacteroides fragilis strain, which has been shown to initiate colon cancer in mice and may also do so in humans.[1. S. Wu et al., "A human colonic commensal promotes colon tumorigenesis via activation of T helper type 17 T cell responses," Nat Med, 15:1016-22, 2009.] This bacterium’s toxin is a metalloprotease that can drive cleavage of the adhesion molecule E-cadherin, leading to the activation of the Wnt/ß-catenin pathway, an overactive pathway in almost all colon cancers. The toxin also activates the transcription factor NF-?B, which plays an important role in the initiation and promotion of epithelial tumorigenesis and is best known as a master regulator of inflammatory response pathways. In this and other ways, this bacterial strain drives inflammation, which creates conditions that promote cancer formation and progression. Much of the current thinking about how bacteria may contribute to cancers, particularly those of the gastrointestinal tract, involves chronic inflammation. (See “An Aspirin for your Cancer?” The Scientist, April 2011.)

While many species of bacteria activate inflammation, it is when bacteria initiate chronic inflammation that cancer risk increases significantly. Inflammatory mediators, such as reactive oxygen and nitrogen species, are part of our defenses against bacterial pathogens, but persistent exposure to these mediators directly damages host DNA and contributes to genomic instability—a common feature of cancer cells. Certain cytokines and chemokines produced by immune cells function as growth factors or promoters of angiogenesis. NF-?B and STATs (signal transducers and activators of transcription), STAT3 in particular, are transcription factors vital to physiologic inflammatory responses, and are key molecular links connecting inflammation to cancer.[2. S.I. Grivennikov et al., "Immunity, inflammation, and cancer," Cell, 140:883-99, 2010.]

The innate immune system’s microbial sensors, which recognize patterns shared across many microbes, have recently been shown to intersect with tumor growth pathways. Several studies in mouse models suggest that Toll-like receptors (a major family of receptors that bind these microbe-associated patterns) and their adaptor proteins, such as MyD88, can promote tumorigenesis by affecting both tumor size and number.

Additionally, the laboratory of Maria Abreu at University of Miami Miller School of Medicine, found that mice deficient in Toll-like receptor-4 were protected from colon cancers that usually arise in the setting of chronic inflammation.[3. M. Fukata et al., "Toll-like receptor-4 promotes the development of colitis-associated colorectal tumors," Gastroenterology, 133:1869-81, 2007.] Conversely, when overexpressed, this receptor was associated with an increased susceptibility to colon cancer. Patients with colitis-associated cancer also had elevated Toll-like receptor-4 levels, raising the possibility of a novel therapeutic target.

To truly understand how gut bacteria might contribute to the initiation of diseases such as cancer, it is vital to clarify, at the molecular level, the beneficial role these microbes play in digestion and metabolism, and the ways that changes in the human diet affect the microbial residents in the gut.

Eating for two

Successful adaptation to the ever-changing human diet is central to the survival of gut microbes. The laboratory of Jeffrey Gordon at Washington University in St. Louis is answering key questions about how diet influences gut bacteria and what has made certain bacteria such successful symbionts. Several other laboratories, such as Andy Goodman’s at Yale, Ruth Ley’s at Cornell, Justin Sonnenburg’s at Stanford, and Peter Turnbaugh’s at Harvard, are now actively investigating the genetic features that allow these bacterial species to rapidly respond to dietary changes. The ‘Western diet,’ a dietary pattern high in fats and simple sugars, can reshape gut microbial ecology and predispose both mice and humans to obesity—a risk factor for cancers of the colon, endometrium (lining of the uterus), breast, esophagus, and kidney. Changing to a plant polysaccharide–rich, low-fat diet reduces weight and shrinks fat stores in humans and mice, and causes marked shifts in gut microbiota. Researchers observed that after these dietary changes had been adopted for long enough to reduce the weight of human subjects and mice, the gut microbiota profiles looked more similar to those of lean control subjects.[4. P.J. Turnbaugh et al., "The effect of diet on the human gut microbiome: a metagenomic analysis in humanized gnotobiotic mice," Sci Transl Med, 1:6ra14, 2009.]

Infographic:Helpful Bacterial Metabolites View full size JPG | PDF
Infographic:Helpful Bacterial Metabolites
View full size JPG | PDF

In a normal gut of a lean individual, bacteria generally do more good than harm. Gut bacteria actively supplement our metabolism. The indigestible leftovers of our diet serve as the major food source for these resident bacteria, the greatest numbers of which reside in the distal gut, or large intestine. They metabolize many dietary fibers that escape host digestion, generating short-chain fatty acids such as acetic, propionic, and butyric acids, which contribute an estimated 10 percent of our daily energy supply.[5. R.E. Ley et al., "Worlds within worlds: evolution of the vertebrate gut microbiota," Nat Rev Microbiol, 6:776-88, 2008.] The amount and variety produced are determined by the types of food ingested, how long the food stays in the gut, and which microbial species are present. While humans have the capacity to synthesize some short-chain fatty acids, the vast majority are produced by gut microbes.

These metabolites do more than just provide us with extra energy. Approximately 95 percent of gut short-chain fatty acids are absorbed and metabolized by the host for a wide range of physiological functions. Microbe-generated acetate, for example, has been shown to bind a G-protein-coupled receptor, GPR43, expressed on immune cells. Deletion of this receptor in mice exacerbated arthritis, asthma, and colitis—diseases characterized by an overactive immune system—suggesting that the microbially produced acetate may help guide the resolution of inflammatory responses.[6. K.M. Maslowski et al., "Regulation of inflammatory responses by gut microbiota and chemoattractant receptor GPR43," Nature, 461:1282-86, 2009.] Acetate also appears to protect the host against infection by pathogenic bacteria, like the intestinal hemorrhage-causing Escherichia coli 0157:H7, by strengthening epithelial barrier function.[7. S. Fukuda et al., "Bifidobacteria can protect from enteropathogenic infection through production of acetate," Nature, 469:543-47, 2011.]

While acetate’s connection to health benefits is clearest, propionic and butyric acids may also be beneficial. Propionic acid appears to modulate T-helper cell immune responses by promoting the adaptive immune response. Butyrate’s role as an important energy source for certain epithelial cell types is well established, as is its inhibition of histone deacetylase enzymes. Some of butyrate’s anticancer effects may involve its ability to alter microRNA expression. A recent study from the laboratory of Eugene Chang at the University of Chicago suggests that butyrate slowed the proliferation of a cancer cell line by reducing miR106b levels. This family of microRNAs plays important roles in regulating cell cycle progression and is often overexpressed in cancers.

From food to cancer

Researchers are beginning to realize that we can’t think of the food we ingest without thinking of the gut bacteria that also ingest our food. One oft-cited example is the polyphenol family of chemicals, predominantly found in coffee, tea, wine, fruits, and vegetables, which have been linked to reducing the risk of cancer. The three main classes of dietary polyphenols include flavonoids, phenolic acids, and lignans. Polyphenols are not digested and absorbed in the upper gastrointestinal tract, but they are readily metabolized in the colon by microbial enzymes.

Infographic: Harmful Bacterial Metabolites View full size JPG | PDF
Infographic: Harmful Bacterial Metabolites
View full size JPG | PDF

While several members of the Bacteroides genus have been shown to metabolize polyphenols, determining which members of the colonic microbial community play a role in the metabolism of polyphenols will require both metabolomic and metagenomic approaches, as well as carefully crafted animal studies and human trials. Investigations headed by Tom van de Wiele’s group in the Laboratory of Microbial Ecology and Technology at Ghent University have shown that the type and quantity of polyphenols consumed by healthy human subjects results in distinct metabolic profiles that are unique to each individual and his or her microbiota. The metabolism of polyphenols changes how they will be absorbed and utilized; therefore, the variability of health benefits observed in epidemiological studies may be attributable to the composition and relative abundance of the gut microbiota. In addition, food isn’t our only source of polyphenols: clinical studies have shown that when human subjects are given a measured quantity of polyphenols, the amount of polyphenols excreted can exceed what was consumed.[8. R.A. Kemperman et al., "Novel approaches for analysing gut microbes and dietary polyphenols: challenges and opportunities," Microbiology,156:3224-31, 2010.]

A number of polyphenols, produced by microbes or ingested directly, are being actively investigated for their anticancer properties. Ellagic acid, which is found in berries and nuts, is one of many plant polyphenol compounds thought to have anti-inflammatory and anticancer effects. Gut microbiota are essential for metabolizing ellagic acid into urolithins—compounds believed to be responsible for reducing inflammation and thereby protecting against cancer. The laboratory of Juan Carlos Espín de Gea at the Spanish National Research Council has investigated the anti-inflammatory effects of urolithins in chocolate. In cell culture, urolithin-A was found to downregulate mRNA expression and protein levels of cyclooxygenase-2—a prostaglandin synthase and a key inflammatory mediator that is inhibited by aspirin and other nonsteroidal anti-inflammatory drugs. They also showed that urolithin-A inhibited the activation of transcription factors like NF-?B and signaling pathways that drive inflammation.[9. A. González-Sarrías et al., "NF-kB-dependent anti-inflammatory activity of urolithins, gut microbiota ellagic acid-derived metabolites, in human colonic fibroblasts," Br J Nutr, 104:503-12, 2010.] Investigators from this lab have also observed similar results in vivo using a rodent model of intestinal inflammation.

Although it is known that a substantial portion of polyphenol metabolites are generated by bacteria in the gut, just how microbiota interact with polyphenols is still not fully understood. In some cases, polyphenols are toxic to microbes. Numerous flavonoid compounds have been able to kill both Gram-positive and Gram-negative organisms in vitro.[10. M. Friedman, "Overview of antibacterial, antitoxin, antiviral, and antifungal activities of tea flavonoids and teas," Mol Nutr Food Res, 51:116-34, 2007.] In addition, it is not known how dietary phenols may alter microbial composition.

In other cases, polyphenols such as the isoflavones produced by soy and other plants act as antioxidants that mitigate oxidative stress, which is often linked to cancer. Just how soy may modify cancer risk is far from clear. Like other antioxidants, isoflavones are thought to reduce the inflammation that predisposes tissues to cancer. The soy isoflavone daidzein is metabolized by certain gut microbes into equol, a plant estrogen. Because of their hormone-like properties, soy isoflavones have been reported to have protective effects against prostate cancer; however, these findings are not consistent across studies. One reason for these inconsistencies could be individual differences in how gut microbes metabolize isoflavones. According to epidemiological studies, only 30–50 percent of the human population is capable of producing equol. Studies of populations that consume a high level of soy, mostly of Asian descent, have found that equol producers may have a greater reduction in cancer risk than those who do not produce equol.[11. J.W. Lampe, "Emerging research on equol and cancer," J Nutr, 140:1369S-72S, 2010.] Generally, interpretation of the soy–cancer prevention literature is challenging. Although more research is needed to understand the role of our gut microbiota in mediating cancer risk, metabolites like urolithins, polyphenols and equol, show promise against cancer.

Our group is studying the effects of dietary interventions that are thought to be beneficial—such as fermented dairy products—and of risk-associated foods like red meat on the microbiota and on colon cancer. We use mouse models of inflammatory bowel disease and colon cancer to understand how diet can impact these diseases. By using mice, we can control many genetic and environmental factors that complicate human studies of the microbiota and diet. In addition, we make use of germ-free mice, in which we can design the microbial communities from scratch by adding back select bacteria. Also, we can transplant human fecal samples into such mice and thus, to some extent, make them better models of human physiology. Our research suggests that one way fermented milk products may confer a health benefit is by indirectly driving shifts in short chain fatty acids; bacteria in the fermented milk actually influence the resident gut microbes to drive these changes.

An incomplete symbiosis

Our gut microbiota, when fed certain foods, can also produce detrimental metabolites that promote cellular proliferation and inhibit apoptosis—circumstances conducive to cancer development. Heterocyclic amines (HCAs)—compounds found in the char that coats any well-done steak—are considered carcinogenic. HCAs are not digested in the small intestine but remain available for fermentation by bacteria in the colon. Once metabolized by gut bacteria, HCAs are converted to electrophilic derivatives that damage DNA, placing people at increased risk for colon cancer.[12. M.M. Huycke, H.R. Gaskins, "Commensal bacteria, redox stress, and colorectal cancer: mechanisms and models," Exp Biol Med, 229:586-97, 2004.]

It will be years before a fecal sample will reveal risk of cancer or the foods that could change it.

Hydrogen sulfide is another metabolite produced by gut bacteria that can damage DNA. Consumption of high-protein foods, particularly red meat, may fuel hydrogen sulfide production by sulfate-reducing gut microbes. Some studies suggest that patients with colon cancer and inflammatory bowel disease may harbor higher levels of such bacteria. Studies by Rex Gaskins’s lab at the University of Illinois at Urbana-Champaign suggest that hydrogen sulfide can contribute to cancer progression when DNA repair mechanisms are impaired. Whether a greater abundance of sulfate-reducing bacteria precedes or is a result of these health conditions, and which host factors contribute, requires further investigation. In high-risk individuals, these metabolites may offer targets for cancer prevention.

“It takes a village”: the power of community

Although the link between gut microbes and cancer risk is becoming clearer, it will probably be years before dropping off a fecal sample at the doctor’s office will generate a report of your cancer risk and a list of foods you should or shouldn’t eat to modify that risk. Further experimentation is needed to understand the metabolic potential and function of the human microbiota. Some of the current bottlenecks are in data processing and analysis.

Indeed, because only a very few gastrointestinal-associated bacterial species, like Helicobacter pylori, have been convincingly linked to cancer, the focus is shifting from single-organism studies to bacterial communities as a factor influencing cancer risk. Worldwide consortia such as the Human Microbiome Project and the Metagenomics of the Human Intestinal Tract project (MetaHIT) are applying sequence-based approaches to study the microbiota of healthy and disease-affected individuals. The emerging field of microbial “omics,” which encompasses metagenomics and metabolomics, is rapidly advancing. Cancer genomics has offered the potential to understand how cancers operate at the molecular level.

Microbial metagenomics may have the potential to improve many aspects of cancer prevention and treatment. Current studies like the esophageal cancer microbiome project, a joint venture spearheaded by Karen Nelson from the J. Craig Venter Institute and New York University’s Zhiheng Pei, aim to identify microbiota-based biomarkers that can identify patients at high risk for developing cancer. Successful microbiota biomarker identification could be used as a prognostic, diagnostic, and management tool, allowing gut microbe testing to become part of the evolving personalized-medicine tool kit.

In cancer care, cancer genomics and pharmacogenomics are increasingly employed to identify which patients will respond to which treatments and whether particular patients are at risk for experiencing dangerous drug toxicities. Enzymes produced by gut microbes can often interact with drug regimens, contributing to side effects or changing how the drug is metabolized by the body. A recent study showed that gut bacterial enzymes called ß-glucuronidases can contribute to the severe diarrhea sometimes associated with a commonly used colon-cancer chemotherapy drug called irinotecan.[13. B.D. Wallace et al., "Alleviating cancer drug toxicity by inhibiting a bacterial enzyme," Science, 330:831-35, 2010.] Selectively targeting these bacterial enzymes reduced a potentially life-threatening side effect of this drug.

The day may not be so far off when fecal samples are biobanked for future transplant, and microbiota associated with a high risk of cancer can be replaced with lower-risk microbiota. Foods or bacterial-directed therapies may be used to re-engineer the microbial communities in the gut by introducing functions that reduce cancer risk. As we come to understand what features constitute a healthy microbiota and how the microbiota changes across the human life cycle, the plasticity and genomic potential of our gut microbes may be tapped as a fountain of youth and health. As far as symbiotic relationships go, ours appears to be continually influenced by dietary patterns that may be altering this relationship in significant ways. A deeper understanding of the effects of dietary intake on our microbiota will hopefully lead us toward a more perfect union.

Michelle Rooks and Wendy Garrett are at Harvard School of Public Health.

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