The bacterial cells harbored within the human gastrointestinal tract (GIT) outnumber the host’s cells by a factor of 10 and the genes encoded by the bacteria resident within the GIT outnumber their host’s genes by more than 100 times. These human digestive-tract associated microbes are referred to as the gut microbiome. The human gut microbiome and its role in both health and disease has been the subject of extensive research, establishing its involvement in human metabolism, nutrition, physiology, and immune function.

Imbalance of the normal gut microbiota have been linked with gastrointestinal conditions such as inflammatory bowel disease (IBD) and irritable bowel syndrome (IBS), and wider systemic manifestations of disease such as obesity, type 2 diabetes, and atopy.

The human digestive system, or the gastrointestinal (GI) tract, begins with the mouth and ends with the anus. The parts of the mouth include the teeth, the gums, the tongue, the oral vestibule (the space between the gums, lips, and teeth), and the oral cavity proper (the space behind the teeth and gums). Other parts of the GI tract are the pharynx, esophagus, stomach, small intestine, large intestine, rectum, and anus (Figure). Accessory digestive organs include the salivary glands, liver, gallbladder, spleen, and pancreas.

The digestive system contains normal microbiota, including archaea, bacteria, fungi, protists, and even viruses. Because this microbiota is important for normal functioning of the digestive system, alterations to the microbiota by antibiotics or diet can be harmful. Additionally, the introduction of pathogens to the GI tract can cause infections and diseases. In this section, we will review the microbiota found in a healthy digestive tract and the general signs and symptoms associated with oral and GI infections.

The digestive system, or the gastrointestinal tract, includes all of the organs associated with the digestion of food.

Anatomy and Normal Microbiota of the Oral Cavity

Food enters the digestive tract through the mouth, where mechanical digestion (by chewing) and chemical digestion (by enzymes in saliva) begin. Within the mouth are the tongue, teeth, and salivary glands, including the parotid, sublingual, and submandibular glands (Figure). The salivary glands produce saliva, which lubricates food and contains digestive enzymes.

(a) When food enters the mouth, digestion begins. (b) Salivary glands are accessory digestive organs. (credit: modification of work by National Cancer Institute)

The structure of a tooth (Figure) begins with the visible outer surface, called the crown, which has to be extremely hard to withstand the force of biting and chewing. The crown is covered with enamel, which is the hardest material in the body. Underneath the crown, a layer of relatively hard dentin extends into the root of the tooth around the innermost pulp cavity, which includes the pulp chamber at the top of the tooth and pulp canal, or root canal, located in the root. The pulp that fills the pulp cavity is rich in blood vessels, lymphatic vessels, connective tissue, and nerves. The root of the tooth and some of the crown are covered with cementum, which works with the periodontal ligament to anchor the tooth in place in the jaw bone. The soft tissues surrounding the teeth and bones are called gums, or gingiva. The gingival space or gingival crevice is located between the gums and teeth.

The tooth has a visible crown with an outer layer of enamel, a layer of dentin, and an inner pulp. The root, hidden by the gums, contains the pulp canal (root canal). (credit: modification of work by Bruce Blaus)

Microbes such as bacteria and archaea are abundant in the mouth and coat all of the surfaces of the oral cavity. However, different structures, such as the teeth or cheeks, host unique communities of both aerobic and anaerobic microbes. Some factors appear to work against making the mouth hospitable to certain microbes. For example, chewing allows microbes to mix better with saliva so they can be swallowed or spit out more easily. Saliva also contains enzymes, including lysozyme, which can damage microbial cells. Recall that lysozyme is part of the first line of defense in the innate immune system and cleaves the β-(1,4) glycosidic linkages between N-acetylglucosamine (NAG) and N-acetylmuramic acid (NAM) in bacterial peptidoglycan (see Chemical Defenses). Additionally, fluids containing immunoglobulins and phagocytic cells are produced in the gingival spaces. Despite all of these chemical and mechanical activities, the mouth supports a large microbial community.

Anatomy and Normal Microbiota of the GI Tract

As food leaves the oral cavity, it travels through the pharynx, or the back of the throat, and moves into the esophagus, which carries the food from the pharynx to the stomach without adding any additional digestive enzymes. The stomach produces mucus to protect its lining, as well as digestive enzymes and acid to break down food. Partially digested food then leaves the stomach through the pyloric sphincter, reaching the first part of the small intestine called the duodenum. Pancreatic juice, which includes enzymes and bicarbonate ions, is released into the small intestine to neutralize the acidic material from the stomach and to assist in digestion. Bile, produced by the liver but stored in the gallbladder, is also released into the small intestine to emulsify fats so that they can travel in the watery environment of the small intestine. Digestion continues in the small intestine, where the majority of nutrients contained in the food are absorbed. Simple columnar epithelial cells called enterocytes line the lumen surface of the small intestinal folds called villi. Each enterocyte has smaller microvilli (cytoplasmic membrane extensions) on the cellular apical surface that increase the surface area to allow more absorption of nutrients to occur (Figure).

(a) The structure of the wall of the small intestine allows for the majority of nutrient absorption in the body. (b) Villi are folds in the surface of the small intestine. Microvilli are cytoplasmic extensions on individual cells that increase the surface area for absorption. (c) A light micrograph shows the shape of the villi. (d) An electron micrograph shows the shape of the microvilli. (credit b, c, d: Modification of micrographs provided by the Regents of University of Michigan Medical School © 2012)

Digested food leaves the small intestine and moves into the large intestine, or colon, where there is a more diverse microbiota. Near this junction, there is a small pouch in the large intestine called the cecum, which attaches to the appendix. Further digestion occurs throughout the colon and water is reabsorbed, then waste is excreted through the rectum, the last section of the colon, and out of the body through the anus (Figure).

The environment of most of the GI tract is harsh, which serves two purposes: digestion and immunity. The stomach is an extremely acidic environment (pH 1.5-3.5) due to the gastric juices that break down food and kill many ingested microbes; this helps prevent infection from pathogens. The environment in the small intestine is less harsh and is able to support microbial communities. Microorganisms present in the small intestine can include lactobacilli, diptherioids and the fungus Candida. On the other hand, the large intestine (colon) contains a diverse and abundant microbiota that is important for normal function. These microbes include Bacteriodetes (especially the genera Bacteroides and Prevotella) and Firmicutes (especially members of the genus Clostridium). Methanogenic archaea and some fungi are also present, among many other species of bacteria. These microbes all aid in digestion and contribute to the production of feces, the waste excreted from the digestive tract, and flatus, the gas produced from microbial fermentation of undigested food. They can also produce valuable nutrients. For example, lactic acid bacteria such as bifidobacteriacan synthesize vitamins, such as vitamin B12, folate, and riboflavin, that humans cannot synthesize themselves. E. coli found in the intestine can also break down food and help the body produce vitamin K, which is important for blood coagulation.

The GI tract has several other methods of reducing the risk of infection by pathogens. Small aggregates of underlying lymphoid tissue in the ileum, called Peyer's patches (Figure), detect pathogens in the intestines via microfold (M) cells, which transfer antigens from the lumen of the intestine to the lymphocytes on Peyer's patches to induce an immune response. The Peyer's patches then secrete IgA and other pathogen-specific antibodies into the intestinal lumen to help keep intestinal microbes at safe levels. Goblet cells, which are modified simple columnar epithelial cells, also line the GI tract (Figure). Goblet cells secrete a gel-forming mucin, which is the major component of mucus. The production of a protective layer of mucus helps reduce the risk of pathogens reaching deeper tissues.

The constant movement of materials through the gastrointestinal tract also helps to move transient pathogens out of the body. In fact, feces are composed of approximately 25% microbes, 25% sloughed epithelial cells, 25% mucus, and 25% digested or undigested food. Finally, the normal microbiota provides an additional barrier to infection via a variety of mechanisms. For example, these organisms outcompete potential pathogens for space and nutrients within the intestine. This is known as competitive exclusion. Members of the microbiota may also secrete protein toxins known as bacteriocins that are able to bind to specific receptors on the surface of susceptible bacteria.

A magnified image of intestinal villi in the GI tract shows goblet cells. These cells are important in producing a protective layer of mucus.

General Signs and Symptoms of Oral and GI Disease

Despite numerous defense mechanisms that protect against infection, all parts of the digestive tract can become sites of infection or intoxication. The term food poisoning is sometimes used as a catch-all for GI infections and intoxications, but not all forms of GI disease originate with foodborne pathogens or toxins.

In the mouth, fermentation by anaerobic microbes produces acids that damage the teeth and gums. This can lead to tooth decay, cavities, and periodontal disease, a condition characterized by chronic inflammation and erosion of the gums. Additionally, some pathogens can cause infections of the mucosa, glands, and other structures in the mouth, resulting in inflammation, sores, cankers, and other lesions. An open sore in the mouth or GI tract is typically called an ulcer.

Infections and intoxications of the lower GI tract often produce symptoms such as nausea, vomiting, diarrhea, aches, and fever. In some cases, vomiting and diarrhea may cause severe dehydration and other complications that can become serious or fatal. Various clinical terms are used to describe gastrointestinal symptoms. For example, gastritis is an inflammation of the stomach lining that results in swelling and enteritis refers to inflammation of the intestinal mucosa. When the inflammation involves both the stomach lining and the intestinal lining, the condition is called gastroenteritis. Inflammation of the liver is called hepatitis. Inflammation of the colon, called colitis, commonly occurs in cases of food intoxication. Because an inflamed colon does not reabsorb water as effectively as it normally does, stools become watery, causing diarrhea. Damage to the epithelial cells of the colon can also cause bleeding and excess mucus to appear in watery stools, a condition called dysentery.

Summary

• The digestive tract, consisting of the oral cavity, pharynx, esophagus, stomach, small intestine, and large intestine, has a normal microbiota that is important for health.
• The constant movement of materials through the gastrointestinal canal, the protective layer of mucus, the normal microbiota, and the harsh chemical environment in the stomach and small intestine help to prevent colonization by pathogens.
• Infections or microbial toxins in the oral cavity can cause tooth decay, periodontal disease, and various types of ulcers.
• Infections and intoxications of the gastrointestinal tract can cause general symptoms such as nausea, vomiting, diarrhea, and fever. Localized inflammation of the GI tract can result in gastritis, enteritis, gastroenteritis, hepatitis, or colitis, and damage to epithelial cells of the colon can lead to dysentery.
• Foodborne illness refers to infections or intoxications that originate with pathogens or toxins ingested in contaminated food or water.

All of the microbial organisms that naturally exist within the gastrointestinal tract.

Microbes on the Human Body

The commensal bacteria that inhabit our skin and gastrointestinal tract do a host of good things for us. They protect us from pathogens, help us digest our food, and produce some of our vitamins and other nutrients. These activities have been known for a long time. More recently, scientists have gathered evidence that these bacteria may also help regulate our moods, influence our activity levels, and even help control weight by affecting our food choices and absorption patterns. The Human Microbiome Project has begun the process of cataloging our normal bacteria (and archaea), so we can better understand these functions.

A particularly fascinating example of our normal flora relates to our digestive systems. People who take high numbers of antibiotics tend to lose many of their normal gut bacteria, allowing a naturally antibiotic-resistant species called Clostridium difficile to overgrow and cause severe gastric problems, especially chronic diarrhea (Figure). Obviously, trying to treat this problem with antibiotics only makes it worse. However, it has been successfully treated by giving the patients fecal transplants from healthy donors to reestablish the normal intestinal microbial community. Clinical trials are underway to ensure the safety and effectiveness of this technique.

This scanning electron micrograph shows Clostridium difficile, a Gram-positive, rod-shaped bacterium that causes severe diarrhea. Infection commonly occurs after the normal gut fauna is eradicated by antibiotics. (credit: modification of work by CDC, HHS; scale-bar data from Matt Russell)

Scientists are also discovering that the absence of certain key microbes from our intestinal tract may set us up for a variety of problems. This seems to be particularly true regarding the appropriate functioning of the immune system. There are intriguing findings that suggest that the absence of these microbes is an important contributor to the development of allergies and some autoimmune disorders. Research is currently underway to test whether adding certain microbes to our internal ecosystem may help in the treatment of these problems, as well as in treating some forms of autism.

Most bacteria that enter the alimentary canal are killed by lysozyme, defensins, HCl, or protein-digesting enzymes. However, trillions of bacteria live within the large intestine and are referred to as the bacterial flora. Most of the more than 700 species of these bacteria are nonpathogenic commensal organisms that cause no harm as long as they stay in the gut lumen. In fact, many facilitate chemical digestion and absorption, and some synthesize certain vitamins, mainly biotin, pantothenic acid, and vitamin K. Some are linked to increased immune response. A refined system prevents these bacteria from crossing the mucosal barrier. First, peptidoglycan, a component of bacterial cell walls, activates the release of chemicals by the mucosa’s epithelial cells, which draft immune cells, especially dendritic cells, into the mucosa. Dendritic cells open the tight junctions between epithelial cells and extend probes into the lumen to evaluate the microbial antigens. The dendritic cells with antigens then travel to neighboring lymphoid follicles in the mucosa where T cells inspect for antigens. This process triggers an IgA-mediated response, if warranted, in the lumen that blocks the commensal organisms from infiltrating the mucosa and setting off a far greater, widespread systematic reaction.

Microscopic creatures—including bacteria, fungi and viruses—can make you ill. But what you may not realize is that trillions of microbes are living in and on your body right now. Most don’t harm you at all. In fact, they help you digest food, protect against infection and even maintain your reproductive health. We tend to focus on destroying bad microbes. But taking care of good ones may be even more important.

You might be surprised to learn that your microbes actually outnumber your own cells by 10 to 1. “The current estimate is that humans have 10 trillion human cells and about 100 trillion bacterial cells,” says Dr. Martin J. Blaser at the New York University School of Medicine.

New techniques allow scientists to study these rich microbial communities and their genes—the “microbiome.” In 2007, NIH launched the Human Microbiome Project to study microbes in and on the body.

Earlier this year, researchers from almost 80 institutions published a landmark series of reports. They found that more than 10,000 different species occupy the human body. The microbiome actually provides more genes that contribute to human survival than the human genome itself (8 million vs. 22,000). Humans need bacteria and their genes more than most of us thought.

One of the most important things microbes do for us is to help with digestion. The mix of microbes in your gut can affect how well you use and store energy from food. In laboratory experiments, transferring bacteria from certain obese mice to normal ones led to increased fat in the normal mice.

Blaser and his colleagues are concerned that changes in our microbiome early in life may contribute to weight problems later. “We’re in the middle of an epidemic of obesity that is very severe,” Blaser says. “It’s relatively recent, it’s widespread across the United States and across the world, and increased calories and decreased exercise seem insufficient to explain this.”

We might be changing our microbiome for the worse, he says, by using antibiotics too often. In a recent NIH-funded study, Blaser’s team found that low-dose antibiotic therapy affected the gut microbiomes of young mice. Antibiotics also altered how the mice used sugars and fats. After 7 weeks, treated mice had up to 15% more fat than untreated mice. This and other studies suggest that gut bacteria can affect both appetite and how you use energy in food.

In related work, Dr. Leonardo Trasande, Blaser and colleagues analyzed data from more than 11,000 children. Although the results weren’t conclusive, they suggest that infants given antibiotics might be at increased risk of becoming overweight. More work will be needed to confirm this connection.

“Microbes in our intestines may play critical roles in how we absorb calories,” Trasande says. “Exposure to antibiotics, especially early in life, may kill off healthy bacteria that influence how we absorb nutrients into our bodies, and would otherwise keep us lean.”

Microbes are also important for your skin, one of the body’s first lines of defense against illness and injury. Skin health depends on the delicate balance between your own cells and the microbes that live on its surface.

“Basically, the healthy bacteria are filling all those little niches so that the more dangerous bacteria can’t get a foothold onto the skin,” says Dr. Julie Segre of NIH.

Segre and other NIH researchers looked at skin microbes collected from different body regions on healthy volunteers. They found that body location has a huge effect on which types of bacteria live. For example, bacteria living under your arms likely are more similar to those under another person’s arm than to the bacteria on your own forearm.

Microbes are also important to the body’s infection-fighting immune system. In one recent study, NIH scientists examined special mice that were born and raised to be germ-free. These mice seemed to have weak immune function. In contrast, normal mice have vibrant bacterial communities and a rich variety of immune cells and molecules on their skin.

The germ-free mice were exposed to Staphylococcus epidermidis, one of the most common bacteria on human skin. Adding this one species of bacteria boosted immune function in the mouse skin. The mice with S. epidermidis were able to defend against a parasite, whereas the bacteria-free mice weren’t.

“We often have a sense that the bacteria that live on our skin are harmful,” Segre says. “But in this study we show that these bacteria can play an important role in promoting health by preventing skin infections from becoming more prolonged, pronounced and more serious.”

There’s strong evidence that the microbes in the female reproductive tract affect reproductive health and help protect against disease. A recent study also found a diverse community of microbes in the male urinary tract and on the penis. NIH-funded researchers are investigating other positive roles for microbes. One major area of research concerns allergy-related conditions, including childhood asthma, skin allergies, hay fever and eczema.

So what can you do to protect against microbes that cause infection but take care of the ones that help you? We know that washing our hands is important for removing harmful microbes—for example, before eating or after using the bathroom.

Other less obvious things can affect your skin microbes, Segre says. The lotions and creams you use can provide a barrier to protect your skin’s moisture, Segre points out, “but in fact you’re also putting a fertilizer onto the microbial garden. You’re really changing the food source for the bacteria that live on your skin.” There’s not one right answer about which skin products are best for you, she says. Experiment to see how different ones affect your skin.

Many researchers worry that some people are trying to get too clean. Blaser thinks that people are using sanitizers and antibiotic products too often these days. “Obviously, there are many bad germs, but I think we’ve gone overboard and it looks like trying to get rid of the bad guys has had a collateral effect on the good guys.”

You’re never alone when it comes to your microbes. But don’t get squeamish about it. Just remember how much you need them.

Protect Your Microbes

• Don’t be scared of microbes. Most actually help you.
• Don’t pressure your doctor to give you antibiotics. They may cause more harm than good.
• Know when to wash your hands—for example, when preparing food and before eating.
• Don’t use antibacterial products you don’t need. Antibacterial soaps have little or no health benefit. And antibacterial versions of household products (like phones and staplers) have not been shown to reduce your risk of infection.
• Don’t go overboard with hand sanitizers. They’re useful in health care settings, but hand washing is a better option in most situations.
• Experiment with different skin moisturizers to see which work best for you.
• Researchers are investigating the potential health benefits of “probiotic” products, which aim to restore a healthy microbe mix, but experts can’t yet make any recommendations.

Everyone has pain or discomfort in their gut occasionally. Maybe you ate something that didn’t agree with you. Or you had an infection that made you sick to your stomach for a few days.

But if pain and other gut symptoms go on for weeks or longer, something more serious might be wrong. Digestive system diseases and disorders are very common. Around 60 to 70 million people in the U.S. live with a digestive disease.

It’s important not to ignore symptoms in your gut. Many digestive disorders are easiest to treat when they first develop.

Potential Causes

One of the most serious gut disorders is inflammatory bowel disease (IBD), although it’s not very common. IBD occurs when immune system cells in the gut overreact to a perceived threat to your body. Often, that “threat” is the normal bugs that make up the microbiome—the microscopic creatures like bacteria, fungi, and viruses—that live in your gut. This overreaction can damage the digestive (gastrointestinal or GI) tract.

The two main types of IBD are ulcerative colitis and Crohn’s disease. “Crohn’s can occur anywhere in the digestive tract, from the mouth to the anus,” says Dr. Judy Cho, an IBD expert at Mount Sinai. Ulcerative colitis happens only in the large intestine.

These two diseases also differ in how deeply they can damage tissue. “Ulcerative colitis causes damage in the gut lining,” explains Dr. Dermot McGovern, who studies IBD at Cedars-Sinai. “Crohn’s disease can go all the way through the gut.” Severe cases of Crohn’s can lead to narrowing of the intestines and even holes in the gut.

Other conditions can harm the lining of the stomach and lead to a type of inflammation called gastritis. The most common cause of gastritis is infection with bacteria called Helicobacter pylori. Other causes include the long-term use of some pain medications. If left untreated, gastritis can lead to painful ulcers.

Twelve percent of people in the U.S. have irritable bowel syndrome (IBS). “This is a very common disorder. It’s characterized by abdominal pain, bloating, and changes in bowel habits,” says Dr. Anthony Lembo, an IBS researcher at Beth Israel Deaconess Medical Center.

Researchers don’t understand exactly what causes IBS. It may have different causes in different people. Sometimes it involves problems with how the brain and gut work together.

Other things that can cause pain and discomfort in the GI tract are acid reflux or food sensitivities.

Pinpointing the Problem

It can be tricky to diagnose a digestive disease because they share a lot of symptoms, explains Cho. Symptoms of many gut conditions include pain, gassiness, bloating, and diarrhea.

“But for IBD, there are several red-flag symptoms,” she says. These are blood in the stool, weight loss, and signs of inflammation found in a blood test. A sign of IBD in children is failure to grow, Cho adds.

IBS can give some people diarrhea and others constipation. Some people go back and forth between the two.

Gastritis and food sensitivities can also cause long-term gut discomfort. To figure out what’s causing gut troubles, doctors may need to run a variety of tests. These can include blood tests and a stool test to look for infection.

Some people may have an imaging test, such as a CT scan. Others may need to have an endoscopy. Endoscopy uses a long, flexible tube with a tiny camera on the end to look in the intestines or stomach.

Treating Pain and Discomfort

While symptoms for different gut disorders can be similar, treatments vary widely. For gastritis caused by bacterial infection, antibiotics are used to kill the germs. If medications are causing gastritis, switching to a different kind of drug will usually allow the stomach to heal.

Food sensitivities can be managed by changing your diet. A nutritionist can help you figure out what foods might be irritating your gut. Acid reflux can also often be improved by changes in your diet and medication.

Treatment isn’t one-size-fits-all for IBS, Lembo explains, because it can have different causes. Some people can get some relief by adjusting their diet. (See the Wise Choices box for foods that can trigger gut symptoms.)

“We also tell patients to eat two to three meals a day, maybe have a snack or two. But don’t eat all day long. Give your gut a chance to rest,” he says.

And while stress doesn’t cause IBS, it can trigger flare-ups of symptoms in many people, says Lembo. Stress reduction strategies and cognitive behavior therapy—a type of talk therapy—can help some people manage symptoms of IBS.

IBD is harder to treat than most gut disorders. “It’s impossible to cure IBD right now,” says Cho. Treatments focus on stopping inflammation long enough to allow the gut tissue to heal, she explains.

Some medications used for IBD control inflammation. Other newer drugs suppress the immune system. But these newer drugs can have serious side effects and are usually only used when others don’t work.

“Research has discovered that the earlier you use these medications, the more likely you are to respond,” says McGovern. So, people with high-risk disease may get these drugs first now, he explains.

Looking for Better Treatments

Researchers are searching for new ways to prevent and manage gut disorders. Lembo, for example, is testing whether peppermint oil can help the gut muscles relax in people with IBS.

Existing treatments for IBD only work for about a third of people who try them. And even then, McGovern says, they may lose their effects over time.

Both Cho and McGovern are working to understand the genetics of IBD. This information could be used at all stages of the disease, explains Cho. For example, if a test could identify children at higher risk of developing IBD later in life, “theoretically it could be prevented,” she says. Strategies could include giving anti-inflammatory drugs before IBD develops or changing the gut microbiome to prevent an immune attack.

“And what we’re all interested in is: Can we use some of these genetic signatures to identify new drug targets for IBD?” adds McGovern. That could also eventually help predict who would most likely benefit from a drug, he says.

One of the newest drugs being tested for IBD was based on a genetic discovery, Cho explains. “There’s increasing precision in treatment,” she says. “Using genetic knowledge to help choose therapies for IBD is something that I think is doable in the next five to 10 years.”

For now, talk with your doctor if gut discomfort or pain are impacting your quality of life. Available treatments can help most people get their insides back in order again.

Gut Trigger Foods

Not all people with gut disorders have problems with the same foods. But some foods that commonly cause gut discomfort include:

• Dairy products
• Caffeine
• Carbonated drinks
• Sugar, candy, and junk food
• Fruit juices
• Beans
• Cruciferous vegetables, like broccoli and cauliflower

Your digestive system is busy. When you eat something, your food takes a twisty trip that starts with being chewed up and ends with you going to the bathroom. A lot happens in between. The health of your gut plays a key role in your overall health and well-being. You can make choices to help your body stay on tract.

Your digestive, or gastrointestinal (GI), tract is a long, muscular tube that runs from your mouth to your anus. It’s about 30 feet long and works with other parts of your digestive system to break food and drink down into smaller molecules of nutrients. The blood absorbs these and carries them throughout the body for cells to use for energy, growth, and repair.

With such a long GI highway, it’s common to run into bumps in the road. About 60 to 70 million Americans are affected by digestive diseases, like gastroesophageal reflux disease (GERD) or irritable bowel syndrome (IBS). GERD happens when your stomach acid and/or contents come back up into your esophagus (swallowing tube) or throat. This causes uncomfortable symptoms like heartburn and indigestion. IBS is a group of symptoms that includes pain in the abdomen and changes in bowel habits. People with IBS may have constipation, diarrhea, or both. Many more people have other digestive problems, like bloating and stomach pain.

“There are many factors that can impact gut health,” says Dr. Lin Chang, a GI expert at the University of California, Los Angeles. How your body’s built, your family and genetic history, how you manage stress, and what you eat can all affect your gut.

“I see a lot of lifestyle-related GI issues, and there are often no quick fixes for that,” she says. “In general, people do well when they create a more routine schedule, eat a healthy diet and smaller more frequent meals, add in some exercise, and get a good amount of sleep.”

Chang studies the connection between stress and IBS. Her research group has found that people who have early life stress are more likely to develop IBS. “However, this increased risk for IBS went down when people confided in someone they trust about the stress they experienced,” she explains. “Finding healthy ways to manage stress is important for GI health, and your health overall.”

What you eat can help or hurt your digestive system, and influence how you feel. “Increasing fiber is really important for constipation,” says Chang. “Most Americans do not eat a lot of fiber so you have to gradually increase the fiber in your diet. Otherwise you might get gas and more bloating, and won’t stick with [the changes].”

Chang says you should eat at least 20–30 grams of fiber a day for constipation. You can spread out your fiber in small amounts throughout the day. Start with small servings and gradually increase them to avoid gas, bloating, and discomfort.

Try to eat fruits and vegetables at every meal. A variety of fruits, vegetables, whole grains, and nuts can provide a healthy mix of different fibers and nutrients to your diet. An added benefit is that the more fiber and whole foods you eat, the less room you’ll have for less healthy options.

But some fiber-rich foods, called high FODMAP foods, can be hard to digest. Examples include certain fruits and vegetables, dairy products, and wheat and rye products. If you have IBS, your doctor may recommend a diet low in FODMAPS.

Researchers are coming to understand the complex community of bacteria and other microbes that live in the human GI tract. Called gut flora or microbiota, these microbes help with our digestion. But evidence has been growing that gut microbes may influence our health in other ways too. Studies suggest that they may play roles in obesity, type 2 diabetes, IBS, and colon cancer. They might also affect how the immune system functions. This can affect how your body fights illness and disease. Recent studies have found that microbes’ effects on the immune system may impact the development of conditions such as allergy, asthma, and rheumatoid arthritis .

You might have heard that probiotics—live microbes that are similar to those found in the human gut—can improve your gut health. These are also called “friendly bacteria” or “good bacteria.” Probiotics are available in dietary supplements and in certain foods, such as yogurt.

There is some evidence that probiotics may be helpful in preventing diarrhea associated with antibiotics and improving symptoms of IBS, but more needs to be learned. Researchers still don’t know which probiotics are helpful and which aren’t. They also don’t know how much of the probiotics people would have to take or who would most likely benefit from them.

Certain food additives called emulsifiers are something else that may affect your gut health. Emulsifiers are added to many processed foods to improve texture and extend shelf life. But studies show they can affect our gut flora.

“Our work and other research indicate that emulsifiers and other food additives can negatively impact the microbiota and promote inflammatory diseases ,” says Georgia State University’s Dr. Andrew Gewirtz. His group has been studying the relationships between food additives, gut bacteria, and disease in mice. The team also plans to examine how different food additives may affect people.

Based on what his team and others have found, Gewirtz advises, “The take home message: Eat a balanced diet and less processed foods.”

“The GI system is complicated and such an important part of our health,” Chang says. “It takes a real partnership between patient and doctor to get to the root of issues. Everyone has to find a healthy routine that works for them.”

She encourages you to take an active role in finding a doctor who makes you feel comfortable. The right doctor will listen carefully to your health history and symptoms. You can help keep your gut in check by talking with your doctor and—together—making the right choices for you.

For Better Gut Health

• Eat slower. Chew your food well before swallowing. It may help you swallow less air and better sense when you’re full.
• Enjoy smaller meals. Eat in moderation to avoid overfilling your stomach and encourage digestion. A packed stomach may also cause reflux, or your food to come back up.
• Set a bedtime for your gut. Try to limit how much you eat after dark. Your GI tract is most active in the morning and daytime.
• Manage stress. Learn healthy ways to reduce stress like relaxation breathing, mindfulness, and exercise. Stress makes it harder to digest your food well.
• Create a routine. Try to eat around the same times each day. Your GI system may do best on a schedule.
• Consider probiotics. Talk with your doctor about taking probiotics (supplemental healthful bacteria). They may ease constipation and IBS symptoms.

Fiber—you know it’s good for you. But if you’re like many Americans, you don’t get enough. In fact, most of us get about half the recommended amount of fiber each day.

Dietary fiber is found in the plants you eat, including fruits, vegetables, and whole grains. It’s sometimes called bulk or roughage. You’ve probably heard that it can help with digestion. So it may seem odd that fiber is a substance that your body can’t digest. Much of it passes through your digestive system practically unchanged.

“You might think that if it’s not digestible, then it’s of no value. But there’s no question that higher intake of fiber from all food sources is beneficial,” says Dr. Joanne Slavin, a nutrition scientist at the University of Minnesota.

Types of Fiber

Different types of fiber can affect your health in different ways. That’s why the Nutrition Facts labels on some foods may list two categories of fiber: soluble and insoluble. Soluble fiber is found in oats, beans, peas, and most fruits. Insoluble fiber is found in wheat bran and some vegetables.

Some soluble fiber is broken down by the complex community of bacteria and other microbes that live in the human gut. These microbes, called gut flora or microbiota, help with our digestion. Emerging research shows they can affect our health in various ways. Studies suggest that they may play a role in obesity, type 2 diabetes, colon cancer, and other conditions. Researchers are now looking at how different types of dietary fibers affect the gut microbiota—and how that, in turn, affects our health.

But soluble and insoluble fiber aren’t always listed separated on labels. Many foods contain both. And both types have health benefits. Experts suggest that men aim for about 38 grams of fiber a day, and women about 25 grams. Unfortunately, in the United States, we take in an average of only 16 grams of fiber each day.

Health Benefits

Some of fiber’s greatest benefits are related to cardiovascular health. Several large studies have found that people who eat the most fiber had a lower risk for heart disease.

High fiber intake—particularly soluble fiber—seems to protect against several heart-related problems. “There is evidence that high dietary fiber consumption lowers ‘bad’ cholesterol concentrations in the blood and reduces the risk for developing heart disease, stroke, and high blood pressure,” says Dr. Somdat Mahabir, a nutrition and disease expert with NIH’s National Cancer Institute.

Fiber can help relieve constipation and normalize your bowel movements. Insoluble fiber is often used to treat or prevent constipation and diverticular disease, which affects the large intestine, or colon.

Fiber may also play a role in reducing the risk for type 2 diabetes , the most common form of diabetes. Fiber in the intestines can slow the absorption of sugar, which helps prevent blood sugar from spiking. “With diabetes, it’s good to keep glucose levels from peaking too much,” explains Dr. Gertraud Maskarinec of the University of Hawaii.

In an NIH-funded study, Maskarinec and her colleagues followed more than 75,000 adults for 14 years. Consistent with other large studies, their research found that diabetes risk was significantly reduced in people who had the highest fiber intake.

“We found that it’s mostly the fiber from grains that protects against diabetes,” Maskarinec says. However, she notes that while high fiber intake may offer some protection, the best way to reduce your risk of diabetes is to exercise and keep your weight in check.

Your weight is another area where fiber might help. High-fiber foods generally make you feel fuller for longer. Fiber adds bulk but few calories. “In studies where people are put on different types of diets, those on the high-fiber diets typically eat about 10% fewer calories,” Slavin says. Other large studies have found that people with high fiber intake tend to weigh less—although that may be because their diets are healthier.

Scientists have also looked into links between fiber and different types of cancer, with mixed results. For example, there is evidence that a high intake of dietary fiber may reduce the risk for colon cancer and colon polyps.

A Fiber-Rich Diet

Experts say that the type of fiber you eat is less important than making sure you get enough overall. “In general, people should not be too concerned by the specific type of fiber,” Mahabir says. “The focus should be more on eating diets that are rich in whole grains, legumes, beans, vegetables, fruits, nuts, and seeds to get the daily fiber requirement.”

Whole grains, fruits, and vegetables are also packed with vitamins and other nutrients, so experts recommend that you get most of your fiber from these natural sources. “Unfortunately, a lot of people tend to pick low-fiber foods. They go for white bread or white rice. Most of the processed foods—foods that are really convenient—tend to be low in fiber,” says Slavin.

For people who have trouble getting enough fiber from natural sources, store shelves are filled with packaged foods that tout added fiber. These fiber-fortified products include yogurts, ice cream, cereals, snack bars, and juices. They generally contain isolated soluble fibers, such as inulin, polydextrose, or maltodextrin. These isolated fibers are included in the product label’s list of ingredients.

However, the health benefits of isolated fibers are unclear. Research suggests they may not have the same effects as the intact fibers found in whole foods. For instance, there’s little evidence that isolated fibers help lower blood cholesterol. They’ve also shown inconsistent effects on the regularity of bowel movements. On the plus side, some studies suggest they might boost the growth of good bacteria in the gut.

The bottom line is that most of us need to fit more fiber into our day, no matter what the source. “It would be great if people would choose more foods that are naturally high in fiber,” Slavin says.

Increase your fiber intake gradually, so your body can get used to it. Adding fiber slowly helps you avoid gas, bloating, and cramps. Eat a variety of fruits, vegetables, whole grains, and nuts to add a mix of different fibers and a wide range of nutrients to your diet. A fiber-rich diet can help your health in many ways.

Tips to Get More Fiber in Your Diet

• Bulk up your breakfast. Choose a high-fiber cereal (5 or more grams per serving) or make a bowl of oatmeal and top it with nuts and fruit.

• Switch to whole grains. Look for bread that lists whole-grain flour as the first ingredient. Experiment with barley; wild or brown rice; quinoa; whole wheat pasta; and bulgur.

• Add a non-starchy vegetable. Keep a bag of frozen mixed vegetables, spinach, or broccoli florets for a quick addition to any pasta sauce or rice dish. Start dinners with a tossed salad.

• Don’t forget legumes. Try peas, different kinds of beans (pinto, kidney, lima, navy, and garbanzo), and lentils.

• Snack on fruit, nuts, and seeds. Grab a piece of fruit such as an apple, pear, or banana. Keep some almonds, sunflower seeds, and pistachios handy. Low-fat popcorn or sliced vegetables and hummus also make a great snack.

Could our own bacteria be helpful in cancer treatment?

Maybe, say researchers sponsored in part by the National Institute of Allergy and Infectious Diseases (NIAID).

Antibiotics are essential to prevent life-threatening and serious bacterial infections in patients undergoing cancer treatment. However, antibiotics also destroy "good" bacteria that prevent infections and enhance immune function.

Fecal microbiota transplantation, also known as FMT, is a new way to replenish "good" bacteria in cancer patients who require stem cell transplants, researchers found.

The process involved using a patient's own stool, known as autologous fecal microbiota transplantation, or auto-FMT for short. Before their stem cell transplantation, the patient's stool was frozen and reintroduced after the stem cell transplant was stable, with the objective of restoring good bacteria to their gut.

While the process might sound strange, it had promising results.

In the study, auto-FMT resulted in the recovery of beneficial gut bacteria to near-normal levels within days for patients. Under more traditional treatment, it can take several weeks for good bacteria to return to normal levels.

"This important study suggests that clinical intervention using auto-FMT can safely reverse the disruptive effects of broad-spectrum antibiotic treatment," says NIAID Director Anthony S. Fauci, M.D. "If validated in larger studies, this approach may prove to be a relatively simple way to quickly restore a person’s healthy microbiome."

The Human Microbiome Project was launched by the National Institutes of Health (NIH) in 2008. One main goal of the project is to create a large repository of the gene sequences of important microbes found in humans, helping biologists and clinicians understand the dynamics of the human microbiome and the relationship between the human microbiota and diseases. A network of labs working together has been compiling the data from swabs of several areas of the skin, gut, and mouth from hundreds of individuals.

One of the challenges in understanding the human microbiome has been the difficulty of culturing many of the microbes that inhabit the human body. It has been estimated that we are only able to culture 1% of the bacteria in nature and that we are unable to grow the remaining 99%. To address this challenge, researchers have used metagenomic analysis, which studies genetic material harvested directly from microbial communities, as opposed to that of individual species grown in a culture. This allows researchers to study the genetic material of all microbes in the microbiome, rather than just those that can be cultured.

One important achievement of the Human Microbiome Project is establishing the first reference database on microorganisms living in and on the human body. Many of the microbes in the microbiome are beneficial, but some are not. It was found, somewhat unexpectedly, that all of us have some serious microbial pathogens in our microbiota. For example, the conjunctiva of the human eye contains 24 genera of bacteria and numerous pathogenic species. A healthy human mouth contains a number of species of the genus Streptococcus, including pathogenic species S. pyogenes and S. pneumoniae. This raises the question of why certain prokaryotic organisms exist commensally in certain individuals but act as deadly pathogens in others. Also unexpected was the number of organisms that had never been cultured. For example, in one metagenomic study of the human gut microbiota, 174 new species of bacteria were identified.

Another goal for the near future is to characterize the human microbiota in patients with different diseases and to find out whether there are any relationships between the contents of an individual’s microbiota and risk for or susceptibility to specific diseases. Analyzing the microbiome in a person with a specific disease may reveal new ways to fight diseases.