The Microbiome Connection

1. IBS and SIBO: You're Not Alone, and You Can Improve

If you come away with only one notion from this book, let it be optimism!

IBS is common. Irritable Bowel Syndrome (IBS) affects millions, with about 11% of the world's population experiencing its symptoms. In the United States, it's estimated that 10 to 15 percent of the population has IBS, making it the most common gastrointestinal disorder. This means that if you're reading this on a bus or train, statistically, one in seven of your fellow passengers likely has IBS.

IBS is costly. The economic and social costs of IBS are significant, with those coping with the condition often missing days of work or school. IBS costs American society more than $21 billion a year in lost productivity at work and in medical expenses, with 13 percent of IBS patients missing at least one day of work or school per month due to their symptoms.

IBS is manageable. Research into IBS, gut motility, the gut's immune system, and the vast inner workings of the gut's microbiome has been groundbreaking. Many, if not most, IBS patients can find partial or complete relief from this often-debilitating disease. With proper diagnosis and treatment, IBS gut pain can be alleviated, leading to an improved quality of life and the ability to engage successfully at work and lead full, active lives.

2. Understanding Your Gut: A Step-by-Step Guide

When you think about eating, your brain tells your gut, “Get ready, food is coming.”

The digestive system is complex. The gut is not just a simple tube that absorbs food, breaks it down, and turns it into waste. It's far more complex, as it's associated with many functions and diseases. The hollow organs that make up the digestive system include the mouth, esophagus, stomach, small intestine, large intestine, and anus.

Each organ plays a role. The mouth starts the process with saliva, the esophagus actively transfers food to the stomach, the stomach grinds the food, the small intestine digests and absorbs, and the large intestine absorbs water. The pancreas, liver, and gallbladder are solid organs of the GI tract, and we will take a look at the appendix as well. Each organ can contribute to bloating, pain, vomiting and diarrhea, or constipation, depending on the disease.

Motility is key. Digestion requires constant, synchronized contractions of the various gut muscles to control the movement of food through the gastrointestinal tract. These contractions are known as gut motility. Motility problems can develop when the nerves and/or muscles of the gut are not working properly. Abnormal gut motility can lead to bloating, pain, nausea, and diarrhea or constipation, all of the symptoms related to IBS.

3. The Gut Microbiome: Your Second Self

We cannot fathom the marvelous complexity of an organic being Each living creature must be looked at as a microcosm—a little universe, formed of a host of self-propagating organisms, inconceivably minute and as numerous as the stars in heaven.

Microbiome's vast influence. The gut microbiome is a vast ecosystem of bacteria, viruses, fungi, and protozoa that can potentially be considered a completely separate organ in the body. This delicate ecosystem can be thrown out of balance, however, and may worsen or lead to chronic diseases such as heart disease, diabetes, and cancer.

Microbiome's components. Your microbiome contains five specific components that promote health and ward off disease: diversity of bacteria and fungi in the gut, distribution of bacteria and fungi, number and composition of bacteria, products of bacteria, and resiliency. A more diverse gut microbiome can lead to a more robust, adaptable immune system.

Microbiome's uniqueness. There's no single normal profile of gut microbiome. Your microbiome is unique to you. There are common classic patterns, but each of us has a distinct microbiome. Your diet, environment, medications, and genetics influence your microbiome, and even your pets can affect your microbiome!

4. Food Poisoning: A Surprising Cause of IBS

Our intent is not to restrict you from traveling or suggest you stop eating in restaurants.

Food poisoning and IBS. One out of nine people who experience food poisoning go on to develop IBS. Food poisoning can introduce harmful pathogens into the microbiome and cause IBS, even many years later. It's also possible that many IBS cases may be secondary to food poisoning or parasitic infections.

Autoimmunity's role. Autoimmunity can be part of this post-infectious disease. An autoimmune disease is best described as a condition in which the immune system mistakenly attacks healthy cells in the body. This concept of autoimmunity in IBS also explains why IBS appears to be more common in women than men, because women are more prone to autoimmune diseases.

IBS blood test. By measuring the specific antibodies to CdtB and vinculin in the blood, we were able to diagnose IBS. This breakthrough led to the first blood test for IBS. If the test is positive, you know you have IBS, which is a real disease that can be caused by food poisoning.

5. SIBO: Symptoms, Diagnosis, and the Breath Test

Many IBS patients like Jennifer have unrecognized SIBO, causing them to suffer through long periods of pain, bloating, and distension, along with the frustration of not having the appropriate treatment.

SIBO and IBS. Up to two-thirds of IBS patients have SIBO. The name of your disease might be IBS, but SIBO is more often its cause. Food poisoning is the most common path to SIBO, but as you'll discover in this chapter, a bowel blockage or any condition that slows down the gut can also cause SIBO.

SIBO definition. SIBO occurs when there are greater than 1000 bacteria per milliliter (>103/mL) in the small intestine. In SIBO, this excessive quantity of bacteria is not an infection, but rather an over-colonization of specific bacteria in an area where they don't belong. The bacteria aren't invading or attacking you; they are your own resident bacteria.

SIBO diagnosis. The primary—and easiest—method of diagnosing SIBO is through a breath test. During the breath test, you'll be asked to give a baseline breath sample and then ingest a sugar substance such as lactulose or glucose. Subsequent breath samples taken every 15 minutes determine if the sugar has been adequately digested by you or by microorganisms in your gut.

6. Three Pillars of SIBO Management: A Comprehensive Approach

The first step in treating SIBO is to understand that SIBO is not a primary disease; in fact, SIBO is a secondary phenomenon that’s caused by other diseases.

Three pillars of SIBO management:

• Identify the cause of SIBO
• Treat the SIBO
• Use techniques (diet, drugs, and others) to maintain control or prevent recurrence of SIBO

Antibiotics for SIBO. The most studied antibiotic for IBS and SIBO is rifaximin. The advantage of rifaximin is that 99.6 percent stays in the gut and is not absorbed by the rest of the body. Rifaximin is FDA-approved for treating IBS with diarrhea.

Prokinetic drugs. After you've successfully removed the imbalance in your microbiome or eliminated excessive bacteria, how do you maintain it? There are drug therapies that can stimulate these cleaning waves, called prokinetic drugs, "pro" for promoting and "kinetic" for movement. That's exactly what they do—promote movement of the gastrointestinal tract.

7. Low-Fermentation Eating: A Diet for IBS and SIBO

With low-fermentation eating, you should be able to travel, and you can go to a restaurant and find food you can eat on almost any menu.

Low-fermentation eating rules:

• Restrict products that contain high levels of carbohydrates or ingredients in food that humans can’t digest, and therefore are digested by bacteria.
• Space meals four to five hours apart.

Foods to avoid. At the top of the list of foods to avoid are non-absorbable sugars, such as sucralose, sorbitol, lactitol, xylitol, and mannitol. Humans can’t digest these artificial sweeteners, and therefore 100 percent of their calories are available for bacteria to digest. Non-digestible sugars will always cause bloating.

Time your eating. We can’t emphasize enough the importance of keeping the gastrointestinal tract’s cleaning waves intact on a regular basis. These cleaning waves (as mentioned in previous chapters) keep the small bowel clean, and they reduce bacteria therein. We recommend waiting four to five hours between each meal as part of low-fermentation eating.

8. Beyond the Basics: What to Do When You're Still Not Better

When we get to this point, depending on your symptoms, we use a more in-depth history and physical examination to pick up clues that you may have something besides IBS or SIBO, or a concomitant factor that adds to your scenario.

Peppermint for IBS. Peppermint has been known to help IBS symptoms for some time, and we’ve seen it work for our own IBS patients. By relaxing the gut muscles, it can relieve cramping.

Serotonin blockers. The 5-HT3 receptor antagonists, also called serotonin receptor antagonists or serotonin blockers, are in a class of medicines that are used for the prevention and treatment of nausea and vomiting caused by chemotherapy, radiation therapy, or post-surgery. An oral version of these drugs can also be used for gastrointestinal problems. The drugs help some patients with IBS diarrhea because they slow down the gut.

Antihistamines. Occasionally, bowel sensitivity is due to the hyperactivity of mast cells and other allergy-related cells. If you can’t decrease your symptoms by modifying your microbiome, adding antihistamines to your treatment may help.

9. Probiotics, Prebiotics, and Fecal Transplants: What's the Evidence?

The notion that probiotic supplements would benefit IBS patients began in the 1980s, and the probiotics frenzy continued through the 2000s.

Probiotics challenges. The two most popular forms of probiotics are Lactobacillus acidophilus and Bifidobacterium bifidum. Some tests of stool samples show lesser amounts of lactobacillus and bifidobacterium in IBS patients as compared with healthy people. Probiotic proponents have seized on these findings as evidence that IBS and other gastrointestinal disorders, including bacterial overgrowth, are due in part to deficiencies in one or both of these two types of bacteria.

Prebiotics and synbiotics. Prebiotics are usually composed of dietary fiber that is designed to feed the bacteria in your gut. A combination of probiotics and prebiotics is called synbiotics because they form a synergy of both. The idea behind synbiotics is that adding prebiotics to a probiotic supplement can help ensure that the digestion-friendly microorganisms arrive in the gut alive and well.

Fecal transplant. A fecal transplant is the transplantation of feces from a healthy donor into another person to restore the balance of bacteria in the gut. Fecal transplant works particularly well to treat Clostridioides difficile infection; in fact, the FDA has approved fecal transplantation for the treatment of recurrent Clostridioides difficile.

10. Myth Busting: Separating Fact from Fiction in IBS and SIBO

Every IBS patient struggles with the emotions of living with IBS, and we don’t dismiss anyone’s feelings.

Myth #1: SIBO is not a real medical condition. This is false. Most gastroenterologists recognize the role of bacterial overgrowth in IBS.

Myth #2: Stomach acid can be replaced with oral supplementation. This is false. Taking a few tablets of hydrochloric acid doesn’t make physiologic sense as SIBO treatment.

Myth #3: IBS is more common in women because they have a lower threshold for pain. This is false. IBS is not a female disease, and has nothing to do with pain tolerance.

Last updated: February 25, 2025