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Bugs in the system: healing IBS naturally

Reading time: 5 minutes

Dr Jenny Goodman solves a patient’s irritable bowel syndrome with a gut-friendly diet and healing herbs and supplements

Gerald, 36, came to me distressed and embarrassed about his gut. He had painful diarrhea and constipation, usually alternating but sometimes both at once, which were seriously disrupting his life.

His doctor had diagnosed anxiety, prescribed antidepressants and recommended a relaxation tape. The antidepressants had made him feel dreadful (and he wasn’t depressed), and the tape had just irritated him. Neither had helped his gut. He was really anxious, however. Of course he was—he never knew when he’d have to rush to a toilet.

It is true that anxiety can exacerbate irritable bowel syndrome (IBS) and trigger an attack, but it is rarely the root cause.

Good vs. bad bacteria

IBS is the body telling us that all is not well with the microbiome, the trillions of microbes that should occupy the colon in symbiotic harmony with us. Symbiosis is a process of “You scratch my back, and I’ll scratch yours.” These tiny bugs digest fiber, turning it into all sorts of goodies for us: vitamin K, B-vitamins like biotin, and crucial short-chain fatty acids like butyric acid. They support our immune function, mental clarity and digestion and generally keep us healthy. What’s not to like?

But, increasingly these days, our gut bacteria get out of balance. Gerald’s stool test showed too few of these friendly, helpful bacteria and an overgrowth of unfriendly bacteria and yeasts (single-celled fungi) that should be a tiny fraction of the creatures in there.

There are several reasons this happens. First, excess sugar intake feeds the wrong bugs and distorts the microbiome. Gerald’s diet diary showed not only sweets but also sources of hidden sugars like processed foods, most of them savory but still full of sugar if you check the ingredients list, which he hadn’t. Dextrose, maltose, sucrose, fructose, lactose, glucose, maltodextrin—they’re all sugar. Gerald was often in a hurry, grabbing breakfast and lunch on the run.

Another factor that damages the microbiome is antibiotics. To treat frequent childhood ear infections and bouts of tonsillitis, Gerald had been given numerous courses of antibiotics. He had also had two chest infections in recent years and again had been given antibiotics.

A sample had never been sent to the microbiology lab for testing to choose the best antibiotic to target the infecting organism. His doctors had just prescribed broad-spectrum antibiotics, which kill a wide range of bacteria, including the essential friendly ones in the gut. When this happens, unfriendly bacteria and fungi take over.

Gut response

It took a while to persuade Gerald to change his diet and cut out all sugar. It involved putting real food in as much as taking the bad stuff out, and that is always challenging for a busy person. But with the help of his wife and his desperation to fix his symptoms, he did manage it.

He noticed improvement within a few months, but cutting out sugar is only the first stage of restoring gut health. Having stopped feeding the bad bugs, we needed to put in some good ones.

So, I prescribed a series of probiotics. It’s important not to get stuck on one brand; we want to imitate nature by cultivating biodiversity in the gut. So, I asked him to rotate brands every four to six weeks (see chart, below, for my preferred products, but there are many other good options). Again, there was further improvement, but not a cure.

The next stage was to attack the unfriendly bacteria and fungi. I started with the gentlest remedies: caprylic acid from coconut, grapefruit seed extract and good old raw garlic (one crushed clove daily with food). After a few weeks, I tested some herbs (see chart, below).

These herbs are powerful and need to be introduced one at a time in slowly increasing doses. Otherwise we risk “die-off,” also known as the Herxheimer reaction, when the unfriendly bugs release their waste products as they die off en masse, making you feel dreadful. So, you have to go slow, and you have to have already “prepared the ground” by cutting out sugar and introducing probiotics before you zap the baddies with these herbs.

By the time we were nearing the end of our herbal treatments, nine or 10 months after his first visit, Gerald’s bowel function was 90 percent recovered. He was fine 90 percent of the time but occasionally had an unexpected attack of diarrhea. We traced this eventually to a food intolerance to raw tomatoes. It hadn’t been a problem before his IBS began five years before.

What happens is unfriendly yeasts that overgrow in the gut change form and produce long filaments that can puncture the gut lining. This leads to “leaky gut” in the small intestine, allowing incompletely digested food particles into the bloodstream, where they produce immune responses—allergic reactions. A food that is harmless when fully broken down causes problems when the gut is leaky.

Leaky gut was, until recently, completely denied and disdained by the orthodox medical establishment. Once someone thought to call it by the more scientific-sounding term “intestinal hyperpermeability,” suddenly it was mainstream and cool.

The final stage of Gerald’s treatment was treatment with substances that let the gut lining heal once the unfriendly fungi are gone: glucosamine, slippery elm, liquorice extract, marshmallow and aloe vera.

After a few months, his treatment was complete. Now he is fine as long as he sticks to the program, which is 99 percent of the time. He can even eat raw tomatoes again, in moderation. On the rare occasion he eats cakes or other sweet stuff, he suffers the next day. I find that such lapses get rarer with time as people’s bodies learn not to crave the stuff that makes them ill.

For Gerald, swapping sugar for a happy gut was certainly worth it.


Gerald’s herbs and supplements plan

I used the herbs and supplements below in combination to help heal Gerald’s gut, but it’s best to get a personalized prescription from a qualified practitioner.


Supplement/herb Preferred products Suggested dosage
Probiotics BioKult Advanced Multi-Strain Formula
Metabolics Combocillus Optibac (all varieties)
Kiki’s Soil-Based Organisms
Follow label instructions
Caprylic acid BioCare Caprylic Acid (672 mg per capsule)


One capsule daily for a week, then two daily for a week, then three daily for the following weeks
Grapefruit seed extract BioCare Biocidin Forte (150 mg per capsule) or
liquid grapefruit extract (36 mg per 3 drops)
Follow the label instructions
Oregano oil, red thyme oil, artemisia, goldenseal root, black walnut, berberine Can be prepared by a medical herbalist in tailored combinations or found in commercial formulas:
Nutri Advanced Berberine + Grapefruit Seed
Nutri Advanced CandiBactin
Follow the recommendations of a medical herbalist or, if using a commercial formula, build up gradually to the dosage on the label
Slippery elm, marshmallow extract, liquorice extract BioCare Slippery Elm Intensive (powder) 3 g daily mixed into yogurt
Glucosamine Allergy Research Group Perm A vite (powder); also contains slippery elm (and other gut-healing ingredients), so can be used instead of BioCare Slippery Elm, but contains stevia, so may be too sweet Follow label instructions
Aloe vera Fushi Organic Aloe Vera Juice Follow label instructions



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