Healthy Gut, Healthy You: A Personalized Plan to Transform Your Health

Written by Dr. Joseph Mercola Fact Checked

Story at-a-glance -

  • If your gut gets inflamed, the inflammation can spread throughout your entire body as it increases many inflammatory cytokines
  • Small intestinal bacterial overgrowth (SIBO) is a very common condition, and if you have it, many of the healthy interventions that are commonly recommended to improve gut health simply won’t work, and will likely make you worse
  • SIBO is caused by an overgrowth of bacteria in the small intestine. Oftentimes, a low-FODMAP diet, which is very low in prebiotic-rich vegetables and fruits that feed bacteria, will resolve the issue
  • Classic symptoms of SIBO include altered bowel function (constipation, diarrhea, or an oscillation between the two), abdominal pain, bloating or discomfort
  • What may appear to be nonceliac gluten sensitivity may actually be FODMAP sensitivity, or a histamine intolerance. Like a low-FODMAP diet, the low-histamine diet can seem paradoxical as it eliminates fermented foods, which are otherwise known to improve gut health

Dr. Michael Ruscio, author of "Healthy Gut, Healthy You: The Personalized Plan to Transform Your Health From the Inside Out," is a clinical investigator who focuses on gastrointestinal (GI) health. I first met Ruscio at Paleo f(x)™ this year in Austin, Texas, where we were on a panel together.

As for so many other health professionals, his career path was an outgrowth of a personal health challenge. Ruscio tells his story:

"In college, I was in pre-med, en route to go into conventional medicine. I actually wanted to be a surgeon. Unbeknownst to me, I ended up coming down with an intestinal parasite. Now, I didn't know I had a parasite. I found that out later. But the symptom that really knocked me down was debilitating insomnia.

If anyone has suffered from insomnia, they know how that can bring your life to a screeching halt. It's terrible; waking up every 45 minutes, [having a] very difficult time to go back to sleep. Therefore, I was tired the next day. I was having brain fog and bouts of depression, but no gastrointestinal symptoms.

I got plugged into the conventional system. I did some evaluations and all the doctors said I was healthy. I was left there with a number of symptoms that had no purported cause, and therefore no solution, so I turned to alternative medicine.

I actually ended up finding one of our mutual friends, Dr. Dan Kalish. He told me he thought I had a parasite. I remember thinking to myself, 'This guy is crazy.' I had never left the country. I had no digestive symptoms. I was only suffering from this insomnia, brain fog, depression and fatigue.

But I figured, 'What do I have to lose?' I did the stool test and determined I had a parasitic infection — a very pathogenic amoeba, Entamoeba histolytica … That taught me a few very important lessons early on in my career. One is that if you're treating symptoms, you're never going to get any better. Two is that a gut problem can manifest solely as nondigestive symptoms."

Gut Dysfunction Can Easily Lead to Systemwide Inflammation

In his book, Ruscio notes that gut dysfunction has the ability to create systemwide inflammation, meaning, if your gut gets inflamed, it can spread throughout your entire body as it increases inflammatory cytokines, including nuclear factor kappa-light-chain-enhancer of activated B cells (NF-ΚΒ). Ruscio explains:

"The connecting point to that is the fact that you have the largest density of immune cells residing in your small intestine. The small intestine, specifically, is where you absorb about 90 percent of your calories. [It's] this selective barrier between the outside world and the inside world.

Food essentially travels from the outside world through your body in this tube that is your digestive tract ... Part of the foodstuffs should be absorbed into your body. That very important selective barrier is predominantly your small intestine … The tool used to help prevent things from getting in that we don't want in[side] is your immune system.

It's a very immuno-active barrier that needs to be selective in letting food in but keeping pathogens out. Of course, when that barrier is malfunctioning, then you can have particles getting in that shouldn't get in. This is where the immune system has to come into play to clean up the mess.

This is likely why we see people who can eat a food and notice a symptom of inflammation in the brain, like brain fog, or inflammation in the joint, joint pain. Clearly, you can have neurological, rheumatological or even dermatological reactions from foods that don't agree with your gut, because of this very broad-acting inflammatory impact …"

How Gut Serotonin Impacts Health

It's widely known that the neurotransmitter serotonin is mostly produced in the gut. Serotonin is converted to tryptophan, then melatonin, so it's great for sleep. However, virtually none of the serotonin produced in your gut actually crosses your blood-brain barrier, so questions remain as to how gut serotonin might influence mental health.

What we do know is that there's a correlation between gut inflammation and mental health issues such as depression and anxiety, likely due to the gut-brain connection via the vagus nerve. Ruscio cites a recent study looking at patients with irritable bowel syndrome (IBS). They found that this IBS population, compared to healthy controls, had higher anxiety and depression scores, and increased fatigue.

"There's likely something going on that affects the brain that occurs in the gut, but whether it's direct or indirect," he says. "I'm not convinced it fully matters, at least not for the purposes of providing people with clinical recommendations … Looking at the observations and the interventions, it does seem here are neurological conditions associated with IBS."

Studies have also shown probiotics are effective against anxiety and depression. Regardless of whether serotonin is a key player in these mental health problems, serotonin serves an important function in your gut, and can be a culprit in some gut problems. Paradoxically, sometimes you may need to eat a diet that appears to be nearly devoid of healthy foods in order to address certain gut problems.

A low-fermentable oligo-, di-, mono-saccharides and polyols (FODMAP) diet, which is very low in prebiotic-rich vegetables and fruits that feed bacteria, has been shown to resurrect serotonin cell density in the gut, as well as peptide YY (PYY) cells in the gut, thereby helping patients to recover from digestive maladies such as SIBO. (PYY is a short amino acid released in your digestive tract in response to feeding, thereby lowering your appetite.)

"Serotonin regulates mortality and also regulates pain," Ruscio explains. "People who have gas pain and bloating, this may be part of the reason why a low-FODMAP diet helps with both of those symptoms."

Small Intestinal Bacterial Overgrowth

Small intestinal bacterial overgrowth or SIBO is a very common condition, and if you have it, many of the healthy interventions that are commonly recommended to improve gut health simply won't work. They'll actually make you worse.

"What happens in [SIBO], as the name kind of hints at, is you have an overgrowth of bacteria in the small intestine. What's interesting here is it's not an infection per se, because it's not bacteria that shouldn't be there. Oftentimes it's bacteria that's normal to the system. It's just overgrown.

In SIBO, our goal [is to re-establish a healthy balance]. One of the ways we can achieve that goal is by using a diet low in FODMAPS, which … essentially just means prebiotics … compounds that feed bacteria."

The classic symptom of SIBO is altered bowel function. Some will have constipation; others diarrhea, while some oscillate between the two. Abdominal pain, bloating or discomfort are also common telltale signs, and estimates suggest SIBO may be an underlying cause in a majority of IBS cases.

Interestingly, SIBO has also been linked to skin conditions such as rosacea, and neurological conditions such as restless leg syndrome. Treating SIBO has also been shown to improve rheumatoid arthritis, and studies have shown an association between SIBO and thyroid autoimmunity and/or hypothyroidism.

"This is where it gets challenging, because we can't put SIBO just in the digestive box," Ruscio says. "There may be someone who has a skin condition and a joint condition that is only attributable to their SIBO. I'd like to paint this perspective for people in terms of how to navigate this.

My philosophy is, once you've taken some steps to generally improve your diet and your lifestyle, if you're still floundering, I think the next best step for most people … would be taking steps to ensure you have optimal gut health. Because there's not necessarily a constellation of symptoms that would say you have SIBO or another gut condition. Rather, I look at it more as a sequencing maneuver."

How to Diagnose and Treat SIBO

According to Ruscio, a breath test is the best method of diagnosis. This involves eating a preparation diet the day before the test, and then collecting a series of breath samples after drinking a solution of either lactose or glucose. Breath samples are typically collected every 15 to 20 minutes for about three hours.

"Essentially, what we're looking for are the changes in the gas levels on those breath samples. Those can tell you if you have SIBO or if you don't have SIBO," he says. As mentioned, a low FODMAP diet — in which you specifically avoid most fruits and vegetables — is often prescribed to address SIBO.

"Every gut is an ecosystem. Every gut does not require the same inputs to thrive. This is one phase where that ecosystem requires a reduction of — at least temporarily — high-FODMAP foods to allow things to rebalance …

You can do [low FODMAP] plus or minus the rules of paleo, meaning if you're going to do a paleo, low-FODMAP diet, you'll have no grains and you'll have no dairy. Some people may prefer that, or some people may prefer the standard low-FODMAP diet, which allows some grains. There's a time and a place, I think, for each. But that's where you can start."

Alternatively, you can perform a urinary organic acid test, which tests for over 100 metabolites in your urine. There are a number of characteristics ones that show up if you have SIBO, so that is an alternative diagnostic strategy.

Gluten Sensitivity Versus FODMAP Sensitivity and Histamine Intolerance

It's worth noting that what may appear to be nonceliac gluten sensitivity may actually be FODMAP sensitivity, or a histamine intolerance. Histamine is a neuroactive compound. It's also a singling molecule for your immune system. And, like a low-FODMAP diet, the low-histamine diet can seem paradoxical, as it eliminates fermented foods, which are high in histamine, as are avocado, spinach and many fishes.

"Why this is important is because if we were living in an overly idealistic situation, then we could just wave a wand and say, 'OK, you're going to go grain-free, dairy-free, low-FODMAP, low-histamine and low-carb.' But if you actually have to do that, things become really challenging.

What I have been seeing in the clinic is patients coming in afraid of food … They come in afraid to eat anything. Some of these patients are literally making themselves sick because they're trying to adhere to two, three, four or five diet rules all at once. This is really pushing me to kind of open my mind a bit on grains.

I used to be much more antigrain. But noticing that some people had bigger dietary battles to fight, like FODMAPS and histamine — if they have to really focus on avoiding FODMAPS and histamine, we've got to give them some room somewhere else. For some, giving them some room to bring back grains into their diets actually is quite helpful …

I was eating, at one point, what I called the 'lazy man's paleo diet.' I'd have a can of tuna with an avocado. That's low-carb. It's quick and easy. I'd wash it down with some sauerkraut and a kombucha. And then at lunch I'd have spinach along with some salmon. A lot of the convenient paleo, low-carb foods are fairly rich in histamine.

I remember very distinctly being at my desk working one day — a beautiful sunny day, with no reason for me not to be happy — and I had this fog over me. I was very irritable.

I was thinking to myself, 'What the heck is going on?' It took me a couple of days to put it together, but I was eating a high-histamine food at every meal. I was just saturating my system with histamine. I just needed to make a simple change of spacing out those high-histamine foods."

In short, whether you're suspecting a nonceliac gluten sensitivity, a FODMAP sensitivity or histamine intolerance, the key is to find a diet that does not irritate your gut. For many, this might be a low-carb, paleo-type approach, potentially with a reduction of FODMAPS and/or histamine-rich foods.

"The nice thing about this is it only takes usually about two weeks to notice if one of these diets is working for you. This is what I walk people through in the book. 'OK. You start here. We'll give this diet a two-week trial, and then re-evaluate.'

You might be done with the diet at that point or you may have to make a tweak and give that another two weeks. It doesn't take long. But it's a series of self-experiments to see what works best for your system. And then once you're feeling well, you know you've gotten the diet that's the best for your unique gut ecosystem."

Acid Reflux May Be Caused by Either Excessive or Insufficient Stomach Acid

Another issue Ruscio discusses in his book is stomach acid. Most who have ulcers or acid reflux have too little acid, not too much, yet they're put on proton pump inhibitors (PPIs) or take over-the-counter antacids, which actually makes the problem worse.

When antacids were first introduced, they were very restricted and patients were told not to take them for more than two weeks. Now you can buy them without prescription and people stay on prescription PPIs for years on end.

"But there are a few important nuances here," he says. "Not everyone has low acid … and not everyone has high acid. You can look at context to help determine, 'Are you someone who should be on supplemental acid or not?'"

According to Ruscio, statistics suggest ulcers are more commonly associated with high acid than low acid, as 6.5 percent of the population has documented ulcers, whereas only 2 percent have documented low stomach acid. "So, there may actually be more people out there with high stomach acid than there are people with low stomach acid," he says.

Those With Anemia or Autoimmune Disease Are at Higher Risk of Low Stomach Acid

However, as Ruscio points out, there also are important nuances involved. For example, if you have a history of anemia or if you have an autoimmune condition, then your risk of low stomach acid is somewhere between 5 and 50 percent. "This doesn't mean that 50 percent of both anemias or autoimmune conditions will have low stomach acid. But you have a range from 5 to 50 percent," he says.

Age can further help you determine where you may fall in this range. Essentially, the older you are, the more likely it is you may have impaired secretion of acid, so you're more likely to have low acid and may do better with acid supplementation.

"There is definitely some nuance there. But it's also important to bear in mind that not everyone does better with acid. Clearly, there are people who do worse from stomach acid supplementation.

Part of the subset that does worse with supplemental acid production are people who have immune reactivity and this food-reactive and histamine-reactive sort of syndrome present, because histamine stimulates stomach acid.

This is why there's literally a drug class or a H2 antagonist, like your Pepcids, that actually block the histamine H2 receptor, and that actually lowers stomach acid.

There's definitely a subset of people who fall into this, [who] react to food and are histamine-intolerant … Giving them acid will make them worse. The answer there is not blocking acid. The answer is to remove the offending factor that's stimulating acid production. There is evidence showing that a low-FODMAP diet can lower histamine eightfold.

There's a number of people who likely have noticed that grains bother their reflux, dairy bothers their reflux, or maybe certain nightshades. Coffee and chocolate also are some foods that can be problematic. Just some simple observations of what your dietary triggers are can remove the stimulus that's causing you to overproduce acid."

Use Food Elimination Diets to Identify Your Acid Triggers

If you have acid reflux or ulcers caused by excess stomach acid and you're trying to wean yourself off antacids, H2 blocker or PPI, it's important to identify what's triggering the excess acid.

"There are a couple of different diets that people can try," Ruscio says. "In the research literature, they're known as either four-, six- or eight-food elimination diets … Essentially, you have to go through some kind of elimination and reintroduction of foods to try to determine what your provocating foods are.

To put it simply, if you want to start with the easier track, start with a six-food elimination or a paleo diet. If you want to start more aggressively, you can go up to a full eight-food elimination or an autoimmune paleo diet. But you're essentially removing foods that may be irritating your system and stimulating histamine. That stimulation of histamine is causing acid."

Some have theorized that SIBO may be a factor in reflux, either through immune system and histamine activation, or because of the gases produced by the overgrown bacteria. Those gases may push the lower esophageal sphincter open, allowing reflux to occur. Hence, a low-FODMAP diet may also be helpful.

"I know this sounds challenging, but we don't want to just say, 'Well, there are a couple of different dietary approaches. I'm not sure which one to do, so I'm just going to take a drug.' It's worse than going through a couple of short experiments to figure out which one of these diets will work well for you.

Because most likely, if you find out which diet works well for you and you resolve your reflux or your heartburn, you'll likely notice other improvements. Your joints may feel looser. You may have better mental clarity. It's worth the effort … Some people may have dysbiosis. SIBO is a type of dysbiosis or imbalance in the bacteria in your gut. Or there may be Helicobacter pylori.

This is where an herbal antimicrobial protocol, especially when paired with a probiotic, can be very effective. I lay this out in the book. If either of these syndromes are present, the book protocol will walk you through exactly how to execute. That can also be helpful."

Other commonsense strategies that can be helpful include inclined bed therapy and avoiding food at least three hours or more before bedtime. Antimicrobial herbs, or alternatively, probiotics, could also be considered.

"People are often looking for the magic product or the magic protocol. They almost never find them because there is no magic protocol. What there is, is a sound process … to rebuild your gut and to balance your gut health — devoid of dogma, devoid of marketing jargon … The magic is in the process, not necessarily in the product," Ruscio says.

Appropriate Use of Digestive Enzymes and Bitters

Digestive enzymes and bitters can also be useful adjuncts when trying to address various gut problems. "I use bitters more. I think bitters are great," Ruscio says. Part of why bitters are so beneficial is because they help repair your gut, and when that happens, the need for aids to increase digestive secretions lessens, as your gut lining produces a fair amount of the digestive enzymes required.

"There's less of a need for enzymatic and digestive support as I've gotten better at healing people's guts," he says. "But I do think, at least in the early phases of someone's healing, when perhaps they're not producing these enzymes as robustly on their own as they should, that using a small dose of hydrochloric acid, a little bit of bile and a blend of different pancreatic enzymes can be helpful."

As a general rule, if you respond positively to supplementation with enzymes, then that tells you that you need the enzymatic support. Over time, as your gut heals, you won't need as much (or any) enzymatic support, as your intestines will create the enzymes you need.

Pros and Cons of Bile Supplementation

As for bile, SIBO can deconjugate your bile, meaning it sort of deactivates it. In this case, eliminating SIBO will restore your ability to use the bile your liver makes. In the meantime, you may benefit from taking supplemental bile, such as ox bile. Keep in mind though that bile can function as a laxative.

"We published a case study a few months ago about a patient who was treated for SIBO … She came into our office for a second opinion. What was happening was people kept saying SIBO was the problem. But the diarrhea and the abdominal pain was solely caused by a reaction to supplemental bile.

She had been taking supplemental bile that had been irritating her gut, causing diarrhea. The only change we needed now was just to get her off of the [ox] bile. There's also a syndrome known as bile acid malabsorption, or bile acid diarrhea. Bile should be secreted at the start of the small intestine, and then it kind of trickles down the small intestine, helping you absorb fats.

At the very end, known as the terminal ileum, that bile is reabsorbed. If that bile does not get reabsorbed and makes its way into the colon, then it can function as an irritant and as a laxative. It's not to say that no one should use bile, but I'm a big advocate of finding the minimal effective dose."

More Information

As a general rule, once you start healing your gut, you should start feeling improvements in a couple of weeks to a few months. That said, some will respond within days, and be fully healed in weeks. It really all depends on what your problem is, and how severe the dysfunction. As noted by Ruscio:

"There's more going on than just the intestinal cells repairing. There are the intestinal cells. There's the local immune system. There's the microflora and the balance of the microflora. All of these things have to kind of integrate. Some of these things feedback on each other.

I should mention, be careful with what you read about SIBO, because some circles would have you believe SIBO is this chronic condition that you can never heal … That's not true for the vast majority of people. The prognosis is much more hopeful for healing the gut than most people realize. Healing can occur within weeks to months for the majority of people."

To learn more, be sure to pick up a copy of "Healthy Gut, Healthy You: The Personalized Plan to Transform Your Health From the Inside Out." It's filled with helpful advice for those struggling with gut issues, including more in-depth details on the topics covered in this interview.