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Invasion of the bad bugs
Doctor Detective with Bryan Walsh


The gastrointestinal tract is one of the most important systems in the body. When our stomachs aren’t happy, neither are we. In this case study, Dr. Detective learns that while taking probiotics can help restore bacterial balance, sometimes it’s not enough to ensure gut health and function.

Eat less and exercise more. It’s generally a great prescription for improving health and improving body composition. However, it doesn’t always work.

Even with an awesome exercise plan and a rock-solid diet, some people suffer from mysterious symptoms and complaints that seem puzzling, given how much effort they put into their fitness and health.

When we meet clients who have problems that exercise and nutrition — not to mention their own doctors — can’t seem to solve, we know there are only a few experts on the planet to turn to. One of them is Bryan Walsh.

Dr. Walsh has a sharp mind, a fitness background, a degree in naturopathic medicine, and extensive additional training and certifications. His wife is a naturopath too. (We bet his kids are the healthiest on the planet.)

When tough cases arise, Dr. Walsh turns from mild-mannered dad and husband into forensic physiologist. He pulls out his microscope, analyzes blood, saliva, urine, lifestyle – whatever he has to, in order to solve the medical mystery.

When Dr. Walsh volunteered to work on a regular case study feature with us, we jumped at the chance. By following along with these fascinating cases, you’ll see exactly how a talented practitioner thinks. You’ll also learn how to improve your own health.

In today’s case study, we meet a young man whose poorly defended stomach was no match for a tripartite army of bacteria, fungus, and parasites.

The gastrointestinal tract is one of the most important systems in the body. Gut problems can cause a host of seemingly unrelated symptoms and make a profound difference to our health and body composition.

In fact, some experts suggest that the microbes found in our gastrointestinal system, called our microflora or microbiome, affect our physiology as much as our own human cells do!

Lots of things can go wrong in the gut, but here are the most common — and often inter-related — issues:

  • poor digestion and absorption of nutrients
  • microbial infection or imbalance
  • inflammation

The client

Steve, a 26 year old male, was referred to our office for a wide variety of symptoms. Over the past few years, he’d seen a number of practitioners.

But his symptoms weren’t diminishing. In fact, some were getting worse.

Steve had seen so many doctors and had researched his problems so thoroughly that he didn’t want to fill out our standard intake forms. Instead, he asked if we could talk about his medical history over the phone before he came in.

As you can see from the picture below, Steve was a bit of a detective himself when it came to his own case.

Considering the evidence already at hand, I asked him to send over any labs he had, and agreed to a short initial consult.


The client’s signs and symptoms

Steve had been experiencing a variety of signs and symptoms for a few years, including, but not limited to:

  • food intolerances, including eggs, dairy, lettuce, processed meat, and chocolate;
  • constipation, gas, bloating, and excessive burping;
  • chronic sinusitis;
  • depression, especially when stressed;
  • low back pain;
  • respiratory issues, including shortness of breath; and
  • generalized fatigue.

He’d been diagnosed with a mononucleosis infection and treated with numerous rounds of antibiotics.

Steve had also taken a couple of other medications during the past year, including acid blockers for heartburn symptoms and nasal steroids for chronic sinusitis.

Together, Steve’s symptoms pointed to some kind of gastrointestinal dysfunction, including possible GI infection and immune system involvement. He’d figured out as much himself.

But what, exactly, was going on? Time for Dr. Detective to get to work.

At this point I didn’t want to re-run more liver tests. I was certain that his liver wasn’t the problem.

The tests and assessments

Blood chemistry panel

Steve sent over his earlier labs, including a salivary adrenal hormone test and a blood chemistry panel.  These tests revealed a few things about Steve:

Marker Result Lab reference range Thoughts
Hemoglobin 15.1 g/dL 14.0-15.0 High-normal – usually dehydration and/or elevated testosterone
RBC 5.21 x10^12/L 4.2-4.9 Elevated – usually dehydration and/or elevated testosterone
Magnesium .79 mmol/l .79-1.00 Borderline low – many potential causes
WBC 3.11 x10^9/L 5.0-8.0 Low – possible chronic immune system involvement
Lymphocytes 47% 20-40% Borderline high – possible viral infection, autoimmunity, other inflammatory process
Phosphorus 0.70 mmol/L 0.87 – 1.45 Low – possible vitamin D deficiency, protein digestion or malabsorption, elevated calcium
Total cholesterol 92 mg/dL 150-200 Low – liver dysfunction, malnutrition, chronic inflammation and/or infection
LDL cholesterol 31 mg/dL <120 Low – similar reasons as low total cholesterol
HDL cholesterol 50 mg/dL >50 Elevated (relative to total levels of cholesterol) – inflammation

Steve also showed low morning and afternoon cortisol. This could indicate an adrenal problem, but in Steve’s case, given the other markers of immune system involvement, I suspected that his immune system was suppressing cortisol production.



The test results

Blood chemistry panel

Steve’s blood panel gave me enough evidence to believe that a stool panel could be another helpful test.

What, exactly, was going on inside Steve’s gut?



Wow. Steve was suffering from a number of fairly significant gastrointestinal infections. Any or all of them could be contributing to his symptoms.

Let’s look a little closer at these findings.

The perfect storm of stomach issues

First, he showed high levels of Mycoplasma Sp., one of the smallest, self-replicating bacteria known in microbiology.  Gastrointestinal mycoplasma infections are associated with a number of different conditions and symptoms.

Next, Steve’s Lactobacillis and Bifidobacter bacteria, also known as probiotics, were normal, likely because he was taking a probiotic product during the time of this test.

Note: We’re often told that taking probiotics is important for gastrointestinal health. This is generally true, and it’s a good idea to take your probiotics. But probiotics aren’t magic; they don’t give you complete immunity against other gastrointestinal problems.

Steve’s test also indicated that he had a Helicobacter pylori infection. H. pylori is a pathogenic bacteria that commonly infects the stomach.

Not only that, but he also had a fairly significant fungal/yeast infection, and a possible parasitic infection.

Bacteria, yeast or fungus, and parasites? Talk about a triple whammy! No wonder he wasn’t feeling too hot.

But to my detective’s eye, these findings were not all that surprising – especially given Steve’s history of antibiotic and acid blocker use.

The role of antibiotics and acid blockers

While antibiotics alter the microbial balance of the gastrointestinal system, they don’t affect parasites or fungus/yeast. So antibiotics kill the good stuff, potentially leaving bad stuff to flourish and even proliferate.

Meanwhile, one of the functions of hydrochloric acid in the stomach is to sterilize our food. Taking acid blockers (as Steve was) might help to settle his discomfort. But in the long run, a low-acid stomach environment let all kinds of pathogens get through.

In fact, many people who take antacids or acid blockers, as well as many older people, have problems because they don’t produce enough stomach acid — rather than too much.

Steve’s stomach’s not so strange

This might sound like a lot. But Steve’s findings are not at all unusual.

Many people unknowingly suffer from some type of gastrointestinal infection, putting up with symptoms like his because they have no idea they might feel any different or any better.

The prescription

Steve showed up with a lot of different symptoms, but given the battle raging in his belly, we decided to focus on his gastrointestinal dysfunctions.

The 4-R protocol

We recommended a “Four-R” protocol:

  • Remove – infections, food sensitivities, and anything else causing inflammation in the GI system.  Often this means trying an elimination diet and adding anti-microbial compounds.
  • Replace – things normally found in the GI tract, which may be somewhat deficient. This might mean adding digestive enzymes and hydrochloric acid.
  • Repair – the gut mucosa with nutrients known to support proper enterocyte (gut cell) function.
  • Re-inoculate – using probiotics.

The outcome

A few weeks into the program, most of Steve’s symptoms  — including gas, burping, and bloating – had almost disappeared. He had more energy and was more able to focus and concentrate.

Even his breathing felt better, though his sinus troubles had not completely resolved.

While I was pleased with Steve’s progress, the detective in me wasn’t completely satisfied. I’ll be running more tests to see what other underlying problems they might reveal.

Summary and recommendations

So what can we take away from Steve’s story?

  1. All body systems depend on good gastrointestinal function. This includes optimal digestion and absorption of nutrients as well as proper microbial balance.
  2. Gastrointestinal infections are more common than many people realize, and can cause a host of seemingly unrelated symptoms.
  3. Taking probiotics is likely important, but does not completely immunize you against other gastrointestinal infections.
  4. Address all levels of gastrointestinal physiology — from bow to stern — to properly restore gut function.
  5. Common medications — such as antibiotics, acid blockers, and antacids — can, if used chronically, disrupt the delicate chemical ecosystem of the GI tract. Use them sparingly.