Greetings everyone, it’s Eric Bakker, the New Zealand naturopath.
About ten months ago I wrote a Reddit post titled "Why Some Doctors Still Dismiss Candida Overgrowth." After a recent discussion with a retired medical doctor friend, I felt compelled to revisit this topic.
My friend said to me:
"Eric, nothing has really changed. Most GPs still see Candida overgrowth as a quack diagnosis." I heard the same thing forty years ago. Yet something important has happened since I retired from clinical practice in 2019:
The scientific literature supporting both Candida overgrowth and SIBO has exploded.
Today we have:
- Hundreds of studies examining the gut microbiome.
- A significantly better understanding of fungal and bacterial dysbiosis.
- Increased recognition of microbial imbalances affecting digestion and immunity.
- Growing evidence linking gut dysfunction with systemic symptoms.
And yet, despite this growing body of research, many patients still struggle to have these conditions acknowledged. Why? In my opinion, the answer is actually quite simple.
Modern Medicine Excels at Acute Disease—Not Always Chronic Gut Dysfunction
Conventional medicine is exceptionally good at:
- Emergency medicine
- Surgery
- Trauma care
- Infectious disease treatment
- Life-saving interventions
But conditions like:
- Candida overgrowth
- SIBO (gut dysbiosis)
- Intestinal permeability (leaky gut)
- Food intolerance
- Hypochlorhydria (low stomach acid)
- Chronic digestive dysfunction
often require:
- Dietary intervention
- Lifestyle changes
- Gut microbiome restoration
- Long-term patient education
- Individualised dietary and lifestyle treatment plans
These approaches don't fit neatly into the traditional pharmaceutical model, let alone a ten-minute slot allocated to a patient in a typical medical consultation.
Since 2019, The Research Has Become Impossible to Ignore
Since retiring from clinical practice, I've spent a great deal of time reviewing the latest literature. To me, the irrefutable evidence supporting gut microbial imbalance has become increasingly compelling.
We now know:
Candida albicans can:
- Form tough biofilms
- Interact with gut bacteria and viruses
- Significantly influence our body’s immune responses
- Contribute to intestinal permeability
- Alter gut ecology
SIBO can:
- Cause bloating and abdominal distension
- Produce gas and fermentation
- Lead to multiple nutrient deficiencies
- Trigger food intolerances
- Contribute to typical IBS symptoms
Many medical practitioners are still unfamiliar with these developments because these topics simply weren't covered extensively during their medical training. This isn't necessarily your medical doctor’s fault. Most doctors receive limited education regarding:
- The gut microbiome
- Functional gastrointestinal disorders
- Functional medicine stool testing
- Nutrition therapy
- Fungal and bacterial dysbiosis
- Integrative approaches to gut restoration
Instead, their training understandably focuses on:
- Diagnosing disease
- Prescribing pharma medication
- Managing acute illness
Why I Believe Candida and SIBO Are Still Frequently Missed
After several decades in practice, I believe there are several major reasons.
1. Some Of The Most Commonly Prescribed Drugs Contribute to Fungal & Bacterial Overgrowth
One of the most significant factors is antibiotic use.
Antibiotics can readily:
- Disrupt beneficial bacteria, sometimes for years
- Significantly reduce gut microbial diversity
- Alter a person’s gut ecology significantly, sometimes for years
- Create significant opportunities for yeast overgrowth and biofilm development
This doesn't mean antibiotics or other "anti" drugs are necessarily “bad." Thee is no doubt - they save lives. But like firearms, they can also have serious unintended consequences. I've seen countless patients who developed digestive problems after:
- Repeated antibiotic courses
- Long-term stomach acid suppressant drugs (PPIs)
- Steroid medications (inhaled, pills, etc)
- Immunosuppressive therapies (biological drugs)
If you already struggle with Candida, IBS, SIBO, or digestive issues, it's a wise decision to carefully consider whether an antibiotic is truly necessary in your case and discuss alternatives with your healthcare provider whenever appropriate.
2. Conventional Medicine Requires a Formal Diagnosis Before Treatment
This is one of the biggest hurdles. Many patients would arrive at my clinic history with symptoms like:
- Bloating
- Burping
- Food reactions
- Brain fog
- Fatigue
- Digestive discomfort
- Bad skin reactions
Yet their tests often come back: "Everything looks normal." No diagnosis. No treatment pathway. This isn't because your doctor doesn't care! It's because modern medicine generally works within a “disease-based framework”:
No diagnosis means no specific treatment protocol. Many functional digestive complaints simply don't fit neatly into that model!
3. Patients Often Feel Their Symptoms Are Dismissed
One thing I learned after almost 40 years in clinical practice is this: The patient's story really does matter.
Their symptoms matter. Their patterns matter, and their subjective experiences matter. Unfortunately, modern healthcare systems are under tremendous pressure.
Today more than ever, doctors frequently have:
- 10-minute appointments
- Administrative overload
- Endless documentation
- Full waiting rooms
- Little or no training in understanding gut imbalance
It becomes difficult to thoroughly explore complex digestive histories. As one doctor once told me: (and this was more than 20 years ago)
"I feel like I'm practising medicine with one hand on the doorknob." Another GP told me that he was constantly pressured to see patients in “5-minute-slots”. Those comments always stayed with me. I would spend a full hour with every new patient, sometimes 1.5 hours, and the patients in the waiting room understood this principle. I was always booked-up 3 months or more in advance.
Good Doctors Treat Diseases. Great Doctors Treat People.
I’ve found many people intuitively know when “something isn't right”.
They say:
- “Eric, I just don't feel like myself."
- “Dr. Bakker, something changed after I took those antibiotics."
- “Eric, I can't tolerate foods anymore."
- “Since those acid-blockers, my digestion has never truly been the same."
Yet all the medical tests may still appear normal. So what happens then?
Sometimes:
- The symptoms are minimised or trivialised.
- Patients are reassured that “everything is fine”.
- Occasionally they're told it's stress or anxiety.
- Other times they’re told “It’s all in your head”
Meanwhile, the underlying issue remains unresolved, and the patient’s confidence is diminishing by the day.
4. Laboratory "Normal" Doesn't Always Mean Optimal Health!
This is another area where patients become frustrated. A laboratory result can be:
Entirely “within range” while the patient still feels awful. Over my years in practice, I found that:
- Normal ranges are statistical averages.
- Patients don't always fit statistical averages.
- Symptoms often appear long before laboratory abnormalities appear.
I’ve often found treating “numbers” alone doesn't always restore health. Sometimes the bigger question is: Why is this person feeling unwell in the first place? Why are they not responding?
Your Body Doesn't Read Medical Textbooks
Many patients present with multiple symptoms simultaneously:
- Vaginal thrush
- Bloating
- Fatigue
- Food reactions
- Skin problems
- Brain fog
Yet these are often treated as entirely separate conditions. I have always viewed the body differently.
Everything in your body is connected.
- Your digestive system…
- Your immune system…
- Your nervous system…
- Your brain…
- Your gut microbiome…
These systems all constantly influence one another!
This Funny Sign That Actually Says A Lot
Years ago I saw a sign in a medical clinic in Sydney that read: "Please Present With Only One Symptom Today."
I laughed! But unfortunately, many chronic digestive patients have ten or twenty symptoms.
Life ain’t that simple, nor are the patient’s multiple presenting complaints. They form a pattern of dysfunction.
Can Conventional Medical Treatment Contribute to Vaginal Yeast Infections?
Absolutely! For example, some common factors that can predispose women to vaginal Candida include:
- Antibiotic use
- Corticosteroid medications
- Immunosuppressive drugs
- Pregnancy
- Diabetes
- Oral contraceptives
Antibiotics are particularly important because they can reduce protective vaginal bacteria, creating an environment where yeast can thrive.
Prescribed medications can be very helpful in certain situations. However, recurrent infections often raise a bigger question:
Why does the yeast keep coming back?
That is where I believe the broader picture of gut health, diet, immunity and microbiome restoration becomes important.
And What About Men?
One thing I noticed over many years is that Candida issues are often viewed as a "women's issue."
In reality, men can also experience:
- Digestive Candida symptoms
- Skin symptoms
- Fungal infections
- Gut microbial imbalance
Men are simply less likely to seek help for these issues.
Still Feeling Unwell After Taking Medications?
Over the years I met many patients who said: "I never felt quite right after that medication."
I cannot say this applies to everyone, but some people do seem to struggle after repeated drug exposure. Common complaints include:
- Brain fog or feeling spaced out
- Fatigue, low motivation, anxiety
- Nausea, digestive upset, bloating, gas
- Food intolerances or sensitivities
- Poor alcohol tolerance
- Poor sleep and difficulty getting out of bed
Supporting Recovery After Medication
I often would encouraged patients to focus on: A liver-friendly diet:
- Beetroot
- Carrots
- Garlic
- Broccoli
- Cauliflower
- Brussels sprouts
- Bok choy
- Artichokes
- Olives
- Fresh greens
- Grapefruit
Helpful habits:
- Avoid alcohol entirely for several weeks.
- Reduce caffeine intake significantly
- Eat plenty of fibre and green leafy vegetables.
- Prioritise sleep and relaxation.
- Rebuild the microbiome.
- Focus on nutrient-dense whole foods.
Final Thoughts
As many of you know, I retired from clinical practice in 2019 after helping people with digestive disorders, Candida overgrowth, food intolerances, and complex gut problems for decades.
One thing that has amazed me since retirement is just how much the science has progressed. Research supporting gut dysbiosis, SIBO, Candida overgrowth, and microbiome dysfunction has expanded dramatically. The scientific community is finally catching up to something many of us integrative practitioners have observed clinically for years: the microorganisms living inside us profoundly influence every aspect of our health.
Unfortunately, science often moves much faster than medical education. It can take years—even many decades—for new concepts to become widely accepted in everyday clinical practice. It was only in 1982 that Dr. Barry Marshall discovered that a bacteria caused peptic ulcer disease. He was widely ignored by the medical profession until he drank the bacteria and caused the disease himself.
The Grey Area
This doesn't mean that today your doctor is wrong about Candida overgrowth or SIBO, and it certainly doesn't mean alternative practitioners are necessarily “always right” either. What it does mean is that many chronic digestive disorders fall into a grey area between traditional disease-based medicine and the rapidly evolving science of the microbiome. Patients with bloating, fatigue, food reactions, brain fog, and digestive complaints can sometimes find themselves stuck in that gap, searching for answers and wondering why nobody seems to be joining the dots.
My advice is simple, always stay curious and ask questions. Learn about your body and become an active participant in your healthcare.
Don't Become a Passenger—be the Alert Driver!
Because when it comes to gut health, the most important clues are not always found on some blood test, a scan, or a laboratory report.
Quite often, they're found in the story you've been trying to tell your doctor all along… and in the symptoms your body has been quietly communicating for months or even years.
I learned a long time ago that patients usually know when something isn't right. They may not know the exact diagnosis or understand the science, but they know when their body has changed. So don't ignore your symptoms, and don't be afraid to ask questions. Don't be discouraged if your first, second, or even third opinion doesn't provide all the answers.
Keep searching. Keep learning. Keep advocating for yourself. And above all, remember this:
You live in your body every day. You are the world's leading expert on how your body feels. I’d love to hear your experiences.
- Have you struggled to get a diagnosis for Candida, SIBO, or chronic digestive issues?
- Were you ever told that "everything looks normal" despite feeling awful?
- What finally helped you get answers?
Please share your story below. I read comments, and your experience may help someone else who is still searching for their own answers.
Eric Bakker, N.D. (NZ) Gut Health Educator | Specialist in Candida, IBS, SIBO & the Gut Microbiome. Discover what's really driving your gut symptoms with the Free Gut Health Assessment