Are Stool Tests Worth It? Gut Health Facts You Should Know
As someone who has been helping people with digestive health for decades, I’ve seen trends come and go. One that has persisted is stool testing — also called fecal testing or gut microbiome testing.
Many functional medicine practitioners, naturopaths, and even conventional doctors recommend it. The idea sounds appealing: send in a small stool sample and get a detailed report on your gut flora. Supposedly, it reveals the root cause of your digestive issues and guides you to the right treatment.
But after decades of helping people heal themselves from Crohn’s, colitis, IBS and SIBO, I can tell you that stool testing is often not worth the hype or the cost.
In this article, I’ll explain why, drawing on my own experience, along with the wisdom of my friend and colleague, Natasha Trenev, founder of Natren Probiotics.
If you’d like to hear our full discussion in detail, here’s the complete video of our conversation:
OR you can listen to the podcast version:
Timestamps:
00:00 – Podcast intro & guest welcome
00:44 – Natasha’s background in digestive health
01:11 – Problems in the supplement industry
01:58 – Intro to stool testing topic
02:48 – Stool test = snapshot in time
03:08 – Overview of digestive tract & gut microbes
03:36 – Why harmful bacteria aren’t always the cause
04:07 – Issues with current stool test methods
04:58 – When stool testing may be valid
05:51 – Same treatment for most gut disorders
06:18 – Broad‑spectrum natural antimicrobials
06:50 – Lifestyle & cultural factors in gut health
07:18 – Microbiome diversity across cultures
08:07 – Antibiotics and gut recovery time
09:00 – Your gut microbiome is unique
09:30 – Hair mineral testing comparison
10:27 – Misleading results & wasted money
11:00 – Bogus probiotic recommendations
11:30 – Dedication to quality probiotics
12:37 – The soil‑based probiotic trend
13:22 – No long‑term safety studies
14:20 – Opportunistic nature of bacteria
15:20 – Risks of aggressive soil bacteria
16:11 – Chemical contamination & health
17:26 – Why Lactobacillus & Bifidobacteria are safe
18:43 – Cultural adaptation to diets
19:47 – The natto example from Japan
20:18 – Traditional food handling
21:09 – Autism rates & gut health
21:53 – Proven gut‑healing protocols
23:01 – Why stool tests miss key microbes
23:40 – Digestive tract function & bacteria
24:51 – Your body rebuilds annually
26:43 – Avoid unsafe probiotics
27:59 – Natren Healthy Trinity formula
28:45 – Why gelatin capsules are best
30:03 – Placing probiotics in correct gut area
31:00 – Importance of bifidobacteria
31:29 – Benefits of Lactobacillus bulgaricus
33:58 – How probiotic strains work together
34:28 – Healing takes time
35:01 – Lifelong probiotic use
36:19 – Processed food damage to gut
37:28 – The potato chip story
38:04 – Fixing supplement industry standards
39:57 – Arsenic in rice research
43:32 – Organic vs regenerative farming
44:05 – Private‑label supplement problems
45:14 – Need for trustworthy health products
45:52 – Daily microbiome care is essential
46:31 – Staying positive & focused
47:53 – Buy from local farmers
48:38 – Nature therapy for gut health
49:57 – Role of social connection
50:53 – Misuse of natural medicines
51:33 – Corporate takeovers of health brands
52:41 – Environmental factors in Crohn’s & colitis
53:13 – Most tests don’t reflect true gut health
54:14 – Return to traditional health wisdom
54:49 – Closing & invitation for questions
What Stool Tests Claim to Measure
Comprehensive stool tests, sometimes called comprehensive stool analysis claim to measure:
- Types of bacteria (good gut bacteria and harmful bacteria)
- Fungi and yeast
- Parasites
- Bile acids and fatty acids
- Inflammation markers
- Nutrient absorption indicators
- Pathogens like Helicobacter pylori (H. pylori)
- Possible signs of leaky gut and intestinal permeability
Some even suggest they can assess the overall health of your microbiome and predict your immune response.
Why Stool Testing Seems Appealing
When you’re dealing with bloating, chronic diarrhea, constipation, abdominal pain, or other digestive symptoms, you want answers.
A stool test seems like a simple way to check your gut microbiota. You imagine taking the results to your healthcare provider and getting a targeted action plan.
For people with inflammatory bowel disease (IBD), irritable bowel syndrome (IBS), ulcerative colitis, Crohn’s disease, or suspected gut inflammation, it sounds like an essential diagnostic to have.
Why Natasha and I Are Skeptical
Natasha has spent over 60 years in the probiotic industry, working with top gastroenterologists, immunologists, and other medical specialists. She has reviewed thousands of research papers on gut microbiota, probiotics, and microbiome tests.
In her experience, stool testing has serious limitations.
Let’s look at them…
A Snapshot in Time
A stool test captures microbial activity at one moment in time. Gut microbes can shift dramatically up to 60% in just 24 hours. Your results today may look very different tomorrow.
Limited View of the Digestive Tract
Your digestive tract is about 27 feet long. Stool forms in the colon; just 9 feet of that length. Many important microbes live in the small intestine or along the gut lining, which stool tests can’t measure accurately. Your colon naturally contains 3-4 lbs of microbes at any time.
Presence Does Not Equal Problem
Finding pathogenic bacteria in a stool sample does not mean they are causing your digestive issues. Some harmful bacteria can live quietly if kept in check by good gut bacteria.
High Cost, Little Impact
Comprehensive stool tests cost anywhere from $400 to $1,500. In most cases, the treatment plan would be the same regardless of the results: remove harmful bacteria, repopulate with good bacteria, make dietary changes, and heal the gut lining.
When Stool Testing Might Be Worth It
There are times when stool testing can be helpful:
- Detecting large-scale gut infections
- Finding high counts of harmful bacteria or parasites
- Investigating chronic diarrhea or blood in the stool
- Guiding targeted antibiotic treatment
Outside of these situations, Natasha and I usually recommend saving your money and focusing on restoring digestive health directly.
Why the Gut Microbiome Matters
Your gut microbiome affects:
- Nutrient absorption and digestion
- Immune system balance and immune response
- Gut-brain axis communication
- Blood sugar regulation
- Mood and cognitive function
- Inflammation control
- Risk for chronic diseases like cardiovascular disease and autoimmune diseases
When your gut microbiota is imbalanced – a condition known as dysbiosis – you may experience digestive problems, chronic diseases, and immune dysfunction.
Good Gut Bacteria vs. Harmful Bacteria
Good Gut Bacteria
- Species like Lactobacillus acidophilus and Bifidobacteria:
- Maintain gut lining integrity
- Reduce gut inflammation
- Aid nutrient absorption
- Support immune function
Harmful Bacteria
Pathogenic bacteria can:
- Damage the gut lining
- Trigger immune responses
- Contribute to IBS, IBD, and leaky gut
- Cause chronic diarrhea and other digestive symptoms
The Problem With Soil-Based Probiotics
Some supplements contain soil-based organisms. These microbes evolved to live in soil, not in the human digestive system. They survive harsh environments by forming spores. While this makes them shelf-stable, it also makes them aggressive. Long-term safety in humans is unknown. Natasha has repeatedly refused to include these in the Natren brand because they are not proven safe.
Proven Alternatives: What Natasha and I Recommend
Use Broad-Spectrum Natural Antimicrobials
Wild oregano oil and olive leaf extract can target harmful bacteria, yeast, and fungi. You don’t need a blood test or stool test to confirm the exact pathogen before starting these.
Garlic, grapeseed extract, and hydrogen peroxide are also effective pathogen-killers, but they don’t tend to be well-tolerated by people with IBD.
For a stubborn, or parasitic infection, use my Quad Synergy protocol.
Repopulate With Safe Probiotics
Natasha formulated Natren’s Healthy Trinity — a trio of well-researched, human-native probiotics:
- Lactobacillus acidophilus for the small intestine
- Bifidobacterium bifidum for the large intestine
- Lactobacillus bulgaricus to stimulate the immune system and help detoxify the gut
These strains have been studied for over 100 years and have decades of proven safety in humans.
Improve Your Diet
- Cut out processed foods and excess sugar, avoid grains
- Eat well-cooked vegetables to nourish gut flora
- Include fermented foods like yogurt from grass-fed milk
Make Lifestyle Changes
- Exercise regularly
- Sleep well
- Manage stress with meditation, breathing exercises, or gentle movement
- Spend time in nature and connect with others
Real-Life Patterns We See
Over and over, Natasha and I see clients spend hundreds on gut microbiome testing only to be told they have dysbiosis or an overgrowth of some bacteria. The treatment? Broad-spectrum antimicrobials and probiotics — exactly what we recommend without the expensive test.
We’ve both helped people recover from severe IBS, IBD, and chronic diarrhea without ever doing a stool test. The same principles apply whether the gut flora is missing bifidobacterium species (for example) or is overrun with pathogenic bacteria.
When to See a Doctor
Seek immediate help if you experience:
- Blood in stool
- Severe abdominal pain; abdomen hard or rigid, not passing gas or stool (could be intestinal perforation)
- Unexplained weight loss
- Persistent vomiting
- High fever
These could signal colon cancer, severe infection, or another urgent health condition.
My Action Plan for Gut Health
- Step 1: Start a proven probiotic routine (I use Natren daily).
- Step 2: Add natural antimicrobials like wild oregano oil if symptoms suggest harmful bacteria.
- Step 3: Shift to a gut-friendly diet — avoid sugar, grains, eat lots of good fat, and well-cooked veggies, chew your pasture-raised meat well before swallowing.
- Step 4: Support your immune and digestive function with lifestyle changes.
- Step 5: Use stool testing only if your symptoms suggest a serious infection or your doctor needs it to guide a specific treatment.
Final Thoughts
Healthy digestion is the foundation of overall health. The digestive tract plays a crucial role in your immune system, nervous system, and mood. Comprehensive stool analysis can have its place, but for most people, investing in proven gut-healing strategies — safe probiotics, dietary changes, and lifestyle adjustments — delivers better results.
As Natasha and I have seen time and again, you don’t need expensive microbiome tests to start healing. You need consistent, safe, and well-researched tools to rebuild the health of your microbiome for life.
You May Also Be Interested In:
- How Ozempic Harms Your Gut and Health
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- Commonly Asked Questions About Jini’s Natural Gut Healing Protocols and Supplements
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