Persistent Gut Symptoms: Why Your Gut Microbiome Is More Than Good and Bad Bacteria
Inside REBALANCE, the third pillar of the Gut Rewire Protocol
In the previous article in this series, I looked at REBUILD, the second pillar of the Gut Rewire Protocol, and why persistent gut symptoms aren't always just about what you eat, but how well you digest it. Now we're moving further along the digestive tract to the next pillar, REBALANCE, and the gut microbiome.
When symptoms such as bloating, constipation or unpredictable bowels persist, it's tempting to focus on whether you have enough "good" bacteria or too many "bad" bacteria. But the microbiome is more complex than that.
Your gut microbiome is an ecosystem, not a list of good and bad bacteria.
About the Gut Rewire Protocol
I developed the Gut Rewire Protocol by bringing together my work as a clinical naturopath and registered psychologist, with a focus on both what's happening physiologically and how changes can be made workable in everyday life.
REBALANCE is the third pillar. It focuses on the gut ecosystem: which microbes are present, the environment they're living in, and how we can support greater microbial and dietary diversity.
Your Microbiome Is More Than a List of Bacteria
The gut microbiome is the community of bacteria, viruses, fungi and other microbes living in your gastrointestinal tract.
These microbes interact with each other, with components of the food you eat and with the environment around them. Some ferment dietary fibres and produce compounds that interact with the gut and our own physiology.
So when I interpret a microbiome test, I'm not just asking:
Which microbes are there?
I'm also asking:
What is happening in the ecosystem around them?
That distinction matters.
Why Gut Bacteria Aren't Simply "Good" or "Bad"
Finding a particular microbe on a stool test doesn't automatically tell us whether it's contributing to your symptoms or whether it needs attention.
Quantity matters
Is it present at a higher or lower level than expected?
Context matters
What else is happening in the microbiome?
Your symptoms matter
Does the result make sense alongside your digestive function, diet, medications and health history?
Treatment priorities matter
Not everything that appears on a microbiome report needs to become something we immediately try to "fix".
A microbiome test gives us information. The important part is deciding what that information means for you.
Microbiome Diversity Matters, But It Isn't the Whole Story
You've probably heard that a diverse microbiome is a healthy microbiome. Diversity is useful information, but it isn't a single score that tells us whether someone's microbiome is "healthy" or "unhealthy". It's one part of a bigger picture.
What I look at | What I'm looking for |
Richness | How many different types of microbes are represented? |
Diversity | How varied is the microbial community overall? |
Quantity | Are particular microbes present at higher or lower levels than expected? |
Composition | Which microbes make up the community? |
Function | What can the results tell me about the gut environment and how it is functioning? |
Environment | What does the test suggest about the conditions in which those microbes are living? |
Overgrowths & parasites | Are there bacterial overgrowths, parasites or other microbes that may be relevant to symptoms or need further attention? |
Your clinical picture | How does all of this fit with your symptoms, diet, medications and health history? |
Finding an overgrowth or parasite doesn't automatically mean we've found the cause of your symptoms. It still needs to be interpreted alongside the rest of the microbiome and your clinical picture.
Your Microbes Eat Too
Different microbes use different components of our diet as fuel. Certain fibres and resistant starches, for example, are fermented by gut bacteria, producing compounds including short-chain fatty acids.
This means food variety matters.
Different plant foods provide different types of fibres and other compounds that feed different microbial populations. Eating a wider variety of plant foods, where tolerated, can help support microbial richness and diversity.
Where relevant, DNA gut testing can also provide information that helps guide longer-term dietary strategies for supporting the gut microbiome.
A diet that becomes increasingly restricted, on the other hand, may provide a narrower range of food for the microbiome.
Different microbes thrive on different foods. Supporting the microbiome isn't just about adding probiotics. It's also about what you're feeding it.
What About Probiotics?
Probiotics can be useful in the right context.
But "probiotic" describes a broad category of supplements. Different products contain different microbes, different strains have different properties, and different doses may be used for different reasons.
So rather than starting with:
"Should I take a probiotic?"
a more useful question is:
"What are we trying to achieve by using one?"
Without a clear answer, adding another probiotic can become another experiment in a long series of experiments.
The aim isn't simply to add more "good" bacteria. It's to consider what the broader gut ecosystem needs.
So What Does REBALANCE Actually Involve?
In practice, I think about REBALANCE in five parts:
Reduce
Reduce the impact of microbes that may be contributing to symptoms.
Support
Help create an environment that supports beneficial microbes.
Feed
Provide the fibres and other nutrients gut microbes use.
Diversify
Gradually increase the variety of foods and fibres where tolerated to support a more diverse microbial ecosystem.
Observe
See how your gut responds and adjust the plan.
Same microbiome result. Different person. Different treatment priorities.
The Goal Isn't a "Perfect" Microbiome
There isn't one ideal microbiome that everyone needs to achieve. The aim is to work out what's relevant to your symptoms, what can realistically be influenced, and what your gut can tolerate now.
That might mean supporting greater food variety, choosing foods that better suit your individual genetic profile, using a targeted probiotic, or reducing the impact of particular microbes.
The goal isn't a page of "perfect" test results. What matters is whether the changes we're making are actually helping you feel and function better.
Next: REWIRE
So far, we've looked at RESET, REBUILD and REBALANCE: gathering and interpreting data, supporting digestive function and working with the gut ecosystem.
But even the most carefully considered treatment plan still has to work in real life.
Knowing that greater food variety might be useful doesn't necessarily make it easy to achieve. Understanding your test results doesn't mean you'll automatically follow a plan when life gets busy or symptoms flare.
REWIRE, the fourth and final pillar of the Gut Rewire Protocol, looks at this part of the process.
In the final article, we'll explore why knowing what to do isn't always enough:
How do you turn a treatment plan into changes that work for you and fit into real life?
This is where gut physiology and behaviour change come together.
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