When people have digestive problems, we often assume there is too much bacteria—some kind of bacterial overgrowth or dysbiosis that needs to be reduced. But there is another possibility that gets much less attention: sometimes there simply aren’t enough microbes in the gut.
I think about the microbiome much like I think about many other things in physiology: as a bell curve. On one end, you can have a very high microbial population, while on the other end, you can have a depressed microbiome, where the overall microbial population is unusually low. Both ends of that curve can cause problems.
Not Every Gut Problem Is an Overgrowth Problem
A high microbial population can create the digestive symptoms we commonly associate with bacterial or microbial overgrowth, but too few microorganisms can also leave the gut dysfunctional.
When the overall microbial population is depressed, I can see gastrointestinal symptoms, poor digestion, inflammation in the intestines, and problems with the intestinal lining. There can also be an environment where pathogenic bacteria begin to grow because there simply aren’t enough healthy bacteria present to maintain balance.
That changes the question we need to ask. Instead of automatically thinking, “What do we need to kill?” we sometimes need to ask, “What is missing?”
The problem is that symptoms alone don’t always tell us which side of the curve we’re on. Someone with too many microorganisms and someone with too few can both have significant digestive complaints, which is why testing can become extremely valuable.
In my practice, I see a depressed microbiome on testing with some regularity. When I show patients what their results actually look like, it can completely change how we approach the problem. What initially looked like a situation that needed more antimicrobial treatment may actually call for something very different. You don’t treat a depleted microbiome the same way you treat an overgrown one.
The OAT Can Help Connect the Dots
One of the tests I find particularly useful for seeing these patterns is the organic acid test, or OAT. The OAT can give us information about microbial activity as well as neurotransmitter-related patterns, and in my experience, people with a depressed microbial population will often also be low on dopamine and catecholamines.
Why would a depressed microbiome affect dopamine? One important reason is amino acid production and metabolism.
Our gut bacteria play an important role in the production and metabolism of amino acids, including aromatic amino acids such as tyrosine and tryptophan. Tyrosine is an important building block for dopamine and other catecholamines, while tryptophan is involved in serotonin production and other important biochemical pathways.
When the microbial population is depressed, we can lose some of that microbial support for amino acid production and metabolism. In other words, a poorly functioning gut may not be adequately providing the biochemical support the brain needs.
This is one reason I often see low microbial populations occurring alongside very low dopamine and catecholamine levels. The gut and brain aren’t operating as two completely separate systems; what happens in the gut can influence the biochemical environment that supports brain function.
FUT2 Can Make a Depressed Microbiome Even More Significant
Genetics can make this situation even more complicated. The FUT2 gene determines whether someone is a “secretor” or “non-secretor,” and one of the things FUT2 influences is the production of 2’-fucosyllactose, or 2’FL, a special prebiotic that helps feed beneficial bacteria in the gut.
2’FL helps support the good bugs while also acting as a decoy for certain unwanted bacteria, making it more difficult for them to attach to the intestinal wall. People with poorly functioning FUT2 genes may not produce enough 2’FL, which can leave beneficial bacteria—particularly Bifidobacteria—without the nourishment they need to thrive.
This matters because these bacteria help produce important amino acids, including tyrosine, tryptophan, and lysine. When you combine a depressed microbiome with a FUT2-related problem, you can have fewer beneficial microbes along with a reduced ability to adequately nourish those microbes.
That combination may make it more difficult for the gut to maintain a healthy microbial environment and provide the amino acids that the brain and nervous system depend on. This is why I like to look at microbiome status, genetics, amino acids, and neurotransmitter patterns together, rather than treating each finding as an isolated problem.
I’ve written more about this relationship in the article here: The FUT2 Genes – A Hidden Cause of Leaky Gut and Leaky Brain.
Stop Trying to Kill What Isn’t There
This is where the distinction between overgrowth and depletion becomes especially important. If someone truly has excessive microbial activity, reducing that overgrowth may be part of the solution. But if the microbial population is already depressed, continuing to focus on killing bacteria isn’t moving us in the right direction.
When the problem is depletion, the goal may instead be to support and rebuild the microbiome. That can include prebiotics, probiotics, nutrient-dense foods, and other strategies designed to create a healthier environment for beneficial bacteria. The specific approach depends on the individual, but the basic principle is simple: if the problem is too little, the answer isn’t more killing.
Look Beyond the Gut
A depressed microbiome doesn’t necessarily occur by itself. When I see this pattern, there may also be low dopamine, low catecholamines, nutritional deficiencies, FUT2 variants, or other signs that the body needs broader support.
That’s why I don’t want to look at one test result and stop there. The gut and brain are deeply connected, and the microbial environment can influence digestion, the intestinal lining, amino acid metabolism, neurotransmitter pathways, and overall brain function.
Dopamine itself is also not simply a matter of “low is bad, high is good.” There is a range, and different parts of that range can create different problems. I’ve written more about low dopamine and its effects here: ADD, ADHD, and Low Dopamine. For more information about the dopamine and catecholamine bell curve, check out this article: Treating COMT and MAO: How COMT Influences the Brain.
The Bottom Line
When it comes to the microbiome, more is not always better—and less isn’t harmless. We hear a lot about bacterial overgrowth, but a depressed microbiome can also contribute to significant digestive dysfunction.
When there aren’t enough beneficial microbes, the intestinal environment can suffer, unwanted bacteria may have more opportunity to grow, and the gut may not adequately support important amino acid pathways. When a depressed microbiome occurs alongside a FUT2 problem, those effects may be compounded.
Testing can help us determine which side of the curve we’re dealing with, and once we know that, the strategy changes. Sometimes the gut doesn’t need more things taken away. It simply needs to be rebuilt.
Looking for Personalized Support?
If you’re struggling with persistent symptoms or health concerns that haven’t improved despite doing all the “right” things, I can help you look deeper.
At Red Mountain Natural Medicine in Boise, Idaho, I work with patients to identify underlying factors that may be affecting their health, including nutrition, gut health, nervous system function, genetics, lifestyle, and other aspects of overall health.
I see patients both in person and via telemedicine. To learn more or schedule a consultation, visit Red Mountain Natural Medicine.
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