"Everything seems to trace back to my gut."
More patients are saying this to me than ever before, and they're not wrong to wonder. Digestion, immune function, mood, skin, even how your hormones metabolize — all of it runs through your gut to some degree. When that system is inflamed or imbalanced, it rarely stays contained to just "stomach issues."
Let's walk through what's actually happening, and what we do about it.
Why Gut Inflammation Doesn't Stay in the Gut
Your gut lining is a single layer of cells, and it's doing a remarkable job: letting nutrients through while keeping bacteria, undigested food particles, and toxins out. When that lining becomes chronically inflamed or more permeable than it should be — sometimes referred to as "leaky gut" — it may allow substances through that shouldn't cross into the bloodstream.
Your immune system, which lives largely in and around your gut, reacts to this. In some people, especially those with a genetic predisposition, ongoing gut inflammation is thought to play a role in triggering or worsening autoimmune conditions, through mechanisms researchers are still actively studying, including something called molecular mimicry, where the immune system mistakes the body's own tissue for a foreign invader after prolonged exposure to gut-derived triggers.
To be clear: gut inflammation isn't the single cause of autoimmune disease — genetics and other environmental factors matter too — but for many patients with autoimmune conditions, addressing gut health is a meaningful part of the overall picture, not an afterthought.
Prebiotics vs. Probiotics: They're Not the Same Thing
These two get used interchangeably a lot, and they do very different jobs.
Probiotics are live beneficial bacteria — think Lactobacillus and Bifidobacterium strains — that you introduce into your gut through food or supplements. They can help repopulate a gut microbiome that's been disrupted by antibiotics, illness, or chronic stress.
Prebiotics are the fiber and plant compounds that feed the good bacteria already living in your gut. Without them, even a great probiotic doesn't have much to "eat" once it arrives. Foods like garlic, onions, asparagus, oats, and slightly underripe bananas are natural prebiotic sources.
Think of it this way: probiotics are the seeds, prebiotics are the soil. You generally want both working together, not one without the other.
What Genova GI Testing Actually Looks At
A basic stool culture only catches a fraction of what's going on. Comprehensive GI testing, like the panels we use through Genova Diagnostics, looks much deeper:
Bacterial balance
Beneficial bacteria levels alongside potentially opportunistic or pathogenic organisms.
Digestive function markers
How well you're breaking down and absorbing fat, protein, and other nutrients.
Inflammation markers
Including calprotectin and eosinophil protein X, which can flag gut inflammation even before symptoms are obvious.
Immune markers
Including secretory IgA, which reflects your gut's frontline immune defense.
Parasites and yeast overgrowth
Which can quietly drive symptoms for years without being caught on standard testing.
Short chain fatty acids
Byproducts of healthy bacterial fermentation that support the gut lining itself.
This kind of testing helps us see the actual landscape of your gut, rather than guessing based on symptoms alone.
Testing for Food Sensitivities
Food sensitivity testing is a genuinely useful tool in our approach, and it's worth understanding what it does and doesn't tell you.
IgG food antibody testing measures your immune system's IgG response to specific foods. Many functional and integrative practitioners, including our team, use this as one piece of a broader picture to identify foods that may be contributing to inflammation, digestive symptoms, or a taxed immune system. It's worth knowing that mainstream allergy societies don't currently endorse IgG testing as a way to diagnose a true food allergy — that's what IgE testing is specifically designed for. IgG results are best used as a starting point for an elimination and reintroduction process, not as a standalone diagnosis.
We may also use IgE testing when a true allergic response (hives, swelling, anaphylaxis-type reactions) is a concern, since that's a different immune pathway entirely and requires a different testing approach.
Why Repair Matters, Not Just Removal
It's tempting to think that removing trigger foods or bad bacteria is the whole job. It isn't. If you remove problem foods or organisms but never repair the gut lining itself, the same sensitivities and inflammation tend to resurface.
We think about gut healing in four parts:
Remove
Pathogenic organisms and foods that are actively driving inflammation.
Replace
Digestive support like enzymes or stomach acid, when your body isn't producing enough on its own.
Repair
Nutrients that directly support the gut lining, such as glutamine, zinc carnosine, and specific fibers.
Repopulate
Reintroducing beneficial bacteria through targeted probiotics, once the environment can actually support them.
Skipping the repair step is one of the most common reasons people feel better temporarily on an elimination diet, then relapse the moment they reintroduce foods. The lining itself needs to heal, not just get a break.
Questions I Get Asked Often
What is the link between gut health and autoimmune disease?
Chronic gut inflammation and increased intestinal permeability are thought to contribute to immune dysregulation in people who are genetically predisposed to autoimmune conditions. It's one factor among several, not a single cause, but it's often an actionable one.
What's the difference between prebiotics and probiotics?
Probiotics are live beneficial bacteria. Prebiotics are the fiber that feeds those bacteria. You typically need both for lasting benefit.
What does a GI stool test check for?
Bacterial balance, digestive function, inflammation markers, immune markers, and the presence of parasites or yeast overgrowth — a much fuller picture than a standard stool culture.
How do I test for food sensitivities?
Through IgG food antibody testing, which many functional medicine practitioners use as a starting point for an elimination and reintroduction process. True allergies are assessed differently, through IgE testing.
What is leaky gut?
A common term for increased intestinal permeability, when the gut lining allows substances through that it normally wouldn't, potentially triggering immune and inflammatory responses.
If This Sounds Like You
If your symptoms keep circling back to your gut, or you have an autoimmune condition and haven't had a real look at what's happening in your digestive system, this is worth exploring properly rather than guessing with another elimination diet.
Ready to take the next step?
Book a consultation with Blaise Integrative Medicine to review your symptoms and build a personalized plan.
This post is for general education and does not replace individualized medical advice.
— Dr. Yana Blaise, DNP, FNP-BC
Blaise Integrative Medicine | Optimize. Restore. Thrive.
