Functional Medicine
Autoimmune Diseases
Med Matrix in South Portland, Maine treats autoimmune conditions (Hashimoto's, lupus, rheumatoid arthritis) by identifying triggers through advanced lab testing. We test thyroid antibodies, inflammatory markers, gut health, food sensitivities, and environmental toxins. Our approach addresses root causes, not just symptoms.
Why Autoimmune Conditions Get Missed for Years
Autoimmune disease happens when your immune system starts attacking your own tissue. It can hit your thyroid (Hashimoto's, Graves disease), your joints (rheumatoid arthritis), your gut (Crohn's, ulcerative colitis), your connective tissue, your skin, your nervous system. There are over 80 recognized autoimmune conditions, and most of them share a frustrating pattern: they take years to diagnose.
The average autoimmune patient sees four to five doctors over a span of four or more years before getting a diagnosis. That's years of being told nothing is wrong. Years of symptoms getting worse while your labs come back "normal." Years of being told it's stress, it's aging, it's in your head.
Here's why it takes so long. Conventional medicine is built around specialties. Your thyroid goes to an endocrinologist. Your joints go to a rheumatologist. Your gut goes to a gastroenterologist. But autoimmune disease doesn't stay in one lane. It's systemic. It crosses every organ system. And when you have fatigue, joint pain, brain fog, gut issues, and skin problems all at once, each specialist looks at their piece and says it's not their department. Nobody puts the picture together.
The other problem is testing. Most primary care doctors don't run autoimmune markers unless you specifically ask. Thyroid antibodies, ANA panels, inflammatory markers like CRP and ESR, specific antibody testing for conditions like lupus or celiac. These tests exist. They're not expensive. They're just not part of a standard panel. So conditions like Hashimoto's (the most common autoimmune disease in the country) go undiagnosed for years because the doctor only checks TSH and calls the thyroid "fine."
We hear this story constantly. Laura, one of our patients, asked her primary care to test her for Hashimoto's. They refused. Her first lab review at Med Matrix revealed it plain as day. Victoria came in with Graves disease, dermatomyositis, type 1 diabetes, and connective tissue disease. Her conventional doctors had her on heavy prescription medications with significant side effects, but nobody looked at root causes. She couldn't get off the couch most days.
“It was looking at more of the root cause, not just treating symptoms. That wasn't working for my symptoms with normal medical doctors.”
Victoria: Root Cause, Not Just Symptom Management
Patient Story
“It was looking at more of the root cause, not just treating symptoms. That wasn't working for my symptoms with normal medical doctors.”
Victoria: Root Cause, Not Just Symptom Management
Patient Story
“There were things on there that I hadn't known. For example, Hashimoto's disease. I had asked my physician to test me for that and they didn't. And that did come up on there.”
Laura: Hashimoto's Discovered After Years of Being Dismissed
Patient Story
Inside Med Matrix
Everything Under One Roof
Advanced testing, personalized protocols, and real results from a team that treats the whole picture.
The Gut-Immune Connection
About 70 to 80 percent of your immune system lives in your gut. That's not a metaphor. The tissue lining your intestines contains the highest concentration of immune cells in your body. When your gut barrier breaks down (what's called intestinal permeability or "leaky gut"), proteins and bacteria that should stay inside your digestive tract leak into your bloodstream. Your immune system reacts. If this goes on long enough, that reaction can become chronic and start targeting your own tissue.
This is why so many autoimmune patients also have gut symptoms. Bloating, constipation, diarrhea, food sensitivities. It's not a coincidence. The gut dysfunction and the immune dysfunction are connected.
Common triggers we test for and address:
- Gut permeability and dysbiosis. Imbalanced gut bacteria, overgrowth of inflammatory species, breakdown of the intestinal lining. We use advanced stool testing and targeted protocols to rebuild gut health.
- Hidden infections. Lyme disease and co-infections, Epstein-Barr virus, other chronic infections can trigger and sustain autoimmune responses. These are almost never tested for in conventional settings.
- Toxin exposure. Mold, heavy metals, pesticides, and endocrine disruptors can push a susceptible immune system over the edge. We assess exposure history and test when indicated.
- Chronic stress and cortisol dysfunction. Long-term stress rewires the nervous system and burns out the adrenal glands. Low cortisol leads to an immune system that's no longer properly regulated. Research supports a direct link between trauma, adverse childhood experiences, and higher rates of autoimmune disease in adulthood.
- Hormonal imbalance. Estrogen, testosterone, and thyroid hormones all influence immune function. Autoimmune conditions disproportionately affect women, and flares often coincide with hormonal shifts (postpartum, perimenopause, menopause).
- Nutrient deficiencies. Low vitamin D, zinc, magnesium, and selenium impair immune regulation. These are simple to test and simple to fix, but they have to be found first.
Trauma and chronic stress create a physiological imprint on the nervous system. When you're in constant fight-or-flight mode, the body starts recognizing its own tissue as foreign. That's not a fringe theory. Research on adverse childhood experiences and autoimmune disease supports this connection directly.
“It was looking at more of the root cause, not just treating symptoms. That wasn't working for my symptoms with normal medical doctors.”
Victoria: Root Cause, Not Just Symptom Management
Watch at 1:00→How Med Matrix Tests and Treats Autoimmune Conditions
We don't start with a diagnosis code and work backward. We start with a full picture of what's happening in your body right now.
Your first visit is a 30-minute testing appointment. We draw a panel of roughly 80 biomarkers and run a full InBody 770 body composition scan. For autoimmune patients, we're looking at everything your other doctors didn't check.
What we test:
- Full thyroid panel (TSH, free T3, free T4, reverse T3, thyroid antibodies for Hashimoto's and Graves)
- Inflammatory markers (CRP, ESR)
- Sex hormones (estrogen, progesterone, testosterone, DHEA)
- Cortisol and adrenal markers
- Metabolic health (fasting insulin, glucose, HbA1c)
- Nutrient levels (vitamin D, B12, ferritin, magnesium, zinc, selenium)
- Body composition (lean mass, visceral fat, hydration)
When indicated, we also run advanced stool testing to evaluate gut microbiome health, intestinal permeability markers, and immune markers in the gut. For patients with suspected Lyme or other chronic infections, we use specialized testing beyond the standard Western blot (which misses a significant percentage of real infections).
One of our 7 providers reviews your full panel, your health history, your medications, and your symptom timeline before you sit down for a one-hour visit. You go through every result together. No rushing. No 10-minute time limit. You leave with a plan that addresses the triggers driving your immune dysfunction, not just the symptoms it produces.
Treatment plans for autoimmune patients often include multiple layers. Gut repair protocols. Targeted supplementation to fill nutrient gaps. Hormone optimization if levels are off. Dietary changes to reduce inflammatory triggers. Stress management and nervous system support. For some patients, peptides like Thymosin Alpha-1 (which modulates T-cell activity) or BPC-157 (which repairs gut lining) become part of the protocol. Everything is individualized. Two patients with Hashimoto's might have completely different root causes and completely different plans.
Real Patients, Real Results
Victoria has multiple autoimmune conditions: dermatomyositis, type 1 diabetes, Graves disease, and connective tissue disease. Before Med Matrix, she was on heavy prescription medications with difficult side effects. Some days she couldn't get off the couch. Quality of life was, in her words, "pretty bad."
Through functional medicine, dietary changes, and targeted supplements, her Graves disease thyroid levels returned to normal in roughly five months. Her joint pain improved significantly. Her fatigue lifted. She describes her quality of life as nearly back to what it was before she got sick. And the cost? She noted it's basically what you'd pay at a regular doctor for co-pays, and the supplements are effective with low side effects.
Laura came to Med Matrix wanting to get off pharmaceuticals. She had high cholesterol, thyroid issues, and persistent fatigue. She'd asked her primary care to test for Hashimoto's. They refused. Her first lab review here revealed Hashimoto's disease. She transitioned to natural thyroid support and targeted supplements. The fatigue lifted. She felt better than she had in years. Her response: "There were things on there that I hadn't known. For example, Hashimoto's disease. I had asked my physician to test me for that and they didn't."
These aren't exceptions. We've treated over 3,000 patients at Med Matrix with a 4.9-star rating across 150+ Google reviews. 7 providers working together, not constrained by insurance. If you've been bouncing between specialists for years without answers, this is the kind of care that puts the pieces together.
“It was looking at more of the root cause, not just treating symptoms. That wasn't working for my symptoms with normal medical doctors.”
Victoria: Root Cause, Not Just Symptom Management
Watch at 1:00→
“There were things on there that I hadn't known. For example, Hashimoto's disease. I had asked my physician to test me for that and they didn't. And that did come up on there.”
Laura: Hashimoto's Discovered After Years of Being Dismissed
Watch at 1:00→What Causes Autoimmune Disease?
Autoimmune disease doesn't appear out of nowhere. Research points to a model called the "triad of autoimmunity": genetic predisposition, an environmental trigger, and intestinal permeability. You can have the genes for Hashimoto's, lupus, or rheumatoid arthritis your entire life and never develop the condition. Something has to flip the switch. That something is almost always environmental.
Gut permeability (leaky gut). When the tight junctions in your intestinal lining break down, proteins and bacterial fragments leak into the bloodstream. Your immune system responds to these invaders, and over time, that response can become self-directed. Research on zonulin (the protein that controls tight junctions) has directly linked intestinal permeability to autoimmune onset. This is why so many autoimmune patients also have digestive symptoms. The gut isn't a bystander. It's often where the disease starts.
Chronic infections. Lyme disease, Epstein-Barr virus (EBV), and other stealth infections can trigger molecular mimicry, where bacterial or viral proteins look similar enough to your own tissue that the immune system gets confused and starts attacking both. EBV reactivation in particular has been linked to multiple sclerosis, lupus, and Hashimoto's in published research. These infections are rarely tested for in conventional settings.
Toxin exposure. Mold mycotoxins, heavy metals (mercury, lead), pesticides, and endocrine disruptors all stress the immune system. For the roughly 25% of the population with genetic susceptibility to mold illness, even brief exposure to a water-damaged building can trigger immune dysfunction that persists long after they leave. We test for these when the clinical picture suggests toxin involvement. Our detoxification page covers this in more detail.
Stress and trauma. The connection between adverse childhood experiences (ACE scores) and adult autoimmune disease is well documented. Chronic stress burns through cortisol reserves. When cortisol is depleted, the immune system loses its primary regulator and becomes hyperactive. This isn't a psychological theory. It's measurable through cortisol testing and supported by population-level data linking trauma exposure to autoimmune diagnosis rates.
Hormonal shifts. Autoimmune conditions affect women at dramatically higher rates than men. Flares often coincide with hormonal transitions: postpartum, perimenopause, and menopause. Estrogen, progesterone, and testosterone all influence immune regulation. When these hormones shift or decline, immune tolerance can break down. This is why hormone optimization is frequently part of an autoimmune treatment plan.
How Do Clinics Personalize Treatment Plans for Autoimmune Diseases?
Two patients with Hashimoto's can have completely different root causes. One might have gut permeability driven by gluten cross-reactivity and a depleted microbiome. The other might have reactivated EBV, tanked cortisol, and mold exposure from a workplace water leak. Same diagnosis, completely different treatment plans.
That's why we don't start with a protocol. We start with data. Your 80+ biomarker panel covers thyroid antibodies, inflammatory markers, sex hormones, cortisol, metabolic health, and nutrient levels. When the clinical picture warrants it, we add advanced stool testing (gut microbiome, permeability markers, immune markers), mycotoxin panels, or specialized infectious disease testing beyond the standard Western blot.
Your provider reviews everything before your 60-minute consultation. Not a summary. Everything. They walk through each result, explain what's driving your immune dysfunction, and build a plan that targets your specific triggers.
Treatment typically involves multiple layers working together:
- Gut repair protocols to restore barrier integrity and rebalance the microbiome
- Targeted supplementation for nutrient gaps (vitamin D, zinc, selenium, magnesium) that directly affect immune regulation
- Hormone optimization when labs confirm imbalance
- Dietary modifications to reduce inflammatory triggers specific to your case
- Stress management and nervous system support to restore cortisol regulation
- Antimicrobial or antiviral protocols when chronic infections are identified
- Peptide therapy (Thymosin Alpha-1 for immune modulation, BPC-157 for gut repair) when appropriate
Progress is tracked through lab retesting, symptom scoring, and body composition scans. Most patients notice improvement in energy and gut symptoms within 4 to 8 weeks. Deeper changes in inflammatory markers and flare frequency build over 3 to 6 months. Recovery is measured in months, not days, but patients who address root causes rather than just suppressing symptoms tend to achieve results that last.
Common Symptoms We See
- Fatigue that doesn't improve with rest or sleep
- Joint pain or stiffness that migrates between locations
- Brain fog, poor concentration, or memory issues
- Digestive problems (bloating, constipation, diarrhea)
- Skin rashes, psoriasis, or unexplained skin changes
- Hair thinning or hair loss
- Recurring low-grade fevers or feeling flu-like
- Sensitivity to cold, especially hands and feet
- Swollen lymph nodes or unexplained swelling
- Symptoms that flare and remit without clear pattern
- Numbness or tingling in hands and feet
- Worsening symptoms during hormonal shifts or high stress
What We Test for This Condition
ANA (Antinuclear Antibody)
Screens for systemic autoimmune activity. Elevated in lupus, Sjogren's, scleroderma, and other connective tissue diseases.
TPO & Thyroglobulin Antibodies
Detects autoimmune thyroid attack. Hashimoto's is the most common autoimmune condition and is frequently missed when only TSH is tested.
hs-CRP
Measures systemic inflammation. Persistently elevated levels indicate ongoing immune activation driving tissue damage.
ESR (Sed Rate)
Another inflammation marker. Used alongside CRP to assess the overall inflammatory burden in autoimmune patients.
Vitamin D (25-OH)
Low vitamin D is strongly associated with autoimmune risk and flare severity. Most autoimmune patients are deficient, especially in Maine.
Cortisol
Your immune system's primary regulator. Depleted cortisol from chronic stress removes the brake on immune hyperactivity.
Fasting Insulin
Identifies metabolic dysfunction and insulin resistance, which drives systemic inflammation that worsens autoimmune conditions.
Full Thyroid Panel (TSH, Free T3, Free T4, Reverse T3)
Autoimmune thyroid disease (Hashimoto's, Graves) requires the complete picture. TSH alone misses the majority of cases.
Sex Hormones (Estrogen, Testosterone, DHEA)
Hormonal imbalance directly affects immune tolerance. Autoimmune flares often track with hormonal shifts.
Ferritin
Iron storage marker. Chronic inflammation can both elevate and suppress ferritin, and iron deficiency worsens fatigue in autoimmune patients.
From Our Podcast
Our providers answer common questions about this condition on the Med Matrix Method podcast.
Leaky Gut Symptoms and the Gut Tests Your Gastroenterologist Is Not Running
- Q:How does leaky gut trigger autoimmune responses?
- Q:What gut tests reveal autoimmune root causes?
Mycotoxin Symptoms: How Hidden Mold Exposure Causes Brain Fog and Fatigue
- Q:How does mold exposure trigger immune dysfunction?
- Q:Why are some people genetically susceptible to mycotoxin illness?
Who Treats This Condition
These providers specialize in this area and review every patient's case personally.
Real Patient Stories
Hear from patients who came to Med Matrix with this condition.
Victoria
Victoria has multiple autoimmune conditions including dermatomyositis, type 1 diabetes, Graves disease, and connective tissue disease. Before Med Matrix, hard prescription medications with significant side effects left her barely able to get off the couch. Through functional medicine, dietary changes, and targeted supplements, her Graves disease thyroid levels returned to normal within roughly five months, her joint pain improved dramatically, and her overall quality of life is nearly back to what it was before.
“It was looking at more of the root cause, not just treating symptoms. That wasn't working for my symptoms with normal medical doctors.”
Laura
Laura came to Med Matrix wanting to get off pharmaceuticals and take an all-natural approach to managing high cholesterol and thyroid issues. During her first lab review with Dr. Rose, she discovered she had Hashimoto's disease, a condition her primary care had declined to test for despite her request. She transitioned to natural supplements for both her thyroid and cholesterol and now feels noticeably better, with more energy and improved overall quality of life.
“There were things on there that I hadn't known. For example, Hashimoto's disease. I had asked my physician to test me for that and they didn't. And that did come up on there.”
Free Resource
Get Your Free Practice Guide
Includes a $100 voucher toward your first visit
Everything you need to make an informed decision: pricing, testing catalog, process timeline, provider bios, and real patient stories. No commitment required.
Free Practice Guide + $100 Voucher
Everything you need before your first visit
STEP 1 OF 3
Enter your email to get instant access
We only accept a limited number of patients per week
EXPLORE
Related Content
Articles, patient stories, and podcast episodes about autoimmune diseases.
FAQ
Autoimmune Diseases FAQ
We work with patients across the full spectrum of autoimmune disease. Hashimoto's thyroiditis, Graves disease, rheumatoid arthritis, lupus, Crohn's disease, ulcerative colitis, psoriasis, multiple sclerosis, dermatomyositis, connective tissue disease, POTS, mast cell activation syndrome (MCAS), celiac disease, and others. We don't treat the diagnosis in isolation. We look at the underlying triggers (gut health, infections, toxins, stress, hormones, nutrients) that are driving the immune response and address those.
A rheumatologist focuses on managing autoimmune symptoms, usually with immunosuppressant medications. That can be necessary and we don't tell patients to stop working with their rheumatologist. But immunosuppressants don't address why your immune system started attacking your own tissue. We look upstream at the triggers: gut dysfunction, chronic infections, toxin exposure, hormonal imbalance, nutrient deficiencies, and chronic stress. Addressing those can reduce flare frequency and severity, sometimes dramatically. Many patients find they can reduce their medication load over time under their specialist's supervision.
We assess dietary triggers as part of the evaluation, and for some patients we use elimination protocols or advanced stool testing to identify inflammatory foods. The standard IgG food sensitivity panels you see marketed online have mixed reliability. We prefer a combination of gut health testing, elimination diets, and symptom tracking to identify what's actually driving inflammation in your specific case. Your provider will recommend the best approach based on your symptoms and lab results.
Initial onboarding runs about $1,200 to $1,500 all-in. That covers your 80-biomarker blood panel, InBody 770 body composition scan, provider prep time, and your full one-hour provider visit. Follow-up visits are $275. If advanced testing is needed (stool testing, DUTCH test, or Lyme panels), there are additional costs your provider will discuss with you. We accept HSA, FSA, CareCredit, and all major cards. New patients get a $100 voucher toward their first visit.
Yes. Many of our autoimmune patients come in already taking medications prescribed by their rheumatologist or specialist. We work alongside those treatments, not against them. Our goal is to address the root triggers so your immune system calms down on its own over time. As that happens, some patients are able to reduce their medications with their prescribing doctor's guidance. We don't tell anyone to stop a medication. That decision is between you and the doctor who prescribed it.
Autoimmune conditions took years to develop, so recovery is measured in months, not days. Many patients notice initial improvements in energy, sleep, or gut symptoms within the first one to three months. Deeper changes in inflammatory markers and flare frequency tend to build over three to six months. Victoria, one of our patients with Graves disease, saw her thyroid levels return to normal in about five months. Your provider will set realistic expectations based on your specific situation and track progress with lab work along the way.
Related Services to Autoimmune Diseases
Your Health, Your Terms
Start Feeling Like Yourself Again
Get your free practice guide and a $100 voucher toward your first visit. No commitment, no pressure.