Conditions We Treat · One Tree Integrative Medicine
Autoimmune Conditions
My immune system is attacking me
and no one can tell me why —
or what triggered it.
Autoimmune conditions occur when the immune system misfires — attacking the body’s own tissues instead of external threats. There are more than 100 recognized types. What they share: chronic inflammation, a body working against itself, and a standard treatment approach that manages the immune response without asking what destabilized it in the first place.
At One Tree, that question — what triggered this — is where the investigation starts. Environmental exposures, gut permeability, chronic infections, hormonal disruption, toxic burden: these are among the most common upstream drivers. They’re also the ones most conventional workups don’t look for.
On this page
What autoimmune conditions are
What actually triggers them
How One Tree investigates
Treatments we use
Conditions in this category
“I’ve been on immunosuppressants for years. They manage the flares. No one has ever asked me what started this.“
What It Is
The immune system, turned against itself.
A healthy immune system distinguishes between the body’s own tissue and foreign threats. In autoimmune conditions, that distinction breaks down — and the immune system begins attacking tissue it should be protecting. The result is chronic inflammation and progressive damage to whichever system or organ is under attack.
The more than 100 recognized autoimmune diagnoses share this fundamental mechanism, even though they present very differently — from joint destruction in rheumatoid arthritis, to thyroid damage in Hashimoto’s, to gut lining in celiac disease, to widespread systemic inflammation in lupus.
Conventional treatment targets the immune response itself — suppressing or modulating it to reduce damage and manage flares. That is often medically necessary. But it doesn’t address the question of what disrupted the immune system’s self-recognition in the first place.
What Triggers It
The upstream question most workups skip.
Autoimmune conditions don’t arise randomly. Research consistently points to a cluster of upstream factors that destabilize immune self-tolerance — individually or in combination. These include:
Gut permeability — A compromised gut lining allows partially digested proteins to enter the bloodstream, triggering immune responses that can cross-react with the body’s own tissue.
Chronic infections — Certain viral and bacterial infections have well-documented associations with autoimmune onset — Epstein-Barr, Lyme, and others can trigger molecular mimicry responses.
Toxic and environmental burden — Heavy metals, mold exposure, and chemical toxins are established immune system disruptors. They rarely appear on standard panels.
Hormonal disruption — Estrogen, progesterone, and thyroid hormones directly regulate immune function. Imbalances can shift the immune system toward inflammatory and autoimmune patterns.
Nutritional deficiencies — Vitamin D, zinc, selenium, and omega-3s are critical to immune regulation. Deficiencies in these are common in autoimmune populations and frequently undetected by standard labs.
Our Approach
We ask what triggered it — not just how to quiet it.
Managing an autoimmune condition and investigating its root cause are two different clinical projects. One Tree focuses on the second — not instead of your existing medical management, but alongside it, looking for what’s sustaining the immune dysregulation.
This typically means going further upstream than standard rheumatology or endocrinology panels — looking at gut barrier integrity, chronic infectious triggers, toxic burden, hormonal environment, and nutritional status. The specific investigation depends entirely on your history, your diagnosis, and what’s already been ruled out.
What We Investigate
Gut permeability and microbiome status · Inflammatory markers beyond standard panels · Full hormonal environment (not just TSH) · Chronic viral and bacterial triggers · Heavy metal and environmental toxin burden · Nutritional deficiencies linked to immune dysregulation · Food sensitivities driving ongoing immune activation · Adrenal and HPA axis function
Conditions in this category
Hashimoto’s thyroiditis
Rheumatoid arthritis
Lupus (SLE)
Celiac disease
Psoriasis & psoriatic arthritis
Inflammatory bowel disease
Multiple sclerosis
Sjogren’s syndrome
Ankylosing spondylitis
Unexplained systemic inflammation
How We Treat It
Treatments we use for autoimmune conditions.
What’s used depends on what the investigation finds. These are the tools most commonly relevant at One Tree for autoimmune cases — each targeting a different part of the picture.
Gut Restoration Protocols
Because gut permeability is one of the most consistent upstream drivers of autoimmune activation, addressing the gut is frequently the most important first step. This involves microbiome mapping, intestinal permeability testing, targeted probiotic and prebiotic protocols, and identifying food sensitivities that are sustaining the immune response with every meal.
Bioidentical Hormone Therapy
Hormones directly regulate immune function. In autoimmune conditions with a hormonal component — Hashimoto’s, lupus, and others that disproportionately affect women — restoring hormonal balance using bioidentical hormones can significantly reduce immune dysregulation and inflammatory burden. Thyroid optimization is a particular focus.
Targeted Nutritional Protocols
Vitamin D deficiency, low zinc and selenium, and insufficient omega-3s are found at high rates in autoimmune populations — and each plays a direct role in immune regulation. Identifying and correcting specific deficiencies (through comprehensive panels, not assumptions) is a core part of every autoimmune protocol at One Tree.
Peptide Therapy
Certain peptides have demonstrated meaningful immune-modulating and anti-inflammatory effects. BPC-157 supports gut barrier integrity and reduces systemic inflammation. Thymosin Alpha-1 directly supports immune regulation and has been used clinically in autoimmune and chronic inflammatory conditions. Used when appropriate to the individual’s case.
What to Expect
From first call to an actual investigation.
Autoimmune cases at One Tree almost always involve a long history — years of symptoms, multiple diagnoses, medications that manage but don’t resolve. That history matters clinically. The intake process is designed to capture it properly.
Free 40-Min Consultation
A direct conversation about your diagnosis, your history, what’s been tried, and what’s never been investigated. Dr. Jamie will tell you honestly whether One Tree’s approach is likely to be useful for your specific situation.
Deep-Dive Intake (60+ min)
A full history covering diagnosis timeline, symptom patterns, prior labs, current medications, diet, environment, and anything you’ve noticed that correlates with flares or remissions.
Targeted Investigation
Advanced labs and functional testing chosen specifically for autoimmune cases — gut, hormones, toxins, infections, nutritional status — going well beyond the standard rheumatology panel.
Your Individualized Protocol
A plan built around what the investigation actually finds. Most autoimmune protocols at One Tree address multiple upstream drivers simultaneously — gut, hormones, nutrition, and inflammation — because they typically interact.
Honest expectations
Autoimmune conditions that have been developing for years don’t resolve quickly. Meaningful improvement is typically measured in months, not weeks.
One Tree doesn’t replace your rheumatologist, endocrinologist, or other specialists. We work alongside your existing care, investigating what they haven’t had time or tools to look for.
Not every autoimmune case has an identifiable upstream trigger that we can address. If that’s the situation, Dr. Jamie will tell you directly rather than recommend treatments unlikely to help.
If your situation is outside what One Tree can meaningfully address, you’ll hear that on the free consultation — not after you’ve already invested in the process.