Healing from the inside out: my Hashimoto's protocol right now
A week and a half ago I started something I've been building toward for a while. A light version of the AIP diet (the Autoimmune Protocol) alongside a gut-healing protocol that my naturopath put together after we got my GI Map test results back. I want to document it here because I think this might be the most significant thing I do for my health this year. And because it's already been a lot.
I knew going in that this protocol was going to be involved. I just didn't fully anticipate what that feels like in practice day to day. Even with calendar reminders for everything, keeping up with it all is genuinely a lot. Two pills upon waking, two with breakfast, a digestive enzyme every single time I eat (that one I keep forgetting), two with dinner, two more after that, and then GI Detox+ to close out the day. All of that layered on top of my regular supplement stack and trying to fit my levothyroxine in at the right time too. I'm getting there. But I wanted to be honest that even with the best intentions and a phone full of reminders, this kind of commitment takes real adjustment.
Before I get into what I'm doing, let me tell you where I am.
I've had Hashimoto's thyroiditis for a little over five years. For those who don't know, Hashimoto's is an autoimmune disease where your immune system attacks your thyroid gland. Over time that attack damages the thyroid's ability to produce hormones, which is why most people with Hashimoto's end up on thyroid medication. I'm currently on 88 micrograms of levothyroxine, and it has been a supportive piece of the puzzle. I have more energy, I can work out consistently, and I feel more like myself than I did for a long time. But it's not the whole answer.
But I still have work to do. My TPO antibodies, which are a marker of autoimmune activity against the thyroid, are still over 900. To put that in context, most labs consider anything under 34 to 35 IU/mL normal. Mine are at 900-plus. That means my immune system is still actively attacking my thyroid, even if the medication is helping manage the symptoms. My goal is to get those numbers down to near zero. That's what Hashimoto's remission looks like.
My fasting insulin is at 7.5, and my naturopath's ideal is closer to 5. That gap matters more than it might seem. Elevated fasting insulin makes it harder to lose weight, increases inflammation, and can interfere with thyroid function. I'm working on this through strength training three times a week, walking four to five times a week, eating in actual meals rather than grazing all day, and CandiBactin-BR, one of my gut protocol supplements, which contains berberine and supports insulin sensitivity as part of what it does.
What the gut test showed
The GI Map test is a comprehensive stool test that looks at what's actually happening in your gut. I would strongly recommend this to anyone with an autoimmune disease who hasn't done one yet. Mine showed three main things to address.
First, I have H. pylori, a bacteria that lives in the stomach. Mine is at a low level, but H. pylori is worth paying attention to when you have Hashimoto's because there is real research suggesting a connection between H. pylori infections and elevated TPO antibodies. Treating it may help bring those numbers down. We'll see.
Second, my good bacteria levels are very low across the board. This is a hallmark of what's often called leaky gut, or intestinal permeability. Basically, my small intestine lining has become permeable, which means food particles are escaping into my bloodstream. My immune system then attacks those particles as foreign invaders. When you already have an overactive immune system from Hashimoto's, that adds a lot of extra inflammatory load on top of everything else.
Third, I have low digestive enzymes, which means I'm not breaking down food as efficiently as I should be. The good news is no parasites, and a lot of the markers that can be really concerning were fine. These three areas are what we're focused on.
What I'm doing about it
My naturopath put together a gut protocol of five specific supplements, and here's the part I loved: she physically tested me for sensitivities to each one through NAET before prescribing them. No guessing. My body responded well to all five, so there was no back-and-forth about what I could tolerate. The five supplements are Pyloricil for the H. pylori, CandiBactin-BR for the dysbiosis and low good bacteria, GI Detox+ as a binder that helps clear what's being stirred up, Digestzyme-V for the low digestive enzymes, and SBI Protect for immune support. I'll be on the gut bacteria protocol for eight weeks and the H. pylori protocol for twelve weeks.
The AIP diet is the dietary piece. AIP eliminates grains, legumes, dairy, eggs, nightshades, nuts, seeds, and most spices for a period of time to reduce the inflammatory load on your system. It's not easy. I love gluten. I love dairy. I love a glass of wine and a dirty martini. But I'm giving myself some flexibility here and calling it light AIP because my goal is progress, not perfection. I'm focused on warm foods in the morning, soups, and meals that are easy on my gut. I'm also using Claude to help me adapt recipes I actually enjoy to fit the protocol, which has been genuinely helpful.
My full supplement stack right now: levothyroxine 88 mcg, NAC and selenium from Thorne (both support thyroid antibody levels), Magnesium Breakthrough, L-glutamine (which helps heal the gut lining), a tribiotic from Arrae, and the five gut protocol supplements from my naturopath.
I've been using LMNT electrolytes on workout days and hot days, and I love them. But I've recently learned that the high sodium content may not be ideal when you're healing H. pylori or leaky gut, so I'm looking to find an alternative for this season of healing. If you have a favorite low-sodium electrolyte that actually tastes good, I would genuinely love to know. Drop it in the comments.
About NAET (the woo woo part)
NAET stands for Nambudripad's Allergy Elimination Technique. I've always leaned toward natural and holistic approaches to health, so the concept wasn't intimidating to me. I just didn't know what it was until my niece started doing it for her eczema and was seeing real results. Her practitioner happened to be very knowledgeable about autoimmune disease specifically, so I tried it.
The way it works is that your body gets tested for sensitivities, and then you go through a clearing process for each one using acupressure points. The idea is that your nervous system learns to stop reacting to those substances as threats. I'm working through the top ten most common allergens first. So far I've cleared eggs, milk proteins, and vitamin C. Seven more to go.
Does it work? I think so. And here's why I find it particularly useful alongside the gut healing protocol: because I have leaky gut, my body is reacting to foods I eat all the time as foreign invaders. If I can clear those sensitivities through NAET while simultaneously healing the gut lining, the theory is that my overall inflammation load goes down significantly. Less for my immune system to react to. Potentially lower TPO antibodies over time. We'll see what the numbers say.
Why I went outside conventional medicine
This is the part that took me the longest to figure out. Even with a functional medicine provider, I was told that Hashimoto's can't be put into remission. That you manage it, you medicate it, and you live with it. I understand why that's the conventional position. But I wasn't willing to accept that there was nothing more to try.
The more I learned about leaky gut and its connection to autoimmune disease, the more it became clear to me that my gut was a missing piece. The research on the gut-thyroid connection, and specifically on H. pylori and Hashimoto's, is genuinely compelling. I needed a practitioner who was willing to dig into that with me, and that meant going to a naturopath.
I'm not anti-medication. My levothyroxine has been life-changing. I'm also not claiming any of this is a cure. But I do believe the gut is the root of so much of what happens in the body, and if I can get mine healthy, I think everything else has a better chance of following.
For anyone who just got diagnosed
You can feel better. I know your body doesn't feel like your own right now. I know you look in the mirror and don't fully recognize yourself. I know you're tired in a way that's hard to explain to people who don't have it. But there is a path through.
Find a care provider who is willing to look for solutions, not just manage symptoms. That might be your regular doctor, a functional medicine doctor, a naturopath, or a nutritionist. It might take a few tries to find the right one. Don't stop looking. And if you haven't done a GI Map test, I would start there. Understanding what's happening in your gut feels, at least for me, like the beginning of understanding what's happening in the rest of my body.
It requires change. It requires hard work. It requires showing up for your own health in ways that feel inconvenient and sometimes expensive and sometimes just annoying. But you really can come out on the other side of this. I'm heading in that direction. And I'll keep bringing you along.
-- Melissa
