How the Autoimmune Protocol Made Me Worse and What Actually Worked

Let me preface this whole story by saying that I don’t think I have an autoimmune disease.  I have lived like a celiac for the last eight years because I exhibited textbook dermatitis herpetiformus when I was eating gluten, because I had a nutritional panel done before and after getting off gluten demonstrating how the simple removal of gluten made me go from malnourished to pretty darn healthy, because I had a positive antibody blood test, because I have a big forehead (fun fact- forehead size can be a more reliable indicator of celiac disease than many other symptoms), and because about a million health issues cleared up when I got off of it. This past year, my 23andme genetic test revealed that I have neither the variant HLA-DQ2 allele nor the HLA-DQ8 allele, which makes it nearly impossible for me to have celiac disease. There’s a small chance I do and I feel no urgency to return to eating gluten (unless I’m in the presence of a Chick-fil-A chicken biscuit), but I think this is still extremely relevant to anyone who does have an autoimmune disease.

Despite having been skinny my entire life, I’ve always been kind of obsessed with food. Always looking forward to the next meal, relishing my time in Whole Foods, baking muffins while listening to Fiona Apple…so naturally, the obsession got cranked up a few notches when I got off gluten. I had to pay even more attention to food than I ever had before. Even seeing the word “wheat” on a label set off alarm bells in my head, triggering an emotional response.

Over the years, I mysteriously started reacting to dairy. I developed chronic sinusitis that wouldn’t go away after six ENTs and about a thousand rounds of antibiotics. It went away when I removed dairy, but then I began having reactions to eggs. I was a little worried, but I didn’t really start freaking out until my fourth food sensitivity came along. That was when I learned about leaky gut and frantically started trying to heal myself. Instead, I ended up having to add several more of my favorites to the banned food list. Desperate, I went on the autoimmune protocol after reading sections from Sarah Ballantyne’s terror-inducing book The Paleo Approach. Nightshades do WHAT to my gut??

This is where things got really weird. After a few months, I started trying to reintroduce foods on the AIP, but anything that wasn’t on the safe list caused intense joint and back pain. I began to develop arthritis EVERYWHERE at the age of 27. My hands hurt, my knees hurt, my wrists and hips had started cracking with every movement – but all this disappeared when I returned to the AIP. Now, AIP enthusiasts will tell you that these foods were bothering you before, but your body had so much inflammation you didn’t notice. I’m here to tell you that they are missing an extremely important factor: the mind-body connection.

Our emotions are energy, and this energy can have an extremely strong impact on our physiology improperly dealt with. Our society tells us that emotional expression indicates weakness, so we repress them – compartmentalize the situation and move on with our lives. When we repress our emotions, this energy can manifest as a cold, back pain, arthritis, even cancer. Big pharma isn’t going to tell you this, but science is catching up – think about all the studies on how stress impacts the body.

I had developed such an emotional connection with food, my body literally started using food as a way to distract me from dealing with emotional “traumas.” My sinus infections developed during the time immediately following a bad breakup when I was still working side-by-side with my ex on a daily basis in a conservative office setting. My egg sensitivity developed when I was living with a passive aggressive roommate who constantly sought out ways to express her disdain for Americans such as myself. My body took the cue that I was a sucker for this method of distraction and began reacting to all the foods I most feared losing. And finally, I developed an intense fear of seeds, nuts, grains, nightshades, and coffee after reading The Paleo Approach and my body responded accordingly to mirror this fear with symptoms.

Can I prove this? No. But I can tell you that a week before I implemented this technique I’m about to share, I had tried reintroducing some non-AIP foods and was in so much pain I could barely walk. Two weeks later, I was back to eating everything with almost no symptoms.

First of all, working with a naturopath to clear these foods energetically did not work because I wasn’t reacting to the foods themselves. What worked was clearing the energy from the emotional situations that occurred around the time that I lost the foods. After my naturopath cleared me on the ex, I could eat dairy for the first time in four years without intense sinus pain or throbbing ears or fits of sneezing. After he cleared me for eggs, I could eat eggs for the first time in three years without these symptoms. Then we worked on my fear of never getting better, and of eating itself.

I read Dr. John Sarno’s book Healing Back Pain: The Mind-Body Connection, which postulates that chronic pain is simply the result of repressed emotions and that once you truly believe it’s not a structural issue, your pain disappears. Dr. Sarno instructs those with chronic back pain to forget the warnings from their doctors about exercise, start running and lifting weights, and the pain would disappear. Since my symptoms were food-induced, I decided I had to disassociate the food from the symptoms.

I reintroduced everything at once – seed based spices, nuts, nightshades, coffee. the works. The pain came back, but I told myself it wasn’t leaky gut – my gut is healed; there is nothing to fear. I began doing a kundalini meditation every day for clearing the subconscious mind because I knew that in order for this to be effective, my subconscious mind had to get the memo. First, my back pain went away. Then my knee pain. I went back to the gym where I used to lift weights and worked through some painful lunges. Then the pain in my toes from the arthritis which had been diagnosed by a foot doctor went away. The pain in my arms and hands hung around the longest – my hands felt numb and my wrists were crackling constantly. After reading that this can be related to an emotion around disliking the work you’re doing on a computer, that finally disappeared as well.

I’m still working on achieving my dream stool on the bristol scale and fully kicking a histamine intolerance, but I am confident that these are emotional issues as well. My entire perspective on myself has completely changed through this experience. I went from viewing myself as a weak, genetically inferior weirdo to a strong, healthy woman who’s basically just like everyone else. I’m beyond thrilled and feel incredibly empowered, and wanted to share this story with the world in case it helps someone…because MAN do I wish someone had told me.

Why I Did The Elemental Diet for SIBO

Small intestine bacterial overgrowth: the suspected source of IBS  in up to 84% of sufferers [R] as well as the inspiration a little game I play with my boyfriend when we’re surrounded by pedestrians called “Pregnant or SIBO?” (That one’s definitely SIBO…)

Antibiotics are likely the most commonly prescribed treatment for SIBO, though herbal treatments have been shown to be just as effective. Or …ineffective, depending on how you look at it. In this study, only 46% of herbal patients cleared the breath test and 34% of antibiotic (Rifaximin) users after a four week course. That’s my first reason for avoiding the antibiotics…

Antibiotics take too damn long and the odds are unimpressive

Four weeks of antibiotics yielded only a 34% success rate? No thank you! I’m impatient. I will take my two weeks of hell-emental, particularly since the success rate has been shown to be 80% for a fifteen day diet [R]. Herbals have been known to take even longer.

Antibiotics probably got me here in the first place

My dermatologist put me on a daily antibiotic in high school for acne, which I was on for six or seven years. By the time I got off it, the evidence of an unhappy gut was strong: I wasn’t absorbing nutrients and debilitating stomach cramps were hitting me in waves. Seven years on the birth control pill followed, during which time I was developing increasing food sensitivities and yeast overgrowth symptoms. Needless to say, my gut was poised and ready for disaster when a violent food poisoning episode hit in spring 2015.

Antibiotics are not selective with the bacteria they destroy – they’re blowing up everything in your gut. When SIBO is caused by an imbalance to begin with, antibiotics are the last thing that is going to restore that balance.

Herbals are powerful and should be used under supervision

I support the use of herbals completely, but they are extremely powerful and I was very cautious about using them on myself without supervision. At the time, I didn’t have a practitioner to work with and even now, my practitioner is a gastro with no herbal training. I realize there are herbal protocols for SIBO all over the Internet, but of course it’s ideal to exercise caution with self treatment.

The elemental diet is the fastest, most effective route

SIBO expert Dr. Allison Siebecker describes the elemental diet as a way to “starve the bacteria, but feed the person, by replacing meals for 2 weeks with an Elemental Formula.  Elemental formulas are powdered nutrients in pre-digested, easily absorbed form.” [R]

You can purchase formulas online, but they’re incredibly pricey and contain unhealthy sugars and fats that can be detrimental – particularly to those who also have leaky gut. Dr. Siebecker created a “homemade elemental diet” recipe with more natural ingredients that costs closer to $200. The drawback of the homemade elemental diet is that it hasn’t been studied, but Dr. Siebecker has used it in her practice with great success.

In a study using the Vivonex Plus elemental formula, 80% of subjects had a negative lactulose breath test on day 15 and that number rose to 85% on day 21. [R]

I feel more energized, clear-headed, and sleep better on the elemental diet

I purchased this shirt at Target to wear ironically during the elemental diet. Treat yoself.

You’d THINK not eating anything for two weeks would make you feel like shit, but I actually felt better much of the time. The greatest benefit I experienced was mental clarity and I suspect this is a result of not having food sensitivity induced brain fog! I also had good energy through most of the day – though I would crash in the evenings.

One extra benefit was that my skin cleared up completely. I went from having big honkin’ cystic zits all over my face to completely clear skin by day 9.

Additionally, I didn’t have to cook for two weeks and was much more mobile than I usually am when doing the autoimmune protocol.

But the elemental diet isn’t all sunshine and aminos

Now that I have offered adequate evidence that the elemental diet is great, I have to tell you: it’s tough. It’s really, really tough. It tastes like puke, you can’t eat any food, and you might have die-off symptoms. I had two die-off episodes, which sounds common in the SIBO support group on Facebook (I would highly recommend joining this group if you plan to do the elemental diet – you will receive much-needed support and accounts of others’ experiences). Some people have no die-off symptoms, like SIBO slayer Katie Caldwell.

Side effects of the elemental diet

Additionally, you risk experiencing candida overgrowth. I developed a yeast infection on day 13 and it sounds like Chris Kresser had a similar experience. I cleared this up in a few days with apple cider vinegar and a supplement and it wasn’t a big deal, but know that this is a possibility.

I do have a handful of tips for making the homemade elemental diet more palatable and reducing nausea:

  1. Separate the ingredients. I put the aminos, multivitamin, and salt in one glass with as little water as needed to dissolve it, and the honey and oil in another with some water.
  2. Don’t take the multivitamin on an empty stomach. Coat your stomach first with some of the oil and wait 15 minutes.
  3. Don’t chug the whole thing- I know you just want to get it over with, but drinking it too quickly can cause nausea. I drank half the oil, waited fifteen minutes, drank the multivitamin and salt with some more oil, waited a few minutes, and then finished both solutions.
  4. My gastro told me that capsules should be okay, and actually I just noticed that Dr. Siebecker’s directions say you can either take the vitamin encapsulated or open the capsule and pour the contents in. I am taking this one step further this time because I just cannot stand the taste of the amino acids and have encapsulated them. This is probably not practical for most people as each meal requires like swallowing like, 20 capsules.
  5. My gastro also said tea should be fine. I had peppermint tea a lot in the beginning, and was thinking that I would blend the coconut oil into the tea this time using an immersion blender so it’s like a creamer. Coffee made this way is delicious! Again, this is fussy and unnecessary, but another coping technique.

Is the elemental diet right for you?

Many practitioners position the elemental diet as a last resort or don’t mention it at all, but it can certainly be the first line of defense with the right mindset. One common concern is potential weight loss, which varies by individual. The elemental diet took me from 107 down to 100 lbs, but I quickly regained the weight when I began eating again. For those who are severely underweight, this diet may not be the right approach. Work with your healthcare team to determine whether this is the right solution for you.


Four Tips for Surviving Business Travel on the Autoimmune Protocol

The dreaded BUSINESS TRIP! It’s happened to me five times since going AIP in February, but I’ve been able to remain compliant every time.

Me in my AIP- enabled high-ish heels at the end of a full day meeting (note: AIP doesn’t, however, support your ability to walk on cobblestone)

Here are my tips for surviving your business trip on the autoimmune protocol:

1. Meal Prep. Okay, this is obvious…

  1. Explain to your company/client/whoever is responsible for your expense reports that you are on a restricted diet to manage your autoimmune disease or health issue and find out if it would be okay to expense a grocery receipt as all your meals. Find out if there is a limit, but you’re likely to be less expensive than all your whiskey guzzling coworkers even if you’re eating grassfed and organic. I usually start freezing leftovers from my cooking a week or two in advance so there is less to do the weekend before the trip. I use mostly plastic tupperware to keep the weight down since I carry all my food on my back, and I pack a pyrex dish in my suitcase for microwaving food at the hotel or on site. Some of my go-to menu items are:
    • Breakfast: Chicken apple sausage, fruit and/or an AIP pancake (At home I eat greens for breakfast too, but I skip ’em on trips for convenience)
    • Snacks: 
      • Roasted cauliflower artichoke hummus (it’s just roasted cauliflower, roasted garlic, a can of artichoke hearts, olive oil, lemon juice, and salt blended in the food processor – SO good! This needs to be frozen before bringing it through security.)
      • Squash flatbread – aka my favorite AIP recipe ever. I use duck fat instead of olive oil, you know, since the client is paying for it and all😉
      • Olives (pour out the juice before bringing it through security)
      • Plantain chips
      • Collagen cake batter bars – I have a coconut sensitivity, so I sub tiger nut butter in for the coconut butter and it’s phenomenal
      • AIP pork rinds
      • Tigernuts – Order the peeled snack pack in advance on Amazon. Contrary to their name, they are not a nut but a slightly sweet tuber. I think they are absolutely delicious and a super simple thing to grab when you’re on-the-go.
      • Sauerkraut – I took a small jar of this both times
    • Meals: If you want to make it really simple, pack a gallon size zipblock bag of salad geens and toss a few cans of tuna into your bag. Chop up veggies of your choice and make a quick dressing-in-a-baggy from olive oil, salt, lemon juice, and spices. As I noted, I also just use leftovers from other meals. 

2. Call ahead.

  • The hotels I have stayed in have two to three microwaves they lend out. Call ahead and make sure you can get one of them placed in your room for your arrival.
  • Almost every restaurant I have gone to with clients has been able to serve me – I just call ahead and make sure they can make me a plain piece of fish and some veggies cooked in olive oil in a clean skillet.

3. Invest in some tools to make your life easier.


  • I travel with this cooler backpack from REI and joke with my coworkers that it’s full of beer because that was actually its God-given purpose. I can fit three days’ worth of snacks and meals, plus ice packs. For flying, I bring it as a carry-on and check my suitcase.
  • This mini portable oven came in handy when I was on a road trip in Norway – I haven’t had to use it for work yet, but if you don’t have access to a microwave this will heat your food up in about 45 minutes to 1 hour. It plugs into the wall, but you can get a power adapter and use it in the car as well.


4. Don’t worry about them; go to bed! 

One of the reasons I hate business trips is because the dinners sometimes go late, and/or I have to work late in my room, and it’s hard to get adequate sleep. Whenever possible, I excuse myself from the table early and return to my room to get ready for bed. Though this probably differs according to company, I have never heard an objection. It was a hard to do at first because I had concern about the perception, but the sleep is worth it to me.


Exocrine pancreatic insufficiency: The Most Overlooked Cause of SIBO?



Small intestine bacterial overgrowth (SIBO) is defined as the presence of excessive bacteria in the small intestine, which doesn’t sound like as big of a beast as it actually can be (1).

According to a study in the World Journal of Gastroenerology, SIBO may be clinically asymptomatic or can resemble irritable bowel syndrome with non-specific symptoms (bloating, flatulence, abdominal discomfort, diarrhoea, abdominal pain). (3) Aside from IBS, there is evidence that SIBO is linked to increased intestinal permeability, aka “leaky gut”(4).

The reason so many people can’t cure their SIBO for good is because they haven’t been able to address the root cause. Root causes can include:

  • Exocrine pancreatic insufficiency (a deficiency of pancreatic enzyme secretion)
  • Low stomach acid
  • Poor intestinal motility (your body’s ability to move food through the digestive tract)
  • Ileocecal Valve Syndrome (the valve between your small and large intestine is either stuck open, causing diahrrea, or stuck shut, causing constipation)
  • Celiac disease complications
  • Prior abdominal surgeries

Exocrine pancreatic insufficency (EPI) isn’t in many of the lists I’ve seen online about SIBO and most doctors don’t know about it in this context, so it’s not surprising that EPI expert Dr. Cynthia Rudert says it’s the number one most overlooked cause of SIBO. This is largely because the lab tests available for analyzing it are either highly inaccurate (lots of false negatives) or extremely invasive.

Diagnosing EPI

So how do you know if you have it then? Well, this is going to sound like an ad for Dr. Rudert BUT…you have to go to an expert who essentially plays detective on your medical history and symptoms, runs the lab work, and tests you on some prescription strength pancreatic enzymes to see if you experience improvement. The symptoms of EPI don’t typically develop until the pancrease has lost 80-90% of its exocrine function (5), but they include:

  • Frequent diarrhea
  • Weight loss
  • Greasy stools that are difficult to flush (people with EPI cannot properly absorb fats, so their stools may float)
  • Gas and bloating
  • Stomach pain


Treating EPI

The good news about EPI is that it’s easy to treat with a pancreatic enzyme replacement therapy, and you don’t have to change your diet further if you’re on the proper enzyme dose. The bad news is that there’s no known “cure” for EPI, and so enzyme replacement may be necessary for a long time, if not forever.

EPI can also cause nutrient malabsorption, particularly in vitamins A, D, E, and K, and so supplementation may be necessary as an additional step (7).