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My Experience with Three Elimination Diets for Gut Health and Lowering Inflammation

Over the past year I’ve tried three different diets to help with my gastrointestinal issues and inflammation: the Low FODMAP diet, the Autoimmune Protocol (AIP) diet, and the Low Histamine diet.

I kept a food journal while I did this to record my reactions and try to pinpoint which foods seemed to be causing me problems. And yes, trying these diets did give me some answers and help me decide which foods hurt me, and which are healing.

If you have wondered about any of these diets, my experiences may help guide you as to which one may be right for you to try.

Elimination Diets

Just to be clear – all three of these are meant to be temporary while resetting your system. Each of them are extremely restrictive in different ways, so they aren’t usually suited for long term adoption.

They are elimination diets – you eliminate certain food groups or specific foods to get your health into a better place. Then you start re-introducing foods, slowly, after giving your body a break from the ones that seem most problematic for you.

The first one I tried was the low FODMAP diet. When I started this diet in January of 2020, I remember thinking that I’d have to do it for six weeks, and I wasn’t sure if I could handle that.

This makes me laugh now – because at this writing, I have been on one or the other of these three different elimination diets for almost a year.

Not only have I survived, but I feel that I’m finally on a path that will bring me healing. Six weeks is not a long time to suss out a hidden health problem – and neither is a year, in fact.

I’m going to provide an overview on my experiences with these three diets and give you the basics on each of them. This article is not meant to be a comprehensive guide to these diets – I just want to give you enough to get you started. I’ll provide additional resources at the end of the article.

Before we get started, just so you know, as a base line, I had already been on a wheat-free, gluten-free, and corn-free diet for several years.

The Low FODMAP Diet

Who it’s for:

This diet is intended for anyone who has been diagnosed with Irritable Bowl Syndrome (IBS). It can also be recommended for SIBO (small intestine bacterial overgrowth).

The idea behind this diet:

Certain foods cause more fermentation in the gut that others. By removing these foods, you can calm your digestive tract and eliminate or lessen your gastrointestinal issues.

FODMAP stands for Fermentable Oligosaccharides Disaccharides Monosaccharides and Polyols. Those are all types of short chain carbohydrates or sugars found in different foods.

These foods are highly fermentable and can cause gastrointestinal issues such as gas, diarrhea, nausea, and constipation, as well as many different types of abdominal pain and discomfort.

And when I say fermentable, yes, it’s the same type of fermentation that happens when you make sauerkraut or sourdough. Bacteria – in this case gut bacteria – break down foods, and in the process create a lot of gas which can cause a lot of pain.

In the case of SIBO, you may have too many of the wrong kinds of gut bacteria and they may be in the wrong place. So with the low FODMAP diet, essentially you stop feeding those bacteria.

Inulin, an undigestible starch found in asparagus, onions, garlic, and artichokes, is good for your gut bacteria if you have a healthy gut microbiome. In the case of FODMAP sensitivities, inulin is to be avoided.

What is eliminated:

Foods are eliminated in groups depending on the type of carbohydrate found in them. You may react to those in one group, but not in another.

Some of the foods that are eliminated include beans, certain vegetables (ie, artichoke, asparagus, cabbage), allium bulbs, wheat, certain fruits (ie, apples, pears), dairy high in lactose, coconut milk, etc.

What you can eat:

Low FODMAP foods, such as gluten-free grains, citrus fruit, under-ripe bananas, lactose-free dairy, eggs, certain vegetables (ie, carrots, radish, spinach), allium greens (chives, scallions), etc.

You’ll find a link to a full list of foods that should be avoided and those that are tolerated at the bottom of this article.

My experience with the low FODMAP diet:

It’s a hard diet to follow. Unless you have a photographic memory, you’ll need a copy of the good and bad foods to refer to at all times.

This diet helped with some of my symptoms, but I had a hard time making sense of my results. Sometimes a food would bother me, other times it wouldn’t. (Now I know why – if you keep reading you’ll find out why.)

The Autoimmune Protocol (AIP) Diet

Who it’s for:

This diet is intended for those with autoimmune conditions, such as hashimoto’s thyroiditis, multiple scelorosis, crohn’s disease, rheumatoid arthritis, etc. There is a large list of autoimmune conditions – if you’re not sure if your diagnosis is autoimmune, look it up. Your doctor may not have told you that your condition is autoimmune.

The idea behind this diet:

Plants have natural defenses to protect them from being eaten, and ensure they can reproduce (usually via their seeds). Those with autoimmune issues have autoimmune systems that are attacking themselves. Eating certain foods apparently exacerbates this response.

What is eliminated:

  • grains and pseudograins
  • nuts
  • seeds
  • dairy
  • eggs
  • legumes
  • nightshades (potatoes, peppers, tomatoes, eggplant, goji berries, groundcherries, etc)
  • spices (most of these are seeds)
  • artificial additives

What you can eat:

  • leafy green vegetables
  • meat and fish
  • non-nightshade vegetables
  • non-nightshade roots and tubers (sweet potatoes, carrots, beets, etc.)
  • non-grain and non-nut flours such as cassava, tigernut, and arrowroot, all of which come from tubers
  • herbs
  • alliums

My experience with the AIP diet:

I was never able to get on the AIP diet in full. I kept almond flour in my diet, which didn’t seem to bother me, as well as eggs. (Eggs did seem to bother me but only sometimes.)

The AIP diet helped with some of my symptoms, but not all of them.

This diet was difficult to master.

Do you think of mustard as being something that comes from seeds? Although this is something I knew very well, when it was lunch time and my stomach was rumbling, somehow I would forget about it… until I ate it and reacted to it. “Oh yeah, mustard comes from mustard seeds, I can’t eat that.”

Or I would eat sausage made with unspecified “spices” and not think about it until afterwards, when inflammation took over my body.

To make up for the lack of grains, I started to use a lot of cassava. I loved baking with cassava and making cassava tortillas (so good!) Unfortunately, eating cassava actually seemed to increase my inflammation.

On the other hand, removing nightshades from my diet was a godsend. I have since retested tomatoes, peppers, and potatoes and found that while potatoes seem to be on my safe list, causing no problems for me, tomatoes, sweet peppers, and hot peppers all wreak havoc in my body, causing bouts of inflammation that it takes me three days to recover from.

The Low Histamine Diet

Who it’s for:

This diet works for those with histamine intolerance. Some of the symptoms of histamine intolerance include: allergy symptoms, breathing issues, heart palpitations, inflammation, GI issues – all of these increase particularly after eating foods high in histamines.

The idea behind this diet:

While histamine is a normal, needed compound in the body, it needs to be cleaned away by an enzyme called DAO. Some individuals don’t produce enough DAO to clean away the histamine, which builds up. Once too much histamine is present, symptoms show up. Amounts of histamine one person has in their body daily can vary depending on diet, lifestyle, and other factors.

I got clued in that this diet might be right for me when I read that histamine intolerance can cause chemical sensitivities.

What is eliminated:

All high histamine foods and histamine-liberating foods are eliminated, such as

  • leftovers
  • fermented foods
  • legumes (including all soy products)
  • tomatoes, hot peppers
  • spinach
  • over-ripe vegetables
  • strawberries, bananas, raspberries, citrus fruit
  • over-ripe fruits
  • aged meats
  • seafood, fish (unless eaten immediately after catching), canned fish
  • most spices
  • wheat
  • buckwheat
  • egg whites
  • sulfites, preservatives, food coloring, gums, and other artificial additives
  • yeast
  • vinegar
  • certain nuts and seeds
  • aged cheeses, fermented dairy (yogurt, kefir)
  • raw milk
  • chocolate
  • raw honey
  • tea, coffee
  • alcohol

There are also some “grey area” foods – some foods are considered high in histamine by some medical sources, but not by others. You have to test these on yourselves to determine whether they trigger you or not.

Some of the “grey area” foods include:

  • berries
  • kiwi
  • stone fruit
  • sweet potatoes
  • other nuts and seeds
  • alliums (garlic, onion, leeks, chives)

What you can eat:

  • freshly prepared foods
  • other veggies
  • potatoes (peeled)
  • other fruits
  • meat (if frozen immediately after slaughter)
  • fish (only if eaten right after being caught)
  • oatmeal, and other grains and pseudograins (except wheat and buckwheat)
  • pasteurized milk, un-aged dairy products
  • egg yolks
  • white chocolate
  • natural sugars, stevia, pasteurized honey

My experience with the Low Histamine diet:

When I tried this diet my body cried out “BINGO!” Suddenly I understood why cauliflower didn’t seem to bother me sometimes, but did other times. Same thing with chicken – and so many other foods.

While following a low histamine diet has been extremely beneficial to me, helping me reduce my inflammation and understand why I often have acid indigestion after eating, it has not been a simple process.

There are a few food lists detailing which foods are high in histamines and which are low – and while the majority of foods on the different lists overlap, there are some contradictions among them. That’s where I’ve had to experiment and see what works for me.

My Takeaway

These three elimination diets have some overlaps. Legumes are eliminated from all three, which explains why all three seemed to help me in some ways. Sadly, beans and other legumes remain on my personal “untolerated” food list.

While the low histamine diet has been the most effective for me in calming my symptoms, histamine intolerance is only the tip of the iceberg, indicative of – most likely – leaky gut syndrome or SIBO.

So while eating a low histamine diet helps, there are some “low histamine” foods which still bother me: all dairy, as well as sweet peppers, for instance. And I’ve noticed that overall I feel better when I keep the proportion of grains in my diet relatively low.

One diet alone doesn’t seem to be the magic bullet to wipe out all of my issues, but so far the low histamine diet has given me the most dramatic results.

As I continue testing for underlying causes, I’ll get more answers. While this process often makes me feel very impatient (I am going on almost a year of this, after all) I’m glad to be on what seems to finally be the right track.

Additional Resources

Please realize that I am not a medical practitioner, and I provide this information simply to give you some ideas to consider on your pathway to healing your gut.

I have found it necessary to be proactive on my health journey, looking for natural solutions that conventional medical doctors aren’t always aware of or able to provide. I know that I am not alone in this situation – there are many others like me, who aren’t getting the help they need from their doctors.

However, if you can work with a naturopathic doctor or functional medicine doctor to help you get to the root of your gastrointestinal issues, do it. At this writing I have started working with a functional medicine doctor myself, and am thrilled to finally have a health care practitioner who sees it necessary to look at my entire health history and not just my current symptoms. You can look for functional medicine doctors right here.

If you’ve had any experience with any of these elimination diets yourself, let me know in the comments – I’d love to hear from you.

And if you’d like more information about the diets mentioned above, here are some sites I have personally found helpful:

Since first writing this, I’ve learned more about why these diets weren’t enough to make me feel great. Read more here:

Gut Health and SIBO – How I Finally Got Diagnosed

Peeling the Onion – My Journey Towards Better Health


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