For many people with gut problems like mine (IBS/IBD), following some gluten-free, low carb diet usually alleviates most of their symptoms within a few weeks/months. But sometimes, for some people, it doesn’t. In that case, specialized diets, all similar, but also each more restrictive than the previous, must be followed. Elimination diets are not as effective in my opinion, because some foods can create irregularity as late as 1-3 weeks after they’re consumed, making it impossible to know which food was the offending one.

I’m not a doctor, but I read and I experiment a lot, so here’s a guide:

1. Start with a doctor’s visit
A stool, allergy and blood tests (and possibly a colonoscopy) can find out if the source of your problem is mechanical, food intolerance, auto-immunity, or an infection. If it’s an infection, e.g. C-Diff, some protozoa like B. Hominis, H. Pylori, listeria etc. then you need antibiotics or a fecal transplant. As bad antibiotics are, these bad organisms can’t always be eradicated with diet, because they are capable of eating everything you eat (while most “good” gut bacteria only feed on carbs). However, new research has shown that home-made kefir can help kill C. Diff (commercial kefir has less potency).

2. Paleo/Primal
This is the least restrictive diet, the most balanced of all in terms of nutrients. It has to be 100% gluten-free to see health benefits. Go for up to 100 gr of “net” carbs per day (for net carbs, just don’t count the fiber). In addition to the Paleo diet, also add this list of superfoods (bone broth is super-important for gut health, for example). Reading online, I found that the vast majority of IBS, GERD, diverticulitis, and Celiac sufferers find relief with plain Paleo. Crohn’s and UC patients range from finding full relief, to partial, to not at all. So for some of these more difficult cases, they have to either add 24-hour fermented home-made goat kefir (while cutting down all other dairy for a while), or read next.

3. SCD
If within a month you have started seeing some results (even if they’re not perfect), stay with Paleo. But if you haven’t seen major results with Paleo/Primal, go for the SCD. The SCD is the same as Paleo, but it does not allow tubers/starches as Paleo does. Regarding its suggestion to go with yogurt, prefer home-made goat kefir instead, which is 5x-10x more potent than yogurt. Retain the list of superfoods from the previous diet, avoid vegetable oils, and supplement with vitamin D3 too if you’re not going out in the sun much. Eventually, if this works, you can revert back to the less restrictive Paleo (+ home-made goat kefir), for life (symptoms will return if you stray away from Paleo).

4. GAPS
If within three months you haven’t seen any good result with the SCD, go for GAPS. GAPS has periods of time where you can’t eat any solid food. When you can eat solid food again, it’s just the same as the allowed food list from SCD. Also, whatever I said above for Paleo/SCD still applies when on the phase where you can eat solid food (goat kefir, superfoods, D3, avoid vegetable oils). GAPS is all about bone broths and probiotic pills, trying to “reset” the gut’s flora. It’s a difficult diet, but it’s effective. Eventually, if this works, you can revert back to the less restrictive Paleo (+ home-made goat kefir), for life (symptoms will return if you stray away from at least Paleo).

5. FODMAPs
If GAPS works while in the “intro” phase, but irregularity returns repeatedly when trying to eat solid food (you’d have to try GAPS for 6 months, coming in and out of its broth phases a number of times), try to cut down FODMAPs. FODMAPs include specific food groups (e.g. onions, brassicas, apples etc) that are allowed in all the above diets, but you can’t consume in this diet. Do remain 100% gluten & grain-free, and avoid vegetable oils while on FODMAPs too though. Also, check your D3 levels.

6. Paleo Auto-Immune Protocol
This is the same as #2 above (Paleo/Primal), but without any dairy, nuts, seeds, fruits, yeasts, eggs, shellfish, pepper spices, and no nightshades (no tomatoes, peppers, eggplants, white potatoes). It’s basically just fat (olive oil, tallow/lard/duck fat), meat/fish/organs (preferably grass-fed/pastured/wild), and veggies/seaweed. This diet is best for people with strong auto-immune problems (e.g. Multiple Sclerosis), but sometimes it works for gut problems too. Don’t stay on this diet for longer than 2-3 months though. Revert back to plain Paleo (+ goat kefir), by introducing small amounts of the non-allowed foods, one by one (allow 1 week before you introduce the next one).

7. Fecal Transplant
If you’re among that 3%-5% of the IBS/IBD patients where none of the above works, then it’s possible that your problem is an infection of an unknown origin, that tests won’t identify. In that case, revert back to Paleo (plus home-made goat kefir), for life, and get a fecal transplant from a healthy donor. Until modern medicine catches up, this is your only hope.

Personally, I was lucky to be able to fix my IBS-D with a mix of Paleo and SCD. That is: Paleo + home-made goat kefir, up to 100 gr of “net” carbs per day (I also followed the Paleo-ketogenic diet for a few months, up to 50 gr “net” carbs per day), vitamin D3 3000 IU per day, and only few tubers/starches. Since almost all these IBS/IBD conditions eventually create malabsorption problems (I was very surprised to find out via a blood test that I was short on B12, since I eat a lot of meat/fish), I supplement a few times a week. I track what I eat via Cronometer, so if I seem short on a nutrient on a weekly basis, I supplement with it once. Put money aside to check your CRP (inflammation), B12, iron, calcium, folate and D3 levels via a blood test every year. It’s all about optimization, especially for us with a sensitive gut.

Good luck!