How to Follow a Low-FODMAP Diet the Right Way Without Causing Imbalances to Your Gut Microbiome

If you’ve been diagnosed with Irritable Bowel Syndrome (aka IBS), SIBO (Small Intestinal Bacterial Overgrowth) or have digestive issues, chances are you’ve heard of the low-FODMAP diet.

Many doctors today recommend the low-FODMAP diet to new IBS patients. Most of the IBS & SIBO patients our team of naturopaths treated have tried the low-FODMAP diet some point.

It’s been gaining a lot of popularity on social media in recent years and a lot of bloggers recommend it too.

Several dozen studies been published about the low-FODMAP diet with results such as:

"The evidence to date indicates that restriction of FODMAPs is an effective dietary intervention for reducing IBS symptoms. There are now well-designed clinical trials to support the efficacy of low FODMAP diet with alleviation of GI symptoms in majority of patients with IBS."

Which is why many patients were shocked to learn that the CanXida team of naturopaths (who actually have experience treating IBS) aren’t big fans of the low-FODMAP diet.

Why? Two reasons.

The first reason is because we’ve seen too many patients make mistakes with this diet. You can see some examples of this if you watch the video below which is from our YouTube channel.

Many patients who learn about the low-FODMAP diet think they need to be on it long term. Or that the low-FODMAP diet is a treatment method for IBS or IBS.

Or that the elimination phase of the low-FODMAP diet is meant to followed indefinitely.

But this isn’t true.

If you look at the original research behind the low-FODMAP diet, which was published in 2001 by Dr. Peter Gibson and Dr. Sue Shepherd at Monash University in Australia, it says the low-FODMAP diet should last 2 to 6 weeks. NO MORE.

After which point you’re supposed to slowly reintroduce most of the foods you eliminated.

And that is because of how restrictive it is.

It takes almost all carbohydrates out of the diet.

Remember, we shape our microbiome & gut bacteria by what we eat. So the more restrictive you are with food, the more restrictive the bacteria will become in the gut.

And over time this can create dysfunction. It can create a situation where if you deviate off the diet, you’ll get sick rather quickly. Which of course will make you think “I need to get back on the FODMAP diet.”

Two of the six major FODMAP groups are prebiotics — foods that feed beneficial bacteria in your gut and make them replicate.

And according to a research study from Monash University (where the low-FODMAP diet was invented), “individuals who stay on the low FODMAP diet develop changes in their gut microbiota.”

Notably, a significant reduction in Bacteroides bacteria, which is a beneficial bacteria that helps regulate your immune system and prevents your gut from being colonized by bad bacteria.

The 2nd reason we’re not fans of the low-FODMAP diet is it doesn’t treat the root cause of IBS/SIBO. It doesn’t eliminate the IBS so you can eat like normal person again when you stop following the diet.

If you want to learn what diet does reverse IBS so you eat normally again, check out our 3-step IBS protocol here.

There are other reasons we don’t recommend the low-FODMAP diet to new patients anymore, but we’re not going to get into them here. You can learn about them if you watch our YouTube video above.

We’re not saying the low-FODMAP diet is useless or you shouldn’t give it a try if you’re struggling with IBS or another gut issue.

A low-FODMAP diet can help you discover which foods are triggering your flare-ups. Just don’t make the mistake of thinking you need to be on low-FODMAP for months or years.

Now with that out of the way, here is the PROPER way to go about a low-FODMAP diet, without it screwing up your gut microbiome.

The 3 Phases of the Low FODMAP Diet

Phase 1: The Elimination Phase

As you likely know, FODMAP stands for Fermentable Oligo-saccharides, Di-saccharides, Mono-saccharides, and Polyols.

The Fermentable part refers to foods which cannot be fully digested or absorbed in the small intestine so ferment in the large intestine (colon).

While saccharides are short-chain carbohydrates (sugars) which are found naturally in many foods. Almost all foods that contain carbohydrates have these sugars.

Most people can tolerate these sugars without any problems (unless they eat a whole lot of them at once) but many patients with IBS tend to react to at least one or two of these groups.

The 4 groups you want to eliminate during Phase 1 are:

Oligosaccharides — these are found in foods like wheat, bread, beans, garlic, and the onion family.

Disaccharides — also known as disaccharide lactose, these are found in most dairy products and anything that contains milk or cream.

Monosaccharides — are found in foods high in fructose such as apples, mangoes, oranges and honey.

Polyols — these are basically sugar alcohols & are found in foods that contain artificial sweeteners like sorbitol and xylitol. Certain natural foods like mushrooms and avocados also contain them.

You need to be very strict during this phase. And that means avoiding ALL of the foods on the following list for a 2 to 6 week period.

FODMAP Foods to Eliminate During Phase 1:

    • Bulgur
    • Couscous
    • Semolina
    • Rye
    • Barley
    • Amaranth

Alternatives that are OK:
Rice, oats, tapioca, potato, buckwheat, corn, and quinoa.

    • White
    • Whole grain, & multigrain
    • Pitta bread
    • Bagels
    • Croissants
    • Muffins
    • Pastries
    • Rye & spelt bread
    • Crumpets
    • Naan

Alternatives that are OK:
Wheat free and gluten free bread. Bread made from oat, rice corn, tapioca, cornflour, millet or potato flour. Sourdough is usually ok in small amounts. Spelt sourdough is usually ok.

    • All wheat flour (including rye & barley)
    • Chickpea flour
    • Coconut flour
    • Soya flour

Alternatives that are OK:
See alternatives listed above. For raising agents, baking powder, baking soda, and arrowroot are ok.

    • All wheat based pasta
    • Gnocchi
    • Chickpea or lentil pasta
    • Ramen, udon or egg noodles

Alternatives that are OK:
Wheat free and gluten free pasta that isn’t made from lentils or other beans. Buckwheat pasta is OK but check ingredients because most buckwheat pasta contains at least 30% to 40% wheat. Rice noodles and kelp noodles are OK.

    • Apples
    • Apricots
    • Avocado
    • Squash
    • Blackberries
    • Cherries
    • Dates
    • Figs
    • Mango
    • Nectarine
    • Peach
    • Pears
    • Plums
    • Watermelon
    • Bell peppers
    • Cucumbers
    • Tomato
    • Olives
    • Pumpkin
    • Any juices or jams that contain the above

Alternatives that are OK:
Bananas, blueberries, cantaloupe, cleminte, grapes, grapefruit, honeydew melon, kiwi, lemon, lime, oranges, pineapples, papaya, pomegranate, raspberry, and strawberry. Keep fruit portion sizes small.

    • Artichoke
    • Asparagus
    • broccoli
    • Brussel sprouts
    • Cauliflower
    • Celery
    • Fennel
    • Garlic
    • Beets
    • Mushrooms
    • Onions
    • Okra
    • Peas
    • Sweet potato
    • Yellow and other sweet corns
    • All beans and pulses (lentils, etc).

Alternatives that are OK:
Alfalfa, asparagus, sugar snap peas, bamboo shoots, beansprouts, carrots, chard, chives, lettuce. bok choy, parsnip, potatoes, raddish, seaweeds, spinach, turnip, red or white cabbage.

    • Pistachio
    • Cashew
    • Coconut (dried) in large amounts

Alternatives that are OK:
All other nuts are OK except peanuts which are best avoided even though they’re FODMAP friendly as our team have observed they tend to cause inflammation in patients with IBS.

Milk products:
    • Whole milk
    • Skim milk
    • Milk from other animals like goats & sheeps
    • Milk powder
    • Evaporated milk
    • Condensed milk
    • Yoghurt, including greek and low fat

Alternatives that are OK:
Lactose free milk, almond or hazelnut milk. rice milk, oat milk. Lactose free milk yogurt is OK. Coconut yogurt is OK. Butter and sour cream are ok. Cream is usually OK in small amounts.

    • Any processed cheeses (the ones with individual slices wrapped in plastic)

Alternatives that are OK:
Cheddar, feta, mozzarella, blue cheese, cream cheese, goats cheese.

    • Honey
    • Agave
    • Fructose syrup (FSCA & others)
    • Sugar free chocolate and other sugar free candy
    • Sorbitol
    • Mannitol
    • Xylitol
    • Isomalt
    • Malt

Alternatives that are OK:
Maple syrup in small amounts is OK. Splenda and aspartame are technically FODMAP friendly sweeteners but you shouldn’t be consuming those if you care about your health.

How Long Should I Stay in Phase 1?

The general advice is 2 to 6 weeks. But most patients will really want to aim for 4 to 6 weeks. Whether you choose to follow it for 4, 5 or 6 weeks should depend on the current health of your gut and the severity of your symptoms.

If you’ve only got mild IBS or SIBO or you consider your symptoms to just be a minor inconvenience, aim for 4 weeks or less.

If you’ve got moderate IBS symptoms or you get flare-ups multiple times a week, aim for 4 to 5 weeks.

If your IBS is severe, aim for the whole 6 weeks.

No matter how severe your IBS or SIBO symptoms currently are or how much relief you get while following the low-FODMAP diet, do NOT go over 6 weeks.

Remember, this is a symptom management diet. It was created to help you identify which specific foods are triggering your symptoms. That way you can remove those specific foods from your diet and add the other foods back in.

You don’t want to be stuck in “symptom reduction mode forever.” You want to heal your IBS so you can live & eat like a normal person again and not worry about FODMAPs at all.

Remember, high FODMAP foods are not bad for you.

Most of the foods listed above contain prebiotics. Prebiotics are complex sugars that feed the good bacteria in your digestive system and make them grow.

These sugars are often locked in plant fiber, which only bacteria is able to break down and access.

They’re necessary for long-term gut health.

Phase 2: The Re-Challenge Phase

The purpose of this stage is to test which FODMAP foods can be reintroduced into the diet without triggering flare-ups.

There is no rule for how long you need to stay in this phase.

Some patients can quickly figure out which foods they react the most to and be done with the Re-Challenge phase in 4 weeks. Others may take 8 or 10 weeks to fully figure everything out.

The easiest way to go about this is to print out or write down all the foods you used to eat but eliminated because they were listed above in the high FODMAP foods section.

You then want to reintroduce one or two of them a time, over a period of 2 to 5 days. For example if you want to add mangos, add fresh or frozen mango to your diet for 2 to 5 days. Start with 1/4th of a mango or half a mango. Then increase the quantity to half a mango or even a whole mango on day 2.

If you don’t get a reaction, it means mango is OK to reintroduce into your diet in phase 3.

Do not continue to eat the mango on a daily basis after you’ve finished your test. Remove the mango from your diet again and move onto the next food.

Take your time and test each food for at least 2 days. Don’t test 10 different foods in 1 day just because your gut has finally calmed down and you haven’t had a flare up in a few weeks.

Be patient. Always start with a small amount and then increase it on the 2nd and 3rd day. Certain foods can take more then 1 day to get to your large intestine. So just because you didn’t react to a food on the first day, it doesn’t mean you won’t react on the 2nd or 3rd.

It’s good to keep a journal during this phase as it can be difficult to track all your results otherwise.

One trick that can speed up this process is to focus on 1 food group at a time. Spend the first week just focusing on fruits, then move onto vegetables and then grains, flours or pasta.

Phase 3: The Adapted FODMAP Diet Phase

Phase 3 is basically the food reintroduction phase.

It’s when you finally reintroduce all the FODMAP foods that you discovered you could tolerate during Phase 2.

You should continue to limit the high FODMAP foods you did react to however (at least until you’ve taken some actions to identify and fix the root cause of your IBS, as we describe in our in-depth guide on how to reverse IBS).

Experiment and see what works for you. Remember that the microbiome is very fluid. It’s always changing in response to the foods you eat and the supplements you take. So just because you can’t tolerate a particular food today, it doesn’t mean you’ll still have that intolerance a month or two from now.

Especially if you take probiotics, as they tend to amplify your results.

Is the Low FODMAP Diet Enough to Fully Eliminate IBS Symptoms?

The low FODMAP diet can lower IBS symptoms though it requires the patient to stay off the high FODMAP foods they reacted to in Phase 2 (potentially indefinitely).

So it’s more of a symptom management diet vs a diet that eliminates IBS entirely so you can eat high FODMAP foods again.

This is where supplements like probiotics come in handy, because while there’s no diet that’s going to eliminate severe IBS on its own, it is possible to achieve this when you combine the proper diet with certain lifestyle changes and a few high quality supplements (such as the CanXida line).

For more information on this topic, see our short article titled: Are Supplements Necessary For Gut Issues Such as Candida, SIBO, & IBS Or Can You Fix These Issues With Diet Alone?

What to Do After the Low FODMAP Diet?

Don’t just stop here. There a ton of additional things you can do really nail IBS (and in many cases, send it into total remission).

Check out the MEVY and Low Allergy Diets, which from our experience working with patients, are far superior to the low-FODMAP diet.

These are well tested diets designed to bring your intestinal fora back into balance. They calm and heal the gut from a multitude of conditions including IBS, SIBO, inflammation, candida overgrowth, leaky gut and more — so you can eat & go to the bathroom like a normal person again.

You can learn more about these diets in our in depth guide titled: How to Heal Severe IBS in 3 Steps Using Just Diet & Supplements – Even When Every Other Diet & Treatment Method Failed You Based on 20 Years of Experience Treating IBS Patients

You may also want to check out these shorter posts on our blog as they contain a lot of information related to IBS & how to heal chronic gut disorders in general.

Before you leave this page, be sure to grab your free PDF copy of our 21-Days To Fix Your Gut Health: A Step-By-Step Guide to Healing Your Gut of Candida, Leaky Gut, IBS, & Almost Any Other Digestive Problem ebook.

This is a special 67-page PDF resource we created in an attempt to give folks struggling with IBS and other chronic gut disorders all the tools & knowledge they need to reverse their condition.

Inside you’ll discover more tips on how to slowly transition to our 3-step diet – as well as everything you need to know about how to shop for fruits, vegetables, herbs, grains & flours, pasta, noodles, beans, nuts, breads, soups, spreads & dips, seafood, poultry, meats, dairy, oils, fermented & cultured foods and more.

It also contains free download links to all our other free resources including a 94-page recipe book we created for gut disorder patients, a 24-page grocery shopping guide PDF, a 64-page workbook & food journal, a 5-page monthly meal planner, a 1 page printable food list & several more free goodies.

You can grab it by clicking the image below.