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The Gut Microbiome & Low FODMAP Diet: Everything You Need to Know

low FODMAP diet Gut microbiome

The low FODMAP diet, created in Melbourne Australia, is one of the best, evidence-based ways to manage irritable bowel syndrome (IBS). However, it is also a very restrictive diet that limits a whole host of healthy foods that would otherwise nurture and improve our gut health. If you are on this diet for a long period of time to investigate your IBS triggers, it is a good idea to take extra steps to ensure that your gut microbiome is nurtured and not neglected. 

What Is The Low FODMAP Diet?

FODMAPs are short chain carbohydrates that are not well digested by the body. Instead of being broken down completely, they ferment in the gut. 

Which is actually part of the reason they are beneficial for gut health. 

But for people suffering from IBS, the consumption of some FODMAPs can result in symptoms such as alterations to bowel movements (constipation, diarrhea or a mix of both), excessive bloating and gas build-up, flatulence, reflux and abdominal pain. 

low and high fodmap foods

The acronym FODMAP stands for:

Fermentable – these types of compounds are broken down (fermented) by bacteria in the large intestine which produces gas

Oligosaccharides (fructans & GOS) – “oligo” means “few” and “saccharide” means sugar. These molecules are made up of individual sugars joined together in a chain

Disaccharides (lactose) – “di” means two. This is a double sugar molecule

Monosaccharides (fructose) – “mono” means single. This is a single sugar molecule

● And Polyols (sorbitol & mannitol) – these are naturally occurring and man-made sugar alcohols

IBS is quite common with 10-20 out of 100 people suffering from IBS symptoms. It typically develops between the ages of 20 and 30 and is twice as common in women

The low FODMAP diet has revolutionized the management of IBS with 70% of those with IBS trialling the diet finding it relieves their symptoms. 

There are three stages to the low FODMAP diet. 

Stage one is the elimination of all moderate to high FODMAP foods. Most plant-based foods have some level of FODMAPs so the complete elimination of them is impossible unless you are following a strictly carnivorous diet, which is not recommended. 

The aim of the diet is to simply eat below a certain level of FODMAPs that is typically fine even for those suffering with severe IBS.

If symptoms resolve after 2-6 weeks on a strict low FODMAP diet, it is time for stage two.

Stage two is the challenge stage. This is where you continue the low FODMAP diet as your base diet but systematically challenge foods from each FODMAP group in varying quantities to see what your individual tolerance is.

This part of the diet is where you gain a lot of insight into your individual triggers and tolerance levels for certain foods.

Stage three, is the reintroduction phase. Now that you know what foods trigger your IBS and what foods do not, you can hopefully reintroduce a lot of foods back into your diet.

This particular part of the diet is often neglected but the creation of a personalised diet that limits IBS symptoms whilst incorporating some moderate to high FODMAP foods is extremely important for long term gut health and overall dietary quality. 

Phases of the low FODMAP diet

What Is The Gut Microbiome?

The gut microbiome is collectively the term used to describe the trillions of microbes which live in our digestive tract, particularly, the lower intestine. 

The microbiota of the gut have an integral role in digestion, immune function, brain health, and metabolism. There have also been more recent links to mood and mental health. 

Bacteria flora gut microbiome

Our microbiome is influenced by a range of factors including:

  • Age
  • Genetics
  • Stress/mood
  • Illness & gut infections
  • Medication use 
  • Diet 
  • Weight

The research of the gut microbiome is still relatively new and there is no current consensus on what is a healthy or ideal gut microbiome. 

At this stage, it is understood that everyone is different and therefore what is ideal can vary. However, diversity of bacteria is important. Such diversity may mean that your gut is in a better position to fight off and resist pathogens.

How Does The Gut Microbiome Affect Human Health?

Gut microbiome and effects on human health

Interactions between the gut microbiome and human health are numerous and complex. 

Dysbiosis of the gut microbiome is the alteration or imbalance of the microbiota that can result from numerous things including poor diet, antibiotics and bowel infections. 

There is growing evidence that dysbiosis of the gut microbiota is associated with the with some intestinal disorders include inflammatory bowel disease, irritable bowel syndrome, and coeliac disease, and even non-gut related disorders such as allergies, asthma, metabolic syndrome, heart disease, and obesity.

Dysbiosis has been linked to many disease states, however, it is unclear in which direction this link occurs. So a bit of a chicken or the egg scenario. Like most things in the gut microbiome space, this research is only emerging and not clear-cut. 

An interesting area of gut microbiome research is in relation to mood and mental health. Gut bacteria produce neurochemicals that the brain and nervous system use to regulate mental processes including processes related to mood, memory and learning. 

Gut bacteria actually produce 95% of the body’s serotonin. So it makes sense that degradation of the gut microbiome and reduction in the specific bacteria that makes serotonin could potentially lead to issues with mood regulation. 

gut and brain axis

How Does The Low FODMAP Diet Affect The Gut Microbiome?

The low FODMAP diet limits prebiotic fibers which can be detrimental to the gut microbiome.

That is why it is important to reintroduce the FODMAPs back into your diet sooner rather than later to help decrease the chances of making your food intolerances worse.

In research, the low FODMAP diet has been shown to alter the gut microbiota by reducing the number of healthy bacteria and the diversity of bacteria.

The low FODMAP diet increases dysbiosis after just 4 weeks.

How To Maintain A Healthy Gut Microbiome On The Low FODMAP Diet

Whilst the low FODMAP diet can negatively alter the gut microbiome, it can still be worth doing for those whose daily life is affected by IBS symptoms.

If you are concerned about your gut health during your time on the low FODMAP diet, there are a few things you can do to nurture the gut microbiome in the meantime

Food Diversity On The Low FODMAP Diet

The American Gut Project found that people who consumed 30 or more plant-based food per week had a more diverse gut microbiome than those who had 10 or less per week.

dietary diversity

Generally, diversity of the gut microbiome is important to have the right balance and array of different microbes with different functions.

Therefore, whilst the low FODMAP diet is very restrictive, try to include as much variety as you can.

It can be quite common for people to avoid diversity on the low FODMAP diet for convenience. But if you are concerned about the effects on gut health, aiming for more variety can be a useful strategy in nourishing your microbiome. 

Eat Low FODMAP, High Fibre Foods With a Focus on Prebiotic-Rich Foods 

Along with general diversity of plant-based foods ensuring that you are getting adequate fiber on a low FODMAP is equally important. 

You can also go a step further and make sure to incorporate sources of prebiotic fibres.

Prebiotic fibers are the preferred fuel source of gut bacteria, and in turn there are several benefits to these kinds of fibers helping probiotics be more effective

The low FODMAP diet does restrict a number of foods that are prebiotic rich. This is because fructans and galacto-oligosaccharides (GOS) are prebiotic fibres.

Prebiotic foods for gut health

But there are still many that you can actively incorporate whilst on the diet, including: 


  • Red or common cabbage, up to 75g
  • Chinese cabbage (wombok), up to 75g
  • Lentils (½ cup canned lentils, 2 tbsp puy lentils)
  • Edamame (½ cup)
  • Sprouted mung beans (⅔ cup)
  • Potatoes (keep the skin on)
  • Chicory, up to 75g
  • Carrots


  • Kiwi fruit
  • Tomatoes
  • Citrus fruits (except grapefruit)
  • Raspberries and strawberries
  • Unripe (green) bananas

Nuts and seeds

  • Chia seeds
  • Pumpkin seeds
  • Walnuts


  • Oats
  • Brown rice
  • Quinoa

You will want to be mindful of the portion sizes you are consuming of many of these foods, as most are low FODMAP in small serves but rapidly become higher FODMAP with increased portion size. 

You can check on this guide to see which serving sizes are okay to include in a low FODMAP diet. 

Also, note that if you are having recurring symptoms on the low FODMAP diet whilst trying to incorporate more of these foods, you may be doing what is called “FODMAP stacking”.

This is when many small portions of low FODMAP foods are consumed and the total load of those FODMAPs is considered high and is resulting in symptoms.

If you are particularly sensitive, be mindful that this can occur with frequent consumption of these foods even in low FODMAP portions. 

Take Probiotics

Probiotics to help nourish the gut microbiome on the low FODMAP diet

Taking probiotics can help to reduce the impact of the low FODMAP diet on the gut microbiome. 

Probiotics are bacteria that assist with diversifying and increasing the colonies of microbiota in the gut.

Probiotic supplements can be made up of a single strain of bacteria or include several strains. 

Different types of bacteria are helpful for different things. The most common and well-researched are species of Lactobacilli and Bifidobacteria. 

IBS patients appear to have lower levels of both species compared to non-IBS sufferers, so it may make sense to take probiotics that include one or both of these strains. 

The research of probiotic use is mixed and it is hard for researchers to pinpoint their effectiveness for different conditions. 

So whilst, probiotics may be useful on a low FODMAP diet, it isn’t clear how effective they will be in minimising dysbiosis.

Avoid Additional Stressors On The Gut Microbiome

There are many dietary and lifestyle habits that can make it difficult for our microbiome to flourish and diversify.

If you are wanting to limit gut microbiome dysbiosis during the low FODMAP diet it can help to limit or avoid:

The low FODMAP diet can be a great solution for the management of IBS. But it can also reduce the health and diversity of your gut microbiome. 

So for the purpose of gut health, it can be important to take additional steps to nourish the gut microbiota during the low FODMAP diet process.

By Leah Higl

Leah is an accredited practising dietitian from Brisbane. She also competes as an under 75kg powerlifter with Valhalla Strength Brisbane. As both an athlete and dietitian, she spends much of her time developing her knowledge and skills around sports nutrition, specifically for strength-based sports. Although, she works with a range of athletes from triathletes to combat sports and powerlifting. Leah also follows a plant-based diet and her greatest passion is fuelling vegan/vegetarian athletes and proving that plant-based athletes can be just as competitive as their non-vegan counterparts.​