The Best Microbiome Diets - How To Improve Gut Health Naturally

June 6, 2023

If you are looking to improve your gut health you might want to consider making some adjustments to your diet. Diet can have a major and nearly instant impact on the health and composition of your gut microbiota. The gut microbiota can in turn can have major effects on your overall health and wellness.

Figuring out the right diet for your gut is not an easy task, so in this blog we are going to review some of those diets. We will also outline the suggested post fecal microbiota transplant (FMT) diets.

  • How does diet affect the microbiome
  • Best diets for gut health
  • Foods that help and hurt your gut
  • How to feed your microbiome post FMT
  • More gut health tips

The diets we will focus on, are aimed at reducing inflammation in the gut and promoting healthy microbial diversity.

How does diet affect the microbiome?

Studies have show that diet has the power to modify the microbial composition of the gut within 24 hours. These alterations in gut bacteria can be both for the better or to the determinant of one's gut health. Specific food groups have been associated with increases or losses in microbiome diversity.

A diet that includes animal protein, for example, correlates with overall microbial diversity. It increases Bacteroides, Alistipes and Bilophilas in the gut. While a high fat diet has been associated with loss of A Muciniphila and Lactobacillus, which are essential to a healthy metabolism.

The impact of diet on gut health: short term and long term

Diet and microbiome composition are undoubtedly linked, and a poor diet can lead to increase risk of microbiome related conditions. As it turns out one of the worst kinds of diet for your microbiome is a western diet. This means high fat, high energy and often, processed foods.

Unfortunately the western diet is one that is becoming increasingly common across the globe due its convenience and low cost. And though diet can alter the microbiome within 24-hours, eating a poor diet consistently can starve your microbes, leading to long term consequences that cannot be reversed.

The cost of a western diet

In a study published in Cell, researchers showed that immigrants to the United States underwent significant loss of microbial diversity upon moving. The researchers believe a large part of the microbiome alterations are due to a change in diet. Specifically citing the western diet as a contributing factor to an “obesity epidemic” among immigrant groups to the US.

Best diets for gut health

There are tons of diets out their that purport to be good for your gut but which are the best? Some people swear by a low fodmap diet, while others believe cutting out animal products is the key to a healthy gut. We are going to outline some of these diets and break down why they are good for your gut.

Each of these diets has its advantages, but it is important before commiting to one that you are informed on which one is best for you. And it is essential to remember that diet is an often overlooked and not particularly well funded area of healthcare and controlled studies on these diets are lacking and evidence of their effectiveness mostly relies on case studies.

Low FodMap diet

The low FodMap diet is designed for those with IBS, focused on cutting out foods high in Fermentable Oligo-, Di-, Mono-saccharides and Polyols. These food groups are fermentable carbs which can cause bloating, gas and other GI symptoms. The rate of symptom improvement by following the low FodMap diet is up to 80%.

Because a lot of high FodMap foods are actually quite good for you and contain things like prebiotics, many suggest utilizing the low FodMap diet as a diagnostic. Doing so by practicing eating low FodMap foods for about a month and then reintroducing food groups in order to assess which foods are triggers for your GI symptoms.

Specific Carbohydrate Diet

The main focus of the Specific Carbohydrate Diet is to cut out foods that consist of hard to digest carbohydrates. That is because those hard to digest carbs can create an overgrowth of certain bacteria in the gut leading to microbial dysbiosis, which many believe is a contributing factors in conditions such as IBD.

The diet was designed by Sydney Haas, MD in the 1920’s for people with IBD (Crohn’s and Ulcerative Colitis), Celiac, Cystic Fibrosis and Diverticulitis. But it has also been suggested to be effective in other conditions associated with microbial imbalances.


AID stands for Anti Inflammatory Diet and it is a modification of the Specific Carbohydrate Diet. The diet was created using updated research on diet and the microbiome. Unlike the SCD, AID includes some easier to digest grains and has a particular focus on prebiotic and probiotic food intake.

To the relief of many this means the diet is less restrictive than the Specific Carbohydrate Diet. Eating food with probiotics and prebiotics is a large pillar of this diet, instead of just restricting inflammatory foods, it also aims to promote the growth of healthy bacteria in the gut. Instead of cutting out whole groups of “hard to digest” foods, it focuses on specific foods that contain things such as trans fats, refined sugar, grains (except oats) and unfermented dairy.

Plant based diet

Though a plant based diet isn’t for everyone, there has been research to suggest it may be beneficial for the microbiome. Even if you do not follow a strictly plant based diet, we could all probably use to get more veggies and fruits. Specifically ones high in fiber, which is a great promoter of gut health and diversity.

A study out of Italy reported that a vegetarian diet provided a richer gut microbiome. It is not clear if this is due to detrimental effects of meat consumption or whether it is a result of higher fiber rich vegetable consumption, over other food groups. Whatever the case, by at least following a part time vegetarian diet can reduce your exposure to the potential dangers of antibiotic fed and processed meat products.

Foods that help and hurt the microbiome

The diets above can be complicated and difficult to follow. If you are just looking to include a few more gut health promoting foods in your diet and cut down on some harmful foods, you’re in luck. Below we will outline the

Processed foods

The main food group you want to avoid if you are trying to protect your microbiome are processed foods. Processed foods are everywhere and can

be hard to avoid, but if you can cut down, you’ll be doing your gut a huge favor.

So what foods are actually processed?

  • Canned foods - specifically those containing added sugar, salt and preservatives.
  • Foods that include ingredients added for flavor or texture - this means sweeteners, emulsifiers, oils, food coloring and preservatives
  • Ready to eat foods - such as crackers, granola, breakfast cereal and deli meats.
  • Pre-made, frozen foods - these are heavily processed foods that contain a lot of preservatives. They are things like frozen pizza and TV dinners.
  • Fast food - much like pre-made foods, fast foods are heavily processed and include tons of preservatives so they can be quickly prepared.

We all need a quick bite sometimes and avoiding processed foods isn’t always an option but try to cut them out where possible.

The magic of fermented foods

Fermented foods have been consumed for thousands of years largely because of their health benefits, of course they also taste good. So, what about them is good for you? Well, naturally fermented foods contain probiotics, which can help enrich your microbiome.

Here are some fermented foods that are easy to add to your diet:

  • Yogurt
  • Kefir
  • Kimchi
  • Sauerkraut
  • Pickles (if naturally fermented)
  • Kombucha
  • Miso

Not all fermented foods contain beneficial probiotics. Many store bought pickles are fermented in vinegar and not using natural processes. Look for the label “naturally fermented” when buying things like pickles and other vinegary treats.

Prebiotic foods

Prebiotics are foods with indigestible fibres that remain undigested by the small intestine and then are fermented by bacteria in the colon. The fermentation of prebiotics feeds bacteria in the gut providing them with a healthy boost.

Here are some common prebiotic foods:

  • Chicory
  • Dandelion
  • Jerusalem artichoke
  • Garlic
  • Onion
  • Leeks
  • Asparagus
  • Bananas
  • Barley
  • Oats
  • Apples
  • Cocoa
  • Flaxseeds
  • Seaweed

While probiotics provide bacteria to the colon, prebiotics feed and help maintain the bacteria that already exist within the colon -- working with the body's natural microbial composition.

How to feed your microbiome post FMT

After FMT you want to make sure you give your microbiome the best chance to benefit from all the incoming microbial material. To do so it is important to eat a well balanced, nutrient rich diet. Eating foods that are both plain enough, to not cause inflammation but also that contain microbe enriching ingredients. High fiber foods are highly suggested, while foods containing sugar and spices should be avoided. It is also important to keep hydrated, as it is not uncommon to experience diarrhea following a fecal transplants. That means you should avoid caffeine and alcohol where possible.

To review...

  • Plain foods like rice, chicken and broth
  • High fibre foods such as bran, whole grains, fruits and vegetables.
  • Hydrate and avoid drinks with alcohol and caffeine

Although this particle protocol for a post FMT diet is not scientifically assessed, it is the recommendation of many medical professionals who perform fecal transplants regularly.

More gut health tips

It's Not Yet Clear How to Boost the Microbiome. But Diet Is the Best Bet

Why is diet so important to the microbiome? This Time article gives an overview of what we know about the microbiome and diet.

How to Improve Gut Microbiome Health: Development from Infant to Adult

Diet, among other things can have detrimental effects on the microbiome. Learn what else might be harming your gut and how you can make it healthier.

Fecal Transplant Guide: How They Work and What They Can Cure

Fecal transplants are emerging as a groundbreaking treatment for illnesses related to microbiome dysbiosis. Learn more about what they are and what they can treat.