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Understanding probiotics, prebiotics, and fermented food: Where to start for a healthier gut.

Updated: Sep 21, 2023

If you're in the gut health space, you've probably heard about probiotics, prebiotics, and fermented foods.

And you've likely gotten opinions about all of them and been told that one or all of them cured your friend so-and-so.

But when you go to the health food store, there are literally hundreds of possible probiotics you could be taking.

Then when you start to add in a prebiotic, you feel even more bloated than you did before.

And you've been drinking kombucha for weeks but the only change you've noticed is a lighter wallet.

Let me help clear up some of this confusion and leave you with practical insight of the world of probiotics, prebiotics, and fermented foods.

First, let's get acquainted with your microbiome

This will clear up why you would take any of these things to begin with. It's good for your gut is the most surface level answer hence the confusion.

upclose picture of microbiome with various different coloured micro-organisms

The gut microbiome is the key player is our digestive functions and really our overall health. The microbiome, is an ecosystem of trillions of bacteria, fungi, and other microorganisms living in our digestive tract. You can learn more about the many functions of the microbiome here.

A healthy microbiome is one that is diverse and abundant in many different types of micro-organisms. In various health conditions and in particular conditions like IBS, heartburn, and constipation we see unbalanced microbiome (a phenomenon we call dysbiosis).

Correcting a dysbiosis is the goal that we are trying to achieve when we incorporate probiotics, prebiotics, and fermented foods.

It's really important to think of your microbiome as an ecosystem. Don't get hung up on good and bad bacteria - it's a oversimplification of a complex system. Think balance instead as we generally want a little bit of everything.

So what exactly are probiotics, prebiotics, and fermented foods?


Probiotics are supplements containing live micro-organisms. They tend to be filled with good ratios of more beneficial organisms that tend to be diminished in dysbiosis.

There is lots of research showing benefits of different probiotics for different conditions. BUT knowing which one is really important to actually see a benefit.

White bottle with 3 pills underneath cartoon of the digestive tract

Probiotics are the most expensive of the 3 and unfortunately cheaper probiotics do tend to work less effectively. And the wrong probiotic can also make symptoms worse.

Probiotics don't actually change the ecosystem of your microbiome they just help changed the function. I don't tend to use probiotics indefinitely but rather use them during strategic times to help shift function in your gut. You can learn all about probiotic specifics from this blog here.

I find probiotics don't work all that well on their own. They work best when in conjunction with nutrition optimizing, sleep, and movement. If you're not there yet, hold off on splurging on the probiotic.


Prebiotics act as food for the beneficial bacteria in our gut. Unlike probiotics, prebiotics are not living microorganisms, but they play a crucial role in maintaining a healthy microbiome.

Photo of prebiotic foods like garlic, onions, leeks, bananas, apples

When we consume prebiotic foods, they reach the large intestine where they are fermented by the gut bacteria, producing short-chain fatty acids (SCFAs), which are essential for a healthy gut lining.

They also help feed a variety of organisms supporting good diversity and balance.

The great thing about prebiotics is that they are much cheaper than probiotics and can create lasting change in our microbiome. You can find prebiotics both in supplemental form and in a wide range of foods such as garlic, onions, legumes, oats, bananas, asparagus, flax seeds, chia seeds, hemp hearts, and most of our veggies.

This is an easy place to start if you're looking to improve your gut health. Plus you'll also get tons of other nutrients from these foods.

However, prebiotics may create problems in an unbalanced microbiome, an unfortunate irony. The most common mistakes I see with prebiotics are taking them too early in a gut healing protocol and taking too large amounts. Both these mistakes make bloating and diarrhea worse.

Always start low and slow with prebiotics. This allows your microbiome to adjust. Some bloating and gas is okay.

If all your symptoms are getting worse no matter what with prebiotics, we may be dealing with a specific type of dysbiosis or overgrowth. Do yourself a favor and consider reaching out for help at this point. Doing cleanses without a plan can make things worse in the long-run.

Fermented Foods

Fermented foods contain both live organisms and food for organisms. They are like a combo of probiotics and prebiotics!

Common fermented foods include yogurt, kefir, sauerkraut, kimchi, miso, sourdough,

Bowls of fermented food like tempeh, kimchi, yogurt, and pickles

kombucha, and all your pickled foods.

Incorporating fermented foods into your diet on a regular basis (few times per week) is a great way to support on-going good gut health!

Can fermented foods work just as well as probiotics? Probably not.

Fermented foods don't contain any where near the bacterial culture levels that we see in probiotics and their specific bacteria is not as specific as what we see in probiotics. Certain yogurts can be a small exception to this rule.

In my practice, fermented foods are brought in to maintain a healthy gut once we've gone through a lot of the healing work. They are not usually part of an active treatment plan.

How to use this information going forward:

The gut is complex but building a healthy gut is not necessarily complicated.

Probiotics, prebiotics, and fermented foods are important aspects for improving microbiome health and this is a key factor when we talk about a healthier gut.

BUT the gut and it's microbiome is also heavily influenced by the gut-brain axis (mind-gut connection), our sleep patterns, our movement, and our hormones.

This is not to say you need to do all these things at the same time, but you can't start and stop with probiotics and prebiotics and except long-term results.

Generally I suggest started small and building up prebiotics and fermented foods in your diet and leave the probiotics until you have an expert guidance.

Looking for more?

The world of gut health can feel overwhelming. There is so much information out there and it's hard to know what you should be following. It can also feel difficult knowing how to start.

This is why I've done the work for you and put the foundations into an easy to follow and practical course. It's backed by evidence, experience, and the results I see with my patients. Best of all, there's no unnecessary food restriction.

If you're someone who is struggling with IBS or think that you might have IBS, then you need to check out The IBS User Guide.

Multiple screens with images from a course called the IBS User Guide

It's all the information you're craving and not getting in your appointments with your doctor. You can access the course at any time but it also runs live 2x/year if that is more your style

If you're someone who struggling with their gut health or perhaps simply interested in learning more about how to improve your gut health, then you need to check out Elevate your Gut

This is full of foundational gut health knowledge to help you gain a solid understanding of what’s going on in your body so you can make tangible changes that benefit your overall health.


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