Published Oct 7  |  7 min read  |  Get the FREE Leaky Gut Recovery Guide

Can probiotics help with your leaky gut?  Yes, but timing is everything and no one else is talking about it.  Let me explain…

I take probiotics daily. When I wake up you might find me popping 1 capsule of Smart Probiotic, a high strength multi-strain probiotic my research team and I spent 3 months researching & developing (available here).

Then at lunch time I might be tucking into an organic jar of ‘live’ sauerkraut. And by dinner I might be eating some unwashed Jerusalem artichoke from the farmers market.

This makes me sound like a beanie-wearing hipster. But I don’t care.

You see, the good bacteria from probiotics have proven to be one of the most important supplements/foods I take to keep my gut in good health.

The funny thing is, this should not be surprising. After all, it turns out our ancestors have been seeking out and consuming lacto-fermented foods – hello yogurt – for well over a million years to help with digestion. (Before we created fire!)

And if you suffer from leaky gut, you could be looking at your new best friend.


…Whilst everyone is telling you to down probiotics like they’re going out of fashion, I have one very important caution in regards to timing.

I recommend that when your gut is at its very worst, you probably want to hold off on probiotics just for a few weeks until you’ve healed it somewhat.

Why leaky gut sufferers should wait a few weeks before taking probiotics

As you know leaky gut syndrome means toxins are able to pass through your gut lining and into your bloodstream. Cue inflammation and immunity problems!

Well, whilst your gut is so hyperpermeable it isn’t a great idea to be downing a whole heap of probiotics. Because even though they are good bacteria, they may similarly be making their way through your (leaky) gut barrier and into your bloodstream.

Instead, of helping re-inoculate your gut, they may end up causing more harm or simply not being used where they should – ie in the gut.

So the simple solution is to first spend a couple weeks healing your leaky gut, so it is less permeable, and there is less bad bacteria in there. All my tips for doing this are in my free leaky gut recovery guide.

When you read my guide you’ll realize that before you start supplementing with probiotics, you’re much better off eating a clean diet (think no processed foods, grains or sugar etc) with digestive enzymes and also megadosing with L-Glutamine.

These 2 supplements will help your gut’s health recover in a more direct way than probiotics. And by doing that they’ll prime it for probiotic use.

For example, whilst probiotics can indirectly aid regeneration of gut lining, L-Glutamine can directly feed the cells so they can rapidly regrow and digestive enzymes can break down particles so there is less irritation of gut lining (amongst other gut benefits).

I’ve written extensively on why these 2 supplements help: glutamine article and digestive enzyme article.

Why your less leaky gut will love probiotics in 2-4 weeks

If you’ve read my free guide on how to tackle your leaky gut, then by about the 3rd or 4th week you’ll be ready to start taking probiotics.

And now that you have patched up the ‘holes’ in your gut, it will be crying out for probiotics as they will help build a healthy layer of good bacteria to protect the gut. Kind of like rebuilding a house and then putting a nice quality roof on top to protect it!

In fact, by this point you’ll find probiotics are the #1 thing to get more of in order to restore your gut health.

Unfortunately, when most people try to explain ‘why’ they help, you’ll get some BS-sounding answer like “gut microbes help maintain your gut lining, so when there is an imbalance cells of gut lining start to deteriorate, which can lead to leaky gut”.

Meh. Vague and incomplete.

So here’s my plain English, but highly specific, explanation of how probiotics (from food or supplements) are the missing piece for us leaky gut sufferers!

  1. Healthy gut flora – supported by probiotics – helps your gut lining’s ‘gatekeepers’ (a.k.a. Tight junctions) decide if something should pass through the lining or not. That means molecules which are good (nutrients) get through and those that are bad, and thus banned from entry (undigested large food particles etc), stay out. By selectively allowing entry you get nutrient absorption.  Fantastic. And by preventing toxins slipping through and into the bloodstream, you help avoid all the immunity responses / inflammation.  Even better.
  2. Good bacteria, from probiotics, helps prevent bad bacteria and yeast from hanging around, which means less leaky gut. It also means that you may be able to say goodbye to related conditions like SIBO and candida, respectively. So it’s no wonder that I sometimes think of probiotics like mini Gandalfs (from Lord of the Rings) shuttling around your intestines yelling at bad bacteria “Thou shall not pass!”. Unsurprisingly probiotics are being used these days to target bad bacteria in other parts of the body too, including your teeth (eg tooth decay and periodontal disease).
  3. Healthy gut flora brought about by probiotic use, can also support leaky gut recovery because it helps us breakdown foods and turn them into nutrients – a more indirect digestion aid than digestive enzymes themselves, but very helpful nonetheless.

Probiotics also work to support your gut health in other ways, such as assisting in the secretion of inflammatory mediators (kinda like organizing your emergency services so they’re not all going around blaring their sirens and causing havoc), supporting secretion of additional intestinal mucus (the protective layer) and even helping in breaking down fiber into beneficial short chain fatty acids like butyrate.

Best of all, probiotics don’t just sound good on paper. Perhaps the coolest thing about them is that recent studies have shown that markers of intestinal permeability decrease dramatically when probiotics are taken!

For example, in this randomized, double-blinded and placebo-controlled study (Int Soc Sports Nutr 2012), zonulin levels in subjects’ feces were significantly reduced after 14 weeks of probiotic use compared to those who didn’t take probiotics.

And since more zonulin means more intestinal permeability, the results indicate probiotics can lead to a healthier intestinal wall.

How can anyone not love these little guys!

Eating v supplementing with probiotics – what’s better?

Eating probiotic-rich foods is a fantastic way to restore your gut flora. A lot of people will turn straight for raw cultured dairy like yogurt or cheese, because, well they taste amazing!

But even in their raw and unflavored state these 2 types of food don’t agree with a lot of people with poor gut health (or even when they recover their gut health).

Worse yet, it is not always easy to find truly raw cultured dairy.

Unsurprisingly, I see people blindly eating processed and flavored yogurts high in sugar, just because some smart marketing people have slapped all kinds of crazy probiotic claims over the labels. A big mistake.

If you really want to enjoy these types of flavors I recommend coconut kefir. Paleo certified and delicious.

Another interesting source of probiotics (and fiber and digestive enzymes) is unwashed fibrous vegetables.

Here you can enjoy soil-based microorganisms in high supply. Plus the soluble fiber in certain vegetables, eg onions, Jerusalem artichokes etc, helps feed the gut flora (I.e. a prebiotic). This probiotic + fiber/prebiotic combo is often found within probiotic supplements themselves (eg FOS, inulin etc), due to the beneficial 2-way relationship.

Importantly, it’s worth noting that prebiotics can feed both good and bad bacteria. That’s another reason why I suggest first spending 3-4 weeks healing your leaky gut, before starting on probiotics and prebiotics.

So unwashed fibrous vegetables are perfect, right?

Well, unfortunately the answer is not simple, because on the health of the soil your vegetables come from. And since you can’t be certain of the origin of store bought vegetables, that is a no for me.

Whilst home-grown is much better, soil testing is a good idea. If you live in a typical, built up area, soil quality might not be great. So be very careful with this approach.

Overall though, I tend to focus my probiotic eating on the hero of vegetable fermentation…cabbage. Whether done German-style (sauerkraut) or Korean style (kimchi), it tastes great!

And to a lesser extent I eat pickles (fermented cucumbers) and peppers – and of course some other varieties of kimchi, eg daikon kimchi.

Of course you can ferment just about any vegetable and end up with a jar of goodness, but the three mentioned above work best in my experience.

But the key is to either make these yourself OR buy organic, refrigerated, ‘live’ versions of them.

Do not buy mass produced, shelf-stable sauerkraut for example. It has likely been pasteurized and all the beneficial bacteria destroyed. Plus these processed versions are usually loaded with other bad stuff from excessive sugar to additives.

Although I would love to say I make my own sauerkraut and kimchi, the truth is I don’t. Life is busy and everything is a tradeoff. So I buy mine from the local organic store.

A lot of people tell me this option is not viable long term though. You see, in order to get a good amount of probiotics from these foods you need to eat quite a lot. And when jars of the high quality, live sauerkraut etc cost $10 – and people go through several a week – the costs really start to add up.

I get that. And that’s one of the many reasons my research team and I spent months formulating a smart, high strength probiotic supplement.  It is such a simple solution for our daily probiotic needs.

But the other reason I use probiotic supplements is to ensure a varied supply of probiotic strains. In other words, to make sure my system is getting a fuller spectrum of strains.  For example, the probiotic we designed has 12 different types of powerful strains.

Supplementation is also smart because even if you eat a lot of probiotic rich foods, you still won’t be getting a high enough dose – especially during the early stages of gut health recovery. (I walk through dosage info below).

Also, to be honest, as much as I love fermented vegetables, they have a lot of ‘taste memory’. Which means you can easily get sick of them if you have them too often. That’s when being able to pop back a flavorless pill or powder of probiotics is so nice!

With all that said, no amount of probiotics in the world will help you if the rest of your diet is bad. So make sure you follow my diet recommendations in this free guide.

How much probiotics should I take?

Unlike a lot of other supplements that can cause problems from overdosing, it’s pretty hard to take too much probiotics.

That said, you can definitely experience some upset stomach issues (gas, rumblings, cramping) when you first start taking probiotics.

The good news is that in most cases this is actually a sign the probiotics are working. You see, during the first week or two of use, the good bacteria will be piling into your system and kicking bad bacteria’s ass. This is known as ‘die off’. And whilst your body is detoxing itself from all the bad bacteria and yeast in your system you’ll probably know it too!

Probiotic dosage recommendations vary widely. And I guess there are a few points of distinction to draw, so you have a complete and balanced answer.

Most people never mention these points of distinction, but they are very important…

  1. Initial dose v long term dose. During the first 2-3 weeks of use I would take a high dose, because at this point my gut is in dire need of good bacteria. Something like 100 billion a day, with half in morning and half before going to bed. Then long term I would be happy with more like 40-50 billion.
  2. Attack dose. I also go with a higher and more frequent dose of probiotics during times when my good bacteria is being wiped out, eg antibiotics, NSAIDs, steroids, acid blockers, food poisoning / diarrhea etc. Once again, this is a temporary upping of the dose.
  3. Support dose. I might also up the dose when good bacteria is being constantly but less severely attacked, eg when traveling and eating low quality meat, drinking chlorinated water, drinking alcohol etc. These all hurt your gut flora.
  4. Quality of probiotic. Probiotics vary in quality greatly! Generic brands or cheap brands tend to sit on shelves for months before even hitting retail stores. And since probiotics decrease in potency over time you can end up with a bottle of probiotics that says 10 billion on the label, but actually only has less than 1 billion live bacteria left!
  5. Presence of prebiotic. Prebiotics such as FOS (fructooligosaccharides) or inulin or best of all, Jerusalem artichoke, in your probiotic can help ferry the probiotics through your acidic stomach by giving them more lasting power. That way they can survive to do their work in the intestines and colon, where they are needed. Ie you enjoy a more complete colonization. Said differently, armed with a prebiotic, you should need less probiotic than otherwise for it to be effective.  But you should not rely on the prebiotic in your probiotic alone for this. Make sure your diet is high in prebiotic foods too, as I talk about in the next point.

When should I take probiotics?

Simple. Take them in the morning when you wake up and just before you eat breakfast.  Here’s why…

…in a 2011 study (Benef Microbes. 2011 Dec 1;2(4):295-303) a team of Canadian researchers actually built an end-to-end fake digestive tract, complete with a fake stomach and intestines.  But of course, they used real acid, enzymes, bile etc to mimic the human experience.

When they fed the mock digestive system a multi-strain probiotic before, during and after meals, they found survival rates were highest when the probiotic was taken between 30 minutes and just when starting a meal.

Conversely, they found probiotics did not survive in high numbers when the supplement was taken 30 minutes AFTER a meal.

One last interesting finding was that survival rates were highest when the meal eaten contained some fat.

So based on this actual study of probiotic survival rates I like to take my probiotic at 6am, which is just when I wake up and usually eat my breakfast.

Ie I take my probiotic when I wake up and then a few minutes later I crawl into the kitchen and rummage around my fridge for a light meal with some fats (hello avocado my good friend!).

And if you are taking a higher than normal dose, split it up, so you take half before breakfast and the other half just before you go to bed.

Importantly, make sure you consume prebiotics and probiotics in food form during the day too. These will play an important role in making sure probiotics get down to where they’re needed and get utilized properly.

I talked about the probiotic-rich foods I eat above. As for prebiotic rich foods, I try to eat garlic, leek, onion and where possible chicory root. But more often I go to asparagus and green bananas. Green bananas in particular carry the added benefit of being a good resistant starch (RS), which works really well to make sure the bacteria in the colon are in good health as well.

In fact, there is growing research on the interplay of resistant starch with probiotics, and your gut flora in general.

Probably the simplest way to get RS prebiotics is through a potato starch flour like Bob’s Milled Potato Flour. You definitely want to ease into this. Don’t megadose! Do the opposite. As it can be fairly tough on your system when you first take it.

Lastly, I just want to reiterate that probiotic and prebiotic foods/supplements are best taken after you’ve been working on healing your gut for 3-4 weeks; ie clean diet, L-Glutamine, digestive enzymes etc. All the things I advise in my free leaky gut recovery guide.

Because only at this point will your gut be really primed for the effects of probiotics/prebiotics, as discussed at the start of this article.

How long should I take probiotics for?

Unlike a lot of other supplements that you might only use for a short period, eg anti-fungals for candida, or you might cycle on and off, eg vitamin D in summer, I take probiotics every day.

The reason I do is to help ensure leaky gut doesn’t come back.

You see, by providing my guts with a constant supply of good bacteria, the balance of good v bad can stay around 80-90% good to 10-20% bad. And that sort of ratio supports a healthy, balanced and stable gut flora.

The good news is that you shouldn’t need to megadose probiotic supplements to help maintain this healthy balance. Instead, simply taking the recommended dose of probiotics (on the label), paired with probiotic-rich foods, will help do the job.

Best type of probiotic to take for people recovering from leaky gut

As you’ll see from the dose comments above, I recommend you take a high potency probiotic with a prebiotic component included (eg FOS, inulin etc). Obviously make sure it is not a generic brand or cheap product.

In addition, you should be looking for a multi-strain probiotic. Importantly, more is not always better.

You see, too many different beneficial bacteria in one probiotic supplement could end up in a bacteria battle royale! This happens when there is too many types and the bacteria end up competing with each other before they can each find their own home in your system.

That’s why I recommend you look for a product with around 10-12 strains.

The 2 most important groups of bacteria are Lactobacillus and Bifidobacterium. So making sure you choose a product with strains from these 2 groups is crucial, eg lactobacillus acidophilus.

Strains like L. Acidophilus, B. Bifidum, L. Salivarius, B. Longum, L. Rhamnous, L. Plantarum (you’ll find this one in fermented cabbage!) are all great and contribute in different ways.

After receiving hundreds of requests from Goodbye Leaky Gut readers, my research team at Essential Stacks and I decided to develop a next generation probiotic-prebiotic complex that ticks all the boxes above.

And the good news is that after months of research and development it is finally available here.

It is the exact probiotic formulation I’ve always been looking for, because it is strong enough to meet our requirements (50 billion CFUs), has 12 different high quality strains, contains 2 premium prebiotics (Inulin and Jerusalem Artichoke), and uses delayed release capsule technology to help the probiotics survive the journey.

This combination means you get your probiotics delivered to the place where they’re actually required (ie your gut).  And this optimal delivery process makes all the difference.

You can purchase Smart Probiotic here on Amazon.

Want a simple solution for your leaky gut that actually works?

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