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The Best Probiotics for SIBO

An important aspect of SIBO treatment is probiotic supplementation. It can be confusing to know which ones to take, when and for how long. If you’re interested in learning more about including probiotic supplementation in your SIBO treatment plan, read on to find out what are the best probiotics for SIBO, how to take them and where to find the right products.

What is SIBO

As the name suggests, small intestinal bacterial overgrowth (SIBO) is when you have too much bacteria in the small intestine. Bacteria are single-celled organisms that are actually essential to human health! However, in order to stay healthy, we need to have the right kinds of bacteria and they need to be in the right places. We have large concentrations of bacteria in the LARGE intestine, as well as on skin. When bacteria are present in large quantities in the SMALL intestine, however, they can disrupt the delicate balance this organ requires in order to carry out the complex processes of digestion.

SIBO is associated with a range of symptoms, including: 

  • Gas
  • Bloating
  • Nausea
  • Fatigue
  • Loss of appetite
  • Feeling of fullness
  • Constipation
  • Brain fog
  • Joint pain
  • Abdominal pain
  • Abdominal distension

Many SIBO symptoms overlap with symptoms of other conditions. Thus, testing is used to confirm diagnosis. If you suspect that you may have SIBO, your doctor can order a breath test.

What are Probiotics

“Probiotics” is just a name that’s been given to bacteria (and other microorganisms) found in food, beverages, supplements and personal care products that have, or may have, health benefits when consumed or applied. 

Probiotics have a range of health benefits, as research continues to demonstrate. When it comes to SIBO, probiotics can be part of a diet-based protocol to treat SIBO, improve outcomes and prevent recurrence.

One question I hear a lot is: “Can I take probiotics while I have SIBO?” Let’s unpack that question. 

Can I take probiotics while I have SIBO? 

Patients often tell me that their doctor told them not to take probiotics until they’re SIBO-free or that they “heard” you shouldn’t take probiotics while you have SIBO. The reasoning is that SIBO is a case of too many bacteria, so we shouldn’t add any more, and that doing so can exacerbate the problem. I want to acknowledge that this reasoning makes some sense and such recommendations come with good intentions. 

However, it’s important that we look at the research so that we’re making the best recommendation possible for patients. So, what does the research say?

  • The results of this randomized prospective pilot study indicated that treatment with probiotic out-performed treatment with the antibiotic metronidazol
  • Another prospective study comparing IBS patients with and without SIBO, found that probiotics were more effective at improving symptom scores for the SIBO patients than those without SIBO

As I’ll describe below, it’s important to keep a broad perspective when treating the microbiome with probiotics. In short, yes it is safe to take probiotics while you have SIBO. In fact, in some cases probiotics can actually treat SIBO.

The Multi-Strain Approach  

As we think about which probiotics are best for SIBO, I think it’s helpful to use the analogy of a garden for the microbiome. After all, the bacteria in our guts are living organisms and create real habitats, of sorts. As with a garden, it’s not just what we plant, but how and in what conditions that matters.

First and foremost, supplementing with probiotics is just not worth it if you’re eating an inflammatory diet, living a sedentary lifestyle, and are stressed out around the clock. Once you’ve addressed those issues, it’s time to determine which probiotics you should be taking, and for how long, which I will outline in the section below.

Another aspect of tending our microbiome garden is what I refer to as the multi-strain approach, and this can be a game-changer in terms of probiotic supplementation. Most probiotic supplements are sold as one- or two-strain formulations. The most popular formulations that I see contain a combination of lactobacillus and bifidobacterium organisms. This class of probiotics is well-researched, which is great. 

However, the research points toward a multi-strain approach as the most effective approach to gut related disorders. That’s why I recommend patients use 3 different formulations together when dealing with SIBO. This is what I’ll summarize below.

The Best Probiotics for SIBO

The probiotic market has exploded over the last decade or so. So, it can feel really overwhelming to determine what you should take for the best results. Many people just choose the most popular brands or the ones with the best marketing. A common question that I get is, “can’t I just eat yogurt to get probiotics?” Many clients also come to me drinking what are really just sodas dressed up to seem healthy, IMHO. These beverages are heavily marketed, and contain prebiotic fibers, apple cider vinegar and probiotics. They’re mostly all sweetened with some type of trendy artificial sweetener, such as stevia or fruit juice concentrate. I recommend foregoing these trendy, shiny products, and getting really high quality probiotics instead. 

I recommend supplementing with probiotic capsules daily. In order to get the therapeutic effect from these products, you need to use the dosage indicated by the research. We can do that by taking capsules, not by drinking soda. 

In order to simplify this as much as possible, I created a protocol on my online dispensary that includes formulations from the following 4 classes probiotics:

  • Lactobacillus
  • Bifidobacterium
  • Saccharomyces boulardii
  • Soil-based Bacillus Strains

You can order directly from this protocol rather than scouring the internet for what you’re looking for. Why order from this protocol? First of all, I’ve taken the leg work out of the process for you. Second, quality is important when it comes to supplements, which are not tightly regulated. Here are some more reasons:

  1. You’ll get a discount. So, they’ll be cheaper right here than other retailers.
  2. Fullscript is a small, innovative company that is making meaningful contributions in the health and wellness space.
  3. Fullscript stands behind the quality of their products and their shipping.

This protocol includes 3 different products. I recommend taking all 3 daily for 1-3 months to start.

How Long to Take Probiotics

How long to continue supplementing with probiotics depends on your individual health history and symptom progression. If you’ve been struggling for a long time (years) with SIBO or other gut issues, you may need to continue taking probiotics for 6 months to a year. Those with less acute issues, and more recent onset may only require 1-3 months of supplementation. 

As always with dietary interventions, I always recommend tracking intake and symptoms via a food journal or diary. You should record what you had to eat or drink, the amount, the time of day and any symptoms and when they occurred. This will help you identify how your symptoms and digestive health are progressing. Sometimes we don’t notice shifts when they happen over a longer period of time. That’s why it’s important to track while you’re running an intervention, whether it’s a dietary restriction or a supplementation protocol. 


Probiotics have been shown to be effective in treating SIBO and improving related symptoms. In order to get the best results, you should take a multi-strain approach, seek out products from reputable sources, be consistent, and record your symptoms and intake. 

Head to my simple and straightforward probiotic protocol to get started today. 

As always, if you need more support with your specific case, you can book an intro call here.

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