Everything you need to know about probiotics

Probiotics have become somewhat of a household staple these days with more and more research coming out on their benefits for our gut microbiome and overall health. But choosing the right one can be overwhelming — how many bacterial strains should it have, which strains are best for your health concern(s), and what about dosing? Let’s simplify things and look at the most important things to consider when choosing a probiotic.

Our microbiome

First, let’s talk about our gut microbiome. Our microbiomes are composed of different microorganisms: bacteria, fungi, and viruses, some of which are “commensal”, meaning they are are neither helpful nor harmful to us. There are also organisms which provide us with health benefits but also benefit themselves from populating our gut. And then there are “opportunistic” organisms, which at normal levels are harmless, however, when levels are imbalanced (which can happen when we suffer from infection, poor digestion, inflammation, or autoimmune conditions), they can become harmful to us. Supplement options that can help support a healthy microbiome include beneficial bacteria that make certain nutrients, protect against harmful infections, and provide anti-inflammatory immune support – AKA probiotic bacteria.

How probiotics help

Probiotic bacteria benefit our gut microbiomes and overall health by decreasing inflammation and strengthening the gut lining (remember the article on inflammation and the gut? If you need a refresher, you can read it here). They also support our immune system, have antibiotic-like effects against harmful microorganisms, and release nutrients that feed the cells in our guts. Suffering from bloating, gas, constipation, or diarrhea can be uncomfortable and may also be a sign that your gut bacteria are imbalanced (dysbiosis). Probiotics help us properly digest and absorb nutrients from food, decrease gas-producing bacteria in our guts, and encourage regular bowel movements. For a probiotic to be effective, it must be able to remain undigested after taking it orally in order to reach our microbiomes. Once probiotic strains reach the gut, they also need to be able to multiply in order to significantly affect the levels of good bacteria in our microbiomes.

Why antibiotics can be harmful to the microbiome

How many times have you been prescribed antibiotics during your lifetime? For most people, the answer is many. Antibiotics work to kill harmful bacteria responsible for infection, however, antibiotics can also wipe out a lot of our good bacteria! This is why sometimes after taking antibiotics, people may notice they catch more cold and flus, experience digestive upset, or feel run-down. Because some of our probiotic, infection-fighting bacteria are killed off, this decreases our immune system function and makes us more susceptible to other infections. It can also affect the levels of potentially harmful bacteria in our guts and cause an opportunistic infection. Clostridium difficilewhich can cause serious digestive upset – is an example of an opportunistic infection acquired in hospitals after antibiotic use. That’s why it’s important to repopulate the microbiome with probiotic (good) bacteria after taking antibiotics or suffering from infection.

Breaking down probiotic strains

Which probiotic strains should you look for? It’s best to consult with a naturopathic doctor who can assess your complete health history, immune function, and any digestive or gastrointestinal concerns in order to find the best fit for you. But below are common probiotic strains with evidence supporting their effectiveness for different health concerns.

  • The most common bacteria in probiotic supplements include Lactobacilli and Bifidobacteria strains. Strains of these bacteria are part of the normal gut flora, but can be decreased in irritable bowel syndrome (IBS), inflammatory bowel disease (IBD), Celiac disease, poor diet, and food poisoning or food sensitivities; they can have their beneficial effects on the microbiome.
  • Lactobacilli – common strains include: L. acidophilus, L. rhamnosus, L. plantarum, L. casei and L. gasseri. Lactobacillus reuteri and Lactobacillus rhamnosus are strains that easily multiply in the gut. Lactobacillus acidophilus is probably the most well-known strain from this bacterial family, as it has been the most frequently used probiotic strain for digestive concerns. Lactobacillus plantarum has been particularly effective in the treatment of IBS.
  • Bifidobacteria – this is one of the most common bacterial families present in our normal gut flora, but these levels are often lower with infection and inflammation. Beneficial strains include B. breve, B. longum, and B. animalis lactis, and B. bifidum.
  • Lactobacillus, Streptococcus and Enterococcus strains are bacteria with the ability to make lactic acid – this helps to prevent harmful bacterial strains from growing in our guts! Streptococcus thermophilus has beneficial effects in IBS and other digestive concerns.
  • Saccharomyces – these strains include S. boulardii and S. cerevisiae, which are actually yeast – not bacteria. Saccharomyces boulardii in particular has beneficial effects in gastrointestinal conditions causing harm to the gut lining, such as infectious diarrhea, IBS, and IBD.
  • More recent research has focused on butyrate-producing probiotic strains. These strains help break down fiber in the gut and as a result make butyrate. Butyrate helps to feed the cells in the intestines, supporting a healthy gut lining. Supplements with these strains are harder to find, but something to look out for! 

Are more strains better? Not necessarily. This can be a bit of a grey area. If choosing a product with multiple bacterial strains, you want bacteria to have a synergistic effect – meaning that they have an even greater beneficial effect combined than each individual strain would on its own. Otherwise, products with multiple strains may be less effective, due to competition between bacterial strains for nutrients in the gut, or prevention of growth of other beneficial bacteria. However, multi-strain probiotics have shown positive results in IBS and other digestive concerns. 

How many CFU (colony forming units) do I need to be taking?

Probiotic dosing is measured in colony forming units (CFU). Many products differ in their CFU levels, which can be quite confusing to navigate. Research suggests that probiotics with at least 10 billion CFU help to support gut health. Higher dosing of 100 billion CFU has been used to help recolonize the gut after antibiotic-associated diarrhea, and dosing up to 500 billion CFU has been used in chronic inflammatory conditions where the gut microbiome is compromised, such as IBD. Dosing is something you should consult with your healthcare practitioner about.

Refrigerated vs non-refrigerated

Most probiotics typically need to be refrigerated – this is because they are live bacteria and require a certain temperature to function best. More recently, some products contain shelf-stable probiotic strains that don’t need refrigeration. Is one better than the other? Ultimately, it really depends on which strains (and how many CFU) the product has and whether these are the right fit for you, but if the product suggests refrigeration it’s best to keep it in the fridge to ensure you’re getting the most benefits.

Probiotics from food?

Diet can be an easy way to add some extra probiotic-support to your microbiome. Probiotic-rich foods include fermented foods such as sauerkraut, kimchi, kefir, tempeh, and yogurt.

As always, it’s best to discuss your specific health concerns with a naturopathic doctor who can help choose a probiotic supplement that’s best for you. But hopefully this information can help you to be more involved in this discussion and make an informed choice!

In good (gut) health,


Images via @nova_probiotics


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Dr. Caroline Lewis (ND MSc) is a Naturopathic Doctor practicing in the Greater Toronto Area. She is passionate about educating women on how to care for their health, so they feel inspired and empowered to reach their highest potential! Her background in Neuroscience, clinical focus in Gut Health, and passion for Holistic Beauty inspire her focus on the gut-brain-skin axis and mind-gut connection. Caroline is also interested in Facial Rejuvenation, Hormone balancing, and Mental Health, and she loves doing Pilates in her free time.