The Functional 4: Best Probiotic Supplements

General Health

written by:

Anya Rosen, MS, RD

Probiotics are all the rage. There are thousands of supplements on the market that not only claim to resolve digestive issues, but also tout numerous other benefits – better skin, stronger immunity, improved energy, weight loss, mental clarity, athletic performance, deeper sleep, etc. Plus, we have millions of influencers who are getting paid by these companies to tell their followers that yes, indeed, their supplement did just that! Listen: I truly wish that there was one magic pill that could do any of the above, but unfortunately it is so rarely that simple. Yes, specific probiotics for specific cases can be an integral part of the healing process – but it requires expert eyes and comprehensive testing to figure out the best probiotic supplements for you.

I’m assuming that you are already familiar with probiotics, so here’s a very basic gist: our gut is filled with hundreds of trillions of microbes, and they are essential for proper body functioning. Probiotics are bacteria (or, sometimes, yeast) that exert beneficial effects on the body – such as the ones listed above. You can find probiotics in some foods that contain live and active cultures, such as yogurt, kefir, kimchi and sauerkraut. Probiotic supplements using specific strains have been studied extensively to treat a variety of health ailments, and the research is certainly promising. 

In this article, I’m going to give you my top four best probiotic supplements that I use in my practice. I have no affiliation with any of these products or brands. However, if you’d like to purchase them at a discount – you can do so by signing up for my virtual dispensary here, which gives you 10% off all supplements plus free shipping. While I hope that you find them helpful, I want you to know that the best way to choose a probiotic supplement (or any supplement, for that matter) is to work with an educated and experienced practitioner who can make recommendations for you based on your body and history.

1. Sacro-B by Thorne

Sacro-B by Thorne contains saccharomyces boulardii, which is actually a yeast-based probiotic. It’s helpful for a variety of gut issues, mainly due to its ability to boost secretory IgA. Secretory IgA is an immunoglobulin that lines the mucus lining of our digestive tract and acts as our immune system’s first-line of defense. S. Boulardii has been shown to help address dysbiosis (AKA an imbalance of good and bad microbes in the gut) by helping fight overgrowth of other pathogens (such as H. Pylori) and improving growth of beneficial intestinal flora. Meanwhile, it also can help with occasional diarrhea – especially when taking antibiotics. 

A common concern that I get around s. Boulardi is that supplementing with yeast can be problematic if there is already overgrowth, such as candida. However, s. Boulardi might actually help fight candida by inhibiting growth and translocation – although the verdict is still out on how effective it is as doing so. Regardless, it will not cause issues if candida overgrowth is present.

2. Ortho Spore IG by Ortho Molecular

Ortho Spore IG by Ortho Molecular kills two birds with one stone. First, it contains bacillus spores: bacillus coagulans, bacillus clausii, and bacillus subtilis. Spore-based (or otherwise known as “soil-based”) strains of probiotics are resistant to harsh environments (e.g. stomach acid) so they can survive until they make their way to the intestines to do their job. Similar to s. Boulardii, spore-based probiotics can help bolster health-promoting, or commensal, bacteria. They also have been shown to impart numerous other benefits, such as increasing short-chain fatty acid production, thereby improving the intestinal barrier and inflammatory response. 

In addition, Ortho Spore IG contains serum-derived bovine immunoglobulin concentrate. This can further improve the gut’s immune response by boosting secretory IgA, as discussed above. Immunoglobulin G (IgG) helps to bind to bacteria and other toxins, promoting a healthier gut environment and lining. 

I find this probiotic supplement to be very well-tolerated and beneficial for patients with small intestinal bacterial overgrowth (SIBO) who tend to have trouble tolerating most probiotic supplements. This is because spore-based probiotics don’t colonize the small intestine, feed the overgrowth bacteria and exacerbate symptoms.

3. ProBiota Bifido by Seeking Health

ProBiota Bifido contains bifido-only probiotic strains, which makes it ideal for those who cannot tolerate lactobacillus – particularly, those who are dealing with histamine intolerance. When you think about histamines, you might think about allergies – and you’re not wrong. Histamines are produced by the immune system whenever it detects a threat and, in excess, causes allergy symptoms such as a runny nose, itching or sore throat, watery eyes, hives or even trouble breathing. Histamines naturally produced in the gut are degraded by the diamine oxidase (DAO) enzyme. There are a variety of variables that can interfere with our bodies’ ability to break down histamines such as overgrowth of bacteria (e.g. morganella, klebsiella, pseudomonas, etc.), hormonal imbalances (e.g. estrogen dominance), certain medications (NSAIDs, acid-blockers, antidepressants, etc.), and more. Lactobacili boosts histamine production, which can further exacerbate symptoms. 

Meanwhile, bifidobacteria can help improve gut health by bolstering levels of commensal bacteria. It has also been associated with other benefits, such as improved blood sugar regulation and immune system responses. Bifidobacteria have also been studied by their ability to convert carbohydrates into butyrate, which fuels intestinal cells and thereby strengthens the gastrointestinal lining. 

4. Fem-Dophilus by Jarrow Formulas

Fem-Dophilus by Jarrow Formulas is my not-so-secret weapon for clients with vaginal health issues such as yeast infections, urinary tract infections (UTIs), or bacterial vaginosis (BV). An imbalance of good and bad bacteria is not a problem that is specific to the digestive tract – it can cause issues in other parts of the body, including the vagina and bladder. Fem-dophilus contains Lacticaseibacillus rhamnosus and Limosilactobacillus reuteri, both of which have been shown in research to help promote vaginal and urinary tract health. 

For acute vaginal issues, I often recommend using Fem-Dophilus as a suppository, inserting one capsule into the vagina at night. Meanwhile, consider broad-spectrum antimicrobials (such as Biocidin) and spore-based probiotics (like Ortho Spore IG, discussed above). If you have a UTI, consider supplementing orally with D-mannose (500mg every 2-3 hours for 5 days or until symptoms are gone). 

Recurrent yeast infections, UTIs or BV are signs that you have gut issues and/or hormonal imbalances. Repeatedly taking antibiotics for them will only make things worse, and likely will perpetuate the cycle (if you have a vagina – you’ve danced that dance at least once before). Definitely reach out for help if this is something that you struggle with.

Best Probiotic Supplements – Bonus Note: Prebiotics

I can’t talk about probiotics without giving a quick mention to prebiotics. Prebiotics are fiber that act as food for probiotics, keeping them alive and well. Good sources of prebiotics are garlic, onions, leeks, asparagus, bananas, oats and many more. The issue, however, is that many people with gut issues do not tolerate prebiotic-rich foods because they are high in fermentable oligosaccharides, disaccharides, monosaccharides and polyols (FODMAPs), leading to excess gas production in susceptible individuals. If that is your case, I caution you that going on a low-FODMAP diet is not the solution; it can further deplete your good microflora, leading to more issues down the road. Instead, you should work with a gut health professional (like us) to help uncover why you cannot tolerate these foods and fix that problem. 

Meanwhile, I’ll leave you with one last supplement recommendation: if you cannot tolerate prebiotic-rich foods, I highly suggest that you try Sunfiber by Tomorrow’s Nutrition. Sunfiber is a prebiotic, soluble fiber that is processed in such a way that it low-FODMAP and does not cause gas or bloating. It is clinically proven to improve digestion (along with numerous other benefits, like better blood sugar stability). Plus, it blends easily and tastelessly into foods or beverages (I like to mix it into oatmeal or a smoothie). Take 1 scoop, which is 7 grams, daily – ideally with breakfast, alongside your probiotic supplement of choice. 

Best Probiotic Supplements – Final Thoughts

With probiotic supplements, it is important to find your Cinderella slipper. If you try any of the above and it makes you feel worse, please stop; just because it’s one of the best probiotic supplements, does not mean that it’s the best for you. If you’re already taking a different probiotic supplement and it makes you feel better, please continue. And if you have recurrent gut issues and can’t get to the bottom of them, please reach out to us for help.

At Birchwell, we team you up with a Registered Dietitian who specializes in functional medicine. They take the time to understand your health from the inside out using advanced lab testing, nutrition, supplements, and lifestyle changes.

Interested in learning more? Book a non-obligation, complimentary discovery call to chat with one of our practitioners and see if our functional health consulting is right for you.


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Anya is a Registered Dietitian, Functional Medicine Practitioner and founder of Birchwell, a virtual integrative health clinic based in New York City.

She specializes in helping her clients identify the root cause of their health concerns through advanced lab testing and her comprehensive assessment. She uses functional diet, supplement, and lifestyle strategies to address any imbalances in the body. Through her integrative and functional nutrition practice, Anya has helped hundreds of adult women and men fix their gut health (e.g. SIBO, reflux, candida, etc.), balance their hormones (e.g. PCOS, peri-menopause, estrogen dominance, etc.), clear their acne or eczema, boost their energy and performance, combat anxiety and depression, improve their body composition, reduce their joint pain - and more.

Anya Rosen, MS, RD, LD, IFNCP, CPT

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