Which is the best probiotic?

In this section we’ll answer the most interesting questions submitted by our followers during the previous week. Today is the turn of one of our French followers, who asks the question mentioned in the title of this post.

These take care of your health, look after them!

Which is the best probiotic? First of all, there’s no specific answer for such a non-specific question. There are thousands of different probiotic brands and even more diseases. We’re not going to give the commercial names of the products as we don’t want to promote any of them specifically. In our opinion most of the probiotic supplements currently available fail to achieve one of their basic goals: reaching the large bowel in an adequate state. Some bacteria, as the ones found in yogurt, can survive the stomach acid. Others can’t. The list below gives credit only to probiotics that have been properly researched and have had some degree of success treating given conditions.

Escherichia coli Nissle 1917: This one had some success treating constipation predominant IBS, dysfunction of intestinal motility and even was considered as effective as Mesalamine in maintaining remission of Ulcerative Colitis. Escherichia coli strain Nissle 1917 has shown to effect the immune system by influencing the maturation and development of the gut-associated lymphoid tissue (GALT) and can regulate the production of some immune mediators. The fact that it comes in an intestinal release form facilitates it reaching the large bowel. This strain persists in the human gut for no more than 14 days so the effects of administration are transient.

Combination of lactic acid bacteria: A famous brand commercializes a mix of 8 lactic acid bacteria that has shown great results both in Ulcerative Colitis and Crohn’s disease. Lactic acid bacteria easily survive the stomach acid so there’s no need for an intestinal release form. The fact that this probiotic is quite expensive and that the same strains can be found in homemade kefir makes us think that fermenting your own milk may be a better alternative. As in the previous one, these strains don’t colonize the human gut so the effect is also transient. If you want to supplement with these bacteria, try to always choose a product with at least 6 different strains and more than 25 billion organisms per dose. Our favourite brands are Now foods and Healthy Origin.

Clostridium butyricum: This particular strain has been used for years in Japan for treating diarrhea and constipation. It’s well studied because it’s one of the strains that produces butyrate. The research points out that the clostridia bacteria may have a huge role in autoimmune disease. The fact that this strain is usually found in the human gut makes it a good option for people with both AI disease and bowel problems. There are basically two products that contain this strain: a Japanese brand called Miyari and another one called Probiotic-3.

Soil based organisms: There’s not much research around these. There has been a huge merchandising around SBO the last five or six years promoting all kind of benefits for the human body. The fact is that these aren’t normal residents in the human gut and although there’s interaction between our body and these organisms we don’t even know if a continuous consumption is safe. There’s also the possibility of an getting an infection that would be very difficult to treat (their spores allow them to resist all kinds of antibiotic therapies), similar to that of a “superbug”. Bacillus subtilis may have an interesting role, but as we don’t have enough experience with it we’ll leave it with a question mark. If after this you’re still thinking about ingesting soil organisms, a better option would be to buy organic vegetables and consume them without washing or just simply working in a garden. There’s basically one product that’s worth the hype: The famous Prescript Assist brand contains many different strains and a huge amount of bacteria per dose. Another great probiotic supplement containing soil based organisms is Garden of Life Primal defense Ultra. This product contains different strains of the most popular probiotic bacteria.

-Bacillus coagulans: This strain seems to improve abdominal pain and diarrhea in patients with IBS. Furthermore, this strains seems to prevent viral respiratory tract infections and reduce symptoms of rheumatoid arthritis. Our favourite Bacillus coagulans brand is Thorne Research.

Saccharomyces boulardii: It’s a well studied fungus. It’s potential role in the treatment of Clostridium difficile infection and Traveler’s diarrhea makes us use it often. It has been used in France for years as treatment for Candida albicans infection as it competes with other fungus in the human bowel. The best products tend to have 5 billion organisms per dose and our favourite is the one produced by NOW foods

Fermented vegetables: Sauerkraut, Pickles, Kimchi and a long etcetera. The second best way of ingesting beneficial and varied bacteria. With a tablespoon full of sauerkraut you’re ingesting more than an entire bottle of certain famous probiotics. Furthermore, some of the strains found in fermented vegetables can persist in the human gut, which is our objective, isn’t it?


It may be as easy as this!

Fecal microbiota transplant: It’s still technically a probiotic. The most promising method for treating several diseases. There’s definitive evidence for using it in Clostridium difficile infection, and there are case reports of complete recoveries in IBS, Ulcerative Colitis, Crohn’s, Rheumatoid Arthritis, Ankylosing Spondylitis, Multiple Sclerosis, Autism and others. The problem is that with the current evidence we still don’t know who may benefit from it, who is the ideal donor and the duration of treatment in each case. The research should go in the direction of sequencing the microbiota in order to match the perfect donor and recipient. Nowadays there are some companies that claim to know how to sequence the human microbiome, and make a lot of money by doing it (a very carefully thought out scam). With the current knowledge there’s no possibility of sequencing the bacterial strains in the human gut one per one, so please find a better way of  spending your money.

-Feed your bacteria: The intestinal microbiota needs soluble fiber, which is usually found in high carb foods such as potatoes or rice. The fact that we promote a low to moderate carb diet for intestinal health and that a lot of people with inflammatory conditions react badly to grains makes us believe that the best source of soluble fiber is psyllium seed powder. There are case reports of people with Ulcerative Colitis going into remission by adding it to their diet and a comparative study with psyllium husk, which is more known, showed bigger production of butyrate after the ingestion of psyllium seed.


Image from Ayers’ page. Scheme resuming the roles of gut flora


  1. -There’s no such thing as “the best probiotic”, they are designed to treat different conditions and the current level of evidence is very low except for treating IBD. Fecal microbiota transplantation is a different story, with huge potential for treating diverse diseases.
  2. -The content of bacterial strains in commercial probiotics is usually lower than  in homemade fermented foods.
  3. -We recommend eating a large variety of fermented foods, dirty organic vegetables and gardening. Our general recommendation is to leave commercial probiotics for special cases such as antibiotic therapy.
  4. -Supplement with soluble fiber such as psyllium seed powder in order to feed your microbiota.
  5. -Different probiotic supplements offer a huge variety of therapeutic options. Bacillus coagulans Lactic acid bacteria, Saccharomyces boulardii, Clostridium butyricum and soil based organisms such as Prescript Assist and Primal Defense are the products that have the biggest scientific support.

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Int J Colorectal Dis. 2012 April; 27(4): 467–474. Published online 2011 December 2. doi: 10.1007/s00384-011-1363-9 PMCID: PMC3307993 A double-blind placebo-controlled trial to study therapeutic effects of probiotic Escherichia coli Nissle 1917 in subgroups of patients with irritable bowel syndrome Wolfgang Kruis, 1 Sigrun Chrubasik,2 Stephan Boehm,1 Christiane Stange,3 and Juergen Schulze


Mutaflor – Chronic Constipation Study MU8902 E.Bruckschen & H.Horosiewicz (1994) MMW;16:241-5

Mutaflor® Chronic Constipation Study MU9202 M.Mollenbrink & E.Bruckschen (1994) Med.Klin89:587-593 Med Klin (Munich). 1994 Nov 15;89(11):587-93.

Treatment of chronic constipation with physiologic Escherichia coli bacteria. Results of a clinical study of the effectiveness and tolerance of microbiological therapy with the E. coli Nissle 1917 strain (Mutaflor)]. Möllenbrink M, Bruckschen E.