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Industry Voices: Designing Probiotics - You Get What You Select For

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By Bernat Olle, PureTech Ventures

A phrase by David Relman in a recent article in the San Francisco Chronicle sums up best how researchers in the microbiome field seem to view commercially available probiotics: "these somewhat irrelevant microorganisms." Data generated to date testing probiotics in a long list of diseases have occasionally shown some beneficial effects. For example, some studies have shown that certain probiotics such as L. rhamnosus GG, L. reuteri, L. casei Shirota, and B. lactis Bb12 can shorten rotavirus diarrhea by more than a day, and a small study showed a mixture of lactobacillus, bifidobacterium and streptococcus strains can reduce pouchitis flares. However, as a whole, the clinical efficacy data with probiotics has not been very convincing. In contrast, their safety track record has been excellent, and many physicians are comfortable suggesting them (often patients ask for them). The food industry certainly deserves credit for having helped establish this safety record.

The recent explosion of high impact research in the field of the human microbiome has both reignited the debate on the clinical track record of probiotics and highlighted that commercially available products have barely scratched the surface in terms of exploring the therapeutic potential of modulating the microbiome.

If (the theory) is broken, fix it

For years, probiotics have been promoted because of their alleged effects in "wellness." Global sales of probiotics (food + supplements) are forecast to reach more than $30 billion by 2015. Much has been written about the failure to support marketing claims on probiotics and the no-nonsense approach that the EFSA has taken toward evaluating such claims. For all the harsh criticism, there is actually some scientific rationale behind the use of probiotics in foods. It just happens to be too simplistic.

The story goes like this. At the beginning of the last century, Elie Metchnikoff observed that in rural areas of Bulgaria, people who had a diet rich in milk fermented by lactic acid bacteria seemed to live longer. Metchnikoff hypothesized that the lactic acid bacteria could be the reason behind the longevity, and proposed that they worked by colonizing the gut, lowering the pH, and inhibiting "bad" proteolytic bacteria such as clostridia. The theory proved to be far too simple. In the 1920s, other researchers showed that Metchnikoff's probiotic (Lactobacillus delbrueckii subspecies bulgaricus) could not colonize the human gut, and what Metchnikoff dubbed as "bad" bacteria now appear to be essential components of the healthy human microbiome.

The next iteration of the theory came in the 1930s. Researchers argued that it would be better to isolate bacteria from the human gut, which makes sense. Attention turned to human-derived lactobacilli and bifidobacteria organisms such as L.acidophilus, L. rhamnosus, L. casei, L. johnsonii  or B. lactis [3]. The narrow focus on lactobacilli seems now a historical vestige, since at the time it was already known that Metchnikoff's theory had holes. The focus on bifidobacteria, on the other hand, was based on observations by Henry Tissier around 1900 showing that these bacteria are dominant in breast-fed infants. However, neither lactobacilli nor bifidobacterium are major colonizers of the adult human gut (Bifidobacteria are dominant in babies during the first months of life, and the rationale for using them in babies may turn out to be sound in some cases).

Yet, somehow, these two genera include, with few exceptions, most of the strains currently used in foods and supplements and which have obtained GRAS (U.S.) or QPS (EU) status. These two groups are considered "safe" based on their history of use, which surely has helped attract attention to them. But it's hard to make a case why many other human commensals shouldn't be just as safe. Yet, they have been systematically ignored. I wonder if what led to that was a perception in the industry that it'd be far easier to commercialize close relatives of established safe strains (that had ambiguous health benefits) than to venture into exploring other gut commensals that might be more relevant to human biology. Whatever the reasons, here we are, 100 years after Metchnikoff's original idea, still making probiotics based on a conceptual framework that we know is flawed.

You're not invited

Currently marketed probiotics don't permanently colonize the gut. Some of these strains were originally isolated from dairy foods or fermented foods and are strangers in the human gut. And the human-derived species of lactobacilli and bifidobacteria mentioned above are often only transiently present in the human gut. Typically they can be found in amounts of 105 to 108 bacteria per gram of feces [4], which is 1,000 times lower than other dominant species of the gut ecosystem. When given exogenously in clinical trials, detecting colonization has been a challenge, since they disappear from the feces soon after administration [5], [6]. They have a hard time crashing the party in the gut. They are outcompeted by a synchronized home team of species that are more efficient at harvesting nutrients and better adapted to the complex human gut ecosystem. And while evidence is starting to emerge that shifts in other dominant commensals are associated with human disease (e.g. [7], [8], [9], [10] ), there is still no compelling association that I am aware of between deficits of any commercial probiotics and disease.

For all these reasons, I think the current paradigm of the single-strain lactobacilli or bifidobacteria probiotic will continue to generate unimpressive data in the clinic (it may remain a marketing success in foods). At the other end of the spectrum, fecal transplants (yes, gross) have shown very promising results in human trials but are likely far too complex to commercialize (they contain undefined communities of 1,000s of bacterial species). Somewhere in the middle, potential future products based on simpler communities of dominant commensals seem worth exploring. Interestingly, the only probiotic approved by the FDA (that I'm aware of) as an animal drug (for prevention of salmonella infections in poultry) is a mixture of 29 indigenous bacterial strains (PREEMPT).

Designing probiotics: You get what you select for

Protein engineers learn by heart the first law of directed evolution: "You get what you select for" (you may not know what the principles that govern the stability or structure of a protein are, but if you apply a selective pressure for, say, thermostability--e.g., a screen that selects proteins that retain activity at high temperature--you will get a thermostable protein). Keeping the distances, you can make an analogy with probiotics. Industry players have selected probiotics without any knowledge of the principles that govern the structure of the human microbiome (which the research community is just starting to figure out). They looked for microbes that would be culturable, tolerant to the acidic environment of fermented milks and yogurts (which lactobacilli can tolerate, unlike other human intestinal species); that would be resilient in environments that have oxygen (unlike most gut anaerobes, many lactobacilli have some tolerance to oxygen and can survive food packaging processes); and that would be resilient to the shear forces encountered during food manufacture (lactobacilli and bifidobacteria have thick cell walls that can sustain high-shear food production processes such as blending [11]). And they deserve a lot of credit for overcoming the technical hurdles of producing live organisms. But they got exactly what they screened for: products with favorable technological properties, but which may be irrelevant to human biology. Somewhat irrelevant. The good news is that we have only seen the tip of the iceberg. New, powerful tools will now enable engineers to look beneath the surface.

Dr. Bernat Olle is a principal at PureTech Ventures. He has been a member of the founding teams of Follica, Vedanta Biosciences and Enlight Biosciences. He serves as the chief operating officer and a member of the board of directors of Vedanta Biosciences. He completed his doctoral work at the Chemical Engineering Department at MIT, where he co-developed a novel method to increase oxygen transfer in bioreactors by using colloidal nanoparticles.