New Pills Deliver Bacteria, Not Drugs, To Cure Us

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It seems that nearly every day, scientists connect another medical condition to atypical gut bacteria populations. Researchers have claimed that gut bacteria play a role not just in digestive health but even in basic brain function and mental health.

Certain bacteria are so clearly good for us that several companies are looking to market pills filled not with chemical drugs, but with bacteria.

bacteria-featA few pharmaceutical startups have already begun testing bacterial medicines in hopes of finding the right strain or stains of bacteria to cure widespread and still mysterious illnesses.

The strongest evidence connects gut bacteria to gastrointestinal conditions, though even there, the science is still too raw to identify the bacterial causes of illnesses. Desperate patients have already turned to fecal transplants to treat such difficult conditions as Clostridium difficile, which causes life-threatening bouts of diarrhea, but it's not clear which donor bacteria do the trick.

Seres Health, an offshoot of Cambridge-based incubator Flagship Ventures, took its previously secret work public last month and is testing a bacterial cocktail to treat C. difficile on human patients.

Seres combs through research on the human biome and runs it through a computational algorithm to identify which communities of bacteria seem to support healthy functions and which are linked to illnesses including C. difficile and inflammatory conditions. The company then assembles bacterial combinations using purified strains.

How a company finds, produces and delivers the organism constitute its intellectual property, which for drug companies is synonymous with profit. Naturally occurring organisms likely cannot be patented in the United States, according to a Supreme Court decision from earlier this year.

pillsMountain View-based Osel is also conducting Phase 2 trials on a medication to treat C. difficile. The company delivers a single bacterial strain in each of its medications, which are usually genetically modified and therefore patentable.

Even at these cutting-edge companies, the state of the science is correlation, not causality. Borrowing big data methods from metagenomics, R&D departments identify patterns of “dysbiosis,” or particular differences in microbiota makeup that could account for negative health impacts, such as Irritable Bowel Disease, obesity, metabolic syndrome and diabetes.

Whether or not the “dysbiosis” causes the diseases, it can be used as a way to identify patients for clinical trials and gauge their responses to treatment.

It seems odd to think that we may soon be taking pills whose mechanisms aren’t fully understood, but that’s nothing new (to wit: antidepressants). What is new is that, instead of annihilating the microbes that live on and in us, these pills would add to their numbers.

Photos: Barbol, Juan Gaertner and Roman Sotola via

Cameron Scott

Cameron received degrees in Comparative Literature from Princeton and Cornell universities. He has worked at Mother Jones, SFGate and IDG News Service and been published in California Lawyer and SF Weekly. He lives, predictably, in SF.

Discussion — 3 Responses

  • Michael K Hurst January 15, 2014 on 7:42 am

    This is a good article about the possibilities from research created as part of the human microbiome project which stand to change the way many health conditions are treated in the coming years. One thing I did want to clarify is that for the treatment of Clostridium Difficile (c. diff) related Colitis, the use of fecal transplants has now gone far beyond a few “desperate patients.” Anti-biotics simply do not work to permanently beat c. diff and the number of doctor using this treatment approach has been rapidly growing especially since last June when the FDA announced it would not enforce INDs before doctors could perform them.
    In addition to their use to treat c. diff, fecal transplants are being studied for use with Ulcerative Colitis, which is considered to be an autoimmune disease even though noticeable differences in gut flora composition are well-documented. I can say that bacteria ended up being the solution for my case of Ulcerative Colitis. Three years ago I read an article in the Journal of Gastroenterology that fecal transplants had been used to successfully treat Ulcerative Colitis in the case of 6 patients. This made sense to me since treatment with antibiotics, sometimes for unrelated conditions had helped bring about a remission of my symptoms several times in the past. So I ended up pursuing this treatment approach in conjunction with a few other treatment approaches and almost 3 years later I am still completely free of any signs or symptoms of the disease. For more information about my experience go to

  • Grim January 17, 2014 on 4:29 am

    We have been basicly built with bugs over a long time.
    To find that they are affected by there environment is not such a far reach be it gut or blood.
    We are what we eat ..causality??
    All those foods out there with chemicals.
    Some or all these chemicals can and will affect us on some level.

  • didibus January 17, 2014 on 8:36 am

    There is something that I find wrong, yet maybe right about all this patentability and profitability. In a way, without the patents and the pills, companies wouldn’t have much incentive to research those areas, because no profit could be made out of them. But it’s also appalling to think a startup is going the extra mile of genetically modifying bacterias, just so it can patent their use. We still haven’t figured out the roles and benefits of non modified bacteria, so to step over that phase, and jump right into genetically modified ones seems far fetched.

    We should also reckon that fecal transplant, is a great way to wreak in the benefits of proper gut bacterias. It’s a super easy, trivial and cheap operation to perform. It’s also a great way to know if the composition is good, it’s basically someone’s else composition, so, you already know it works to some extent.

    Yet, pharmaceuticals and the medical industry has little interest in fecal transplant. That is because there is nothing to sell, and therefore, no profit to be made. This is why they are spending a lot of time researching ways to recreate the composition of the bacterial guts in a lab. That way, they can patent the process, and sell pills.

    I wish their was a solution to this problem. It’s a shame that a lot of medical breakthrough are put aside, or ignored for long periods of time, because they don’t have as much commercial potential. I don’t know what could be made, but I wish something was.