National Geographic

A Living Drug Cocktail

We know that the 100 trillion microbes in the human body are important to our health. What’s harder to know is how to use them to make us healthy.

Normally, our resident microbes–the microbiome–carry out a number of important jobs for us, from fighting off pathogens to breaking down food for us. If they get disrupted, we  suffer the consequences. Sometimes antibiotics can upset the ecological balance in our bodies so severely, for example, that rare, dangerous species can take over.

For decades, doctors and scientists have searched for microbes that can promote our health by taking up residence in our bodies. They’ve had some modest success in treating people by giving them a single species at a time. (Don’t be fooled by all the so-called probiotic foods and pills you can buy over the counter–few, if any, have ever been scientifically shown to be effective.) Part of the problem has been that scientists haven’t been terribly systematic about searching for microbes. Very often, their most important standard for a probiotic germ is not its healing power, but its ability to survive in food, or packed into a pill.

Scientists have also had some limited success at the other end of the spectrum, by exploiting much of the microbiome’s diversity at all once. For some people with deadly gut infections, for example, the only cure is to get a so-called fecal transplant from a healthy donor. Fecal transplants show a lot of promise, but scientists don’t have a clear idea of how they work. A stool sample is loaded with hundreds of different species, any one of which might be either essential for overthrowing pathogens or just along for the ride.

In Nature today, a team of scientists report taking an important step forward in microbiome-based medicine. They searched for species methodically, in the same way medicinal chemists search for new drugs. They have pinpointed a handful of species living in the human gut that collectively show signs of fighting effectively against some autoimmune diseases.

Scientists have long suspected that the immune system would benefit from microbiome-based medicine. That’s because immune systems depend on the microbiome to develop normally in the first place. As a child’s immune cells grow and divide, they pick up signals from the microbes. Those signals teach the immune system to become tolerant. They can still recognize a dangerous pathogen and kill it, but they spare the beneficial bugs. And they also become less likely to overreact to a harmless molecule or our own tissues.

One important group of immune cell involved in this tolerance are known as Tregs (short for the CD4+ FOXP3+ T regulatory cells). They are abundant in the microbe-packed gut, where they help to broker a truce between host and the germs that live there. Tregs also depend on the microbiome for their very existence. When scientists rear mice without any germs at all, the animals develop very few Tregs. And as a result their immune system becomes prone to raging out of control.

A number of experiments have hinted that abnormal levels of Tregs are behind some autoimmune gut diseases, such as colitis, which causes chronic inflammation in the large intestines and diarrhea. This raises the possibility that a treatment for colitis would be to bring Tregs back to normal levels. Perhaps among all the bacteria in the gut, scientists could find the ones that sent the signals to the Tregs.

Over the past few years, Kenya Honda of the University of Tokyo and his colleagues have been hunting for those species. They started by testing out subsets of the microbiome to find groups of species that could foster the growth of Tregs. Raising healthy mice, they collected the mouse droppings, which contained lots of bacteria. They treated the droppings with chloroform, which kills most bacteria. The only microbes that survived were species that make spores tough enough to withstand the chemical.

When the scientists gave those spore-forming bacteria to germ-free mice, the level of Tregs in the animals went up. That didn’t happen when the scientists gave the mice other kinds of bacteria instead.

This discovery didn’t pinpoint exactly which bacteria were fostering Tregs. But it certainly narrowed down the line-up of suspects dramatically. And it also prompted Honda and his colleagues to start acting more like a drug company testing promising new compounds. In fact, Honda co-founded a company called Vedanta Biosciences for that express purpose.

Their goal now became finding a species, or a group of species, that live in humans, and which promote the growth of Tregs in the gut. Rather than taking the kitchen-sink approach of fecal transplants, they would try to deliver a surgically precise germ.

They took stool samples from a healthy Japanese volunteer and doused them with chloroform, so that once more they only had to contend with spore-forming species. Then they inoculated germ-free mice with different combinations of the surviving bacteria. After letting the bacteria grow in the mice, they then inspected the animals to see if any of them had high levels of Tregs as a result. They did find some of those combinations, and they went on narrowing down the suspects until  they were left with just seventeen species, along belong to a type of bacteria called Clostridia.

One particularly interesting result of the experiment was that they couldn’t get these good results from any fewer than those seventeen species. On its own, each of the species was unable to foster the immune cells. It may be a combination of signals from all seventeen species that promotes the Tregs.

The researchers wondered if these seventeen species played a special role in autoimmune diseases in humans. To find out, they looked at the microbiomes from health people and people with colitis. The seventeen species tended to be rarer in the sick people.  Perhaps, the researchers reasoned, losing this network of microbes weakens the signals that keep Treg levels normal. The immune system spins out of control, leading to colitis.

If that were true, then giving someone a pill with all seventeen species might be an effective way to fight colitis. But Honda and his colleagues weren’t ready to start inoculating people with Clostridia. Clostridia is a huge group of species that includes some very nasty characters that cause diseases like tetanus and botulism. They would have to do some preliminary work first.

All seventeen species were new to science (something that’s pretty typical for microbiome research), so the scientists sequenced their genomes. None of the seventeen species carried genes for toxins or other disease-causing proteins. From an inspection of their DNA, at least, the microbes looked safe.

Next, the scientists tested the bacteria out on mice. They gave the microbes to animals either suffering from colitis or from allergy-triggered diarrhea. In both cases, the bacteria raised the level of Tregs dramatically in the guts of the mice. The mice also partly recovered from their diseases. The mice with colitis had less inflammation, and the mice with diarrhea had healthier stool.

From here, the Vedanta researchers eventually hope to get to clinical trials on humans. As I wrote in April, turning bugs into drugs is a big challenge on many levels. For one thing, the FDA doesn’t have a long tradition of approving such research. And while Honda and his colleagues have certainly gone a long way to pinpointing how microbes foster Tregs, they have yet to work out the precise balance of signals that really matters to the immune system.

Nevertheless, a seventeen-bug cocktail would be appealing in many ways. For one thing, the microbes are regular residents of the human gut, dwelling there for people’s entire lifetime. And they only live in the gut, and not the heart or the liver or some other organ. Both these facts suggest that such a cocktail would be unlikely to cause harmful side effects. What’s more, the microbes would be able to deliver a steady, long-running dose of the chemicals necessary to keep Treg levels healthy.

The new study also points to a way to systematically search the microbiome for treatments for other diseases. It’s possible that small teams of other species handle other jobs in the body. They may nurture other types of immune cells, for example. Or they may send signals into the body that regulate body weight. By winnowing down the microbiome, scientists may be able to deploy those elite units to fight other diseases.

[Update: Nature paper link fixed]

There are 7 Comments. Add Yours.

  1. Daniel Sprockett
    July 10, 2013

    Hi Carl, the link to the Nature paper is broken.

    [CZ: Thanks for pointing that out. It's fixed now.]

  2. Carol M
    July 11, 2013

    Fascinating set of studies, fascinating article. Could preliminary results obtained so far be too good to be true?It all sounds too easy.

  3. Monica Metzler
    July 15, 2013

    So interesting! Really enjoying watching this whole area grow.
    (FYI – typo in second sentence of penultimate paragraph — “their” for “there.”)

    [CZ: Thanks. Fixed]

  4. Hubert P
    July 18, 2013

    Nice article indeed!
    The same concept (i.e. using a defined group of bacterial species to try and mimic properties of a full microbiota) has also been exploited in the case of fecal transplants.
    As you said, they are mostly used is to treat otherwise recurrent and potentially deadly gut infections which are caused by Clostridium difficile, another example of nasty species from the genus Clostridia. These infections are linked to a state of dysbiosis -perturbation of the intestinal ecosystem and the gut microbiota- and cause debilitating diarrhea which can lead to severe illness and death if left untreated.
    Fecal transplant is the most effective way of curing the infection, with a success rate of around 98% and almost no relapse, as opposed to approximatively 25% chance of relapse with antibiotic treatment, which is due to the ability of C. difficile to create spores resisting the antibiotics (this is reviewed in the following article: http://www.giejournal.org/article/S0016-5107(13)01587-3/abstract. Unfortunately it is not freely available). But as it is the case in the Treg study, a source of concern is that the gut microbiota from a healthy donor can contain bugs that could be nasty to the patient, since his/her whole intestinal tract is affected by the disease.
    To overcome this issue, a UK group took stool samples from a healthy donor and incubated them twice in liquid culture to “purify” cultivable species. The following is pretty similar to what has been done in this paper: they characterized and used 6 of the isolated bacterial species as a representative group of a healthy flora that they then transplanted in mice infected by a highly contagious strain of C. difficile. As it is the case here, the bacterial mixture was enough to cure the infection, but not the bacterial species alone.
    The main hypothesis explaining the success of this transplant is that the transplanted bacteria serve as a primer group that re-creates a healthy microbiota. This microbiota will then compete with C. difficile for food sources, and since it is more efficient, will help to get rid of it. The paper describing these experiments was published in PLoS pathogens last year. It is therefore open access, and there is a nice figure at the end summarizing the working hypothesis (you can find it at http://www.plospathogens.org/article/info%3Adoi%2F10.1371%2Fjournal.ppat.1002995).
    I’m done; hopefully this was not to long. I’m passionate about research concerning the gut microbiota in health and diseases and will actually begin my PhD thesis in that area. I just thought I would add my two cents if you don’t mind : )

    • Stephen
      July 18, 2013

      If I may ask comment to the following…

      I believe that while Antibiotics Do Kill “most” of their Targeted Bad Bugs, they also Kill the majority of beneficial Good Bugs in our Guts.

      Still further, I believe that unless this decimated Gut is not aggressively Re-populated with Good Bugs / Probiotics .. opportunistic / faster moving Bad Bugs will establish Gut / Pathogenic Bad Bug Dominance .. not only compromising daily food Breakdown/ Absorb .. but over time will compromise Gut Integrity itself i.e. Leaky Gut.

      That this Pathogenic Bad Bug Dominance will remain until they are Replaced by Good, or the host is no more.

      Thoughts / Guidance Welcome

      Thoughts welcome

      • Hubert P
        July 19, 2013

        Indeed, antibiotics are pretty undiscriminating and eliminate good bugs as well as nasty ones. However, they will not wipe out everything since their target is usually specific to a group of bacteria: for example, penicillin and its derivatives are mostly targeting gram-positive bacteria. Still, you can compare it to bombing a whole town to get rid of a few harmful bad guys: efficient, but with a lot of collateral damage.

        With that in mind, what you say is right: when the gut microbiota is weakened by antibiotics, opportunists can rise in numbers and colonize the niche that was occupied before. But once again, this does not occur every time.

        And antibiotics can work against nasty bugs such as C. difficile. They are however less efficient in this case than fecal transplant, and the main issue is recurrent reinfections: if all C. difficile bugs are not destroyed by the antibiotics, you pretty much go back to 0, but the risk of a subsequent relapse after a new round of treatment increases.
        Still according to the first paper I mentionned, “Patients who have 1 recurrence have up to a 45% chance of a second recurrence, and after a second recurrence, up to 65% of patients will have a third.”

        • Stephen
          July 19, 2013

          Thank You for your Reply Thoughts…

          I make mention to another great Carl Z article in WIRED Magazine / Oct 2011 which caught my Eye relative to Antibiotic & Gut Health… specifically .. “Even Two years out, the Flora had not regained their former diversity “

          To me, this is Health Troubling given the importance of GUT Mediated Immunity, the liberal dispense of Antibiotics and the lack of focus on Gut Health in today’s modern society.

          You can imagine all the Negative Health Ripples caused by GUTs that have yet to achieve Health after a Protocol of Antibiotics.

          Antibiotics = MicroBiome Killer
          Studies have revealed some alarming costs of taking Antibiotics, which don’t discriminate between disease-causing bacteria and our natural MicroBiome.

          Graphed below is the diversity of gut bacteria from one important genus (Bacteroides) in a patient who took a weeklong course of clindamycin; different colors represent the different species.

          For nine months after exposure, the subject’s gut was left with nothing but one type, a clindamycin-resistant strain of Bacteroides thetaiotaomicron.

          Even Two years out, the Flora had not regained their former diversity.

          Illustration: Teagan White
          Sources: baby: Ruth E. Ley, Cornell University; mouth: Egija Zaura, University of Amsterdam and Free University Amsterdam; antibiotics: Janet K. Jansson, Lawrence Berkeley National Laboratory; fat: Peter J. Turnbaugh, Washington University in St. Louis

          • By Carl Zimmer
          • Wired October 2011

          http://www.wired.com/magazine/2011/09/mf_microbiome/

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