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How to Program One of the Gut’s Most Common Microbes

Last month, I wrote a feature for New Scientist about smart probiotics—bacteria that have been genetically programmed to patrol our bodies, report on what they find, and improve our health. Here’s how the piece began:

“[There’s a] growing club of scientists who are tweaking our microbiome—the microbes that live in or on our bodies—in pursuit of better health. They are stuffing bacteria with circuitry composed of new combinations of genes, turning them into precision-targeted micro-drones designed to detect and fix specific problems.

Some lie in wait for pathogens like P. aeruginosa or the cholera bacterium Vibrio cholerae, releasing lethal payloads when they have the enemy in sight. Some use the same tactics to attack cancer cells. Others can sense signs of inflammation and release chemicals that could help to treat chronic conditions like inflammatory bowel disease. And these tricks aren’t just confined to the lab. In the next 18 months, at least one start-up is expected to put its newly created synthetic bugs into clinical trials with real people. Welcome to the age of smart probiotics, where specially designed bacterial rangers patrol the gut, reporting on the state of the environment, eliminating weedy species, and putting out fires.”

This work is part of the growing field of synthetic biology, which brings the principles of engineering to the messy world of living things. Synthetic biologists treat genes as “parts”, which they can pick from a registry, combine into “circuits” or “modules”, and stuff into a living “chassis”. Rather than modestly modifying one or two genes, they remix large networks, to produce yeast that can brew antimalarial drugs instead of beer,  cells that self-destruct if they turn cancerous, or microbes that can sense and quench inflammation in the gut.

Initially, these microbiome engineers started by modifying the obvious laboratory darlings, like Escherichia coli, or species used in probiotic yoghurts, like Lactobacillus. These bacteria have been studied for a long time and are easy to manipulate. But they are actually relatively rare in our guts. They also lack staying power, which is why the current generation of probiotics don’t colonise the people who swallow them, and rarely deliver on their fabled health promises.

If you want to turn a microbe into a gut ranger, you’re better off starting with a species that’s well-adapted there. And there are few better choices than Bacteroides thetaiotamicron—B-theta to its friends. Collectively, the Bacteroides genus makes up between 30 and 50 per cent of the microbes in a Western person’s gut. They’re exquisitely attuned to that environment and they’re excellent colonisers. And B-theta is arguably the best-studied of them. It was an early star of the microbiome craze: by working on this microbe back in the 1990s, pioneers like Jeff Gordon began to understand how important gut bacteria are to our lives.

Now, Mark Mimee and Alex Tucker from MIT have hacked B-theta, creating a small library of biological parts that can be used to programme it.

They started by building circuits that can permanently activate a given gene, and then tune its activity to a specific level within a 10,000-fold range. They tested these circuits by hooking them up to a gene that makes a glowing enzyme, and showed that they could precisely set the brightness of the glow.

Next, they created inducible circuits, which would activate a target gene only when they receive some kind of external trigger, like a drug or a dietary nutrient. When the trigger arrives, the circuit produces an enzyme that cuts out a particular piece of DNA, flips it around, and glues it back into place. A microbe that carries this circuit has memory—by inverting its DNA, it permanently records its encounter with the triggering substance. Mimee and Tucker could then tell if the trigger was present by sequencing the right region and looking for the inversion. They had effectively turned B-theta into a journalist that could sense and report on the events in a gut.

Finally, the team created circuits that can inactivate specific genes in B-theta. They used a powerful new technique called CRISPR interference, in which an enzyme called Cas9 is guided to a specific stretch of DNA. Cas9 normally acts like a pair of scissors that cuts whatever DNA it encounters. But in CRISPR interference, the scissors have been blunted. Rather than cutting a target gene, Cas9 just sits there, stopping other enzymes from activating it.

Mimee and Tucker connected Cas9 to genes that sense external triggers, so they could unleash it when they wanted. Then, they used different guide molecules to target Cas9 to specific genes. Now, they could inactivate those genes whenever they wanted, by delivering the right trigger. “It’s a flexible strategy for turning off any gene you want,” says Timothy Lu, who led the study.

A cynic might say that these circuits already existed, and the team just repurposed them for use in B-theta. But that was not easy. Unlike E.coli, which grows with ridiculous ease, B-theta is exquisitely sensitive to oxygen. To work with it, the team had to exclude the omnipresent gas by buying an anaerobic chamber. They also had to develop new ways of introducing foreign DNA into the bacterium—something that’s easy to do in E.coli, but harder in several other species.

Synthetic biology projects have often advanced to this point and then face-planted. Circuits that look good on paper and work in a dish will then fail when they’re incorporated into an actual cell or, in the case of gut microbes, when those cells are loaded into an animal. Pamela Silver from Harvard Medical School achieved one of the first successes last year by programming E.coli with a memory switch, and testing it in mice Lu’s team have now done the same. When they gave their programmed microbes to mice, everything worked. The inducible memory switches turned on when the mice ate the right triggers, as did the Cas9 suppressors. “We were surprised at how well they did,” says Lu.

“This is a beautiful, elegant piece of work that shows the power of synthetic biology to make a previously challenging organism immediately accessible to the scientific community,” says Michael Fischbach from the University of California, San Francisco, who is also programming his own microbes. “Bacteroides is an ideal ‘chassis’: a friendly bacterium that colonizes the gut professionally.”

“This study provides a nice proof of concept that portable components can be combined and function in this gut commensal,” agrees Justin Sonnenburg from Stanford University, who has been working with B-theta for decades and is also engineering it. This rapidly expanding direction for gut microbiota research will eventually give us new insight into microbiota-host interaction and medically useful microbes.”

By that, he means that programmed gut microbes could tell us a lot more about the gut than we currently know. The organ is still a bit of a black box.Food goes in and, some 8.5 metres later, waste comes out. Yes, we roughly understand what happens in the middle, but the details are still elusive. When Sonnenburg applied for his position at Stanford, an interviewer asked him: “What a single cell has experienced while transiting the digestive tract? If there’s a little inflammation, has it experienced that? Does it stick around eating plant polysaccharides? How could you tell?” Those are the kinds of questions that he, Lu, and others hope to address with their microbial reporters.

They also want to connect detection circuits to therapeutic ones, so that microbes can not only spot early signs of infections and chronic diseases, but also correct them. You could imagine handing out these sentinel microbes to people in the midst of epidemics, like the cholera outbreak that is still raging in Haiti. Alternatively, soldiers and tourists could take them before travelling abroad to regions with a high risk of diarrhoeal diseases. The possibilities are vast.

Reference: Mimee, Tucker, Voigt & Lu. 2015. Programming a Human Commensal Bacterium, Bacteroides thetaiotaomicron, to Sense and Respond to Stimuli in the Murine Gut Microbiota. Cell Systems http://dx.doi.org/10.1016/j.cels.2015.06.001

8 thoughts on “How to Program One of the Gut’s Most Common Microbes

  1. Stumbled upon your microbiome article while researching copulatory differences between chickens and ducks, and found it to be utterly fascinating. Want to read much more of your writings. Thanks so much.

  2. Interesting how the crowd that rails against “Genetically Modified Organisms” — or GMO for short — is the same crowd that loves probiotic foods ranging from yoghurt to fermented products to capsules containing so-called probiotic bacteria. The natural conclusion is that folks who use these supplements are themselves “GMO.”

  3. Jay, there is nothing about purposefully ingesting microorganisms that would cause DNA to be artificially edited. What are you on about, exactly?

  4. The engineering is all well and good Ed, but there’s a big missing piece: what foods contain B-theta or how one would go about obtaining it as a supplement?

  5. The article only mentions that Bacteroides thetaiotaomicron is well adapted to the gut, it is anaerobic, identified as friendly but gives no further detail as to how it functions which is of significant importance.

    Second, usually the process of genetic modification involves additional marker genes which are also alien to the host. There are a number of studies that indicate that the process or existence of genetic modification in food plants produces inflammation in the gut when consumed in animals, as well as infertility. What then will be the results of introducing genetically modified microbes to the gut, no matter how well intentioned someone might be?

    DNA is an incredibly complex structure about which current science knows some parts and pieces but as a whole is not yet well understood. Especially when it is now known that specific genes have more than one role or capability and the spacing of genes plays another role. This obviously adds a whole new layer whose ramifications as yet are not considered. When we consider the many real consequences of “Murphy’s Law” scientific enthusiasts of GM are playing in the dark. Until it is very well understood from extensive laboratory research, which is still a probable distant future, it is a highly irresponsible game that corporate researchers are playing. It is the rush for profit without common sense.

    John Weiss, your Luddites happen to include Nobel Laureates in the biological sciences.

    1. Thoughtful answer John. What you say is true. So far, the only GMOs that are in common use are modifications which produce resistance to herbicides. Modifying gut bacteria, as you point out , is another ball of wax. ONTOH no risk, no gain. We cannot know the results of gut bacteria modification if we don’t do it. It appears that there are better ways than the current methods of gut flora/fauna modification which is rather a shotgun approach. Look what happened to the Luddites! Perhaps one could argue that the simple approach to life (none of those lousy Jacquard machines in my neighborhood!) is a better way. I disagree, and Nobel Laureates aside, I say forge ahead. But test it on mice first!

      1. John Weiss, your statement “no risk no gain” does not bear up in the everyday world. People who are successful in life are normally very risk adverse, that is how they became successful. They invent or find something that by demonstration they know works and follow through with it. My point about GM is that it is not known yet how genetics really work, and by a very credible view of life, biological sciences as a whole are still quite distant from having a good understanding of the origins of life.

        Scientists have found that if we poke this or that we get a reaction, and that this reaction looks interesting and this one doesn’t. Yet as to really understanding how that reaction came about and what are its consequences and ramifications it is still largely unknown. Playing in the dark is opening up to have all kinds of undesired consequences as further research on GMOs is illustrating. One is that GMOs are not identical with their non GM counterpart while industry wishes to falsely represents otherwise; they may look the same but chemically they are not.

        To get a better idea let’s take your loom analogy. We could say that your Jacquard loom, in this case representing the reality of DNA, functions with twelve layers of warp and weft and is capable of displaying exquisitely elaborate designs. You are giving this loom to a craftsman who has worked all of his life with a backstrap loom doing two dimensional imaging. You realize that the loom can produce some really beautiful products, but like the craftsman you have no idea how the loom works to be able to train him how to use it. However you give it to him saying play with it and we’ll hope for the best. No pain no gain, right? Eventually if, and this is a pretty big if, the craftsman is able to leave almost all of his preconceptions and experience about weaving behind, he may finally be able to produce something worthwhile. And if he is not very careful and able to think in a whole new inter-dimensional manner he is going to produce a lot of knots.

        If we look at the cutting edge of physics we will find that the universe is non-material, it is an intelligently organized collection of different vibrations of energy that most likely have the inter-dimensional qualities analogous to the Jacquard loom. Genes are material structures and are represented by the backstrap loom. The actual gap of scientific understanding between the non-material intelligently governed quantum field and the material chemical and biological state of the gene is enormous. As you say further research needs to be done.

        The Nobel Laureates of whom I speak are the ones saying it needs more testing before it is ignorantly unleashed on the natural world, which foolishly has already been done. Monsanto has repressed internal research that showed problems with animals. There is no study on humans to demonstrate if it is safe or not. There are a number of animal studies that show harm is present as I mentioned the studies that indicate inflammation and infertility from consumption of GMO feed.

        The health effects have not been researched by industry and the political policy has been to leave it to industry to do the research. That is an obvious big conflict of interest as Monsanto has well demonstrated. The bio-tech industry basically sat down with government and constructed the approval process mostly on their terms from the start. It’s one thing to want to see an industry blossom and quite another to irresponsibly throw caution to the wind as you are recommending and government has done.

        Is the priority of government to encourage business at whatever cost or is it to assist and protect its population as a whole? I will suggest that its real purpose is to serve the population as a whole. Unfortunately the way government is presently structured its primary role is to maintain the current power hierarchy. At this time at the top of the power hierarchy sit large corporations. When meaningful change does come it always comes from outside of government.

        The revolving door between industry and government is another part of the problem. Some years ago when Monsanto gained approval for their controversial recombinant growth hormone for dairy cattle (there were substantial counter indications) the application was written by a lawyer who stepped into a position on the FDA to approve the very same application. On leaving the FDA not long after the lawyer became a vice president at Monsanto. These types of deals are a regular occurrence in Washington DC.

        I am completely for new knowledge and responsible research. As human beings we have a tremendous capacity for learning and invention. This can come as a shortsighted impatient avaricious search for power which is all too common in the prevalent corporate model of business; or it can come from a wise, judicious and heart centered intelligence that takes a wide enough view to include all possible consequences. The idea of Murphy’s Law is to adequately study one’s self and surroundings to avoid the dangers that are definitely present; not to throw caution to the wind in the vain hope (and yes, it’s definitely a form of vanity) that something might come of it.

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