Can Your Microbiome Be Genetically Engineered to Make You Healthy?

Some people just know what they want from an early age. “I asked my parents for a microscope at age 6. I don’t have a memory of myself not wanting to be a scientist,” recalls synthetic biologist Carlotta Ronda. “I like creativity, and I almost ended up doing some kind of artistic major in college. But being a scientist is just embedded in every fiber of myself.”

Her desire to combine creative problem-solving with her scientific curiosity drew her toward genetic engineering, and her early research career focused on the then-new technique of genome editing using CRISPR-Cas9. “I would say that I’m in between a biologist and an engineer,” she says. “CRISPR wasn’t born as a genome-editing tool — it was discovered by microbiologists as an immune system for bacteria. You need the synthetic biology approach to repurpose it and create a new tool that can open up new ways to study the cell you’re interested in.”

Ronda’s current research develops new techniques to better understand and manipulate the human gut microbiota — the symbiotic bacteria that live inside our gastrointestinal tracts. Over the past decade, these microorganisms have been found to play a role in facilitating and regulating not just human digestion but also immunological and neurological processes. “We need to understand the fundamental mechanisms that are involved in the interaction between ourselves and our commensals,” Ronda says, “but there are not many tools to do it.” An edited version of our conversation follows.

Why is it difficult to learn about the microorganisms living inside our gut?

If you think about it, the gut is a black box. You can’t just open people up and look at what the bacteria are doing. You can study fecal matter, but that is a result of bacteria living in the colon, which are different from those living in the small intestines. So we can’t access them, and we cannot cultivate them easily in the laboratory either, unfortunately. They’re very resistant to cultivation, and they have specific nutrient requirements. So my goal is to devise new systems to try to assess these complex communities and work with them in situ — in the actual gut.

Why do we need genetic engineering tools to do this?

The way scientists usually try to understand the functions of parts in a complex system — like one cell in a tissue, or a node in a network — is to modify it. You “knock it out,” or put more of it in, and then you observe how the system reacts to figure out the interactions.

The microbiome is a complex community. It’s a network of nodes. And to understand the function of each node within the network and how the network interacts with the host — which is us — you need to modify those nodes, those bacteria. Using genetic engineering, I can perturb this community to understand the function of specific components of it.

You previously relied on CRISPR, but in your current work, you created a new system called MAGIC. What is that?

MAGIC stands for metagenomic alteration of gut microbiome by in situ conjugation. It is a completely new system that allows us to genetically engineer complex bacterial communities in situ. MAGIC does not involve CRISPR; rather, it relies on a different microbial system that is based on the natural ability of bacteria to exchange DNA. A perfect example is antibiotic resistance: To survive, bacteria under antibiotic selection use this mechanism to exchange the antibiotic resistance genes. My system repurposes this ability to move genetic material from one bacterium to another, to deliver genes that encode a function that I have programmed them for.

So that’s how you modify the gut microbiome and then observe the effects?

Exactly. The major advantage of using this system is that you don’t introduce lots of new bacteria to the environment — you just use the community that’s already adapted to being there. If you try to put new bacteria in your gut — which is what fecal transplants are supposed to do — it’s not a sure thing that they will stick around. There are some studies on fecal transplants that show that they are not as efficient or effective as we think because the native microbiota of the host can be recalcitrant to accepting the bacteria from the donor, because they’re not adapted exactly to the host’s gut environment. It’s a very competitive system, and sometimes the donor bacteria will just be outcompeted right away.

Could this technique someday be used therapeutically, like fecal transplants are?

It is a very interesting therapeutic approach because I could insert a new genetic function in your own microbiome, which would mean you can have your own microbiome producing a compound or drug that is good for you. Maybe that’s an anticancer drug. Or let’s say you suffer from depression. Instead of taking an antidepressant like Prozac, you could get your own gut bacteria to produce serotonin, and affect your brain chemistry via the gut-brain axis. Right now, I’m actually testing a compound called butyrate that is known to increase memory, decrease inflammation and help to prevent neurodegenerative disease.

One benefit of traditional medications is that you can stop taking them once they’re no longer needed. How would that work if your own gut is manufacturing one of these compounds?

There are different strategies. One is to program a “suicide” system that you genetically encode when you set the function of the payload. For example, the presence of certain stimuli — like a specific sugar you would ingest in milk or in a supplement — could activate the suicide mode, and so then the therapeutic function would disappear.

What’s in store for the future of microbiome research?

There are so many open questions. Viruses and the human virome are going to become an important field of study, too. But I think the big question is, are we going to change our paradigm about understanding bacteria, where they go from being bad guys to being an integral part of our life? I mean, if you look at germ-free laboratory mice, which lack any microorganisms on or in their bodies, they have so many problems. They’re so incredibly sick, and also mentally impaired. We’ve been using antibiotics to destroy bacteria because we are used to associating bacteria with disease, but I’m so fascinated by the fact that every day we discover more and more about how we have co-evolved with them. They’re an integral part of our lives, and that’s that.