What’s the Right Way to Regulate Gene-Edited Crops?
In the next few decades, humanity faces its biggest food crisis since the invention of the plow. The planet's population, currently 7.6 billion, is expected to reach 10 billion by 2050; to avoid mass famine, according to the World Resource Institute, we'll need to produce 70 percent more calories than we do today.
Imagine that a cheap, easy-to-use, and rapidly deployable technology could make crops more fertile and strengthen their resistance to threats.
Meanwhile, climate change will bring intensifying assaults by heat, drought, storms, pests, and weeds, depressing farm yields around the globe. Epidemics of plant disease—already laying waste to wheat, citrus, bananas, coffee, and cacao in many regions—will spread ever further through the vectors of modern trade and transportation.
So here's a thought experiment: Imagine that a cheap, easy-to-use, and rapidly deployable technology could make crops more fertile and strengthen their resistance to these looming threats. Imagine that it could also render them more nutritious and tastier, with longer shelf lives and less vulnerability to damage in shipping—adding enhancements to human health and enjoyment, as well as reduced food waste, to the possible benefits.
Finally, imagine that crops bred with the aid of this tool might carry dangers. Some could contain unsuspected allergens or toxins. Others might disrupt ecosystems, affecting the behavior or very survival of other species, or infecting wild relatives with their altered DNA.
Now ask yourself: If such a technology existed, should policymakers encourage its adoption, or ban it due to the risks? And if you chose the former alternative, how should crops developed by this method be regulated?
In fact, this technology does exist, though its use remains mostly experimental. It's called gene editing, and in the past five years it has emerged as a potentially revolutionary force in many areas—among them, treating cancer and genetic disorders; growing transplantable human organs in pigs; controlling malaria-spreading mosquitoes; and, yes, transforming agriculture. Several versions are currently available, the newest and nimblest of which goes by the acronym CRISPR.
Gene editing is far simpler and more efficient than older methods used to produce genetically modified organisms (GMOs). Unlike those methods, moreover, it can be used in ways that leave no foreign genes in the target organism—an advantage that proponents argue should comfort anyone leery of consuming so-called "Frankenfoods." But debate persists over what precautions must be taken before these crops come to market.
Recently, two of the world's most powerful regulatory bodies offered very different answers to that question. The United States Department of Agriculture (USDA) declared in March 2018 that it "does not currently regulate, or have any plans to regulate" plants that are developed through most existing methods of gene editing. The Court of Justice of the European Union (ECJ), by contrast, ruled in July that such crops should be governed by the same stringent regulations as conventional GMOs.
Some experts suggest that the broadly permissive American approach and the broadly restrictive EU policy are equally flawed.
Each announcement drew protests, for opposite reasons. Anti-GMO activists assailed the USDA's statement, arguing that all gene-edited crops should be tested and approved before marketing. "You don't know what those mutations or rearrangements might do in a plant," warned Michael Hansen, a senior scientist with the advocacy group Consumers Union. Biotech boosters griped that the ECJ's decision would stifle innovation and investment. "By any sensible standard, this judgment is illogical and absurd," wrote the British newspaper The Observer.
Yet some experts suggest that the broadly permissive American approach and the broadly restrictive EU policy are equally flawed. "What's behind these regulatory decisions is not science," says Jennifer Kuzma, co-director of the Genetic Engineering and Society Center at North Carolina State University, a former advisor to the World Economic Forum, who has researched and written extensively on governance issues in biotechnology. "It's politics, economics, and culture."
The U.S. Welcomes Gene-Edited Food
Humans have been modifying the genomes of plants and animals for 10,000 years, using selective breeding—a hit-or-miss method that can take decades or more to deliver rewards. In the mid-20th century, we learned to speed up the process by exposing organisms to radiation or mutagenic chemicals. But it wasn't until the 1980s that scientists began modifying plants by altering specific stretches of their DNA.
Today, about 90 percent of the corn, cotton and soybeans planted in the U.S. are GMOs; such crops cover nearly 4 million square miles (10 million square kilometers) of land in 29 countries. Most of these plants are transgenic, meaning they contain genes from an unrelated species—often as biologically alien as a virus or a fish. Their modifications are designed primarily to boost profit margins for mechanized agribusiness: allowing crops to withstand herbicides so that weeds can be controlled by mass spraying, for example, or to produce their own pesticides to lessen the need for chemical inputs.
In the early days, the majority of GM crops were created by extracting the gene for a desired trait from a donor organism, multiplying it, and attaching it to other snippets of DNA—usually from a microbe called an agrobacterium—that could help it infiltrate the cells of the target plant. Biotechnologists injected these particles into the target, hoping at least one would land in a place where it would perform its intended function; if not, they kept trying. The process was quicker than conventional breeding, but still complex, scattershot, and costly.
Because agrobacteria can cause plant tumors, Kuzma explains, policymakers in the U.S. decided to regulate GMO crops under an existing law, the Plant Pest Act of 1957, which addressed dangers like imported trees infested with invasive bugs. Every GMO containing the DNA of agrobacterium or another plant pest had to be tested to see whether it behaved like a pest, and undergo a lengthy approval process. By 2010, however, new methods had been developed for creating GMOs without agrobacteria; such plants could typically be marketed without pre-approval.
Soon after that, the first gene-edited crops began appearing. If old-school genetic engineering was a shotgun, techniques like TALEN and CRISPR were a scalpel—or the search-and-replace function on a computer program. With CRISPR/Cas9, for example, an enzyme that bacteria use to recognize and chop up hostile viruses is reprogrammed to find and snip out a desired bit of a plant or other organism's DNA. The enzyme can also be used to insert a substitute gene. If a DNA sequence is simply removed, or the new gene comes from a similar species, the changes in the target plant's genotype and phenotype (its general characteristics) may be no different from those that could be produced through selective breeding. If a foreign gene is added, the plant becomes a transgenic GMO.
Companies are already teeing up gene-edited products for the U.S. market, like a cooking oil and waxy corn.
This development, along with the emergence of non-agrobacterium GMOs, eventually prompted the USDA to propose a tiered regulatory system for all genetically engineered crops, beginning with an initial screening for potentially hazardous metaboloids or ecological impacts. (The screening was intended, in part, to guard against the "off-target effects"—stray mutations—that occasionally appear in gene-edited organisms.) If no red flags appeared, the crop would be approved; otherwise, it would be subject to further review, and possible regulation.
The plan was unveiled in January 2017, during the last week of the Obama presidency. Then, under the Trump administration, it was shelved. Although the USDA continues to promise a new set of regulations, the only hint of what they might contain has been Secretary of Agriculture Sonny Perdue's statement last March that gene-edited plants would remain unregulated if they "could otherwise have been developed through traditional breeding techniques, as long as they are not plant pests or developed using plant pests."
Because transgenic plants could not be "developed through traditional breeding techniques," this statement could be taken to mean that gene editing in which foreign DNA is introduced might actually be regulated. But because the USDA regulates conventional transgenic GMOs only if they trigger the plant-pest stipulation, experts assume gene-edited crops will face similarly limited oversight.
Meanwhile, companies are already teeing up gene-edited products for the U.S. market. An herbicide-resistant oilseed rape, developed using a proprietary technique, has been available since 2016. A cooking oil made from TALEN-tweaked soybeans, designed to have a healthier fatty-acid profile, is slated for release within the next few months. A CRISPR-edited "waxy" corn, designed with a starch profile ideal for processed foods, should be ready by 2021.
In all likelihood, none of these products will have to be tested for safety.
In the E.U., Stricter Rules Apply
Now let's look at the European Union. Since the late 1990s, explains Gregory Jaffe, director of the Project on Biotechnology at the Center for Science in the Public Interest, the EU has had a "process-based trigger" for genetically engineered products: "If you use recombinant DNA, you are going to be regulated." All foods and animal feeds must be approved and labeled if they consist of or contain more than 0.9 percent GM ingredients. (In the U.S., "disclosure" of GM ingredients is mandatory, if someone asks, but labeling is not required.) The only GM crop that can be commercially grown in EU member nations is a type of insect-resistant corn, though some countries allow imports.
European scientists helped develop gene editing, and they—along with the continent's biotech entrepreneurs—have been busy developing applications for crops. But European farmers seem more divided over the technology than their American counterparts. The main French agricultural trades union, for example, supports research into non-transgenic gene editing and its exemption from GMO regulation. But it was the country's small-farmers' union, the Confédération Paysanne, along with several allied groups, that in 2015 submitted a complaint to the ECJ, asking that all plants produced via mutagenesis—including gene-editing—be regulated as GMOs.
At this point, it should be mentioned that in the past 30 years, large population studies have found no sign that consuming GM foods is harmful to human health. GMO critics can, however, point to evidence that herbicide-resistant crops have encouraged overuse of herbicides, giving rise to poison-proof "superweeds," polluting the environment with suspected carcinogens, and inadvertently killing beneficial plants. Those allegations were key to the French plaintiffs' argument that gene-edited crops might similarly do unexpected harm. (Disclosure: Leapsmag's parent company, Bayer, recently acquired Monsanto, a maker of herbicides and herbicide-resistant seeds. Also, Leaps by Bayer, an innovation initiative of Bayer and Leapsmag's direct founder, has funded a biotech startup called JoynBio that aims to reduce the amount of nitrogen fertilizer required to grow crops.)
The ruling was "scientifically nonsensical. It's because of things like this that I'll never go back to Europe."
In the end, the EU court found in the Confédération's favor on gene editing—though the court maintained the regulatory exemption for mutagenesis induced by chemicals or radiation, citing the 'long safety record' of those methods.
The ruling was "scientifically nonsensical," fumes Rodolphe Barrangou, a French food scientist who pioneered CRISPR while working for DuPont in Wisconsin and is now a professor at NC State. "It's because of things like this that I'll never go back to Europe."
Nonetheless, the decision was consistent with longstanding EU policy on crops made with recombinant DNA. Given the difficulty and expense of getting such products through the continent's regulatory system, many other European researchers may wind up following Barrangou to America.
Getting to the Root of the Cultural Divide
What explains the divergence between the American and European approaches to GMOs—and, by extension, gene-edited crops? In part, Jennifer Kuzma speculates, it's that Europeans have a different attitude toward eating. "They're generally more tied to where their food comes from, where it's produced," she notes. They may also share a mistrust of government assurances on food safety, borne of the region's Mad Cow scandals of the 1980s and '90s. In Catholic countries, consumers may have misgivings about tinkering with the machinery of life.
But the principal factor, Kuzma argues, is that European and American agriculture are structured differently. "GM's benefits have mostly been designed for large-scale industrial farming and commodity crops," she says. That kind of farming is dominant in the U.S., but not in Europe, leading to a different balance of political power. In the EU, there was less pressure on decisionmakers to approve GMOs or exempt gene-edited crops from regulation—and more pressure to adopt a GM-resistant stance.
Such dynamics may be operating in other regions as well. In China, for example, the government has long encouraged research in GMOs; a state-owned company recently acquired Syngenta, a Swiss-based multinational corporation that is a leading developer of GM and gene-edited crops. GM animal feed and cooking oil can be freely imported. Yet commercial cultivation of most GM plants remains forbidden, out of deference to popular suspicions of genetically altered food. "As a new item, society has debates and doubts on GMO techniques, which is normal," President Xi Jinping remarked in 2014. "We must be bold in studying it, [but] be cautious promoting it."
The proper balance between boldness and caution is still being worked out all over the world. Europe's process-based approach may prevent researchers from developing crops that, with a single DNA snip, could rescue millions from starvation. EU regulations will also make it harder for small entrepreneurs to challenge Big Ag with a technology that, as Barrangou puts it, "can be used affordably, quickly, scalably, by anyone, without even a graduate degree in genetics." America's product-based approach, conversely, may let crops with hidden genetic dangers escape detection. And by refusing to investigate such risks, regulators may wind up exacerbating consumers' doubts about GM and gene-edited products, rather than allaying them.
"Science...can't tell you what to regulate. That's a values-based decision."
Perhaps the solution lies in combining both approaches, and adding some flexibility and nuance to the mix. "I don't believe in regulation by the product or the process," says CSPI's Jaffe. "I think you need both." Deleting a DNA base pair to silence a gene, for example, might be less risky than inserting a foreign gene into a plant—unless the deletion enables the production of an allergen, and the transgene comes from spinach.
Kuzma calls for the creation of "cooperative governance networks" to oversee crop genome editing, similar to bodies that already help develop and enforce industry standards in fisheries, electronics, industrial cleaning products, and (not incidentally) organic agriculture. Such a network could include farmers, scientists, advocacy groups, private companies, and governmental agencies. "Safety isn't an all-or-nothing concept," Kuzma says. "Science can tell you what some of the issues are in terms of risk and benefit, but it can't tell you what to regulate. That's a values-based decision."
By drawing together a wide range of stakeholders to make such decisions, she adds, "we're more likely to anticipate future consequences, and to develop a robust approach—one that not only seems more legitimate to people, but is actually just plain old better."
Two-and-a-half year-old Huckleberry, a blue merle Australian shepherd, pulls hard at her leash; her yelps can be heard by skiers and boarders high above on the chairlift that carries them over the ski patrol hut to the top of the mountain. Huckleberry is an avalanche rescue dog — or avy dog, for short. She lives and works with her owner and handler, a ski patroller at Breckenridge Ski Resort in Colorado. As she watches the trainer play a game of hide-and-seek with six-month-old Lume, a golden retriever and avy dog-in-training, Huckleberry continues to strain on her leash; she loves the game. Hide-and-seek is one of the key training methods for teaching avy dogs the rescue skills they need to find someone caught in an avalanche — skier, snowmobiler, hiker, climber.
Lume’s owner waves a T-shirt in front of the puppy. While another patroller holds him back, Lume’s owner runs away and hides. About a minute later — after a lot of barking — Lume is released and commanded to “search.” He springs free, running around the hut to find his owner who reacts with a great amount of excitement and fanfare. Lume’s scent training will continue for the rest of the ski season (Breckenridge plans operating through May or as long as weather permits) and through the off-season. “We make this game progressively harder by not allowing the dog watch the victim run away,” explains Dave Leffler, Breckenridge's ski patroller and head of the avy dog program, who has owned, trained and raised many of them. Eventually, the trainers “dig an open hole in the snow to duck out of sight and gradually turn the hole into a cave where the dog has to dig to get the victim,” explains Leffler.
By the time he is three, Lume, like Huckleberry, will be a fully trained avy pup and will join seven other avy dogs on Breckenridge ski patrol team. Some of the team members, both human and canine, are also certified to work with Colorado Rapid Avalanche Deployment, a coordinated response team that works with the Summit County Sheriff’s office for avalanche emergencies outside of the ski slopes’ boundaries.
There have been 19 avalanche deaths in the U.S. this season, according to avalanche.org, which tracks slides; eight in Colorado. During the entirety of last season there were 17. Avalanche season runs from November through June, but avalanches can occur year-round.
High tech and high stakes
Complementing avy dogs’ ability to smell people buried in a slide, avalanche detection, rescue and recovery is becoming increasingly high tech. There are transceivers, signal locators, ground scanners and drones, which are considered “games changers” by many in avalanche rescue and recovery
For a person buried in an avalanche, the chance of survival plummets after 20 minutes, so every moment counts.
A drone can provide thermal imaging of objects caught in a slide; what looks like a rock from far away might be a human with a heat signature. Transceivers, also known as beacons, send a signal from an avalanche victim to a companion. Signal locators, like RECCO reflectors which are often sewn directly into gear, can echo back a radar signal sent by a detector; most ski resorts have RECCO detector units.
Research suggests that Ground Penetrating Radar (GPR), an electromagnetic tool used by geophysicists to pull images from inside the ground, could be used to locate an avalanche victim. A new study from the Department of Energy’s Sandia National Laboratories suggests that a computer program developed to pinpoint the source of a chemical or biological terrorist attack could also be used to find someone submerged in an avalanche. The search algorithm allows for small robots (described as cockroach-sized) to “swarm” a search area. Researchers say that this distributed optimization algorithm can help find avalanche victims four times faster than current search mechanisms. For a person buried in an avalanche, the chance of survival plummets after 20 minutes, so every moment counts.
An avy dog in training is picking up scent
Sarah McLear
While rescue gear has been evolving, predicting when a slab will fall remains an emerging science — kind of where weather forecasting science was in the 1980s. Avalanche forecasting still relies on documenting avalanches by going out and looking,” says Ethan Greene, director of the Colorado Avalanche Information Center (CAIC). “So if there's a big snowstorm, and as you might remember, most avalanches happened during snowstorms, we could have 10,000 avalanches that release and we document 50,” says Greene. “Avalanche forecasting is essentially pattern recognition,” he adds--and understanding the layering structure of snow.
However, determining where the hazards lie can be tricky. While a dense layer of snow over a softer, weaker layer may be a recipe for an avalanche, there’s so much variability in snowpack that no one formula can predict the trigger. Further, observing and measuring snow at a single point may not be representative of all nearby slopes. Finally, there’s not enough historical data to help avalanche scientists create better prediction models.
That, however, may be changing.
Last year, an international group of researchers created computer simulations of snow cover using 16 years of meteorological data to forecast avalanche hazards, publishing their research in Cold Regions Science and Technology. They believe their models, which categorize different kinds of avalanches, can support forecasting and determine whether the avalanche is natural (caused by temperature changes, wind, additional snowfall) or artificial (triggered by a human or animal).
With smell receptors ranging from 800 million for an average dog, to 4 billion for scent hounds, canines remain key to finding people caught in slides.
With data from two sites in British Columbia and one in Switzerland, researchers built computer simulations of five different avalanche types. “In terms of real time avalanche forecasting, this has potential to fill in a lot of data gaps, where we don't have field observations of what the snow looks like,” says Simon Horton, a postdoctoral fellow with the Simon Fraser University Centre for Natural Hazards Research and a forecaster with Avalanche Canada, who participated in the study. While complex models that simulate snowpack layers have been around for a few decades, they weren’t easy to apply until recently. “It's been difficult to find out how to apply that to actual decision-making and improving safety,” says Horton. If you can derive avalanche problem types from simulated snowpack properties, he says, you’ll learn “a lot about how you want to manage that risk.”
The five categories include “new snow,” which is unstable and slides down the slope, “wet snow,” when rain or heat makes it liquidly, as well as “wind-drifted snow,” “persistent weak layers” and “old snow.” “That's when there's some type of deeply buried weak layer in the snow that releases without any real change in the weather,” Horton explains. “These ones tend to cause the most accidents.” One step by a person on that structurally weak layer of snow will cause a slide. Horton is hopeful that computer simulations of avalanche types can be used by scientists in different snow climates to help predict hazard levels.
Greene is doubtful. “If you have six slopes that are lined up next to each other, and you're going to try to predict which one avalanches and the exact dimensions and what time, that's going to be really hard to do. And I think it's going to be a long time before we're able to do that,” says Greene.
What both researchers do agree on, though, is that what avalanche prediction really needs is better imagery through satellite detection. “Just being able to count the number of avalanches that are out there will have a huge impact on what we do,” Greene says. “[Satellites] will change what we do, dramatically.” In a 2022 paper, scientists at the University of Aberdeen in England used satellites to study two deadly Himalayan avalanches. The imaging helped them determine that sediment from a 2016 ice avalanche plus subsequent snow avalanches contributed to the 2021 avalanche that caused a flash flood, killing over 200 people. The researchers say that understanding the avalanches characteristics through satellite imagery can inform them how one such event increases the magnitude of another in the same area.
Avy dogs trainers hide in dug-out holes in the snow, teaching the dogs to find buried victims
Sarah McLear
Lifesaving combo: human tech and Mother Nature’s gear
Even as avalanche forecasting evolves, dogs with their built-in rescue mechanisms will remain invaluable. With smell receptors ranging from 800 million for an average dog, to 4 billion for scent hounds, canines remain key to finding people caught in slides. (Humans in comparison, have a meager 12 million.) A new study published in the Journal of Neuroscience revealed that in dogs smell and vision are connected in the brain, which has not been found in other animals. “They can detect the smell of their owner's fingerprints on a glass slide six weeks after they touched it,” says Nicholas Dodman, professor emeritus at Cummings School of Veterinary Medicine at Tufts University. “And they can track from a boat where a box filled with meat was buried in the water, 100 feet below,” says Dodman, who is also co-founder and president of the Center for Canine Behavior Studies.
Another recent study from Queens College in Belfast, United Kingdom, further confirms that dogs can smell when humans are stressed. They can also detect the smell of a person’s breath and the smell of the skin cells of a deceased person.
The emerging avalanche-predicting human-made tech and the incredible nature-made tech of dogs’ olfactory talents is the lifesaving “equipment” that Leffler believes in. Even when human-made technology develops further, it will be most efficient when used together with the millions of dogs’ smell receptors, Leffler believes. “It is a combination of technology and the avalanche dog that will always be effective in finding an avalanche victim.”
Living with someone changes your microbiome, new research shows
Some roommate frustration can be expected, whether it’s a sink piled high with crusty dishes or crumbs where a clean tabletop should be. Now, research suggests a less familiar issue: person-to-person transmission of shared bacterial strains in our gut and oral microbiomes. For the first time, the lab of Nicola Segata, a professor of genetics and computational biology at the University of Trento, located in Italy, has shown that bacteria of the microbiome are transmitted between many individuals, not just infants and their mothers, in ways that can’t be explained by their shared diet or geography.
It’s a finding with wide-ranging implications, yet frustratingly few predictable outcomes. Our microbiomes are an ever-growing and changing collection of helpful and harmful bacteria that we begin to accumulate the moment we’re born, but experts are still struggling to unravel why and how bacteria from one person’s gut or mouth become established in another person’s microbiome, as opposed to simply passing through.
“If we are looking at the overall species composition of the microbiome, then there is an effect of age of course, and many other factors,” Segata says. “But if we are looking at where our strains are coming from, 99 percent of them are only present in other people’s guts. They need to come from other guts.”
If we could better understand this process, we might be able to control and use it; perhaps hospital patients could avoid infections from other patients when their microbiome is depleted by antibiotics and their immune system is weakened, for example. But scientists are just beginning to link human microbiomes with various ailments. Growing evidence shows that our microbiomes steer our long-term health, impacting conditions like obesity, irritable bowel syndrome, type 2 diabetes, and cancer.
Previous work from Segata’s lab and others illuminated the ways bacteria are passed from mothers to infants during the first few months of life during vaginal birth, breastfeeding and other close contact. And scientists have long known that people in close proximity tend to share bacteria. But the factors related to that overlap, such as genetics and diet, were unclear, especially outside the mother-baby dyad.
“If we look at strain sharing between a mother and an infant at five years of age, for example, we cannot really tell which was due to transmission at birth and which is due to continued transmission because of contact,” Segata says. Experts hypothesized that they could be caused by bacterial similarities in the environment itself, genetics, or bacteria from shared foods that colonized the guts of people in close contact.
Strain sharing was highest in mother-child pairs, with 96 percent of them sharing strains, and only slightly lower in members of shared households, at 95 percent.
In Italy, researchers led by Mireia Valles-Colomer, including Segata, hoped to unravel this mystery. They compared data from 9,715 stool and saliva samples in 31 genomic datasets with existing metadata. Scientists zoomed in on variations in each bacterial strain down to the individual level. They examined not only mother-child pairs, but people living in the same household, adult twins, and people living in the same village in a level of detail that wasn’t possible before, due to its high cost and difficulties in retrieving data about interactions between individuals, Segata explained.
“This paper is, with high granularity, quantifying the percent sharing that you expect between different types of social interactions, controlling for things like genetics and diet,” Gibbons says. Strain sharing was highest in mother-child pairs, with 96 percent of them sharing strains, and only slightly lower in members of shared households, at 95 percent. And at least half of the mother-infant pairs shared 30 percent of their strains; the median was 12 percent among people in shared households. Yet, there was no sharing among eight percent of adult twins who lived separately, and 16 percent of people within villages who resided in different households. The results were published in Nature.
It’s not a regional phenomenon. Although the types of bacterial strains varied depending on whether people lived in western and eastern nations — datasets were drawn from 20 countries on five continents — the patterns of sharing were much the same. To establish these links, scientists focused on individual variations in shared bacterial strains, differences that create unique bacterial “fingerprints” in each person, while controlling for variables like diet, demonstrating that the bacteria had been transmitted between people and were not the result of environmental similarities.
The impact of this bacterial sharing isn’t clear, but shouldn’t be viewed with trepidation, according to Sean Gibbons, a microbiome scientist at the nonprofit Institute for Systems Biology.
“The vast majority of these bugs are actually either benign or beneficial to our health, and the fact that we're swapping and sharing them and that we can take someone else's strain and supplement or better diversify our own little garden is not necessarily a bad thing,” he says.
"There are hundreds of billions of dollars of investment capital moving into these microbiome therapeutic companies; bugs as drugs, so to speak,” says Sean Gibbons, a microbiome scientist at the Institute for Systems Biology.
Everyday habits like exercising and eating vegetables promote a healthy, balanced gut microbiome, which is linked to better metabolic and immune function, and fewer illnesses. While many people’s microbiomes contain bacteria like C. diff or E. coli, these bacteria don’t cause diseases in most cases because they’re present in low levels. But a microbiome that’s been wiped out by, say, antibiotics, may no longer keep these bacteria in check, allowing them to proliferate and make us sick.
“A big challenge in the microbiome field is being able to rationally predict whether, if you're exposed to a particular bug, it will stick in the context of your specific microbiome,” Gibbons says.
Gibbons predicts that explorations of microbe-based therapeutics will be “exploding” in the coming decades. “There are hundreds of billions of dollars of investment capital moving into these microbiome therapeutic companies; bugs as drugs, so to speak,” he says. Rather than taking a mass-marketed probiotic, a precise understanding of an individual’s microbiome could help target the introduction of just the right bacteria at just the right time to prevent or treat a particular illness.
Because the current study did not differentiate between different types of contact or relationships among household members sharing bacterial strains or determine the direction of transmission, Segata says his current project is examining children in daycare settings and tracking their microbiomes over time to understand the role genetics and everyday interactions play in the level of transmission that occurs.
This relatively newfound ability to trace bacterial variants to minute levels has unlocked the chance for scientists to untangle when and how bacteria leap from one microbiome to another. As researchers come to better understand the factors that permit a strain to establish itself within a microbiome, they could uncover new strategies to control these microbes, harnessing the makeup of each microbiome to help people to resist life-altering medical conditions.