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Nature

17
Dec

Small Is Big: How Bacteria Will Make Our World Cleaner and Healthier

During her training as a soil scientist, Janet Jansson never imagined that she’d end up poring over gene sequences from a person’s intestines. The affable native of New Mexico had gone through the usual motions on the way to her first professorship—a Master’s in soil microbiology, a Ph.D. in microbial ecology, and a postdoc in biochemistry to round things out. For 20 years, she used every known trick to coax soil microbes into divulging their secrets. When those didn’t work, she developed her own, including an early and widely-cited method for purifying DNA from bacteria living in soil. It was gratifying work, if not the most high profile.

That would soon change, though. In 2000, Jansson, then a professor at Södertörn University in Sweden, was teaching a class with Charlotta Edlund, a colleague who studied microbes from a medical perspective. The two shared a mutual passion for microscopic life, but their research approaches couldn’t have been more different. Unlike bacteria which thrive in the human body, soil microbes are incredibly difficult to cultivate in the lab—you can’t just inoculate a Petri dish and return in the morning. So Jansson and other soil microbiologists had created an entirely new suite of tools.

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Enterococcus faecalis, a common bacterium in the human microbiome

As Jansson and Edlund talked shop over the course of the semester, Jansson recalls her colleague wondering if the techniques used to study soil microbes might be useful in a project on antibiotic resistance that relied on fecal samples. “That was before the human microbiome was cool,” Jansson says. “That’s how it started. And then I got very interested in it.”

Like many ideas whose time is right, Jansson wasn’t alone in her foray into the human microbiome. “There were several soil microbiologists that started to do the same thing as me. Just independently, without knowing,” she recalls. “At that time, methods-wise, technique-wise, the environmental field was farther ahead than the clinical field, whereas in the past, it has been the reverse.”

That reversal would end up changing the way we understand the microbial world. Rather than assuming bacteria and other microorganisms lead lives that occasionally intersect with the macroscopic world, we would come to learn that microbes exert their influence in various and surprising ways. But as we discover more about the remarkable diversity in the microbial world, we’re learning that we may be able to use them as allies in everything from advanced medical treatments to farming and environmental remediation.

A Slick Solution

Jansson’s lab had already expanded well beyond soil microbes by the time an explosion rocked the Deepwater Horizon oil rig in April 2010. Her research group, now at the Lawrence Berkeley National Laboratory in Berkeley, California, was investigating how microbial enzymes might help suck more oil out of a well. To do that, they had been developing complex methods to extract DNA from oil. “We had already worked out all of those methods at the time the spill happened,” Jansson says.

The Gulf of Mexico is littered with natural oil seeps, which some species of bacteria thrive on. In a way, the spill was a seep of massive proportions, and it had the potential to drastically alter the Gulf’s microbial communities, benefitting some types while harming others. Jansson and one of her collaborators, Terry Hazen, also a microbiologist at the Berkeley Lab, asked BP, which was already funding Jansson’s work on oil and microbes, if they would be willing to back a study of Gulf bacteria populations. They agreed, sending microscopes, freezers, grad students, and postdocs out on boats to survey the waters.

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Firefighting ships attempt to put out the blaze on the Deepwater Horizon.

Jansson’s team was in charge of the DNA extraction part, which would help identify which types of bacteria were thriving and where. Comparing water samples taken both in and out of the plume of oil, Jansson and her colleagues noticed distinct differences. Of the 951 taxa that were present in the plume, 16 of those were booming compared with levels in normal sea water. Nearly all of the prospering taxa could either degrade oil or kick their reproduction into high gear when oil is present in cold water.

Their study confirmed what many suspected—that certain members of the Gulf’s natural bacterial communities would chomp away at the oil over time, eventually bringing water quality back up to more normal levels. But more intriguingly, the methods Jansson and her team developed could also be used for environmental monitoring. They showed it is possible to use specific bacterial taxa, or even individual genes, as bioindicators. Instead of using complicated chemical tests to ascertain water quality, scientists in the field could draw a sample of water and run it through a cheap sequencer that would look for particular genetic markers that correlate with oil concentration.

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Dolphins swim next a plume of crude released in the Deepwater Horizon oil spill.

Beyond environmental monitoring, Jansson and her group’s work could lead to new ways to clean up oil spills. If we could harness the Gulf’s oil-loving bacteria, they could be used to mop up a spill more quickly. “If you did have an oil spill in the future, you could maybe try to enrich similar microorganisms that have those properties,” Jansson speculates. By building up beneficial populations in and around a spill, the damaging oil could be dissipated more quickly. All by using bacteria that occur naturally in the Gulf.

Living Sensors

Jansson and her colleagues’ work in the Gulf of Mexico is relatively cutting edge, which is to say that it’s not quite ready for widespread use. Jansson’s research is like the early stages of R&D in a long, multi-year development process of a new product. Someday, we may be able to clean up a spill without nasty chemicals or dig up a scoop of soil and run it through a sequencer that can sense subtle but significant changes in microbial communities. But we’re not there yet.

“That should be possible,” says van der Meer, a professor of microbiology at University of Lausanne in Switzerland. “But then you’re talking more about very complicated systems,” he says. “People have tried to develop chips to get very rapid ID of which functional capacity a bacterial community has, but even that requires quite a bit of interpretation before you can get a reasonable signal. We’re speaking about weeks of analysis.”

To bridge that gap, van der Meer has been developing test kits that, rather than sense changes in microbial communities, have the necessary bacteria locked inside. The kits rely on the microbes instead of the more traditional chemicals to test for various contaminants, including arsenic, oil, and other pollutants, for less cost.

One of van der Meer’s bioreporters is a nonpathogenic form of E. coli that has a gene inserted into an appropriate part of its genome that, when in the presence of arsenic, produces a protein that glows green. Green fluorescent protein, or GFP, is a standard technique that’s used in labs across the world to see if a gene is active or not. Van der Meer’s innovation was to take that process out of the lab and into the field.

To get them to the field, van der Meer freeze-dries the cells into a powder. When he needs to use the test, he reconstitutes them by adding a few drops of water. (Other labs transport bacterial spores, which require a few hours to “wake up.”) Once awake, he exposes the bacteria to the water or soil he’s looking to test. If a contaminant like arsenic is present, then the cells will glow green.

Van der Meer’s bioreporters aren’t in mass production currently, but its not hard to imagine that being far off. Once the bacteria have been sensitized to a particular chemical or contaminant, the assays cost less than one cent to produce. Packaging, shipping, and marketing will add to the cost, but with such a low starting point, bioreporters could be far more affordable and thus available to poorer parts of the world. After all, why shouldn’t they know what’s in their drinking water, too?

Agricultural Judo

While van der Meer has been using bacteria to sense what might be wrong with our environment, other scientists have been using strains to encourage what’s right with it. Soil microbiologists—including Jansson—have been studying the intimate relationship between bacteria and plants. The development of genetic surveys has clarified that picture, and over the years, that’s led plant physiologists and soil microbiologists to speculate on various ways to use microbes to boost crop yields.

After decades of research on fertilizers, pesticides, and plant genetics, agricultural science is increasingly focusing its attention on microbes. “You have kind of those three general areas of how we improve crops: Crop genetics, chemicals, and bacteria,” Kloepper says. “We’re in the mature state now where we’re looking at those not as competition, but as a blend of what we offer to growers.”

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Soil microbes play an intimate role in plant growth. Boosting beneficial bacteria can raise crop yields.

There are a few different ways we can use microbes in agriculture. Seeds can be coated with a polymer containing beneficial microorganisms, giving the new plant a head start. Microbes can also be mixed in with fertilizer or stirred into irrigation water. Once they form their association with the plant, beneficial bacteria can increase root and shoot growth, fix nitrogen for the plants, and wick up nutrients in the soil that would be otherwise out of reach or unobtainable.

Another approach is called “predictive agriculture.” “This is a relatively very new area,” Jansson says. While still years off, researchers today are using a variety of tools to study which microbes thrive when crop yields are high. Once those populations are characterized, Jansson says, then scientists can ask, “Is there some way we can manipulate the environment to enhance their survival?”

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Beneficial bacteria can be applied in a number of ways, including in irrigation water.

While the current tenor of the field has been more early-phase than market-ready, that may change soon. “The benefits of the microbes are being investigated like they’ve never been investigated before,” Kloepper says. “I think we’re on the cusp of making some real breakthroughs.”

If we’ve known about beneficial soil bacteria for years, why has it taken so long for the field to thrive? One reason is certainly our ability to inexpensively sequence DNA and RNA from soil, making it easier than ever to survey microbial communities. Beyond the genetic revolutions, there also may be a more esoteric reason. Kloepper suspects our interest in plant-microbe interactions has been fueled, in part, by our growing familiarity with the human microbiome. “Our food understanding kind of mirrors our understanding in health,” he says. As scientists learn more and the public becomes more accustomed to the idea of microbial helpers, Kloepper says, “why wouldn’t we use it in agriculture?”

The Gut-Heart Connection

Our understanding of microbial worlds has grown quickly under the tutelage of soil scientists and plant microbiologists, but it has positively exploded when medicine has entered the fray. By collaborating with microbiologists like Jansson, doctors and medical researchers have begun to map out and leverage the ecosystem within our bodies.

Unlike Jansson, Stan Hazen stumbled into his study of the human microbiome. Hazen, a cardiovascular specialist and researcher at the Cleveland Clinic, was analyzing archived blood samples of thousands of patients, some of whom suffered a heart attack or stroke or had died, trying to see if any patterns stood out. One that did was the blood level of a compound known as TMAO. The compound changes the way cholesterol is metabolized, causing it to build up in people’s arteries. Hazen and his team had a smoking gun, but they initially didn’t know what was pulling the trigger—what was producing all this TMAO in people with cardiovascular problems.

“We essentially reverse engineered where it came from and discovered that it was a by-product of gut flora metabolism,” Hazen says. More than that, he and his team learned that TMAO levels were higher among red meat eaters, meaning that it wasn’t red meat, per se, that causes heart disease, but its interaction with the bacteria in our gut. “This metabolite alters, literally, how cholesterol is sensed by cells in the artery wall.”

To Hazen, the revelation that microbes in our guts could be causing atherosclerosis changed the way he thought about the human body. Instead of focusing drug development on processes that are entirely human, maybe it should look at the microbiome, too, he thought. “Can we drug the microbiome?” Hazen wonders. He thinks so and is currently testing a drug that will block the enzyme in bacteria that produces TMAO, halting the chain reaction before it can even begin.

“That’s a really a big and fundamental shift in how we think about treating diseases,” Hazen says. “If we give a drug to a bacteria, it’s usually an antibiotic to kill it. Instead of killing it, we’re talking about making an inhibitor of just a specific enzyme.” He’s optimistic the approach will yield benefits outside of atherosclerosis, including other ailments like diabetes and obesity. “Any place where bacteria are thought to be playing a role,” he says.

Drugging the microbiome may not be the only way medicine can use the microbiome to its advantage. Cambridge, Massachusetts-based startup Seres Health is developing a microbe-containing pill to combat infections of Clostridium difficile, a bacterium that causes diarrhea, colon inflammation, and, in some cases, death. The current cutting-edge procedure for treating C. difficile is a fecal transplant, where bacteria from a healthy person’s gut are isolated, cultured, and injected into the patient’s colon. Seres is hoping a simple pill can replace that process.

Probiotic pills have been on the market for years, but the way they were developed and how they are marketed put Seres in a different class. Many existing probiotic pills are sold as supplements, so their claims aren’t verified by the FDA. Seres, though, will be seeking FDA approval for their pill, meaning it will be classified as a drug rather than a supplement.

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Clostridium difficile is a bacterial infection that can be fought using transplanted gut bacteria from a healthy donor.

Seres and other companies hoping to produce scientifically-tested, FDA-regulated probiotic pills have a difficult road ahead of them. The human microbiome is dauntingly complex, and we have only begun to understand how many different species it contains and what role they play. Injecting a new player into the mix could disrupt the ecosystem in unexpected ways.

Still, as genetic sequencing techniques improve, our understanding of the human microbiome is likely to improve. Rather than relying on chemical formulas, we may be able to take drugs containing a specific suite of bacteria to subtly alter our microbial ecosystem to treat a number of different diseases, from acute intestinal infections like C. difficile to chronic ailments like clogged arteries.

Assembling the Puzzle

Despite the breakneck pace of discovery, we’re still very much in the early days of learning what we can do with the microbiome and what it can do for us. There’s a long road ahead, and the speed with which we travel down it is dependent on new investigative techniques like the sort that Jansson’s lab are developing. She calls her method an “omics” approach, meaning she’s drawing on genomics, metabolomics, proteomics, and so on, all techniques that rely on huge amounts of data to distill insights into genetics, metabolism, proteins, and more.

Developing lab protocols to purify the necessary materials is a challenge, but even more constraining are computing resources. “It’s hard to even weed through the data,” Jansson says. “You need supercomputing facilities and really massive statistical analyses to be able to go through these data sets.”

Our primitive understanding of the microbiome’s diversity is also holding us back. Where we once thought there were perhaps a few thousand species, now “reasonable estimates are more on the order or millions or hundreds of millions,” according to Jonathan Eisen, an evolutionary biologist at the University of California, Davis.

Jansson is hopeful that by mapping that diversity, we can gain a better understanding of the role bacteria play in the environment and in our bodies—and how we can use them. “A lot of bioinformatics tools are being developed,” she says. “We’re pretty close to being able to deal with massive amounts of these signature gene sequences.”

Sequencing techniques and supercomputing promise to deepen our understanding of microbial communities, but at its heart, the field is dependent on something more personal and less quantifiable—scientific collaboration. After all, without partnerships like Jansson and her colleague Charlotta Edlund’s, we may still be in the dark about the diversity and significance of the microbiome. But with them, we’ve changed the way we treat diseases, clean up the environment, and grow food. Who knows what comes next?