Gut bacteria's shocking secret: They produce electricity

Date:

September 12, 2018

Source:

University of California - Berkeley

Summary:

To date, most electricity-generating bacteria have come from weird environments, but researchers have found more than 100 in the human microbiome, both pathogenic and probiotic. They were unsuspected because they employ a different and simpler extracellular electron transfer system, which may prove useful in creating bacterial batteries. Their electrogenic ability may be important in infectivity, or in how they ferment cheese and yogurt.

Listeria bacteria transport electrons through their cell wall into the environment as tiny currents, assisted by ubiquitous flavin molecules (yellow dots).

Credit: Amy Cao graphic. Copyright UC Berkeley

While bacteria that produce electricity have been found in exotic environments like mines and the bottoms of lakes, scientists have missed a source closer to home: the human gut.

University of California, Berkeley, scientists discovered that a common diarrhea-causing bacterium, Listeria monocytogenes, produces electricity using an entirely different technique from known electrogenic bacteria, and that hundreds of other bacterial species use this same process.

Many of these sparking bacteria are part of the human gut microbiome, and many, like the bug that causes the food-borne illness listeriosis, which can also cause miscarriages, are pathogenic. The bacteria that cause gangrene (Clostridium perfringens) and hospital-acquired infections (Enterococcus faecalis) and some disease-causing streptococcus bacteria also produce electricity. Other electrogenic bacteria, like Lactobacilli, are important in fermenting yogurt, and many are probiotics.

"The fact that so many bugs that interact with humans, either as pathogens or in probiotics or in our microbiota or involved in fermentation of human products, are electrogenic -- that had been missed before," said Dan Portnoy, a UC Berkeley professor of molecular and cell biology and of plant and microbial biology. "It could tell us a lot about how these bacteria infect us or help us have a healthy gut."

The discovery will be good news for those currently trying to create living batteries from microbes. Such "green" bioenergetic technologies could, for example, generate electricity from bacteria in waste treatment plants.

The research will be posted online Sept. 12 in advance of Oct. 4 print publication in the journal Nature.

Breathing metal

Bacteria generate electricity for the same reason we breathe oxygen: to remove electrons produced during metabolism and support energy production. Whereas animals and plants transfer their electrons to oxygen inside the mitochondria of every cell, bacteria in environments with no oxygen -- including our gut, but also alcohol and cheese fermentation vats and acidic mines -- have to find another electron acceptor. In geologic environments, that has often been a mineral -- iron or manganese, for example -- outside the cell. In some sense, these bacteria "breathe" iron or manganese.

Transferring electrons out of the cell to a mineral requires a cascade of special chemical reactions, the so-called extracellular electron transfer chain, which carries the electrons as a tiny electrical current. Some scientists have tapped that chain to make a battery: stick an electrode in a flask of these bacteria and you can generate electricity.

The newly discovered extracellular electron transfer system is actually simpler than the already known transfer chain, and seems to be used by bacteria only when necessary, perhaps when oxygen levels are low. So far, this simpler electron transfer chain has been found in bacteria with a single cell wall -- microbes classified as gram-positive bacteria -- that live in an environment with lots of flavin, which are derivatives of vitamin B2.

"It seems that the cell structure of these bacteria and the vitamin-rich ecological niche that they occupy makes it significantly easier and more cost effective to transfer electrons out of the cell," said first author Sam Light, a postdoctoral fellow. "Thus, we think that the conventionally studied mineral-respiring bacteria are using extracellular electron transfer because it is crucial for survival, whereas these newly identified bacteria are using it because it is 'easy.'"

To see how robust this system is, Light teamed up with Caroline Ajo-Franklin from Lawrence Berkeley National Laboratory, who explores the interactions between living microbes and inorganic materials for possible applications in carbon capture and sequestration and bio-solar energy generation.

She used an electrode to measure the electric current that streams from the bacteria -- up to 500 microamps -- confirming that it is indeed electrogenic. In fact, they make about as much electricity -- some 100,000 electrons per second per cell -- as known electrogenic bacteria.

Light is particularly intrigued by the presence of this system in Lactobacillus, bacteria crucial to the production of cheese, yogurt and sauerkraut. Perhaps, he suggests, electron transport plays a role in the taste of cheese and sauerkraut.

"This is a whole big part of the physiology of bacteria that people didn't realize existed, and that could be potentially manipulated," he said.

Light and Portnoy have many more questions about how and why these bacteria developed such a unique system. Simplicity -- it's easier to transfer electrons through one cell wall rather than through two -- and opportunity -- taking advantage of ubiquitous flavin molecules to get rid of electrons -- appear to have enabled these bacteria to find a way to survive in both oxygen-rich and oxygen-poor environments.

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Story Source:

Materials provided by University of California - Berkeley. Original written by Robert Sanders. Note: Content may be edited for style and length.

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Journal Reference:

1. Samuel H. Light, Lin Su, Rafael Rivera-Lugo, Jose A. Cornejo, Alexander Louie, Anthony T. Iavarone, Caroline M. Ajo-Franklin, Daniel A. Portnoy. A flavin-based extracellular electron transfer mechanism in diverse Gram-positive bacteria. Nature, 2018; DOI:10.1038/s41586-018-0498-z

MOTH GUT BACTERIA COULD HELP CREATE NEW ANTIBIOTICS

S. Thiessen, MPI for Chemical Ecology

The cotton leafworm, Spodoptera Littoralis, holds a bacterium in its gut capable of fending off unwanted, deadly microbes.

THIS BENEVOLENT BACTERIA FENDS OFF DEADLY MICROBIAL INVADERS

By Claire Maldarelli

Moths are herbivores. The last thing they want are tiny bugs in their bellies. But they give a pass to one bacterium—E. mundtii. In fact, they allow it to proliferate uncontrolled inside their guts as they grow. And for a long time, scientists couldn’t figure out why. But a recent study in the journal Cell Chemical Biology suggests that this bacterium secretes a toxic substance that kills off other invading—and often deadly—bacteria, thereby securing itself a prime spot in the moth’s gut.

Scientists have known for a while that this species exists in high numbers inside the larval gut of a particular moth species, the cotton leaf worm, S. Littoralis. A 2012 study found that that this one species alone makes up about 40 percent of the entire microbial makeup of that moth's gut. In trying to make sense of this, they found that young S. Littoralis larvae had an abundance of Enterococcus, the family that E. mundtii belongs to, in their guts. But the guts of older larvae seemed to be dominated only by E. mundtii.

What was causing this significant change? Researchers took a group of Enterococcus bacteria from the young larvae and watched how they interacted with each other. They found that E. mundtii were able to outlive the rest by secreting a toxic peptide that not only killed off other Enterococcus bacteria but also a multitude of other harmful, invading bacteria that would have otherwise had a good chance of killing the moth.

Aside from this being an extremely effective way to survive and live on to adulthood, it also demonstrates a natural mechanism through which microbes prevent other microbes from killing their hosts. How will this help us humans? The researchers think this idea of using one ‘safe’ species of bacteria to fend and kill off invading, toxic bacteria could be an effective way to create new types of antibiotics. In fact, E. mundtii could be particularly useful—according to the researchers, it seems to selectively kill off common food-borne pathogens, like L. monocytogenes as well as toxic bacteria like certain strains of E. faecalis and Streptococcus, while leaving healthy bacteria alone.

Novel methods to combat bacterial infections in humans are sorely needed. Just last week, a woman in Nevada died of a superbug that was resistant to every known and available antibiotic on the market. Instances like these are a reminder that antibiotic resistance continues to loom in our near future. Deadly bacteria quickly evolve so to survive the antibiotics that once killed them off, so fighting their increasing resistance to drugs is a never-ending tug-of-war. But if we can come up with new methods—like using other bacteria to fend them off—we may be able to slow down the instances of these infections.

For now, the researchers are eager to see if this type of symbiotic defense mechanism exists in other insects as well, and if so, how exactly it works. There’s a high chance that it does, the scientists note, given that insects are remarkably resistant to infection compared to other animals. Perhaps with more research we can adopt some of these remarkable mechanisms as well.

Having worms can be good for the gut

THE WORM TURNS  Intestinal parasites may have an upside. Researchers have discovered that people with whipworms (Trichuris trichiura, left) and mice with Heligmosomoides polygyrus (right) have fewer inflammation-provoking bacteria than they do without the worms. 

Parasites trigger immune reaction that can calm inflammation

BY 

TINA HESMAN SAEY

Parasitic worms may hold the secret to soothing inflamed bowels.

In studies of mice and people, parasitic worms shifted the balance of bacteria in the intestines and calmed inflammation, researchers report online April 14 in Science. Learning how worms manipulate microbes and the immune system may help scientists devise ways to do the same without infecting people with parasites.

Previous research has indicated that worm infections can influence people’s fertility (SN Online: 11/19/15), as well as their susceptibility to other parasite infections (SN: 10/5/13, p. 17) and to allergies (SN: 1/29/11, p. 26). Inflammatory bowel diseases also are less common in parts of the world where many people are infected with parasitic worms.

P’ng Loke, a parasite immunologist at New York University School of Medicine, and colleagues explored how worms might protect against Crohn’s disease. The team studied mice with mutations in the Nod2gene. Mutations in the human version of the gene are associated with Crohn’s in some people.

The mutant mice develop damage in their small intestines similar to that seen in some Crohn’s patients. Cells in the mice’s intestines don’t make much mucus, and more Bacteroides vulgatus bacteria grow in their intestines than in the guts of normal mice. Loke and colleagues previously discovered that having too much of that type of bacteria leads to inflammation that can damage the intestines.

In the new study, the researchers infected the mice with either a whipworm (Trichuris muris)or a corkscrew-shaped worm (Heligmosomoides polygyrus). Worm-infected mice made more mucus than uninfected mutant mice did. The parasitized mice also had less B. vulgatus and more bacteria from the Clostridiales family. Clostridiales bacteria may help protect against inflammation.

“Although we already knew that worms could alter the intestinal flora, they show that these types of changes can be very beneficial,” says Joel Weinstock, an immune parasitologist at Tufts University Medical Center in Boston.

Both the increased mucus and the shift in bacteria populations are due to what’s called the type 2 immune response, the researchers found. Worm infections trigger immune cells called T helper cells to release chemicals called interleukin-4 and interleukin-13. Those chemicals stimulate mucus production. The mucus then feeds the Clostridiales bacteria, allowing them to outcompete the Bacteroidales bacteria. It’s still unclear how the mucus encourages growth of one type of bacteria over another, Loke says.

Blocking interleukin-13 prevented the mucus production boost and the shift in bacteria mix, indicating that the worms work through the immune system. But giving interleukin-4 and interleukin-13 to uninfected mice could alter the mucus and bacterial balance without worms’ help, the researchers discovered.

Loke and colleagues also wanted to know if worms affect people’s gut microbes. So the researchers took fecal samples from people in Malaysia who were infected with parasitic worms.  

After taking a deworming drug, the people had less Clostridiales and more Bacteriodales bacteria than before. That shift in bacteria was associated with a drop in the number ofTrichuris trichiura whipworm eggs in the people’s feces, indicating that getting rid of worms may have negative consequences for some people.

Having data from humans is important because sometimes results in mice don’t hold up in people, says Aaron Blackwell, a human biologist at the University of California, Santa Barbara. “It’s nice to show that it’s consistent in humans.”

Worms probably do other things to limit inflammation as well, Weinstock says. If scientists can figure out what those things are, “studying these worms and how they do it may very well lead to the development of new drugs.” 

Gut reaction

In normal mice (top), the cells lining the intestines form fingers reaching toward the hollow center. In mice with a mutation in the Nod2 gene (middle), the intestinal lining is often swollen and damaged (an abscess shown). But infecting mutant mice with a whipworm (Trichuris muris) can restore the gut to health (bottom) by promoting mucus production and shifting the mix of bacteria that live the intestines.

Citations

D. Ramanan et al. Helminth infection promotes colonization resistance via type 2 immunity.Science. Published online April 14, 2016. doi: 10.1126/science.aaf3229. 

D. RAMANAN ET AL/SCIENCE 2016

Gut microbes signal when dinner is done

LOSS OF APPETITE  Experiments show that helpful gut bacteria like this E. coli K12 produce proteins that could influence the appetite of mice and rats.

After eating, bacteria tell host to quell hunger

BY 

CHRIS SAMORAY

Gut bacteria are not polite dinner guests. They fill up fast and tell their host to quit eating, too.

After only 20 minutes, helpful E. coli populations that live in animal guts produce proteins that can curb how hungry its animal partner is, researchers show November 24 in Cell Metabolism. In mice and rats, the proteins stimulated brain-body responses that led the animals to eat less. The new findings indicate that gut microbes could be more involved with regulating food intake in animals, including humans, than previously thought.

“It suggests that the growth and activity of the microbiome might specifically regulate appetite and feeding behavior,” says Kevin Murphy, an endocrinologist at Imperial College London not involved with the study.

Food provides loads of nutrients to the gut. There, microbes use the nourishment to maintain population size. In the lab, Sergueï Fetissov and colleagues found that E. coli populations stopped growing 20 minutes after receiving nutrients. Upon hitting the 20-minute mark, the microbes also made some different proteins than before and boosted production of the protein ClpB, which mimics a hormone in humans that acts on appetite. When the E. coli stopped growing, they produced “two times as much of this protein,” says Fetissov, a physiologist at Rouen University in France.

Proteins from the E. coli no-growth stage were then injected in rats and mice. Compared with rodents that didn’t receive the proteins, those that did ate less and had higher levels of ClpB in their guts. The researchers also found that the protein encouraged the release of peptide YY — a hormone associated with reduced appetite — and stimulated nerve cells that decrease hunger levels.

 The E. coli proteins seem to influence feeding behavior in the rats and mice. But it’s too soon to say whether the results are applicable to humans. “Further work is required to determine how physiologically relevant the findings are,” Murphy says.

The interaction between gut microbes and host organisms isn’t well understood, Fetissov says, so it’s important to study pathways and mechanisms that relate to food intake. Human gut microbes, for instance, may play a role in obesity, and he says that studies like this could help explain links between microbes and human health.

WHAT DOES YOUR GUT MICROBIOME LOOK LIKE?

Katherine Harmon Courage

SCIENTISTS CAN NOW SEE HOW DIET IMPACTS THE GUT AND ITS MICROBES—AND YOU CAN, TOO

Inside your gut

Quantitative Imaging of Gut Microbiota Spatial Organization

Your large intestine may not usually be a pretty place, but for scientists wielding a new technique to map out every last bacterium and undigested food particle, it can become a marvel. The results, described in the October issue of Cell Host & Microbe paint a stunning visual picture of a delicate dance between necessary microbes and the sensitive gut wall—kept in balance by a crucial layer of mucus. This image shows a detail taken from a mouse's gut that has been colonized with human gut microbes; the mucus layer is dyed green, the gut wall cells are tinted blue, and two phyla of bacteria common in a human gut are also marked: Firmicutes in yellow and Bacteroidetes in fuchsia. Such never-before-seen detail will help researchers better understand how diet can impact gut microbes and our health.

The microbes in your gut depend on you to feed them well. A steady diet of complex fibers keeps them happy—and by extension, may keep you healthier. The microbiota have been linked to weight, gut health, allergies and even mood. Studies have shown that when the host (you) fails to supply the hungry hordes of beneficial microbes with what they want, the populations can change, and can even start to threaten the gut's thin lining. But we have been unable to see exactly whether—and how—these shifts were happening.

Fiber-deprived

Quantitative Imaging of Gut Microbiota Spatial Organization

We depend on the mucus layer (pictured in green) to protect our gut wall. Even beneficial microbes in our gut can cause the immune system to activate if they get too close. A normal, healthy mucus layer is pictured on the left, showing the microbes (red) and food particles (yellow) far away from the host tissue (blue) when mice were on a standard diet. But when mice didn't eat any fiber (a favorite food of gut microbes, also known as "microbiota-accessible carbohydrates" or "MACs"), the mucus wall shrank, allowing microbes uncomfortably close to the gut tissue. Why the shrinkage? When microbes don't have dietary fibers to munch on, they eat the mucus instead.

Now a team at Stanford University has created an elegant method of peering inside the gut—at cell-level resolution—to see what is going on. The researchis in the October issue of Cell Host & Microbe.

The big picture

Quantitative Imaging of Gut Microbiota Spatial Organization

This slice shows how the mucus lining (green) surrounds undigested food (blue)—in this case plant matter—in the large intestine. This comprehensive, high-resolution view of a tiny (9-millimeter) sample was made by stitching together 40 different images.

Most of our understanding about gut microbes—and any impact diet has on them—has come from poop. Researchers can run a quick genetic scan on a smudge of a fecal sample, assessing which microbes are there, and in what abundances. But from this mixed-up pile, there is no way to know where in the gut the microbes are living—or how they are interacting with one another or with you. "Mapping the spatial organization of this microbial community is a fundamental aspect of understanding its biology," says Justin Sonnenburg, a microbiologist at Stanford and coauthor of the new paper. "Without this information, we will struggle to make sense of how these microbes are contributing to our health or why interactions go awry and cause disease."

Missing clusters

Quantitative Imaging of Gut Microbiota Spatial Organization

Researchers found that mice colonized with human gut microbes and fed a normal, healthy diet had clusters of different types of bacteria (Bacteroidetes in red andFirmicutes in green). When mice lacked fiber in their diet, however, this organization disappeared, and members of these two microbe phyla were scattered randomly within the large intestine. You can also see that the space (black) between the microbes and the host tissue (blue) is thinner in the no-fiber diet.

"This is a huge advance," says Eric Martens, an assistant professor of microbiology at the University of Michigan Medical School, who also studies the impact of fiber on gut microbes and the gut's mucus layer and was not involved in the new research. "Since we are just beginning to understand the mechanisms and functions of the hundreds of species of bacteria that inhabit the gut, understanding how these organisms pack together, organize, and reproduce in such a dense and tightly confined space provides enormous insight," he says.

Up-close companions

Quantitative Imaging of Gut Microbiota Spatial Organization

A closer look comparing the healthy diet (left) and the fiber-deficient diet (right) shows how different the distributions of the microbe types are. Bacteria in theBacteroidetes phylum are in red, and those in the Firmicutes phylum are in green. The standard diet on the left also appears to contain more Firmicutes overall than the fiber-free diet on the right, which could have implications for what happens in the gut—and by extension, the host.

Sonnenburg and his colleagues fed mice (colonized with human gut microbes) standard and fiber-deficient diets. They then carefully preserved thin slices of the mouse intestines and added special dyes to mark different microbes, undigested food, the essential mucus layer and the gut wall. With so many minute sample slices to analyze, they also developed software to help compute the spatial relationships.

Building the barrier

Quantitative Imaging of Gut Microbiota Spatial Organization

The crucial mucus layer that protects our gut is constantly being renewed. This image of a standard mouse gut shows a close-up of mucus (green) being formed by goblet cells (in pockets surrounded by blue host tissue) and then released into the mucus barrier. "The mucus forms sheets that build on top of each other, forming a boundary," explains Kristen Earle, a graduate researcher in microbiology and immunology at Stanford University and co-author of the new study. "On top of this layer is a looser layer, that forms a habitat for bacteria."

In being able to actually see what was happening on these different diets, the researchers found that when the fiber was reduced, the mucus layer shrank—likely due to starved microbes eating it—from approximately 51 micrometers to just 31, allowing the microbes closer to the sensitive wall of the intestine. And as Sonnenburg notes, "we know that part of maintaining harmony between our resident microbes and our intestinal tissue is separation of the two"—namely by the mucus layer.

Crowded field

Quantitative Imaging of Gut Microbiota Spatial Organization

The highest concentrations of bacteria are found in the large intestine, where they break down fibers and other compounds our body couldn't process on its own. This image shows a mat of bacteria in a normal mouse fed on a healthy diet.

As this mucus layer shrank, mice missing the fiber in their diet also had more markers of inflammation. This can be triggered by the immune system attempting to keep bugs where they belong—in the gut. "Over long periods of time, low levels of inflammation can lead to many different types of problems, including colitis or even cancer," Sonnenburg says. (But, he cautions, the experiments have only been in mice—and over a short time period—so how the findings translate to us and our long-term health remain to be seen.)

Strange powers

Quantitative Imaging of Gut Microbiota Spatial Organization

Although fewer and farther-between, bacteria in the small intestine seem to play a role in shaping the landscape there. The small intestine is lined with protrusions called villi, which help increase the body's ability to absorb nutrients from food passing through. In mice fed a standard diet, there was a small amount of an antimicrobial compound (called REG3B, noted by coloring antibodies to this compound in red) at the base of the villi. But this microbe-deferring compound was prevalent through the villi when mice ate a fiber-free diet. Researchers are still investigating what this might mean for health.

In addition to the shrinking mucus layer, the researchers were also able to see that changing the diet altered the way bacteria were organized in the gut. On a standard diet, two categories of bacteria were usually found in clumps of similar cells. But without fiber, these groupings vanished, and the microbes were more evenly distributed.

Ronan O'Connell, of University College Dublin's Conway Institute of Biomolecular and Biomedical Research, has been using laser microscopy to parse the structure of the gut microbiota in healthy people as well as those with diseases of the intestinal tract. He notes that the new imaging technique "beautifully illustrates the complexity of the host-microbiome interface," adding that it might some day be able to be used to study the differences in healthy and diseased guts in humans. Sonnenburg and his group are, in fact, already looking to expand the work to humans.

In the meantime, the new software used for this work (called BacSpace) is available to other groups, and, Sonneburg notes, he hopes sharing it will "propel this field forward rapidly." Martens, for one, is enthusiastic about the potential for this visual approach. "One can imagine turning up the resolution to the species level, instead of just phyla."

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