Posts Tagged ‘bacteria’

By Michael Le Page

Eating too much salt may impair the body’s ability to fight bacterial infections, according to studies in mice and in 10 human volunteers.

Christian Kurts at the University Hospital of Bonn in Germany and his team first showed that mice given a high salt diet were less able to fight kidney infections caused by E. coli and body-wide infections caused by Listeria monocytogenes, a common cause of food poisoning.

“The bacteria caused more damage before the immune system got rid them,” says Kurts.

Next, the team gave 10 healthy women and men who were 20 to 50 years old an extra 6 grams of salt a day on top of their normal diet, in the form of three tablets a day. After a week, some of their immune cells, called neutrophils, had a greatly impaired ability to engulf and kill bacteria compared with the same tests done on each individual before they took extra salt.

The team didn’t examine the effect of high salt intake on the body’s ability to fight viral infections.

The World Health Organization recommends that people eat no more than 5 grams of salt a day to avoid high blood pressure, which can cause strokes and heart disease. In the UK, people eat 8 grams on average, suggesting many consume as much or more than the volunteers in the study.

The team thinks two mechanisms are involved. First, when we eat lots of salt, hormones are released to make the body excrete more salt. These include glucocorticoids that have the side effect of suppressing the immune system throughout the body.

Second, there is a local effect in the kidney. Kurts found that urea accumulates in the kidney when salt levels are high, and that urea suppresses neutrophils.

Journal reference: Science Translational Medicine, DOI: 10.1126/scitranslmed.aay3850

https://www.newscientist.com/article/2238629-eating-too-much-salt-seems-to-impair-bodys-ability-to-fight-bacteria/?utm_source=NSDAY&utm_campaign=8ea0a51a66-EMAIL_CAMPAIGN_2020_03_25_04_56&utm_medium=email&utm_term=0_1254aaab7a-8ea0a51a66-374123611

by CARLY CASSELLA

The way oral bacteria sets up shop in our mouths is not unlike how we humans settle into our cities, a new study has found.

There’s a reason bacteria are said to live in ‘colonies’, and the more we learn about how these tiny architects build their communities, the more familiar their behavior seems to us.

A new study following how multiple individual settlers develop into microcolonies has found growth patterns and dynamics that mirror our own urban inclinations.

“We take this ‘satellite-level’ view, following hundreds of bacteria distributed on a surface from their initial colonisation to biofilm formation,” says Hyun Koo from the University of Pennsylvania.

“And what we see is that, remarkably, the spatial and structural features of their growth are analogous to what we see in urbanisation.”

Just as in nature, bacteria in your mouth live in complex structures known as biofilms. In fact, 99.9 percent of prokaryotes live crammed together with millions of other neighbours in one of these settlements.

Biofilms are everywhere, but if they’re on your teeth, we refer to them as plaque. This dense and sticky deposit is hard to remove, thereby protecting resident microbes from environmental assaults, like toothpaste, floss or even antibiotics.

It builds up when several individual settlers develop into microcolonies, but exactly how this happens remains underexplored.

Using the oral bacterium Streptococcus mutans, researchers have shown that microbial cells settle at random and regardless of the surface type. Nevertheless, only a subset of colonisers actually begin clustering, expanding their scope “by amalgamating neighboring bacteria into densely populated microcolonies.”

“We thought that the majority of the individual bacteria would end up growing,” says Koo. “But the actual number was less than 40 percent, with the rest either dying off or being engulfed by the growth of other microcolonies.”

Once the clusters arise, something really curious happens: they begin to interact with one another, growing and organising into densely populated “micron-scale microcolonies that further expand and merge” to form a biofilm superstructure.

This sort of cooperation is interesting, as previous studies have reported bacterial competition in other species, especially when there was a scarcity of nutrients.

In this case, the nutrients only impacted the actual forming of the colonies. After that, “the individual microcolonies (distant or in close proximity) continued to grow without disruption until merging with each other, and the merged structures behaved and grew like a single new harmonised community,” the researchers write.

Only when more antagonistic foreign species were introduced did it affect that seemingly peaceful unit, and the growth of the microcolonies was lowered.

“These communities (microcolonies) can expand and merge with each other in a collaborative fashion, without competition between adjacent communities,” the authors conclude.

It’s the type of growth that indicates “communal behavior between microorganisms”, and it looks similar to human urbanisation, where some settlers stay static, while others grow into villages that further expand into densely-populated microcolonies or cities, which then merge into microbial megacities.

Of course, there are limits to this idea of bacterial urbanisation. The authors aren’t saying microbes build traffic signs, roads and supply lines, but the general idea is the same and it can not only help us tackle infections better, it might also help us build more sustainably.

“It’s a useful analogy, but it should be taken with a grain of salt,” Koo says. “We’re not saying these bacteria are anthropomorphic. But taking this perspective of biofilm growth gives us a multiscale, multidimensional picture of how they grow that we’ve not seen before.”

The study was published in Nature Communications.

https://www.sciencealert.com/bacteria-settle-into-complex-structures-just-like-humans-settle-into-cities

Researchers have engineered Escherichia coli bacteria to make energy exclusively from carbon dioxide, according to a paper published November 27 in Cell.

E. coli are normally heterotrophs—organisms that get their energy sources from ingesting organic compounds, such as glucose—but the new study shows that they can be turned into autotrophs, making their own energy by turning carbon dioxide from the atmosphere into biomass.

“I find it fundamentally amazing that an organism which evolved over billions of years to live a heterotrophic lifestyle can so quickly and completely change into an autotroph,” Dave Savage, a biochemist at University of California, Berkeley, who was not involved with the study, tells The Scientist in an email. “It suggests that metabolism is extremely malleable.”

This process of using inorganic carbon to make biomass, called carbon fixation, could be used to solve “some of the biggest challenges of humanity today,” Ron Milo, a systems biologist at the Weizmann Institute of Science in Israel and the lead author of the paper, tells The Scientist. For example, increasing carbon fixation in plants generates more biomass, which could increase the world’s food supply.

The team set out to make E. coli—a “very genetically malleable model organism,” says Milo—fix carbon as a step toward sustainable industrial processes such as creating biofuel.

E. coli doesn’t normally have molecular mechanisms in place to use CO2, so the researchers gave it genes for the ability to fix carbon that were based on the gene sequence of carbon-fixing Pseudomonas bacteria. These changes weren’t enough to force the bacteria to switch to being autotrophic, so the team also disabled three genes involved in heterotrophic metabolism and put the bacteria into growth chambers with limited amounts of sugar, which starved them. In this environment, there was an advantage for bacteria that used CO2 instead of the finite sugar supply, and the researchers wanted to see if the bacteria could evolve to only use CO2.

The E. coli were grown on sodium formate, a carbon molecule that donates the necessary electrons during the process of making energy, but doesn’t contribute to biomass. The air in the growth chambers was also enriched with carbon dioxide.

After approximately 200 days, the bacteria relied completely on carbon dioxide from the air to generate biomass while taking in formate as a necessary ingredient for the chemical reactions. When the scientists analyzed the bacterial genome, they found that the bacteria evolved to use carbon dioxide as their energy source after as few as 11 mutations. Some of the changes occurred in genes related to carbon fixation, while others were in genes that are known to mutate in other lab evolution experiments or have no known role in energy production from CO2.


Heterotrophic E. coli (left) produce biomass from sugar, but lab-evolved autotrophic E. coli from the new study (center) use CO2 instead. The authors envision autotrophic E. coli that use renewable energy and have no net carbon emissions in the future (right).

“It’s a proof of concept for the field, that you can really rewire . . . the metabolic features of living organisms from scratch. It’s an exciting step forward,” Tobias Erb, a synthetic biologist at the Max Planck Institute for Terrestrial Microbiology in Germany who wrote a commentary on the study, tells The Scientist. However, “if the strain that they created [is] of biotechnological relevance in the future . . . I think is still up to debate,” he says.

For instance, the autotrophic E. coli currently produce more carbon dioxide as a byproduct than they take in. This could be solved by producing formate from carbon dioxide in the future, so that there are no net carbon dioxide emissions.

In addition, the researchers used high carbon dioxide levels in the bacteria’s growth chambers—around 10 percent of the air—but it’s only 0.04 percent of Earth’s atmosphere. “We’re interested to see if we could move it towards ambient carbon dioxide levels, meaning that one could use the ambient atmosphere that has much less [carbon dioxide], 400 parts per million,” says Milo.

“It’s an interesting concept now. Whether it actually is something that becomes useful in terms of application, that’s another question,” Patrik Jones, who studies microbial metabolic engineering at Imperial College London and was not involved with the study, tells The Scientist. “It’s definitely a step towards that direction . . . But then I think it’s important to realize that there are more steps needed in order to utilize this.”

ABOVE: FLICKR.COM, NIAID
Researchers have engineered Escherichia coli bacteria to make energy exclusively from carbon dioxide, according to a paper published today (November 27) in Cell.

E. coli are normally heterotrophs—organisms that get their energy sources from ingesting organic compounds, such as glucose—but the new study shows that they can be turned into autotrophs, making their own energy by turning carbon dioxide from the atmosphere into biomass.

“I find it fundamentally amazing that an organism which evolved over billions of years to live a heterotrophic lifestyle can so quickly and completely change into an autotroph,” Dave Savage, a biochemist at University of California, Berkeley, who was not involved with the study, tells The Scientist in an email. “It suggests that metabolism is extremely malleable.”

This process of using inorganic carbon to make biomass, called carbon fixation, could be used to solve “some of the biggest challenges of humanity today,” Ron Milo, a systems biologist at the Weizmann Institute of Science in Israel and the lead author of the paper, tells The Scientist. For example, increasing carbon fixation in plants generates more biomass, which could increase the world’s food supply.

The team set out to make E. coli—a “very genetically malleable model organism,” says Milo—fix carbon as a step toward sustainable industrial processes such as creating biofuel.

E. coli doesn’t normally have molecular mechanisms in place to use CO2, so the researchers gave it genes for the ability to fix carbon that were based on the gene sequence of carbon-fixing Pseudomonas bacteria. These changes weren’t enough to force the bacteria to switch to being autotrophic, so the team also disabled three genes involved in heterotrophic metabolism and put the bacteria into growth chambers with limited amounts of sugar, which starved them. In this environment, there was an advantage for bacteria that used CO2 instead of the finite sugar supply, and the researchers wanted to see if the bacteria could evolve to only use CO2.

The E. coli were grown on sodium formate, a carbon molecule that donates the necessary electrons during the process of making energy, but doesn’t contribute to biomass. The air in the growth chambers was also enriched with carbon dioxide.

After approximately 200 days, the bacteria relied completely on carbon dioxide from the air to generate biomass while taking in formate as a necessary ingredient for the chemical reactions. When the scientists analyzed the bacterial genome, they found that the bacteria evolved to use carbon dioxide as their energy source after as few as 11 mutations. Some of the changes occurred in genes related to carbon fixation, while others were in genes that are known to mutate in other lab evolution experiments or have no known role in energy production from CO2.

Heterotrophic E. coli (left) produce biomass from sugar, but lab-evolved autotrophic E. coli from the new study (center) use CO2 instead. The authors envision autotrophic E. coli that use renewable energy and have no net carbon emissions in the future (right).
GLEIZER ET AL.
“It’s a proof of concept for the field, that you can really rewire . . . the metabolic features of living organisms from scratch. It’s an exciting step forward,” Tobias Erb, a synthetic biologist at the Max Planck Institute for Terrestrial Microbiology in Germany who wrote a commentary on the study, tells The Scientist. However, “if the strain that they created [is] of biotechnological relevance in the future . . . I think is still up to debate,” he says.

For instance, the autotrophic E. coli currently produce more carbon dioxide as a byproduct than they take in. This could be solved by producing formate from carbon dioxide in the future, so that there are no net carbon dioxide emissions.

In addition, the researchers used high carbon dioxide levels in the bacteria’s growth chambers—around 10 percent of the air—but it’s only 0.04 percent of Earth’s atmosphere. “We’re interested to see if we could move it towards ambient carbon dioxide levels, meaning that one could use the ambient atmosphere that has much less [carbon dioxide], 400 parts per million,” says Milo.

“It’s an interesting concept now. Whether it actually is something that becomes useful in terms of application, that’s another question,” Patrik Jones, who studies microbial metabolic engineering at Imperial College London and was not involved with the study, tells The Scientist. “It’s definitely a step towards that direction . . . But then I think it’s important to realize that there are more steps needed in order to utilize this.”

Emily Makowski is an intern at The Scientist. Email her at emakowski@the-scientist.com.

https://www.the-scientist.com/news-opinion/lab-evolved-e–coli-makes-energy-solely-from-carbon-dioxide-66788?utm_campaign=TS_DAILY%20NEWSLETTER_2019&utm_source=hs_email&utm_medium=email&utm_content=80070748&_hsenc=p2ANqtz-_mk5jB1Vyqx3xPsKPzk1WcGdxEqSmuirpfpluu4Opm4tMO6n7rXROJrCvQp0yKBw2eCo4R4TZ422Hk6FcfJ7tDWkMpyg&_hsmi=80070748

By Priyanka Runwal

From spooky abandoned houses to dark forest corners, spider webs have an aura of eternal existence. In reality, the silk threads can last hours to weeks without rotting. That’s because bacteria that would aid decomposition are unable to access the silk’s nitrogen, a nutrient the microbes need for growth and reproduction, a new study suggests.

Previous research had hinted that spider webs might have antimicrobial properties that outright kill bacteria. But subjecting the webs of three spider species to four types of bacteria revealed that the spiders use a resist strategy instead, researchers report October 23 in the Journal of Experimental Biology.

The scientists “challenge something that has gone significantly overlooked,” says Jeffery Yarger, a biochemist at Arizona State University in Tempe, who wasn’t involved in the research. “We just assumed [the silk] has some kind of standard antimicrobial property.”

Spiders spin strings of silk to trap food, wrap their eggs and rappel. Their silk webs can sport leaf debris for camouflage amidst tree canopies or leftover dead insects for a meal later. These bits and bobs lure bacteria and fungi involved in decomposition to the web, exposing the protein-rich web silks to the microbes.

“But [the microbes] don’t seem to affect spider silk,” says Dakota Piorkowski, a biologist at Tunghai University in Taichung, Taiwan.

To check if the silk was lethal to bacteria, Piorkowski’s team placed threads from three tropical spider species — giant golden orb weaver (Nephila pilipes), lawn wolf spider(Hippasa holmerae) anddome tent spider (Cyrtophora moluccensis) — in petri dishes and grew four types of bacteria, including E. coli, in perpendicular lines across the silk. “The idea is that if the silk has antibacterial properties, you should see no growth between the piece of silk and … bacteria,” Piorkowski says.

There was no evidence of this “clear zone” of dead bacteria in spots where the bacteria came in direct contact with the silk, the researchers found. So the team then tested if the silk kept hungry bacteria at bay by blocking them from its nitrogen reserves. Wetting the silk threads with an assortment of nutrient solutions showed that the bacteria readily grew on all three types of spider silk when extra nitrogen was available. That indicated that the bacteria are capable of growing on and possibly decomposing the silk, as long as the threads themselves aren’t the only source of nitrogen.

The researchers hypothesize that an outer coating of fat or complex protein on the silk may block bacteria’s access to nitrogen.

Randy Lewis, a spider silk biologist at Utah State University in Logan, cautions against ruling out antibacterial features in all spider silks, though. Underground webs of tarantulas (SN: 5/23/11), for example, can face environments rife in microorganisms compared with that experienced by aerial web-spinning spiders, he says, and may need the extra protection.

Spider webs don’t rot easily and scientists may have figured out why

microbial-activity-in-the-mouth-may-help-identify-autism-in-children

Weight gain trajectories in early childhood are related to the composition of oral bacteria of two-year-old children, suggesting that this understudied aspect of a child’s microbiota — the collection of microorganisms, including beneficial bacteria, residing in the mouth — could serve as an early indicator for childhood obesity. A study describing the results appears September 19 in the journal Scientific Reports.

“One in three children in the United States is overweight or obese,” said Kateryna Makova, Pentz Professor of Biology and senior author of the paper. “If we can find early indicators of obesity in young children, we can help parents and physicians take preventive measures.”

The study is part of a larger project with researchers and clinicians at the Penn State Milton S. Hershey Medical Center called INSIGHT, led by Ian Paul, professor of pediatrics at the Medical Center, and Leann Birch, professor of foods and nutrition at the University of Georgia. The INSIGHT trial includes nearly 300 children and tests whether a responsive parenting intervention during a child’s early life can prevent the development of obesity. It is also designed to identify biological and social risk factors for obesity.

“In this study, we show that a child’s oral microbiota at two years of age is related to their weight gain over their first two years after birth,” said Makova.

The human digestive tract is filled with a diverse array of microorganisms, including beneficial bacteria, that help ensure proper digestion and support the immune system. This “microbiota” shifts as a person’s diet changes and can vary greatly among individuals. Variation in gut microbiota has been linked to obesity in some adults and adolescents, but the potential relationship between oral microbiota and weight gain in children had not been explored prior to this study.

“The oral microbiota is usually studied in relation to periodontal disease, and periodontal disease has in some cases been linked to obesity,” said Sarah Craig, a postdoctoral scholar in biology at Penn State and first author of the paper. “Here, we explored any potential direct associations between the oral microbiota and child weight gain. Rather than simply noting whether a child was overweight at the age of two, we used growth curves from their first two years after birth, which provides a more complete picture of how the child is growing. This approach is highly innovative for a study of this kind, and gives greater statistical power to detect relationships.”

Among 226 children from central Pennsylvania, the oral microbiota of those with rapid infant weight gain — a strong risk factor for childhood obesity — was less diverse, meaning it contained fewer groups of bacteria. These children also had a higher ratio of Firmicutes to Bacteroidetes, two of the most common bacteria groups found in the human microbiota.

“A healthy person usually has a lot of different bacteria within their gut microbiota,” said Craig. “This high diversity helps protect against inflammation or harmful bacteria and is important for the stability of digestion in the face of changes to diet or environment. There’s also a certain balance of these two common bacteria groups, Firmicutes and Bacteroidetes, that tends to work best under normal healthy conditions, and disruptions to that balance could lead to dysregulation in digestion.”

Lower diversity and higher Firmicutes to Bacteroidetes (F:B) ratio in gut microbiota are sometimes observed as a characteristic of adults and adolescents with obesity. However, the researchers did not see a relationship of weight gain with either of these measures in gut microbiota of two-year-olds, suggesting that the gut microbiota may not be completely established at two years of age and may still be undergoing many changes.

“There are usually dramatic changes to an individual’s microbiota as they develop during early childhood,” said Makova. “Our results suggest that signatures of obesity may be established earlier in oral microbiota than in gut microbiota. If we can confirm this in other groups of children outside of Pennsylvania, we may be able to develop a test of oral microbiota that could be used in clinical care to identify children who are at risk for developing obesity. This is particularly exciting because oral samples are easier to obtain than those from the gut, which require fecal samples.”

Interestingly, weight gain in children was also related to diversity of their mother’s oral microbiota. This could reflect a genetic predisposition of the mother and child to having a similar microbiota, or the mother and child having a similar diet and environment.

“It could be a simple explanation like a shared diet or genetics, but it might also be related to obesity,” said Makova. “We don’t know for sure yet, but if there is an oral microbiome signature linked to the dynamics of weight gain in early childhood, there is a particular urgency to understand it. Now we are using additional techniques to look at specific species of bacteria–rather than larger taxonomic groups of bacteria–in both the mothers and children to see whether specific bacteria species influence weight gain and the risk of obesity.”

In addition to Makova, Craig, Paul, and Birch, the research team includes Jennifer Savage, Michele Marini, Jennifer Stokes, Anton Nekrutenko, Matthew Reimherr, and Francesca Chiaromonte from Penn State, Daniel Blankenberg from the Cleveland Clinic, and Alice Carla Luisa Parodi from Politecnico di Milano. INSIGHT (Intervention Nurses Start Infants Growing on Healthy Trajectories) is coordinated through the Penn State Milton S. Hershey Medical Center.

This work is supported by the National Institute of Diabetes and Digestive and Kidney Diseases (NIDDK); the Penn State Eberly College of Science; the Penn State Institute for Cyberscience; the National Center for Research Resources and the National Center for Advancing Translational Sciences of the National Institutes of Health (NIH); and the Pennsylvania Department of Health using Tobacco CURE funds.

http://science.psu.edu/news-and-events/2018-news/Makova9-2018

bacteria-crop750
Listeria bacteria transport electrons through their cell wall into the environment as tiny currents, assisted by ubiquitous flavin molecules (yellow dots). (Amy Cao graphic, copyright UC Berkeley)

By Robert Sanders

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.

UC 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.

microbebattery611
A microbial battery made with newly discovered electrogenic bacteria. Electrodes (CE, WE) are placed in jars full of bacteria, producing up to half a millivolt of electricity. Ajo-Franklin photo.

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.

Other co-authors are Lin Su and Jose A. Cornejo of Berkeley Lab and Rafael Rivera-Lugo, Alexander Louie and Anthony T. Iavarone of UC Berkeley. The research was funded by the National Institute of Allergy and Infectious Diseases of the National Institutes of Health and the Office of Naval Research.

http://news.berkeley.edu/2018/09/12/gut-bacterias-shocking-secret-they-produce-electricity/


When scientists add code to bacterial DNA, it’s passed on to the next generation.

By Bryan Nelson

The way DNA stores genetic information is similar to the way a computer stores data. Now scientists have found a way to turn this from a metaphorical comparison into a literal one, by transforming living bacteria into hard drives, reports Popular Mechanics.

A team of Harvard scientists led by geneticists Seth Shipman and Jeff Nivala have devised a way to trick bacteria into copying computer code into the fabric of their DNA without interrupting normal cellular function. The bacteria even pass the information on to their progeny, thus ensuring that the information gets “backed up,” even when individual bacteria perish.

So far the technique can only upload about 100 bytes of data to the bacteria, but that’s enough to store a short script or perhaps a short poem — say, a haiku — into the genetics of a cell. For instance, here’s a haiku that would work:

Bacteria on
your thumb
might someday become
a real thumb drive

As the method becomes more precise, it will be possible to encode longer strings of text into the fabric of life. Perhaps some day, the bacteria living all around us will also double as a sort of library that we can download.

The technique is based on manipulation of an immune response that exists in many bacteria known as the CRISPR/Cas system. How the system works is actually fairly simple: when bacteria encounter a threatening virus, they physically cut out a segment of the attacking virus’s DNA and paste it into a specific region of their own genome. The bacteria can then use this section of viral DNA to identify future virus encounters and rapidly mount a defense. Copying this immunity into their own genetic code allows the bacteria to pass it on to future generations.

To get the bacteria to copy strings of computer code instead, researchers just book-ended the information with segments that look like viral DNA. The bacteria then got to work, conveniently cutting and pasting the relevant section into their genes.

The method does have a few bugs. For instance, not all of the bacteria snip the full section, so only part of the code gets copied. But if you introduce the code into a large enough population of bacteria, it becomes easy to deduce the full message from a sufficient percentage of the colony.

The amount of information that can be stored also depends on the bacteria doing the storing. For this experiment, researchers used E. coli, which was only efficient at storing around 100 bytes. But some bacteria, such as Sulfolobus tokodaii, are capable of storing thousands of bytes. With synthetic engineering, these numbers can be increased exponentially.

http://www.mnn.com/green-tech/research-innovations/stories/bacteria-can-now-be-turned-living-hard-drives