Bacteria - Latest Research

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Oil-eating bacteria found at the bottom of the ocean
"We know more about Mars than the deepest part of the ocean," researcher Xiao-Hua Zhang said.
By Brooks Hays


Scientists used a submersible to collect microbial samples from the Mariana Trench in the Pacific Ocean. Photo by UEA

April 12 (UPI) -- Scientists have discovered oil-eating bacteria in the planet's deepest oceanic trench, the Mariana Trench.
An international team of researchers, including scientists from Britain, China and Russia, used a submersible to collect microbial samples from the trench, which bottoms out at 6.8 miles below sea level. For reference, the peak of Mount Everest is 5.5 miles above sea level.


Only a few expeditions to the Mariana Trench have been made, and the latest is one of the first to focus on the trench's microbial communities.
"We know more about Mars than the deepest part of the ocean," Xiao-Hua Zhang, a research professor at the Ocean University in China, said in a news release.
RELATED Even deep sea creatures are eating plastic

When researchers analyzed the microbial samples collected during the expedition, they found a new group of hydrocarbon degrading bacteria. They published the results of the study Friday in the journal Microbiome.

Hydrocarbons are organic compound made up of only hydrogen and carbon atoms. They're found in crude oil and natural gas, among other places.

"These types of microorganisms essentially eat compounds similar to those in oil and then use it for fuel," said Jonathan Toddy, researcher at the University of East Anglia. "Similar microorganisms play a role in degrading oil spills in natural disasters such as BP's 2010 oil spill in the Gulf of Mexico."

RELATED Bacteria in the human body are sharing genes, even across tissue boundaries

Researchers were surprised by the abundance of the oil-eating bacteria in the trench. Nowhere else on Earth are oil-eating bacteria so proportionally dominant.
To better understand where the microbes are getting their sustenance, scientists collected water samples the entire length of the water column, from sea surface to the sediments at the bottom of the Mariana Trench.

Scientists found the oil-eating microbes as deep as 4 miles beneath the ocean surface, and researchers suspect the microbes live at even greater depths.

RELATED Scientists find tanner crabs feeding on seafloor methane vent

The bacteria are likely deriving a significant portion of their food from pollution that sinks from the ocean surface. But scientists also found evidence that some of the hydrocarbons are sourced from below.

"To our surprise, we also identified biologically produced hydrocarbons in the ocean sediment at the bottom of the trench," said UEA researcher Nikolai Pedentchouk. "This suggests that a unique microbial population is producing hydrocarbons in this environment."

In addition to providing sustenance, researchers suspect the hydrocarbons help microbes survive the crushing pressures of extreme ocean depths.

Oil-eating bacteria found at the bottom of the ocean
 

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Hydrocarbons are organic compound made up of only hydrogen and carbon atoms. They're found in crude oil and natural gas, among other places.
"These types of microorganisms essentially eat compounds similar to those in oil and then use it for fuel," said Jonathan Toddy, researcher at the University of East Anglia. "Similar microorganisms play a role in degrading oil spills in natural disasters such as BP's 2010 oil spill in the Gulf of Mexico."
I find this to be normal. Its a well known fact that some types of microorganisms do consume +H and C/CO2 and then convert that to alcohol and use it as a fuel. No matter what restaurant the food is coming from I will eat the food.:-F
 

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I find this to be normal. Its a well known fact that some types of microorganisms do consume +H and C/CO2 and then convert that to alcohol and use it as a fuel. No matter what restaurant the food is coming from I will eat the food.:-F
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Bacteria behave as individuals when navigating a maze
"There is biochemical noise in every cell," researchers reported. "As a fundamental random component, this causes diversity of appearance and behavior."

By Brooks Hays
April 24, 2019 / 11:52 AM

In the maze, some bacterial cells quickly found their way to the highest concentration of the attractant, while others got lost swimming down the wrong channels. Photo by ETH Zurich

April 24 (UPI) -- When researchers placed bacteria in a maze, they found genetically identical sells exhibited individuality.

Scientists reported the unexpected discovery this week in the journal Nature Communications.

Even the simplest life forms, microorganisms, can sense and respond to their environment. Bacteria, for example, move toward food and away from harmful substances. The strength of their response reflects the concentration gradient of the substance they're reacting to.

This motility strategy is called chemotaxis, and until now, scientists assumed the ability was uniform among the cells of a single bacteria species or population.

The latest research showed that is not the case.

To study the movement pattern of individual bacterial cells, scientists developed a microfluidic system featuring an arrow of narrow channels that branch out atop a thin glass plate.

Researchers allowed a chemical attractant to spread out across the family tree-like maze, with the tips of some branches featuring higher concentrations. All the bacteria cells were released at the base of the tree, where the attractant's concentration was weakest.

When the cells encountered a fork in the maze, they had to decide whether to keep swimming in the same direction, following the increasing concentration levels, or reverse course and follow a different branch.

Scientists observed some cells easily making their way toward the branches with the highest concentration, while others struggled to navigate the maze.

While every cell has the same genetic coding, the results of the new study demonstrate the epigenetic diversity of each bacteria cell. Genes are expressed differently in each cell, producing biochemical diversity.

"There is biochemical noise in every cell. As a fundamental random component, this causes diversity of appearance and behavior," researchers reported.

Researchers suggest the biochemical variation present in different bacteria cells likely provides an evolutionary advantage. While cells adept at chemotaxis can travel to sources of food more efficiently, cells with less positional awareness are more likely to happen upon new sources of food.

"Non-genetic diversity has long been known in the biomedical life sciences; for example, it is thought to play a role in antibiotic resistance," said Roman Stocker, a professor of environmental engineering at ETZ Zurich. "Now, environmental scientists have shown that this diversity also affects fundamental behaviors of bacteria, such as locomotion and chemotaxis -- further expanding the concept of bacterial individuality."

 

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March 25, 2019
Bacteria can travel thousands of miles through the air
Scientists identified commonalities among the genetic and evolutionary histories of bacteria communities living thousands of miles apart.
By Brooks Hays
Researchers collected bacteria from hot springs in Italy, Russia and Chile's El Tatio region, pictured here. Photo by Yaroslav Ispolatov/Rutgers University


March 25 (UPI) -- Scientists previously thought bacteria needed a host to travel the globe. However, new research suggests bacteria can travel thousands of miles through the air.

"Our research suggests that there must be a planet-wide mechanism that ensures the exchange of bacteria between faraway places," Konstantin Severinov, a professor of molecular biology and biochemistry at Rutgers University, said in a news release. "Because the bacteria we study live in very hot water -- about 160 degrees Fahrenheit -- in remote places, it is not feasible to imagine that animals, birds or humans transport them."

Severinov and his colleagues estimated atmospheric currents ensure distant and remote parts of the world share common bacteria.

To better understand the links between faraway bacterial communities, scientists studied the genetic signatures left by interactions between bacteria and viruses.

Bacteriophages, viruses that infect bacteria, are everywhere. They are the most abundant life form on the planet. They also have a significant -- and measurable -- influence on microbial communities.

For the study, Severinov and his research partners collected Thermus thermophilus bacteria from hot springs across the globe -- in Chile, Italy and Russia. The samples were separated by thousands of miles.

When bacteria is infected by viruses, "molecular memories" are stored in sections of bacterial DNA called CRISPR arrays. The surviving bacteria cells pass on the snippets of viral DNA, the memories, to the next generation.

Before the study, scientists hypothesized the molecular memories of bacteria living on opposite sides of the planet would be quite different. Researchers also assumed the bacteria species would be shaped by unique evolutionary histories.

"What we found, however, is that there were plenty of shared memories -- identical pieces of viral DNA stored in the same order in the DNA of bacteria from distant hot springs," Severinov said. "Our analysis may inform ecological and epidemiological studies of harmful bacteria that globally share antibiotic resistance genes and may also get dispersed by air instead of human travelers."

Scientists shared their surprise findings Monday in the journal Philosophical Transactions of the Royal Society B. In followup studies, study authors plan to use planes, drones and research balloons to study bacteria in air samples collected at different altitudes across the globe.

 

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April 16, 2019
Bacteria use viruses to differentiate themselves from their competitors
"Now we show cells utilize viruses to distinguish themselves from closely related bacteria," researcher Thomas Wood said.

By
Brooks Hays


The photo shows a virus particle carried by some bacteria strains. The phage allows the bacteria to recognize itself and gain a competitive advantage over its competitors. Photo by Sooyeon Song and Missy Hazen

April 16 (UPI) -- Normally, bacteria and viruses are enemies, but new research suggests a viral infection can offer bacteria some benefits -- chiefly, the ability to distinguish friend from foe.

"This is the first evidence that cells can distinguish themselves from related competitors through the use of a virus," Thomas Wood, researcher at Pennsylvania State University, said in a news release. "The implications are that we should re-evaluate the relationship between a virus and its cellular host in that there are sometimes benefits to having a viral infection."

Scientists discovered the phenomenon after observing a stark demarcation line between two strains of the bacteria Escherichia coli K-12, but no such divide between identical clones.

The related rivals steered clear of one another, while the identical strains swam toward one another. To find out why, scientists surveyed 4,296 single-gene knockouts in the genome of Escherichia coli K-12. Researchers determined only one mutation caused the demarcation line to disappear.

The mutation involved a gene that is used in viral replication. According to their analysis, the virus-related proteins produced by the gene allow for bacterial self-recognition.

Scientists were also able erase the demarcation line by silencing the bacteriophage genomes that have weaved their way into the bacteria's genome. These leftover viral genes don't produce active phage particles, nor do they rupture host cells.

When scientists exposed bacteria to a related virus, the old viral genes were activated and began producing phage particles for the new virus.

The latest findings -- published Tuesday in the journal Cell Reports -- suggest the newborn particles help bacteria distinguish itself from closely related competitors.

The new virus and old viral genes allow bacteria to organize into groups. Their power in numbers allows the bacteria to bully competitors.

"Bacteria are frequently thought of as living individually, but in fact they can forage for food as groups," Wood said. "In order to act as a group, they must be able to distinguish themselves from other bacteria. In one type of social activity, when they communicate, bacterial cells secrete chemical signals to communicate. Now we show cells utilize viruses to distinguish themselves from closely related bacteria."

Experiments showed the virus doesn't attack its host cells. Instead, the virus attacks other bacteria cells that don't carry the virus. The host helps the virus reproduce, and the virus takes out the bacteria's competitors.


 

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Bacteria in the human body are sharing genes, even across tissue boundaries
"The horizontal exchange between microbes in our bodies is about 30 percent higher than what you'll find on the rest of the planet," researcher Gustavo Caetano-Anollés said.
April 11, 2019
By Brooks Hays

Researchers have identified instances of horizontal gene transfer between bacteria in the human body, a finding that researchers say could help in understanding antibiotic-resistant forms of bacteria. Photo by qimono/Pixabay



April 11 (UPI) -- Microbes in the human body are swapping genes with one another, according to a new study. Some bacteria genes can even travel across tissue barriers without their microbial hosts.


Scientists were able to identify instances of "horizontal gene transfer" using a new molecular data-mining method.

"Horizontal gene transfer is a major force of exchange of genetic information on Earth," Gustavo Caetano-Anollés, a professor of crop sciences and genomic biology at the University of Illinois, said in a news release. "These exchanges allow microorganisms to adapt and thrive, but they are likely also important for human health. There are some bacteria that cannot live outside our bodies and some without which we cannot live."

Because horizontal gene transfer has enabled the proliferation of antibiotic resistance among pathogens, an improved understanding of the phenomenon has public health implications.

For the new study, scientists constructed family trees of the thousands of microbes that colonize the human body. Powerful computers and sophisticated algorithms helped scientists analyze the relationships among the different trees and differentiated between genes that were shared via inheritance and genes that were acquired via horizontal gene transfer.

"Most current methods for determining horizontal gene transfer compare DNA features or statistical similarity between genomes to identify foreign genes," said Arshan Nasir, researcher at COMSATS University in Pakistan. "This works fairly well for relatively recent gene transfers, but often fails to identify transfer events that occurred millions or billions of years ago."

The new analysis method allowed Caetano-Anollés and Nasir to overcome this problem. Their work -- detailed this week in the journal Scientific Reports -- showed microbes in the human body exchange genes very freely.

"The horizontal exchange between microbes in our bodies is about 30 percent higher than what you'll find on the rest of the planet," Caetano-Anollés said. "This implies that our bodies provide a niche that is unique and facilitates innovation at the microbe level."

Scientists determined the majority of gene transfer activity, 60 percent, occurs between microbes living in different parts of the body -- microbes in gut sharing genes with bacteria living in the blood, for example.

"Some of these could be very old gene transfer events that happened before the microbes colonized the human body," Nasir said. "It also could be that some bacteria colonize different human body sites at different time points in an individual's lifespan. The others could be the result of the transfer of bacterial DNA from one site to another, perhaps through the blood. We need further experimental evidence to test this tantalizing possibility."

By teasing out which portions of microbial genomes were inherited and which were transferred, scientists can gain new insights into the evolutionary histories of different bacteria strains, as well as their evolutionary relationships with the human body.

 

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Sequencing of human gut genome reveals nearly 2,000 unknown bacteria species
"Research such as this is helping us create a so-called blueprint of the human gut," researcher Trevor Lawle said.
By Brooks Hays
Feb. 12, 2019



New research revealed thousands of new bacteria species inside the human gut. Photo by Pixabay/CC


Feb. 12 (UPI) -- Scientists at the European Molecular Biology Laboratory have identified nearly 2,000 previously unknown bacterial species living in the human gut.

Researchers with the lab's European Bioinformatics Institute collected gut cultures from study participants around the world. The microbiologists used a variety of computational methods to sequence the genes found in the samples.

Studies show the communities of microbes living inside the intestines play a vital role in human health. Dozens of maladies have been linked to imbalances within the gut microbiome. Research even suggests gut bacteria influences gene expression.

Despite increasing numbers of microbiome studies, scientists' understanding of the communities of microorganisms occupying the human gut -- the gut microbiota -- remains incomplete.

To better understand which gut microbes are shared by humans and why they thrive inside human intestines, scientists are developing new ways to efficiently sequence the genomes of gut microbiota.

"Computational methods allow us to understand bacteria that we cannot yet culture in the lab," Rob Finn, researcher at the European Bioinformatics Institute, said in a news release. "Using metagenomics to reconstruct bacterial genomes is a bit like reconstructing hundreds of puzzles after mixing all the pieces together, without knowing what the final image is meant to look like, and after completely removing a few pieces from the mix just to make it that bit harder."

"Researchers are now at a stage where they can use a range of computational tools to complement and sometimes guide lab work, in order to uncover new insights into the human gut," Finn said.

In addition to finding commonalities among human gut microbiota, new sequencing techniques are revealing unique geographical differences among the microbial communities found in the guts of disparate populations. The microbiome inside the human gut evolves in response to a person's diet and environment.

"We are seeing a lot of the same bacterial species crop up in the data from European and North American populations," Finn said. "However, the few South American and African datasets we had access to for this study revealed significant diversity not present in the former populations. This suggests that collecting data from underrepresented populations is essential if we want to achieve a truly comprehensive picture of the composition of the human gut."

According to the researchers, the techniques used to mine public databases of gastrointestinal bacteria for new species can be easily reproduced for future studies. Scientists detailed their efforts in the journal Nature.

"Research such as this is helping us create a so-called blueprint of the human gut, which in the future could help us understand human health and disease better and could even guide diagnosis and treatment of gastrointestinal diseases," said Trevor Lawley, researcher at the Wellcome Sanger Institute.

 

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Activating large silent genes allows bacteria to synthesize new molecules
By Brooks Hays
Jan. 2, 2019

Scientists have developed a way to unmute large, silent genes, allowing for the production of new molecules. Photo by Caroline Davis2010/Flickr

Jan. 2 (UPI) -- When researchers stripped away repressors thwarting the expression of big, silent genes in Streptomyces bacteria, they unlocked the genetic building blocks of several new molecules.

Because Streptomyces bacteria synthesizes several molecules used in antibiotics and anti-cancer drugs, scientists hope their work will lead to the discovery of new therapeutic agents.

"There are so many undiscovered natural products lying unexpressed in genomes. We think of them as the dark matter of the cell," Huimin Zhao, a chemical and biomolecular engineering professor at the University of Illinois, said in a news release. "Anti-microbial resistance has become a global challenge, so clearly there's an urgent need for tools to aid the discovery of novel natural products. In this work, we found new compounds by activating silent gene clusters that have not been explored before."

Small silent gene clusters have previously been unmuted using CRISPR technology, but larger silent gene clusters have been difficult to unlock.

To free up the large gene clusters in Streptomyces, researchers inject the bacteria with copies of the target DNA fragments. Scientists dubbed the copies transcription factor decoys. Zhao deployed the clones in an effort to lure away the silencing agents. Their subterfuge worked.

"Others have used this similar kind of decoys for therapeutic applications in mammalian cells, but we show here for the first time that it can be used for drug discovery by activating silent genes in bacteria," said Zhao.

According to Zhao, the new method -- described in the journal Nature Chemical Biology -- doesn't disrupt the natural genome.

"It's just pulling away the repressors," he said. "Then the genes are expressed naturally from the native DNA."

The decoys deployed by Zhao and his colleagues enabled the bacteria's previously silenced gene cluster to produce eight new molecules, but so far, scientists have identified the structure of just two and described only one in detail.

In follow up studies, scientists plan to precisely describe the structure and characteristics of all eight. Researchers also plan to test whether any of the new molecules boast anti-microbial, anti-fungal, anti-cancer or other potentially useful biological properties.

 

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Germ-Killing Brands Now Want to Sell You Germs
The world’s best-known antibacterial labels are pouring millions into probacterial health and beauty startups.
April 22, 2019 By Caroline Winter
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Photo illustration: Nitrosomonas. Photographer: Brea Souders for Bloomberg Businessweek

It was a snowy week in February 2009 when David Whitlock packed up his three-bedroom apartment near Cambridge, Mass., and moved into his van. Then 54 years old, the inventor had spent all his money, almost half a million dollars, on worldwide patent filings for a newfound obsession: a type of bacteria, culled from soil samples, that he theorized would improve skin disorders, hypertension, and other health problems. “It was the most important thing I could work on,” Whitlock says. “But I knew I needed patents, otherwise I wouldn’t be able to get anyone interested.”

To make his white Dodge Grand Caravan habitable, Whitlock sawed down his queen-size bed frame and squeezed it in. He donated or abandoned most of his furniture, storing his lab equipment in a barn owned by his business partner, Walter “Hilly” Thompson. Then Whitlock drove to his former employer, cement company Titan America LLC, where he still had an office and did some consulting. Without asking permission, he pulled into the parking lot and made it home for the next four and a half years. “I found that if I stayed fully dressed and got inside two sleeping bags, I could tolerate it,” he says of the coldest winter nights.

relates to Germ-Killing Brands Now Want to Sell You Germs

Whitlock
Photographer: Brea Souders for Bloomberg Businessweek


Every so often, he would coat himself in a concoction made with his homegrown bacteria, a ritual he’d begun years earlier in the belief it would improve his overall health and all but eliminate the need to bathe or use soap. Then he’d spend the day in his office, tirelessly researching microbes.
“A lot of people gave me shit for living in my car,” Whitlock says. “But it was like nothing, trivial.” His real problem was finding investors, a challenge exacerbated by his autism spectrum disorder. To get his message out, he relied mainly on Thompson. Most everyone dismissed the duo’s idea as nuts.

Today things look very different. Whitlock lives in an apartment, and his startup, AOBiome Therapeutics Inc., has raised almost $100 million. The company is seeking to become the first to get Food and Drug Administration approval for pharmaceutical-grade topical live bacteria, with six clinical trials under way to treat acne, eczema, rosacea, hay fever, hypertension, and migraines.

AOBiome’s cosmetics branch, Mother Dirt, already counts tens of thousands of customers for its products, including the spray Whitlock developed from his bacterial elixir; they’re sold online, at natural beauty and food retailers, at Whole Foods Market stores in the U.K., and, starting in June, in the U.S. Several of Whitlock’s early investors are so enthusiastic about AOBiome that they’ve adopted his hygiene habits. “I haven’t used soap or shampoo or antiperspirant or deodorant or toothpaste or mouthwash in five or six years,” says entrepreneur and venture capitalist Lenny Barshack.

The company’s message fits well with a growing body of research into the human microbiome showing that some bacteria are not only good but also vital. Microbial imbalances play a role in many conditions, including allergies, autism, cancer, depression, irritable bowel syndrome, and obesity. Also, probiotics and prebiotics—which refer, respectively, to beneficial live microbes and the ingredients that promote their growth—are a new frontier in health and beauty.

From 2015 to 2016, equity funding for companies invested in the so-called microbiome jumped from $173 million to $728 million, according to CB Insights, a company that tracks the tech market. Last year the figure rose to $939 million. The global market for probiotic supplements reached $5 billion in 2017, according to the International Probiotics Association, making it the fastest-growing supplement category in the world.

Even corporations that built brands dedicated to killing bacteria are investing in microbiome research and startups, sometimes on the sly. In 2016 the Clorox Co., maker of microbe-annihilating Clorox Bleach, acquired Renew Life Formulas Inc., which sells prebiotic and probiotic supplements. This January, Unilever Ventures Ltd., the conglomerate’s investment arm, took a minority stake in Gallinée, a tiny London-based startup whose slogan is “Happy skin needs happy bacteria.”

The German chemicals giant BASF is 3D-printing artificial skin and embedding it with bacteria to develop treatments for aging, pigment disorders, and pollution exposure. And last October, AOBiome licensed Whitlock’s bacteria spray to MBX LLC, which trademark and company documents reveal to be a shell company owned by S.C. Johnson & Son Inc., maker of Windex, Drano, and Raid.

relates to Germ-Killing Brands Now Want to Sell You Germs

Whitlock’s mug, unwashed for many years.
Photographer: Brea Souders for Bloomberg Businessweek


The term “microbiome” is widely traced to a 2001 Scientist magazine article that deployed it “to signify the ecological community of commensal, symbiotic, and pathogenic microorganisms that literally share our body space.” That group includes fungi, viruses, and bacteria, some of which help produce vitamins, hormones, and other chemicals vital to our immune system, metabolism, mood, and much more. In the typical person, these microorganisms account for about 2 pounds and roughly as many cells as the ones containing human DNA.

In recent decades our microbiomes have been altered by poor dietary habits; overuse of disinfectants, antibiotics, and other germ fighters; dwindling contact with vital environmental microbes, including those carried by wildlife and livestock; and the rise in cesarean section births, which don’t immerse babies in the valuable bacteria found in the birth canal. According to one 2015 study, Americans’ microbiomes are about half as diverse as those of the Yanomami, an isolated Amazonian tribe.

A series of studies begun in 1998 examined the relationship between bacteria and disease incidence in the Finnish-Russian border region of Karelia, where people share similar genetics. On the richer, cleaner Finnish side, people were as many as 13 times likelier to suffer from inflammatory disorders as on the Russian side, where the majority live in rural homes, keep animals, and tend their own gardens.

A comparable American study, published in 2016, examined the genetically similar Hutterites of South Dakota and Amish of Indiana. The Hutterites, who use pesticides and industrial farming techniques, had higher asthma incidence, 23 percent, than almost any other U.S. group. Among the Amish, who farm without chemicals and rely on manpower and horses, the condition is quite rare. To see whether each community’s respective bacterial populations were affecting people’s health, researchers collected dust samples from Hutterite and Amish bedrooms, mixed them with egg proteins, then gave them to mice with an egg-protein allergy. The mice exposed to Hutterite dust developed extreme asthmatic symptoms, whereas those exposed to Amish dust exhibited almost no allergic response.

These and many more studies have some scientists fearing that people, especially in the West, are cleaning themselves sick. The trick for companies hoping to cash in on the countervailing trend will be to figure out which microbes help restore human health. It won’t be easy. “Most of the species in our body don’t have names. They’ve not been cultured,” says Robert Dunn, a professor of applied ecology at North Carolina State University, whose most recent book, Never Home Alone, details the relationship between nature and health. “Nobody has studied them in any real detail.”
“That first winter, I did start to smell,” Whitlock recalls. Instead of giving up, he doubled down

Whitlock’s passion for microbes began around 2000. “No one was talking about this stuff back then,” he says, sitting in a conference room at AOBiome’s headquarters in Cambridge. At 64, he’s bald on top, with wispy gray hair around his ears. His daily uniform consists of large wire-rimmed glasses, well-worn jeans, hiking boots, and a flannel shirt. For the record, he has no discernible odor.

His autism is pronounced enough that he didn’t notice when all his colleagues dressed like him on his birthday in 2015. Nor did he recognize me the third time we met for an interview. But in conversation he’s open and funny about his passions and quirks. Among the latter is his habit of drinking multiple cups of black coffee a day from a sludge-coated mug advertising the antidepressant Zoloft, which he’s been taking for decades. “I haven’t washed it in probably 20 years,” he says. In an effort to improve his longevity, Whitlock eats only one meal a day: typically a breakfast pile of oats, dried blueberries and raisins, prunes, mushrooms, and a half-pound of shredded mozzarella. For an entire year, he tells me, he also ate hard-boiled eggs with the shells still on. “That wasn’t an experiment. I just thought it was a good idea—and it wasn’t,” he says, shaking his head. “Shells have sharp edges.”

Whitlock holds bachelor’s and master’s degrees in chemical engineering from the Massachusetts Institute of Technology. Before starting AOBiome, he invented a more environmentally friendly cement production process and, together with Thompson, co-founded Separation Technologies Inc., which Titan America bought in 2002. He didn’t begin thinking in earnest about biology until a fateful date with a bubbly fifth grade teacher. Why, she asked him, did her horse roll in the dirt, even in the cool springtime months before biting insects had hatched? “I was her Mr. Scientist friend, and I tried to find an answer,” Whitlock says. The romance didn’t flourish, but his curiosity did; he read hundreds of scientific papers and grew fascinated by a type of bacteria, found in soil and other natural environments, that derives energy from ammonia rather than organic matter.
That gave him an idea: What if these ammonia-oxidizing bacteria, or AOB, transformed sweat into something beneficial? Further study proved his hunch correct. AOB, it turns out, convert ammonia into nitrite, a molecule with anti-infective properties, and nitric oxide, which Science magazine declared “molecule of the year” in 1992. “It helps maintain blood pressure by dilating blood vessels, helps kill foreign invaders in the immune response, is a major biochemical mediator of penile erections, and is probably a major biochemical component of long-term memory,” the magazine’s editor wrote. In 1998 three Americans won the Nobel Prize in medicine for discovering that nitric oxide transmits chemical signals important to a wide range of health-related functions.

Hooked, Whitlock began collecting soil samples from stables and fields, then analyzing them in a makeshift basement lab. Eventually he extracted an AOB called Nitrosomonas eutropha, which he describes as “relatively athletic.” He coaxed it to multiply in an ammonia solution using a set of tanks and jury-rigged aquarium bubblers. To test its efficacy, he began running experiments on himself. That’s when he stopped showering. “That first winter, I did start to smell,” he recalls.

Instead of giving up, he doubled down: “I had the idea, if I wear a sweater, I will sweat more, release more ammonia to the AOB, and they will make nitrite, and that will suppress the bacteria that are causing the odor.” When that worked, he tried sleeping encased in a giant plastic bag fashioned from a computer-server dust cover, in the hope that minimal airflow would increase nitric-oxide absorption. That investigation ended after Whitlock broke out in a rash. He also gauged his nightly erections with a volume-measuring device called a plethysmograph, on the theory that more nitric oxide would mean increased blood flow. (He says it did.)

All the while, Thompson was raising money to fund additional research and clinical trials. “I was trying to find people who’d listen and not write David off as some kook,” he says. “David is a very gentle, brilliant man who really cares about people and helping the world, and money was not that big a driver for him.” Even though Thompson didn’t fully understand AOB himself, he spent about $600,000 across 12 years to pay Whitlock a minimal monthly stipend and cover patent, equipment, and legal expenses. He was just about to run out of funds when another investor stepped in: Jamie Heywood, co-founder of PatientsLikeMe, an online info-sharing network. Three years earlier, Whitlock had presented Heywood with a tinfoil-wrapped Poland Spring bottle filled with his microbial elixir. “Here’s my drug,” he said. “Try it.”

Heywood did, and he and his teenage daughter came to swear by it. He recalls thinking he’d be the only one willing to invest with “this crazy guy from MIT who looks like he’s homeless.” But he concluded that the idea was too important to ignore. He also found the underlying science compelling. “It’s a bacterial delivery of a necessary drug,” he says. “You can’t just dump nitric oxide in the system. You have to enhance the body’s ability to operate its own system more effectively.”

Heywood’s group raised an initial round of $1.4 million, recruited a chief executive officer, and retested Whitlock’s science under the banner of AOBiome. “We wanted to see: Is there a bug? What’s its sequence? Can you grow it? Does it do anything? Do any of David’s radical self-experimentation claims hold up?” he says. After the bacteria proved safe, the team began testing on independent human subjects.

One of these early experimenters was the writer Julia Scott, who described her monthlong “No-Soap, No-Shampoo, Bacteria-Rich Hygiene Experiment” in a cover story for the New York Times Magazine. Initially her hair turned dark with grease, and she began to smell. But after the second week, she detected a wonderful change in her skin. “It actually became softer and smoother, rather than dry and flaky, as though a sauna’s worth of humidity had penetrated my winter-hardened shell,” she wrote. “And my complexion, prone to hormone-related breakouts, was clear. For the first time ever, my pores seemed to shrink.” The article prompted so many inquiries that AOBiome’s web host began bouncing emails, thinking a spam attack was under way.

The team hadn’t intended to introduce a cosmetic brand, but it seized on the opportunity, rebranding its side project Mother Dirt in 2015. The company outsourced the bacteria farming to a bioreactor operator in India, where regulations are less stringent and landlords less squeamish. From there, the AOB were refrigerated and shipped in high concentrations to a monoseptic factory outside Boston for dilution and bottling. (Full disclosure: I was among the early adopters and still occasionally use the spray on my face in humid summer months. At $49 for a 3.4-ounce bottle, it’s a bit pricey, though, and I’ve had mixed results.)

In 2017, Mother Dirt recorded revenue of $2.6 million for its cosmetic spray and a microbiome-neutral cleanser, shampoo, and moisturizer. Some of those sales were to MBX, the shell company registered to S.C. Johnson, under a resale agreement struck that October for every market except China. (The plan is to introduce the cosmetic spray there starting next year.) S.C. Johnson declined to comment on its foray into marketing live bacteria, and AOBiome executives say they’re prohibited from talking about the deal.

relates to Germ-Killing Brands Now Want to Sell You Germs

A petri dish at AOBiome.
Photographer: Brea Souders for Bloomberg Businessweek


In November, beauty experts convened at a stuffy London conference center for the third Skin Microbiome Congress. Many conglomerates were on hand, including BASF, Bayer, Coty, Merck, Nestlé, L’Occitane, L’Oréal, and Unilever, but representatives from startups did most of the talking.
Featured brands included Yun Probiotherapy, a Belgian startup that encapsulates live bacteria and mixes it into creams, and Esse Probiotic Skincare, a company headquartered in South Africa that offers genetic sequencing of the skin microbiome, as well as live-bacteria serums and bacterial spa treatments.

Whitlock wasn’t in attendance—he tends to avoid conferences—but a few kindred spirits were. Esse’s founder, Trevor Steyn, told me he takes the youngest of his seven children outside to eat a weekly spoonful of dirt. “I let them choose where they want to get it from,” he said. “We live in a very rural area outside Durban.”

The picture was very much of a still-gestating industry. “We don’t think it’s mainstream, and we don’t think it’s going to be mainstream next year or the year after that,” Jasmina Aganovic, president of Mother Dirt, told an audience of roughly 200. “All of us are here and dedicated to what we’re doing because we see a long-term vision.”

L’Oréal was among the few big brands to host a talk, demonstrating how harsh cleansers dry out the skin and damage the microbiome, and how some moisturizers begin to revive bacteria populations after a few hours. (Months after the talk, the French giant announced a partnership with UBiome Inc., a Silicon Valley startup with patented technology for analyzing the human microbiome.) L’Oréal-owned La Roche-Posay also held a talk touting the brand’s thermal spring, which contains diverse bacteria that seem to ameliorate inflammatory skin disorders such as psoriasis; in addition to appearing in cosmetic products, the spring’s waters draw some 8,000 patients each year.

Most of the other large companies just took notes. “The big players come to these conferences and kind of sit on the sidelines,” says Marie Drago, founder of Gallinée, the Unilever-backed happy-bacteria startup. “They have a branding problem to figure out because, for so many years, they’ve been pushing antibacterial products.” “We’ve got far more to lose,” says Geoff Briggs, technology manager for Walgreens Boots Alliance Inc. “If a niche brand is out there and the claims don’t stack up, nobody really cares in the wider world. But if we put something out on a shelf and it doesn’t work, doesn’t support the claims we’re making on it, then it ruins our brand.”

Some companies, including Estée Lauder Inc., have quietly incorporated bacterial ingredients since the 1970s. But “quietly” is the key word, because most consumers still equate microbes with bad skin. Until the science and marketing advance, top companies seem content to invest in smaller brands that can lead the trend while they discreetly pursue their own research. That said, Briggs suggests that all the major personal-care—and even home-care—brands could be at least microbiome-friendly in the next decade.

Getting there could mean eliminating some of the haziness around the category. The FDA still has no precise definition for “probiotic.” And in contrast with the food industry, which defines it as a live microbe with proven health benefits, skin-care brands apply it liberally, to live bacteria, to dead and ruptured bacteria, and more. Then again, loose definitions haven’t hurt sales of products labeled “natural” or “organic.”
relates to Germ-Killing Brands Now Want to Sell You Germs

A multiwell plate showing the presence of nitrite, which turns pink with an added reagent.
Photographer: Brea Souders for Bloomberg Businessweek


In some respects, the new microbe-oriented brands are trying to restore an earlier, more natural relationship between humans and the environment. And it’s true that people have been exploring microbial beauty and health treatments since before Robert Hooke and Antonie van Leeuwenhoek discovered microorganisms circa 1665. Cleopatra was said to have bathed in donkey’s milk, which is chock-full of prebiotics. In China, where human stool has been used as medication since at least the fourth century, a 16th century doctor named Li Shizhen penned a recipe for “yellow soup”—a broth made from fresh, dried, fermented, or infant feces—to treat gastrointestinal illnesses.

The potential health benefits of bacteria were expressly recognized as early as 1905, when Elie Metchnikoff, a colleague of Louis Pasteur, hypothesized that Bulgarians’ relative longevity owed not to their yogurt-heavy diet, but more specifically to the lactobacilli used to ferment the yogurt. Soon thereafter, a German doctor, following in the footsteps of the Chinese, created a cure from the excrement of a soldier who’d been the only one in his battalion to evade dysentery during World War I; the doctor’s formulation is still sold as a treatment for digestive problems in Europe, under the Mutaflor label.

It wasn’t until about 15 years ago that scientists developed genetic sequencing tools allowing them to better tally microbial populations and study how their presence or absence affects human health. The advent of improved and cheaper technology has in turn made it possible for a market in microbiome therapeutics to emerge. Tiny for now, the sector could grow to $10 billion by 2024, according to IP Pragmatics Ltd., a London consulting firm. “Every company that does anything with human health is exploring the microbiome,” says Jack Gilbert, professor and microbiome researcher at the University of California at San Diego. “The microbiome, over the next 5, 10 years—I hope—will lead to a revolution in personalized treatments.” This could span everything from acne medications to cancer immunotherapy.

“The idea that a single microbe is going to be a fix-all for people of different backgrounds seems somewhat simple”

Sorting out the medicine from the proverbial snake oil will involve clinical trials. Currently only a few dozen companies worldwide are conducting them, and AOBiome, like many of the others, has its share of skeptics. Among the doubters is Dunn, the applied-ecology professor and author. There’s little evidence, he says, that Whitlock’s N. eutropha was ever a permanent resident of our ancestors’ skin. And he doubts that one type of bacteria alone could significantly improve health outcomes. “The idea that a single microbe is going to be a fix-all for people of different lifestyles and context and genetic backgrounds all around the world seems somewhat simple,” he says.

There’s even a risk, he adds, that Whitlock’s bacteria could become an unchecked invasive species: “One worry is that it becomes the cane toad of the skin and has unanticipated consequences that spread throughout the ecosystem.” Asked about this possibility, AOBiome says it has performed safety testing and that if anything were to go wrong, its AOB are so slow to reproduce that people would only need to take a soapy shower to kill them.

AOBiome’s double-blind trial for acne will soon enter its final, human-testing phase. The company says its initial findings show that its pharmaceutical-grade spray, which is roughly five times as concentrated as its cosmetic spray, led to a 48 percent reduction in pimples and red bumps, compared with a 32 percent reduction for those who’d used a placebo. The spray also decreased skin pH, which is considered a beneficial effect, and resulted in a 300-fold decrease in Staphylococcus aureus, a strain known to cause eczema. Preclinical trials for acne also turned up an interesting side effect of Whitlock’s spray: It caused a medically significant drop in blood pressure. To follow up, AOBiome is now conducting clinical trials for an AOB nasal spray.

The company’s six active trials are being funded almost entirely by one investor: Jun Wang, the former CEO of a research center called the Beijing Genomics Institute and the founder of ICarbonX, a Chinese artificial intelligence health company valued at $1 billion. Wang, like other investors, is devoted to Whitlock’s spray and says his friends and family are self-experimenting to see how it holds up against conditions such as migraines and pollution-induced skin woes. “It has become very popular in my circle,” he says, speaking to me over Skype from China. Now chairman of AOBiome, he says he hopes to turn the Cambridge startup into a pipeline for bacteria-based drugs. The company is considering whether to set up additional labs in China and has begun generating a diverse library of AOB for further study. “AOB is just the first bacteria we’re working on,” Wang says. “We are thinking about how to do gold mining in the bacteria world.”

On a rainy evening in November, Whitlock meets me at Summer Shack, a giant seafood restaurant off a busy thruway near AOBiome’s office. Outside stands a statue of a New England fisherman, its elongated, blocky proportions resembling those of an Easter Island head. Inside the waiting area, a video demonstrates how to shell a lobster.

Whitlock was never very involved in Mother Dirt (“I’m cosmetic-challenged”), and he says he’s impatient for AOBiome’s clinical trials to prove the theories from his minivan days. The company’s mission is personal for him. In addition to autism, he suffers from anxiety, depression, hypertension, and post-traumatic stress disorder from being bullied as a child. He’s convinced his bacteria have improved these conditions, although he’s careful to emphasize that he has no clinical proof. “Before, I could never have sat here and talked like this with a stranger,” he tells me. “I want a billion people to use this every day.”

When the waitress comes to take drink orders, Whitlock sticks with water. Alcohol, he explains, might harm the AOB population he’s been cultivating on his skin. “They’re very sensitive,” he says.

 

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Researchers reveal how bacteria can adapt to resist treatment by antibiotics
April 24, 2019
by Lisbeth Heilesen,
Aarhus University

In a joint collaboration, researchers from Denmark and Switzerland have shown that bacteria produce a specific stress molecule, divide more slowly, and thus save energy when they are exposed to antibiotics. The new knowledge is expected to form the basis for development of a new type of antibiotics.

All free-living organisms are under constant pressure to survive. Darwin dubbed this "survival of the fittest" and thus described how the best adapted species would have most offspring and therefore eventually end up propagating itself.

This fundamental principle is particularly prominent in the world of microorganisms, where free-living bacteria live in a constant fight to be the most well adapted and thus those who divide fastest in any given natural habitat. But when bacteria at the same time are exposed to deadly antibiotics, this fight becomes a question of balancing fitness, i.e. the ability to divide fast, with tolerance towards antibiotics. This amazing adaptability of bacteria is a contributing factor to the severity of infectious diseases in humans, including tuberculosis and severe urinary tract infection, for which the disease often resurfaces after treatment has ended.

In a new research paper, just published in the high-impact journal Molecular Cell, researchers from Aarhus University have collaborated with experts from the University of Copenhagen and the technical university ETH Zürich in Switzerland and taken a close look at how bacteria handle this difficult balancing act. The results show that bacteria very quickly reduce their rate of cell division when exposed to antibiotics in order to maintain the highest possible tolerance, but quickly start growing again when the substances are removed and fitness is the most important factor.

Bacteria save up energy
At the molecular level, the researchers in the group of Asc. Prof. Ditlev Egeskov Brodersen from the Department of Molecular Biology and Genetics at Aarhus University have been able to show that the effect is mediated by an enzyme within the bacteria, capable of saving up molecular energy in the form of constituents of cellular DNA, which can be used for rapid regrowth when the antibiotic treatment is ceased. When the bacteria are exposed to antibiotics, they immediately start breaking down substituents of DNA (the so-called nucleotides), into smaller parts that are then stored in the cell.

The researchers have shown that bacteria produce a specific stress molecule called (p)ppGpp upon exposure to antibiotics that makes the enzyme more active. This thus means that the saving up of energy happens extra fast when the bacteria are exposed to stress. Using an advanced analytical method called X-ray crystallography, the researchers have been able to generate detailed 3-D pictures of the enzyme, both in its normal state and when bound to the stress molecule. The results surprisingly show that the enzyme opens up when the stress hormone is present, and thus functions much more efficiently because the nucleotides can more easily access the active site where the breakdown process takes place.

It is expected that the new knowledge about the molecular basis for the reaction of bacteria to antibiotics can be used to develop a whole new type of antibiotics that prevent bacteria from saving up energy and thus adapting to the treatment.

 

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Bacteria used to produce synthetic mother-of-pearl
Ben Coxworth
April 23rd, 2019

A sample of the artificial nacre, deposited on a glass slide
A sample of the artificial nacre, deposited on a glass slide(Credit: University of Rochester / J. Adam Fenster)

Besides simply looking nice when used in jewellery, mother-of-pearl is also one of nature's hardest, stiffest, most stable materials. Scientists have now utilized bacteria to develop a cheap and eco-friendly method of replicating it, for possible use in a variety of areas.

Also known as nacre, mother-of-pearl is the hard iridescent coating found on the outside of pearls, and the inside of certain mollusc's shells. Featuring a brick-wall-like microstructure, it's composed of stacked brick-like calcium carbonate plates, joined together via a biopolymer "mortar."
Synthetic versions of it have already been created, by teams from the University of Cambridge, the CNRS lab, and ETH Zurich. All of the techniques that were used, however, have incorporated either harsh chemicals or large expenditures of energy. Led by Assoc. Prof. Anne S. Meyer, a team at New York's University of Rochester set out to develop a synthetic nacre-production method that was easier on the environment.

The resulting technique involves mixing urea with Sporosarcina pasteurii bacteria and a calcium source, then dipping a glass slide into the solution. A reaction between the urea and bacteria causes a thin layer of calcium carbonate to crystallize onto the slide.

That slide is then placed in a beaker containing a solution of the bacteria Bacillus licheniformis. After that beaker has been left in an incubator for a period of time, the bacteria forms a layer of sticky polymer on top of the existing calcium carbonate layer.

By going back and forth between the two processes, the scientists can build up successive alternating layers of the calcium and the polymer. The final coating is tougher and stiffer than most plastics, yet is also quite lightweight and flexible. It isn't ready quickly, though – one combined calcium/polymer layer currently takes about one day to synthesize, and is just five microns thick.

To that end, Meyer and colleagues are now working on speeding up the production process, and making the layers thicker. It is hoped that the coating could ultimately be applied to a variety of materials, or even produced as a stand-alone material.

Possible applications include its use in lightweight aircraft or other vehicles, as a coating that prevents cracks and corrosion in structures, or as a sustainable food packaging material. Additionally, because the synthetic nacre is biocompatible, in could be used in the construction of implants or artificial bones.

A paper on the research was published this week in the journal Small.

Source: University of Rochester

 

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E-cigarette fluids and cartridges contain ‘bacteria and fungi toxins’, study finds

Contaminants known to cause asthma and other lung diseases ‘add to the growing concerns’ about vaping

E-cigarette cartridges and vape liquids are contaminated with bacteria and fungi that could cause lung infections and asthma, a study has found.

A quarter of the 75 brands of US vaping products studied by Harvard researchers showed traces of bacteria – and four out of five had fungal contamination. The study included sealed and refillable products.

The researchers looked for chemical markers that can trigger lung conditions such as asthma, including bacterial endotoxins produced by the E coli bug, and β-D-glucan, part of the cell wall of invasive fungi.

These bacteria and fungi by-products have been shown to cause “acute and chronic respiratory effects”, said senior author and environmental geneticist Professor David Christiani.

He added: “Finding these toxins in e-cigarette products adds to the growing concerns about the potential for adverse respiratory effects in users.”

The findings, published in the journal Environmental Health Perspectives, come as academics warned that UK health authorities are ignoring the potential risks of vaping being used as a quitting aid for smokers.

E-cigarettes are considerably safer to smoke as they contain nicotine but not tobacco, which produces hundreds of cancer-causing chemicals when burnt. However, that does not mean they are harmless.

Professor Martin McKee this week warned they have not existed for long enough to fully understand their impact.

There have been several studies with animals and humans which suggest that additives and flavourings used to help form vapour may have long-term negative effects.

One University of Birmingham study found that condensed vapour can interfere with the immune system’s ability to clean up the lungs.

If vapours are also introducing potentially harmful invaders this could have major effects, particularly with rising levels of resistance to antibiotic and antifungal treatments.

The Harvard study found 17 of 75 products (23 per cent) showed traces of endotoxins and 61 of 75 included glucans.

Bacterial contaminants were more common in tobacco and menthol flavourings, while glucans were more common in fruit flavourings and cartridge refills, suggesting differences in manufacturing were to blame.

The authors said these findings should be considered when drawing up regulatory policies, however independent experts said the findings needed to be tested in real world settings.

Dr Penny Woods, chief executive of the British Lung Foundation, said the results were “interesting” but preliminary, adding that the UK has ”different, tighter e-cigarette regulations” than the American market.

“We do need to keep adding to our knowledge on the long-term effects of e-cigarettes, however we know that vaping is 20 times less harmful than smoking,” she added.

 

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