Tag: microbe

Astronomers Spot Possible Signs Of Extraterrestrial Life In Venus’s Clouds

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There may be bizarre microbes living in the sulfuric acid-laden clouds of the hothouse planet, scientists said.

By Seth Borenstein

Astronomers have found a potential sign of life high in the atmosphere of neighboring Venus: hints there may be bizarre microbes living in the sulfuric acid-laden clouds of the hothouse planet.

Two telescopes in Hawaii and Chile spotted in the thick Venutian clouds the chemical signature of phosphine, a noxious gas that on Earth is only associated with life, according to a study in Monday’s journal Nature Astronomy.

Several outside experts — and the study authors themselves — agreed this is tantalizing but said it is far from the first proof of life on another planet. They said it doesn’t satisfy the “extraordinary claims require extraordinary evidence” standard established by the late Carl Sagan, who speculated about the possibility of life in the clouds of Venus in 1967.

“It’s not a smoking gun,” said study co-author David Clements, an Imperial College of London astrophysicist. “It’s not even gunshot residue on the hands of your prime suspect, but there is a distinct whiff of cordite in the air which may be suggesting something.”

As astronomers plan for searches for life on planets outside our solar system, a major method is to look for chemical signatures that can only be made by biological processes, called biosignatures. After three astronomers met in a bar in Hawaii, they decided to look that way at the closest planet to Earth: Venus. They searched for phosphine, which is three hydrogen atoms and a phosphorous atom.

On Earth, there are only two ways phosphine can be formed, study authors said. One is in an industrial process. (The gas was produced for use as chemical warfare agent in World War I.) The other way is as part of some kind of poorly understood function in animals and microbes. Some scientists consider it a waste product, others don’t.

Phosphine is found in “ooze at the bottom of ponds, the guts of some creatures like badgers and perhaps most unpleasantly associated with piles of penguin guano,” Clements said.

Study co-author Sara Seager, an MIT planetary scientist, said researchers “exhaustively went through every possibility and ruled all of them out: volcanoes, lightning strikes, small meteorites falling into the atmosphere. … Not a single process we looked at could produce phosphine in high enough quantities to explain our team’s findings.”

That leaves life.

The astronomers hypothesize a scenario for how life could exist on the inhospitable planet where temperatures on the surface are around 800 degrees (425 degrees Celsius) with no water.

“Venus is hell. Venus is kind of Earth’s evil twin,” Clements said. “Clearly something has gone wrong, very wrong, with Venus. It’s the victim of a runaway greenhouse effect.”

But that’s on the surface.

Seager said all the action may be 30 miles above ground in the thick carbon-dioxide layer cloud deck, where it’s about room temperature or slightly warmer. It contains droplets with tiny amounts of water but mostly sulfuric acid that is a billion times more acidic than what’s found on Earth.

The phosphine could be coming from some kind of microbes, probably single-cell ones, inside those sulfuric acid droplets, living their entire lives in the 10-mile-deep clouds, Seager and Clements said. When the droplets fall, the potential life probably dries out and could then get picked up in another drop and reanimate, they said.

Life is definitely a possibility, but more proof is needed, several outside scientists said.

Cornell University astronomer Lisa Kaltenegger said the idea of this being the signature of biology at work is exciting, but she said we don’t know enough about Venus to say life is the only explanation for the phosphine.

“I’m not skeptical, I’m hesitant,” said Justin Filiberto, a planetary geochemist at the Lunar and Planetary Institute in Houston who specializes in Venus and Mars and isn’t part of the study team.

Filiberto said the levels of phosphine found might be explained away by volcanoes. He said recent studies that were not taken into account in this latest research suggest that Venus may have far more active volcanoes than originally thought. But Clements said that explanation would make sense only if Venus were at least 200 times as volcanically active as Earth.

David Grinspoon, a Washington-based astrobiologist at the Planetary Science Institute who wrote a 1997 book suggesting Venus could harbor life, said the finding “almost seems too good to be true.”

“I’m excited, but I’m also cautious,” Grinspoon said. “We found an encouraging sign that demands we follow up.”

NASA hasn’t sent anything to Venus since 1989, though Russia, Europe and Japan have dispatched probes. The U.S. space agency is considering two possible Venus missions. One of them, called DAVINCI+, would go into the Venutian atmosphere as early as 2026.

Clements said his head tells him “it’s probably a 10% chance that it’s life,” but his heart “obviously wants it to be much bigger because it would be so exciting.”

https://www.huffpost.com/entry/venus-possible-life_n_5f5f878ac5b68d1b09c5ab9b

Scientists Awaken Deep Sea Bacteria After 100 Million Years

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The microbes had survived on trace amounts of oxygen, and were able to feed and multiply once revived in the lab.


These bacteria, glowing green in this microscopy image, were revived from deep sea sediment more than 100 million years old.

by Amanda Heidt

Microbes extracted from deep sea sediments that settled during the age of the dinosaurs have been revived in the lab after eons spent in a dormant state. Despite needing oxygen to survive, the bacteria were able to make due with only trace amounts and almost no food for more than 100 million years. Once reanimated, most of the microbes were able to feed and multiply with seemingly no ill effects attributed to their long period of rest.

“The most exciting part of this study is that it basically shows that there is no limit to life in the old sediments of Earth’s oceans,” Steven D’Hondt, an oceanographer at the University of Rhode Island and a coauthor of the study, tells Reuters. “Maintaining full physiological capability for 100 million years in starving isolation is an impressive feat.”The endeavor, described Tuesday (July 28) in Nature Communications, shows just how little is known about the physiological limits of life on Earth, the authors report.

Researchers have long looked to the Earth’s most extreme corners to study the limits of life, including the deep sea, and lead author Yuki Morono, a geomicrobiologist at the Japan Agency for Marine-Earth Science and Technology, wanted to know just how high a tolerance bacteria have for conditions that would prove fatal for other organisms.

Morono collected sediment cores during a research cruise in 2010 aboard the JOIDES Resolution, a floating lab that operates 24 hours a day during scientific voyages. The team targeted the South Pacific Gyre off the east coast of Australia, often called an ocean desert because it lacks the nutrients needed to support even most plankton. As a result, very little organic matter falls to the seafloor more than three miles below.

Across the length of the roughly 250-foot cores, the team collected samples of clay spanning a deposition period between 13 million years ago and almost 102 million years ago. With the samples in the lab, they added nutrients such as nitrogen and carbon—food to jump start any life inside. For up to 557 days after, Morono would extract small chunks of sediment and dissolve them in water, searching for living cells. While a sample of sediment taken from a more oxygen-rich layer of the sea floor might contain more than 100,000 cells per cubic centimetre of mud, Science reports, these deep sea samples might initially only have 1,000 cells in that same volume.

Over time, the microbes began to multiply, a finding Morono initially attributed to “some mistake or a failure in the experiment,” he tells The Guardian. They ruled out contamination from other sources of seawater in the lab, ultimately confirming that what they were seeing was real. In many samples, as many as 99 percent of the microbes were revived. After 68 days, the total number of cells had increased by four orders of magnitude, up to 1 million cells per cubic centimetre.

A genetic analysis showed that the microbes were fairly diverse, representing 10 major groups of bacteria, some of which are widespread throughout other parts of the ocean. Kenneth Nealson, an environmental microbiologist retired from the University of Southern California who was not involved in the study, tells Science this finding “suggests that learning to survive under conditions of extreme energy limitation is a widespread ability,” a useful trick for microbes when food is scarce.

The relatively slow accumulation of sediments in the South Pacific Gyre ended up being key to the cells’ survival, The Guardian reports. When sediment builds up quickly, the pressure pushes out any oxygen that might otherwise linger between the grains to keep aerobic microbes alive. The authors report that if sediment accumulates at a rate of no more than three to six feet every 1 million years, it can remain oxygenated enough to support bacteria.

Some researchers are now pointing to what these findings might mean for the search for life on other planets, as they broaden what environments can be considered amenable to life. Speaking to Science, Andreas Teske, a microbiologist at the University of North Carolina, Chapel Hill, who was also not involved with the new study, says that even if a planet’s surface looks barren, “it may be holding out in the subsurface.”

https://www.the-scientist.com/news-opinion/scientists-awaken-deep-sea-bacteria-after-100-million-years-67778?utm_campaign=TS_DAILY%20NEWSLETTER_2020&utm_medium=email&_hsmi=92321648&_hsenc=p2ANqtz-_CJvqIFUkIbgjmnSDIBINFzIXb2lAmiW6BrZS2DJ6_X9ZLjddemUBo7JRpNuc3zOJJTboLcWUF_yU3_wh4ALU8z1w_XA&utm_content=92321648&utm_source=hs_email

Auto-brewery syndrome

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Microbes can produce so much alcohol that people become drunk—and sustain liver damage—without touching any booze.

by Ed Yong

The man’s troubles began in 2004, when, having moved from China to attend college in Australia, he got really drunk. That would hardly have been a noteworthy event, except that the man hadn’t consumed any alcohol—only fruit juice.

The bizarre incident soon turned into a pattern. About once a month, and out of the blue, he’d become severely inebriated without drinking any alcohol. Over time, the episodes became more severe and more frequent. He lost jobs because people suspected him of being a closet drinker. He was frequently hospitalized. In 2011, he returned to China and his mother cared for him while monitoring him with a Breathalyzer. His blood-alcohol levels, she found, would erratically and inexplicably soar to 10 times the legal limit for driving.

In June 2014, at the age of 27, he was admitted to the intensive-care unit of Chinese PLA General Hospital, in Beijing. At one point, so much alcohol was on his breath that he couldn’t sleep through the night. Another time, he threw up and blacked out after chugging some soda water. A CT scan showed that his liver was damaged, inflamed, and riddled with fatty deposits.

The man was diagnosed with a rare condition aptly known as auto-brewery syndrome, in which microbes in a person’s gut ferment carbohydrates into excessive amounts of alcohol. The earliest cases were documented in Japan in the 1950s, and a few dozen more have been reported since, in people all over the world, and even in children as young as 3. The microbial culprits are usually yeasts—the same fungi used to brew beer and wine—and the condition can often be treated with antifungal drugs.

But those drugs didn’t work on the Chinese patient. Baffled, a team of doctors, led by Jing Yuan from the Capital Institute of Pediatrics, analyzed the man’s stool samples and found that the alcohol in his body was being produced not by yeast, but by bacteria. During his first episode in the hospital, Klebsiella bacteria had bloomed so vigorously that it made up 19 percent of the microbes in his gut, and became 900 times more common than in healthy people.

Klebsiella pneumoniae is extremely common in both soils and human bodies. Though usually harmless, it’s also an opportunistic pathogen that can cause severe infections if given the chance. And while Klebsiella is not known for intoxicating its hosts, Yuan’s team found that the patient had two particular strains that can churn out alcohol. Many gut microbes do this, but at such low levels that their boozy by-products are easily removed by the liver. The Klebsiella strains in Yuan’s patient were exceptions: At one point, they produced so much of the stuff that it was as if the man had knocked back 15 shots of whiskey. “We were surprised that bacteria can produce so much alcohol,” Yuan says.

Auto-brewery syndrome is extreme, but it has similarities to other, milder and more prevalent conditions. For example, people with nonalcoholic fatty liver disease (NAFLD) build up fatty deposits in their liver in the style of heavy drinkers, despite touching little or no alcohol. This condition is very common, affecting 30 to 40 percent of American adults; the causes are still unclear and likely varied. Yuan wondered if Klebsiella might be involved, and when she analyzed 43 Chinese people with NAFLD, she found that 61 percent had the same high-alcohol strains as the man with auto-brewery syndrome. By contrast, just 6 percent of people with a healthy liver carry those strains.

To see if those strains were actually causing fatty livers, the team fed them to mice that had been raised in sterile conditions and lacked microbes of their own. Within two months, the rodents had signs of liver disease, inflammation, and scarring, comparable to mice that had been drinking alcohol itself. The same thing happened if the team transplanted the stool from an NAFLD patient into germ-free mice, but not if they first removed the alcohol-making Klebsiella using a virus—a phage—that specifically kills those strains. Although studies in mice should be treated with caution, Yuan nonetheless suggests that these strains could be an important cause of NAFLD, through the alcohol they produce.

Other researchers have suggested this before. In 2000, Anna Mae Diehl from Johns Hopkins University noticed that obese mice often have alcohol on their breath, which goes away after antibiotic treatment. “Intestinal production of ethanol may contribute to the genesis of obesity-related fatty liver,” she speculated. Two groups later showed that alcohol-producing microbes are more common in the guts of people with NAFLD than in those of their healthy peers.

While Yuan’s team pointed their fingers at Klebsiella, “it was found in only 60 percent of the human subjects they studied with NAFLD,” says Susan Baker at the State University of New York at Buffalo. “Others have identified other likely bacteria as possible culprits.” She cautions against focusing on any specific microbe, and instead considering the entire ecosystem of the body—bacteria, yeasts, viruses, gut cells, immune cells, liver, and all.

Yuan agrees. She notes that NAFLD is a complex and varied condition, and that even if Klebsiella does turn out to be a cause, it would be one of many. It also raises several questions: Why do some strains produce so much alcohol? Where do they come from? What makes them bloom so vigorously in people such as the unfortunate Chinese man who launched this study—genetics, diet, or something else? And perhaps most important, what can be done about them?

Phages might eventually help, as they did in Yuan’s mice. But for her patient with auto-brewery syndrome, simpler measures did the trick. He was treated with an antibiotic and put on a no-sugar, no-carbohydrate diet for three weeks. His intoxication symptoms eventually subsided, and two months later he was released from the hospital.

https://amp.theatlantic.com/amp/article/598414/

Keeping gut bacteria in balance could help delay age-related diseases

On By A.P.In ageing, aging, gut, gut bacteria, MedicineLeave a comment

Why do some people remain healthy into their 80s and beyond, while others age faster and suffer serious diseases decades earlier? New research led by UCLA life scientists may produce a new way to answer that question—and an approach that could help delay declines in health.

Specifically, the study suggests that analyzing intestinal bacteria could be a promising way to predict health outcomes as we age.

The researchers discovered changes within intestinal microbes that precede and predict the death of fruit flies. The findings were published in the open-source journal Cell Reports.

“Age-onset decline is very tightly linked to changes within the community of gut microbes,” said David Walker, a UCLA professor of integrative biology and physiology, and senior author of the research. “With age, the number of bacterial cells increase substantially and the composition of bacterial groups changes.”

The study used fruit flies in part because although their typical life span is just eight weeks, some live to the age equivalent of humans’ 80s and 90s, while others age and die much younger. In addition, scientists have identified all of the fruit fly’s genes and know how to switch individual ones on and off.

In a previous study, the UCLA researchers discovered that five or six days before flies died, their intestinal tracts became more permeable and started leaking.

In the latest research, which analyzed more than 10,000 female flies, the scientists found that they were able to detect bacterial changes in the intestine before the leaking began. As part of the study, some fruit flies were given antibiotics that significantly reduce bacterial levels in the intestine; the study found that the antibiotics prevented the age-related increase in bacteria levels and improved intestinal function during aging.

The biologists also showed that reducing bacterial levels in old flies can significantly prolong their life span.

“When we prevented the changes in the intestinal microbiota that were linked to the flies’ imminent death by feeding them antibiotics, we dramatically extended their lives and improved their health,” Walker said. (Microbiota are the bacteria and other microorganisms that are abundant in humans, other mammals, fruit flies and many other animals.)

Flies with leaky intestines that were given antibiotics lived an average of 20 days after the leaking began—a substantial part of the animal’s life span. On average, flies with leaky intestines that did not receive antibiotics died within a week.

The intestine acts as a barrier to protect our organs and tissue from environmental damage.

“The health of the intestine—in particular the maintenance of the barrier protecting the rest of the body from the contents of the gut—is very important and might break down with aging,” said Rebecca Clark, the study’s lead author. Clark was a UCLA postdoctoral scholar when the research was conducted and is now a lecturer at England’s Durham University.

The biologists collaborated with William Ja, an assistant professor at Florida’s Scripps Research Institute, and Ryuichi Yamada, a postdoctoral research associate in Ja’s laboratory, to produce an additional group of flies that were completely germ-free, with no intestinal microbes. Those flies showed a very dramatic delay in intestinal damage, and they lived for about 80 days, approximately one-and-a-half times as long as the animal’s typical life span.

Scientists have recently begun to connect a wide variety of diseases, including diabetes and Parkinson’s, among many others, to changes in the microbiota, but they do not yet know exactly what healthy microbiota look like.

“One of the big questions in the biology of aging relates to the large variation in how we age and how long we live,” said Walker, who added that scientific interest in intestinal microbes has exploded in the last five years.

When a fruit fly’s intestine begins to leak, its immune response increases substantially and chronically throughout its body. Chronic immune activation is linked with age-related diseases in people as well, Walker said.

Walker said that the study could lead to realistic ways for scientists to intervene in the aging process and delay the onset of Parkinson’s disease, Alzheimer’s disease, cancer, stroke, cardiovascular disease, diabetes and other diseases of aging—although such progress could take many years, he said.

Among New York Subway’s Millions of Riders, a Study Finds Many Mystery Microbes

On By A.P.In Kebmodee, Medicine, microbiology, Nature, ScienceLeave a comment

Have you ever been on the subway and seen something that you did not quite recognize, something mysteriously unidentifiable?

Well, there is a good chance scientists do not know what it is either.

Researchers at Weill Cornell Medical College released a study on Thursday that mapped DNA found in New York’s subway system — a crowded, largely subterranean behemoth that carries 5.5 million riders on an average weekday, and is filled with hundreds of species of bacteria (mostly harmless), the occasional spot of bubonic plague, and a universe of enigmas. Almost half of the DNA found on the system’s surfaces did not match any known organism and just 0.2 percent matched the human genome.

“People don’t look at a subway pole and think, ‘It’s teeming with life,’ ” said Dr. Christopher E. Mason, a geneticist at Weill Cornell Medical College and the lead author of the study. “After this study, they may. But I want them to think of it the same way you’d look at a rain forest, and be almost in awe and wonder, effectively, that there are all these species present — and that you’ve been healthy all along.”

Dr. Mason said the inspiration for the study struck about four years ago when he was dropping off his daughter at day care. He watched her explore her new surroundings by happily popping objects into her mouth. As is the custom among tiny children, friendships were made on the floor, by passing back and forth toys that made their way from one mouth to the next.

“I couldn’t help thinking, ‘How much is being transferred, and on which kinds of things?’ ” Dr. Mason said. So he considered a place where adults can get a little too close to each other, the subway.

Thus was the project, called PathoMap, born. Over the past 17 months, a team mainly composed of medical students, graduate students and volunteers fanned out across the city, using nylon swabs to collect DNA, in triplicate, from surfaces that included wooden benches, stairway handrails, seats, doors, poles and turnstiles.

In addition to the wealth of mystery DNA — which was not unexpected given that only a few thousand of the world’s genomes have been fully mapped — the study’s other findings reflected New York’s famed diversity, both human and microbial.

The Bronx was found to be the most diverse borough in terms of microbial species. Brooklyn claimed second place, followed by Manhattan, Queens and Staten Island, where researchers took samples on the Staten Island Railway.

On the human front, Dr. Mason said that, in some cases, the DNA that was found in some subway stations tended to match the neighborhood’s demographic profile. An area with a high concentration of Hispanic residents near Chinatown in Manhattan, for example, yielded a large amount of Hispanic and Asian genes.

In an area of Brooklyn to the south of Prospect Park that roughly encompassed the Kensington and Windsor Terrace neighborhoods, the DNA gathered frequently read as British, Tuscan, and Finnish, three groups not generally associated with the borough. Dr. Mason had an explanation for the finding: Scientists have not yet compiled a reliable database of Irish genes, so the many people of Irish descent who live in the area could be the source of DNA known to be shared with other European groups. The study produced some less appetizing news. Live, antibiotic-resistant bacteria were discovered in 27 percent of the collected samples, though among all the bacteria, only 12 percent could be associated with disease. Researchers also found three samples associated with bubonic plague and two with DNA fragments of anthrax, though they noted that none of those samples showed evidence of being alive, and that neither disease had been diagnosed in New York for some time. The presence of anthrax, Dr. Mason said, “is consistent with the many documented cases of anthrax in livestock in New York State and the East Coast broadly.”

The purpose of the study was not simply to satisfy scientific curiosity, the authors said. By cataloging species now, researchers can compare them against samples taken in the future to determine whether certain diseases, or even substances used as bioterrorism weapons, had spread.

City and transit officials did not sound grateful for the examination.

“As the study clearly indicates, microbes were found at levels that pose absolutely no danger to human life and health,” Kevin Ortiz, a spokesman for the Metropolitan Transportation Authority, said in an email. And the city’s health department called the study “deeply flawed” and misleading.

Dr. Mason responded by saying he and his team had simply presented their complete results.

“For us to not report the fragments of anthrax and plague in the context of a full analysis would have been irresponsible,” he said. “Our findings indicate a normal, healthy microbiome, and we welcome others to review the publicly available data and run the same analysis.”

Thanks to Kebmodee for bringing this to the attention of the It’s Interesting community.