Tag Archives: microbes

Your microbiota will be having non-stop sex this Valentine’s Day

Even if you’re alone this Valentine’s Day, there’s no need to worry: some parts of your body will be getting plenty of action. In fact, your body will host a veritable carnival of the sensual in your tummy, as your microbiota will engage in an orgy of sex and swinger’s parties — where they’ll be swapping genes instead of keys.

A medical illustration of drug-resistant, Neisseria gonorrhoeae bacteria. Original image sourced from US Government department: Public Health Image Library, Centers for Disease Control and Prevention. Image in the public domain.

The salacious gene

Imagine you have a severe disease with a very unusual cure: you can treat by making love with someone who then passes on the necessary genes to cure your ailment. It is, as they say, sexual healing. Using sex to protect or heal themselves is precisely what bacteria can do, and it’s a crucial defense mechanism.

In the past, the research community thought bacterial sex (or conjugation, as scientists call it) was a terrible threat for humans, as this ancient process can spread DNA capable of conveying antibiotic resistance to their neighbors. Antibiotic resistance is one of the most pressing health challenges the world is facing, being projected to cause 10 million deaths a year by 2050.

But there’s more to this bacterial sex than meets the eye. Recently, scientists from the University of Illinois at Urbana-Champaign and the University of California Riverside witnessed gut microbes sharing the ability to acquire a life-saving nutrient with one another through bacterial sex. UCR microbiologist and study lead Patrick Degnan says:

“We’re excited about this study because it shows that this process isn’t only for antibiotic resistance. The horizontal gene exchange among microbes is likely used for anything that increases their ability to survive, including sharing vitamin B12.”

For well over 200-years, researchers have known that bacteria reproduce using fission, where one cell halves to produce two genetically identical daughter cells. However, in 1946, Joshua Lederberg and Edward Tatum discovered bacteria could exchange genes through conjugation, an entirely separate act from reproduction.

Conjugation occurs when a donor and a recipient bacteria sidle up to each other, upon which the donor creates a tube, called a pilus that attaches to the recipient and pulls the two cells together. A small parcel of DNA is then passed from the donor to the recipient, providing new genetic information through horizontal transfer.

Ironically, it wasn’t until Lederberg met and fell in love with his wife, Esther Lederberg, that they made progress regarding bacterial sex.

Widely acknowledged as a pioneer of bacterial genetics, Esther still struggled for recognition despite identifying the horizontal transfer of antibiotic resistance and viruses, which kill bacteria known as bacteriophages. She discovered these phages after noticing small objects nibbling at the edges of her bacterial colonies. Going downstream to find out how they got there, she found these viral interlopers hiding dormant amongst bacterial chromosomes after being transferred by microbes during sex.

Later work found that environmental stresses such as illness activated these viruses to replicate within their hosts and kill them. Still, scientists assumed that bacterial sex was purely a defense mechanism.

Esther Ledeberg in her Stanford lab. Image credits: Esther Lederberg.

Promiscuity means longevity

The newly-published study builds on Esther’s work. The study authors felt this bacterial process extended beyond antibiotic resistance. So they started by investigating how vitamin B12 was getting into gut microbial cells, where the cells had previously been unable to extract this vitamin from their environment — which was puzzling as, without vitamin B12, most types of living cells cannot function. Therefore, many questions remained about how these organisms survived without the machinery to extract this resource from the intestine.

The new study in Cell Reports uses the Bacteroidetes species, which comprise up to 80% of the human microbiome in the intestines, where they break down complex carbohydrates for energy.

“The big, long molecules from sweet potatoes, beans, whole grains, and vegetables would pass through our bodies entirely without these bacteria. They break those down so we can get energy from them,” the team explained.

This bacteria was placed in lab dishes mixing those that could extract B12 from the stomach with some that couldn’t. The team then watched in awe while the bacteria formed their sex pilus to transfer genes enabling the extraction of B12. After the experiment, researchers examined the total genetic material of the recipient microbe and found it had incorporated an extra band of DNA from the donor.

Among living mice, something similar happens. When the group-administered two different subgroups of Bacteroidetes to a mouse – one that possessed the genes for transferring B12 and another that didn’t — they found the genes had ‘jumped’ to the receiving donee after five to nine days.

“In a given organism, we can see bands of DNA that are like fingerprints. The recipients of the B12 transporters had an extra band showing the new DNA they got from a donor,” Degnan said.

Remarkably, the team also noted that different species of phages were also transferred during conjugation, exhibiting bacterial subgroup specificity in some cases. These viruses also showed the capacity to alter the genomic sequence of its bacterial host, with the power to promote or demote the life of its microbic vessel when activated.

Sexual activity in our intestines keeps us healthy

Interestingly, the authors note they could not observe conjugation in all subgroups of the Bacteroidetes species, suggesting this could be due to growth factors in the intestine or a possible subgroup barrier within this large species group slowing the process down.

Despite this, Degnan states, “We’re excited about this study because it shows that this process isn’t only for antibiotic resistance.” And that “The horizontal gene exchange among microbes is likely used for anything that increases their ability to survive, including sharing [genes for the transport of] vitamin B12.”

Meaning that bacterial sex doesn’t just occur when microbes are under attack; it happens all the time. And it’s probably part of what keeps the microbiome and, by extension, ourselves fit and healthy.

Different cities have their own microbial fingerprint, a global study reports

An international team of researchers says that every city has its own fingerprint — in the shape of pathogens.

Prague.
Image credits Denis Poltoradnev.

The largest ever genetic study of urban microbiomes (including both surfaces and the air in 60 cities worldwide) reports that each city has its own microbial fingerprint. The project sequenced and analyzed samples from public transit systems and hospitals in cities around the world, identifying thousands of viruses, bacteria, and two archaea not found in reference databases.

Roughly 4,730 different samples, taken from cities on six continents over the course of three years were used as part of this study, the team explains. The analysis also revealed a set of 31 species that were found in 97% of the samples.

Microunique

“Every city has its own ‘molecular echo’ of the microbes that define it,” says senior author Christopher Mason, a professor at Weill Cornell Medicine (WCM) and the director of the WorldQuant Initiative for Quantitative Prediction.

“If you gave me your shoe, I could tell you with about 90% accuracy the city in the world from which you came.”

This study is the first systematic, worldwide catalog of urban microbial ecosystems, according to the authors. Despite the breadth of the results here, the team is confident that any subsequent sampling of this kind will continue to find new species.

The paper draws its roots in 2013, when Mason started collecting and analyzing microbial samples in the New York City subway system. After publishing his findings, Mason was contacted by other researchers from around the world who wanted to perform similar analyses in their own cities. So he worked out a protocol that they could follow, posting it on YouTube. Samples were to be collected using DNA- and RNA-free swabs and sent to a lab at WCM for analysis along with controls. Most of the analysis part was handled by an Extreme Science and Engineering Discovery Environment (XSEDE) supercomputer in Pittsburgh.

Two years later, in 2015, Mason created the International MetaSUB (Metagenomics and Metadesign of Subways and Urban Biomes) Consortium to better handle all the data people were sending him. Samples from air, water, and sewage were now coming in from across the world in addition to those from hard surfaces.

Such genomic studies can help detect outbreaks of both known and unknown infections and can help us keep tabs on the levels of antibiotic-resistant microbes in different urban environments. It’s also a very useful tool when analyzing the evolution of microbial life.

“There are millions of species on Earth, but we have a complete, solid genome reference for only 100,000 to 200,000 at this point,” Mason says, explaining that the discovery of new species can help with the building of microbial family trees to see how different species are related to one another.

“Based on the sequence data that we’ve collected so far, we’ve already found more than 800,000 new CRISPR arrays,” he says. Additionally, the findings indicate the presence of new antibiotics and small molecules annotated from biosynthetic gene clusters (BGCs) that have promise for drug development.

These samples led to the results published in this paper: 4,246 known species of microorganisms were identified worldwide, 31 of which were present in 97% of all samples from urban areas.

“One of the next steps is to synthesize and validate some of these molecules and predicted  biosynthetic gene clusters (BGCs), and then see what they do medically or therapeutically,” Mason says. “People often think a rainforest is a bounty of biodiversity and new molecules for therapies, but the same is true of a subway railing or bench.”

The paper “”A global metagenomic map of urban microbiomes and antimicrobial resistance” has been published in the journal Cell.

Microbial earthly life could survive on Mars, at least for a time

In a new study, NASA and German Aerospace Center scientists found that Earth microbes can withstand Martian conditions, which means we could use them there, but they could also pose risks for astronauts.

Sturdy microbes

You’re never really alone. You’ve got a gazillion tiny critters on yourself at any given moment. Most are harmless. Some can be useful — and of course, some can be harmful.

Try as we might (and space agencies do try), there’s no realistic way to eliminate all microbes from a crewed mission. Even with all the available decontamination procedures, you can’t really kick all off them from everywhere. If (or perhaps when?) we fly astronauts to Mars, the mission will bring some microbes along, like it or not.

Some have suspected that this wouldn’t matter at all, because the microbes just wouldn’t be able to survive on Mars. But a new study says otherwise.

“We successfully tested a new way of exposing bacteria and fungi to Mars-like conditions by using a scientific balloon to fly our experimental equipment up to Earth’s stratosphere,” reports Marta Filipa Cortesão, joint first author of this study from the German Aerospace Center, Cologne, Germany. “Some microbes, in particular spores from the black mold fungus, were able to survive the trip, even when exposed to very high UV radiation.”

The endurance of microbes and their ability to withstand Martian conditions is important for any human Mars mission. For one, they could be dangerous for astronauts, or confuse them — finding life forms on Mars would be exciting, but not if you’ve brought them yourself from Earth. But microbes could also help a potential research station or colony, helping with things like making water or fuel.

“With crewed long-term missions to Mars, we need to know how human-associated microorganisms would survive on the Red Planet, as some may pose a health risk to astronauts,” says joint first author Katharina Siems, also based at the German Aerospace Center. “In addition, some microbes could be invaluable for space exploration. They could help us produce food and material supplies independently from Earth, which will be crucial when far away from home.”

Mars, on Earth

Quartz disc with dried Aspergillus niger spores, before being placed in the aluminum sample carriers that went on the Trex-box. Image credits: German Aerospace Center (DLR).

To find out whether microbes could survive on Mars, researchers sent them into the stratosphere on a balloon mission. There, the microbes were kept at Martian pressure and in a specially-prepared artificial Martian-mimicking atmosphere.

“The box carried two sample layers, with the bottom layer shielded from radiation. This allowed us to separate the effects of radiation from the other tested conditions: desiccation, atmosphere, and temperature fluctuation during the flight. The top layer samples were exposed to more than a thousand times more UV radiation than levels that can cause sunburn on our skin.”

Not all the microorganisms made it back, but some did, like the black mold Aspergillus niger, for instance. Aspergillus niger is less likely to cause human disease than some other Aspergillus species. However, many useful enzymes are produced using the industrial fermentation of the mold.

Next, researchers have to build a larger catalog of what microbes might survive the trip to Mars and use the information to prepare accordingly for future Mars missions.

“Microorganisms are closely-connected to us; our body, our food, our environment, so it is impossible to rule them out of space travel. Using good analogies for the Martian environment, such as the MARSBOx balloon mission to the stratosphere, is a really important way to help us explore all the implications of space travel on microbial life and how we can drive this knowledge towards amazing space discoveries.”

The study has been published in Frontiers.

Wildfire smoke can carry microbes that cause infectious diseases, researchers find

Breathing wildfire smoke, even in low amounts, means you’re exposed to noxious gases, plant material, and incinerated synthesis materials. It’s bad enough, especially for those with respiratory conditions. But there’s more: the haze can also be loaded by microbes, a new study showed.

Image credit: Flickr / BLMidaho

Wildfires over the past 3 years have resulted in lengthy episodes of smoke inundation across major metropolitan areas in Australia, Brazil, and the United States. In 2020, air quality across the western United States reached and sustained extremely unhealthy to hazardous levels for successive weeks from August through November.

Although the pulmonary and cardiovascular consequences of human exposure to smoke particulate matter are extensively researched, there remains little recognition or monitoring of microbes, a smoke component with potentially important health repercussions that has only just started to be studied.

That’s why a pair of researchers, Leda Kobziar and George Thomson, published a perspective piece, calling for a multidisciplinary approach from fire ecology to epidemiology to better characterize these microbes and determine how they might be making wildfire smoke even worse for human health.

“It’s not just comprised of particulate matter and gases, but it also has a significant living component in it,” Kobziar told Wired. “Wildfire smoke may actually spread beneficial organisms for an ecosystem but what might the consequences be for the spread of pathogens that we know are airborne?”

Wildfires are a source of bioaerosols, airborne particles made of fungal and bacterial cells and their metabolic byproducts. Once they are in the air, these small particles can travel hundreds or even thousands of miles. The extent will depend on the fire behavior and atmospheric conditions, eventually being deposited or inhaled.

But shouldn’t the microbes get burned in the flames? Not necessarily, the researchers argue. Wildfires burn at different intensities at different spots as they move around. This means complete combustion happens simultaneously with incomplete combustion, leaving lots of pockets in which microbes can survive the blaze.

Instead of dying, microbes can be transported in wildfires smoke emissions. They are basically hitchhikers on charred carbon and water vapor. While microbial concentration in smoke is higher near the fire source, these microbes may be active agents spreading infection, the researchers argue in their piece.

“The diversity of microbes we have found so far in the very few studies that have been done is impressive,” said Kobziar in a statement. “These taxa (groups of living organisms) were not found in non-smoky air in the same locations prior to the fire, proving that combustion and its associated winds aerosolize microbes.”

For example, there’s the fungus genus Coccidioides, a species that lives in soil. If a fire disrupts a landscape, it affects the soil directly by burning it with flames but also indirectly, as the hot and rising air creates an atmospheric void near the surface. This can produce strong winds that move the earth, aerosolizing the fungi and altering the local microecosystem.

A firefighter can then inhale that air filled with microbes, which can create a condition known as coccidioidomycosis, or valley fever, with symptoms such as fever and shortness of breath. This can then progress to pneumonia or meningitis. Coccidioidomycosis is actually very common among firefighters.

This could easily get more severe. Wildfires are getting bigger because of climate change and researchers are reporting an increase in the number of people in the American West infected with mycoses. Fungal spores “can at as an allergen and initiate asthma,” Mary Prunicki, from Stanford University, told Wired.

Studies with hurricanes and storms had shown that microbes agents can travel very long distances, but no one was able to prove a similar journey for bacteria in a smoke plume. But the ability of smoke to travel around the world suggests that it could be a “missing link” in explaining some patterns of infection.

“When infections are detected in patients, the potential causal agents that are screened are based on what is known to be endemic in a given region,” said Kobziar. “However, smoke blurs the lines between regions.”

The perspective piece was published in Nature.

Could bacteria take up jobs mining in space? Turns out, they could

This year has certainly been all about microbes, and a new paper keeps this trend going — but not how you’d expect.

Sphingomonas desiccabilis growing on basalt rock.

Microbes can help extract economically-important materials from rocks in zero-gravity, a new paper reports. The findings showcase the potential of microscopic life in such applications even in space. They also point to the possibility of ‘biomining’ being used as a critical transition step before settling another planet.

The smallest miners

Rare earth elements are, as their name suggests, quite rare. But they’re also critical for high-tech applications due to their often-unique physical and chemical properties. Due to their rarity, such elements are very challenging and expensive to mine and refine, and we’re limited in how much we can produce. Demand for such materials will soon outstrip supply. One solution, however, may lie just above the skies.

Having the ability to identify and isolate rare earth elements will be extremely important for humanity as we seek to expand to other worlds — bonus points if we can do it easily and cheaply. Microbes are already used in this role on Earth, and the new study reveals that they can work just as well in low- or zero-gravity conditions.

The team worked with three species of bacteria (Sphingomonas desiccabilis, Bacillus subtilis, and Cupriavidus metallidurans) in microgravity conditions that simulated the environment aboard the ISS or that on Mars. They measured how efficiently these could leech 14 rare earth elements from basalt rocks, which are very similar to those on the surface of the Moon and Mars. Trials on Earth were carried out in parallel with these experiments to give the team a control group in normal gravity conditions.

All in all, S. desiccabilis successfully extracted the elements from rocks in all three gravity conditions. It was quite effective across all conditions and showed the highest extraction efficiency (around 70%) of all the bacteria tested with the elements Cerium and Neodymium. The other two species were either less effective in low gravity conditions (compared to normal gravity), or were completely unable to perform the task.

The findings suggest that not all the species we use for mining here on Earth would function well, or at all, in other gravity conditions. However, they also clearly show that some of these species would. Identifying which ones these are will be a species-by-species process, but it would definitely pay off in the long term.

That being said, the idea of carrying microorganisms from Earth to another planet is quite a philosophical can of worms. While it may definitely help us extract the things we need from deposits far away, such a step risks fundamentally altering (or replacing) a celestial body’s biosphere.

The paper “Space station biomining experiment demonstrates rare earth element extraction in microgravity and Mars gravity” has been published in the journal Nature Communications.

Scientists find evidence of ocean crust microbes living beneath the seafloor

Microbiologist Ginny Edgcomb (left) and Gaëtan Burgaud cultured fungal colonies from rock samples deep within the seafloor. Credit: Tom Kleindinst, © Woods Hole Oceanographic Institution.

Scientists have found evidence of active microbial communities living in the oceanic crust hundreds of meters beneath the seafloor, proving that life can find a way under even the most extreme and remote conditions.

Rock cores drilled from an undersea mountain in the Indian Ocean revealed that bacteria, fungi, and single-celled organisms called archaea live in cracks and fissures in the dense rock of the ocean’s lower crust. The scientists discovered that the rock samples contained biosignatures of life, including DNA and lipid biomarkers, and messenger RNA extractions showed that some of the cells were actively dividing.

Beneath the soft sediments of the seafloor sit layers of basaltic and gabbro rocks that make up the oceanic crust. Scientists know that life exists in seafloor sediments, but only one previous study in the Atlantic Ocean probed the oceanic crust for signs of life. In the latest research, scientists recovered rock from 750 meters into the lower crust and performed a host of laboratory tests in search of microbial activity.

Beneath the soft sediments of the seafloor sit layers of basaltic and gabbro rocks that make up the oceanic crust. Scientists know that life exists in seafloor sediments, but only one previous study in the Atlantic Ocean probed the oceanic crust for signs of life. In the latest research, scientists recovered rock from 750 meters into the lower crust and performed a host of laboratory tests in search of microbial activity.

“These [communities] can basically be hanging out for millions of years in a very quiescent state,” study author and associate scientist Virginia Edgcomb, from Woods Hole Oceanographic Institution, said. “I’m sure even the active microbes are carrying on at a very slow rate relative to those near the surface, but nevertheless, they’re buzzing along.”

The latest research, published today in the journal Nature, suggests that survival in the deep biosphere depends on underground fluid flow. As seawater entrains deep in the crust, it travels through cracks in the rock, some microfine and others as large as, or even larger, than spaghetti noodles. The fluid likely carries organic matter from the ocean, said Edgcomb, and the team found signs of life clustered around these nutrient highways.

A thin section of the rock core shows distinct minerals (colored) and a small cavity where fluid may have flowed through, delivering organic matter that fuels subsurface microorganisms. Credit: Frieder Klein/WHO.

Many of the microorganisms match those observed in other extreme environments, like hydrothermal vents, said Edgcomb. But unlike what Edgcomb expected, the underground life relied on both fixing chemicals for energy and co-opting organic matter floating in the fluid. Messenger RNA analysis revealed that the microbes can recycle amino acids or lipids of dead (or even living) matter. Steven D’Hondt, a professor at the University of Rhode Island who was not involved with the research, said this “runs counter to standard assumptions about subseafloor crustal life.”

“The readiness of that community to consume organic matter suggests that it is metabolically linked to the broader world (e.g., the ocean) via ocean circulation,” D’Hondt said.

It’s unclear whether these results can apply to other areas of the ocean’s lower crust. The research team extracted cores from the undersea mountain Atlantis Bank where the lower crust is exposed at the ocean bottom, which is unusual—normally, thousands of meters of sediment would cover it. The site gave the research team unprecedented access to the lower crust, but future research must confirm whether life is possible with upper crust and bottom sediments still intact.

The latest study shows that “life finds a way,” said Jennifer Biddle, an associate professor at the University of Delaware who did not take part in the study. Earth’s lower oceanic crust could be an analogue to how life might survive on other planets, Biddle added.

Edgcomb cautions that the biomass in the study was extremely low: The cells are just “barely eking out a living,” she said. Still, “the lower ocean crust is one of the last frontiers of the exploration for life on Earth,” Edgcomb said. “We have a better understanding that the lower crust does indeed host viable and, in some cases, active microbial cells.”

—Jenessa Duncombe (@jrdscience), Staff Writer

This article was originally published on Eos Magazine and was republished under a CC BY-NC-ND 3.0 license.

Microbes discovered in the ocean’s crust rely on recycling to survive

Extreme and remote conditions don’t seem to be an impediment for microbe communities, according to a new study, which found some of them living in the crust of the ocean far beneath the seafloor and relying on recycling to survive.

A detailed look at the rocks. Credit Woods Hole Oceanographic Institution

Researchers found bacteria, fungi, and archaea (single-celled organisms) in rocks at about 700 meters below the bottom of the Indian Ocean. The finding was possible by looking at rock samples from the Atlantis Bank, a part of the seafloor where rock is exposed close to the surface.

The microbe communities were living in the cracks and fissures of the rock, according to researchers at the Woods Hole Oceanographic Institute. The rock samples had biosignatures of life such as DNA and lipid biomarkers, while messenger RNA extractions showed some cells were still active.

The fact that there’s life in seafloor sediments isn’t new, but only one study in 2010 had looked at the oceanic crust in the Atlantic Ocean for signs of life. Ocean crust covers nearly 70% of the earth’s surface and is made up mainly by the gabbroic layer. Gabbro is intrusive igneous rock.

“These [communities] can basically be hanging out for millions of years in a very quiescent state,” study author and associate scientist Virginia Edgcomb said in a statement. “I’m sure even the active microbes are carrying on at a very slow rate relative to those near the surface, but nevertheless, they’re buzzing along.”

The study claimed that the survival of the bacteria, fungi, and archaea relied on underground fluid flow. Seawater travels through the cracks in the rock, carrying organic matter down from the ocean. The researchers found signs of life in those currents of seawater.

At the same time, the study found a set of survival strategies used by the microorganisms. Some showed the ability to store carbon in their cells, while others were able to process nitrogen and sulfur to generate energy, recycle amino acids, and produce vitamins.

Steven D’Hondt, a professor at the University of Rhode Island who was not involved with the research, told EOS that this “runs counter to standard assumptions about subseafloor crustal life” and that “the readiness of that community to consume organic matter suggests that it is metabolically linked to the broader world.”

Whether the results can be applied to other areas of the ocean’s lower crust is still an open question. The study focused on the Atlantis Bank, where the lower crust is exposed at the ocean bottom, an unusual phenomenon. Future research will have to confirm whether life is possible with the upper crust and bottom sediments still intact.

The study was published in the journal Nature.

Sanitizing homes gets rids of bacteria but makes room for fungi

Researchers have found that using cleaning products is effective at eradicating bacteria. However, the downside is cleansing the home of bacteria makes room for other microbes, such as fungi.

The findings were reported by researchers at the University of Oklahoma, who compared the microbial diversity in rural and urban homes from Peru and Brazil. They took samples from four locations in increasingly urban settings: from huts in the rainforest to city apartments in Manaus, the capital and largest city of the Brazilian state of Amazonas.

Samples were taken off the walls, floors, and countertops of the homes, as well as skin swabs from pets and people.

As the researchers converged towards more urban homes, bacterial diversity decreased, including so-called ‘good’ bacteria, some of which live in our gut. Meanwhile, fungal diversity actually increased in urban homes. Among them are fungi from the Malassezia genus, which contains strains that are known to cause infections.

This is probably due to the cleaning solutions that specifically target bacteria. Fungi, which have thick cell walls, are much harder to kill than your run-off-the-mill bacteria. And since urban homes are such good insulators, trapping CO2 and blocking sunlight, they’re also hospitable environments for the fungi. These differences in bacteria and fungi were also found on the skin of humans, not just in their homes.

“Maybe they’re scrubbing away all the bacteria and now you have this big open surface for fungi to grow on; maybe [the fungi] are also becoming more resistant to the cleaning agents that we use,” Laura-Isobel McCall, a biochemist at the University of Oklahoma, told NPR.

Besides bacteria, fungi, and some parasites, the researchers also tested the chemicals found inside the apartments. They found many more synthetic chemicals inside urban homes than in rural ones, sourced from items such as building materials, medications, and personal care products. In other words, urban environments are extremely artificial compared to rural ones — and these findings likely aren’t limited to Peru and Brazil.

If anything, this study shows that our efforts to sanitize our homes may never be satisfying. When you throw out one kind of germs, you’re just making room for other germs to break in.

The findings appeared in the journal Nature Microbiology.

Molecules in mucus subdue microbes to make them harmless

More than 200 square meters of our bodies — including the digestive tract, lungs, and urinary tract — are lined with mucus. Far from being a gross waste product, this slippery secretion produced by, and covering, the mucous membranes serves an important physiological purpose.

It has been established that mucus is the body’s security bouncer physically trapping pathogens, toxins, and fine particles like dust and pollution. The cells of the immune system in the mucus then attack and neutralize the invading germs before they get the opportunity to spread throughout the body and cause infection. In some instances, mucus is coughed up or expelled – which is the body’s way of forcing the pathogens out of the body. Mucus also lubricates the eyes so they can blink and the throat so it can swallow. It also serves as a lubricant under the skin’s surface to help minimize friction between the organs.

New research at the Massachusetts Institute of Technology (MIT) and published in Nature Microbiology shows one of mucus’s unexpected beneficial properties: mucus contains sugars that can interfere with bacteria’s communication and behavior, effectively stopping the formation of dangerous, tough biofilms and making them harmless.

The research was funded by the National Institute of Biomedical Imaging and Bioengineering, the National Institutes of Health, the National Science Foundation, the National Institute of Environmental Health Sciences, and the MIT Deshpande Center for Technological Innovation.

Katharina Ribbeck and her colleagues study compounds called mucins in mucus. Mucins are long polymers, or molecular chains, densely studded with sugars. They “look like mini bottlebrushes,” Ribbeck said, except bristling with sugar molecules where whiskers would be.

“What we have in mucus is a therapeutic gold mine,” said Ribbeck, the Mark Hyman, Jr. Career Development Professor of Biological Engineering at MIT. “These glycans have biological functions that are very broad and sophisticated. They have the ability to regulate how microbes behave and really tune their identity.”

Ribbeck and others have shown that mucus can stop microbes from binding to surfaces. Researchers focused on how glycans were interacting with an opportunistic microbial pathogen called Pseudomonas aeruginosa, the bacterium commonly causing serious infections in people with weak immune systems and cystic fibrosis patients.

They found that when bacteria were exposed to glycans isolated from mucus, they were disarmed; the microbes stopped attaching to or killing host cells, halted production of toxic molecules, and microbial genes that are involved in bacterial communications weren’t expressing. The new study is the first to “identify that the glycan component” — that is, the sugars grafted to the mucins — “is responsible for suppressing antagonistic microbial behaviors.”

They now plan to study the impact of individual glycans out of hundreds that can be found in mucus. They also want to investigate how glycans affect other kinds of pathogens like Candida albicans and Streptococcus bacteria. They already know that glycans can stop Streptococcus from sharing genes, a primary way that drug resistance spreads among microbes.

“What we find here is that nature has evolved the ability to disarm difficult microbes, instead of killing them. This would not only help limit selective pressure for developing resistance, because they are not under pressure to find ways to survive, but it should also help create and maintain a diverse microbiome,” Ribbeck says.

Scientists, including Ribbeck, are also looking into the development of artificial mucus, which might be a new approach to fighting pathogens that does not involve traditional antibiotic drugs.

“Farm air” can protect children from asthma

Your grandma was probably right: rural, farm-like air is better for your health, at least asthma-wise. The key? Microbes.

Farm air might ward off asthma, the new study reports.

In recent years, the incidence of asthma in children has been increasing. Although the causes are not exactly clear, the phenomenon has been linked with urbanization, and particularly the lack of certain microbes. The relationship between the microbial world and asthma is not well understood, but there does seem to be a connection between the two. Researchers also figured out something strange: children on farms don’t really get asthma. Now, they’re starting to understand why this is happening.

Previous research has suggested that exposure to rural house dust can reduce the incidence of asthma, although it’s not exactly clear what particular species of the microbiota contribute to this.

Researchers from Finland led by Pirkka Kirjavainen studied the indoor dust microbiota from the rural and suburban homes of 395 Finnish children. They discovered a very distinct pattern associated with farm homes — a pattern which was not present in urban areas.

“The microbial composition in farm homes was clearly distinct from that in non-farm homes,” the researchers write.

The lower incidence of asthma in rural areas is well known, but the team wanted to see if this can be traced to or compared with the microbiota. So they replicated the microbe patterns found in farms and applied it to the homes of 1,031 German children, showing a reduced risk of asthma in children living in non-farm homes where the microbiota resembled that of the Finnish farm homes. This strongly supports the idea that the microbes themselves were providing the asthma-protective effect.

“The indoor dust microbiota composition appears to be a definable, reproducible predictor of asthma risk and a potential modifiable target for asthma prevention,” the team continues.

It may seem counterintuitive that microbes have a protective effect, but by this point, it’s not exactly surprising. Although there are some substantial knowledge gaps on this issue, it’s become increasingly clear that the microbiota plays a much more important role than we thought, affecting our bodies in a number of ways. Since the dawn of our species, humans have adapted to live in rich microbial communities, and urbanization is changing that faster than the microbiota can adapt.

This isn’t the first study to find that farm air wards asthma. Future research will attempt to better define the species responsible for this phenomenon and better study how their protective effect can be replicated to reduce the asthma risk for children.

Molehill.

Researchers, at long last, develop effective tool to study soil-borne microbes

Novel research is allowing us to see what different microbes in the soil are up to.

Molehill.

Image via Pixabay.

Researchers from the Department of Energy’s Lawrence Berkeley National Laboratory (Berkeley Lab) report being the first to successfully isolate active microbes from a soil sample. These germs underpin life on Earth today, so the research has the potential to branch out into many other fields including ecosystem science, environmental rehabilitation, and agriculture.

Soil searching

Soils are probably the most diverse microbial communities on the planet,” said Estelle Couradeau, first author of the study. “In every gram of soil, there are billions of cells from tens of thousands of species that, all together, perform important Earth nutrient cycles. They are the backbone of terrestrial ecosystems, and healthy soil microbiomes are key to sustainable agriculture.”

“We now have the tools to see who these species are, but we don’t yet know how they do what they do. This proof-of-concept study shows that BONCAT is an effective tool that we could use to link active microbes to environmental processes.”

For the past two years, Couradeau and her co-authors have been collaborating with other researchers in a Berkeley Lab-led scientific focus area called ENIGMA (Ecosystems and Networks Integrated with Genes and Molecular Assemblies) to better understand soil microbiomes. ENIGMA’s projects are of great interest to researchers in the field of biology, energy, and Earth sciences.

Soil microbes are hard to study because they won’t grow in lab cultures, and because they come in an extremely wide palette in natural habitats. Many of these microbes as much as 95% at a time, according to the team can also lie inactive at any given time, further complicating efforts to tie their activity to observed effects. Because of this, researchers usually study such microbes by collecting samples and then sequencing bulk DNA to determine which strains are present therein. However, most of the commonly used techniques can’t differentiate active microbes from those that are dormant or from free-floating bits of DNA found in soil and sediment.

Sleeper cells

“There are many barriers to measuring microbial activities and interactions,” said Trent Northen, lead author and director of biotechnology for ENIGMA

Enter BONCAT (Bioorthogonal Non-Canonical Amino Acid Tagging), a microbial sorting tool that allows researchers to tell apart active vs inactive microbes in a sample. Northen’s team is the first one to successfully use this technique on a sample of soil, and they hope the research will help us understand how soil microbiomes affect large-scale environmental events. BONCAT was developed by Caltech geneticists in 2006 as a way to isolate newly made proteins in cells, and was later adapted into a tool that could identify active, symbiotic clusters of dozens to hundreds of microbes within ocean sediment. Further refinement of this method led to the development of BONCAT Fluorescent Activated Cell Sorting (BONCAT+FACS), which is able to detect individual active microbes.

With BONCAT+FACS, researchers sort through single-celled organisms using a fluorescent tagging molecule, which binds to a modified version of methionine (an amino acid). A fluid solution containing the modified methionine is introduced to a sample of microbes, and those that are active — i.e. that are synthesizing proteins — will incorporate the modified methionine into their structures. The process is much more streamlined and reliable than previous microbial identification methods, and only takes a few hours to perform (which means it can tag active cells even when they are not replicating).

The team spent three months tweaking and optimizing the technique, which resulted in a protocol that can smoothly and reliably identify active microbes in a sample — “most importantly”, according to a press release accompanying the study, the technique “gives very reproducible results”.

“BONCAT+FACS is a powerful tool that provides a more refined method to determine which microbes are active in a community at any particular time,” said  Rex Malmstrom, co-author of the study who previously worked on refining BONCAT for marine use.

“It also opens the door for us to experiment, to assess which cells are active under condition A and which cells become active or inactive when switched to condition B.”

“With BONCAT, we will be able to get immediate snapshots of how microbiomes react to both normal habitat fluctuations and extreme climate events—such as drought and flood—that are becoming more and more frequent,” said Northen.

BONCAT+FACS will be available through the user programs set up by the Department of Energy’s Joint Genome Institute (JGI), the authors write. They hope to promote research in other lines of study, among which they cite assessing antibiotic susceptibility in unculturable microbes and investigating the completely unknown roles of Candidatus Dormibacteraeota, a phylum of soil bacteria, found across the world, that appear to remain dormant most of the time. The technique will also help fill in the gaps of our understanding of environmental functions and point the way for new research into drought-resistance in crops, the sustainable production of fuel and other bioproducts, environmental rehabilitation, and many others.

The paper “Probing the active fraction of soil microbiomes using BONCAT-FACS” has been published in the journal Nature.

Antibiotics.

Study proposes five new rules to prevent antibiotic resistance “disaster”

Efforts to fight antibiotic resistance aren’t “nearly radical enough” today, according to a new study.

Antibiotics.

Image credits Emilian Danaila.

Relying too much on reducing antibiotic use and implementing new drugs could lead to “disaster”, says Dr. Ben Raymond, of the University of Exeter. In a new study, Dr. Raymond proposes five rules for the “sustainable use” of antibiotics which would help us maintain the efficiency of this class of drugs and prevent antibiotic resistance from becoming a deadly problem.

Resistance fighters

“People think the best way to tackle antibiotic resistance is to give out fewer antibiotics and find new drugs. Those are important steps, but this approach alone is not nearly radical enough,” says Dr. Raymond, of the Centre for Ecology and Conversation on the University of Exeter’s Penryn Campus in Cornwall.

“Even if we can keep finding new drugs, disaster will follow if we use them in the same way as we use current ones. No drug yet discovered is evolution proof, and the typical practice of using single drugs at once, in unprotected ‘monotherapies’ is unsustainable.”

What he proposes instead is a multi-pronged approach intended to prevent what the World Health Organisation calls “a post-antibiotic era in which common infections and minor injuries can once again kill.” The measures include taking steps to protect new drugs before resistance becomes a problem, diversifying the range of antimicrobials currently in use to avoid relying too much on a handful of drugs (which also speeds up the evolution of resistance for those drugs), and using data to design management plans for particular superbugs.

“This ‘business as usual’ approach can be disastrous, as exemplified by the history of resistance in gonorrhoea and the emergence of untreatable infections,” Dr. Raymond explains. “Resistance to new antibiotics can become widespread in two or three years, so new drugs must be partnered with more sustainable patterns of use.”

The five ‘rules’ outlined in the study are:

  1. Prevention. Echoing the old adage, Dr. Raymond wisely notes that “resistance is easier to deal with before it becomes severe.” Avoiding heavy use of single drugs for extended periods of time creates less evolutionary pressure for its active compound (i.e. bugs have less need and opportunities opportunity to develop resistance to a particular compound, as they don’t see it that frequently).
  2. Don’t rely on “fitness costs.” Some approaches call for break periods in the use of a particular drug, in the hope that bacteria resistant to it will die off to their competition because they carry resistance genes that are no longer useful (i.e. genetic dead weight.) While the idea behind the approach can work, resistance to a drug does not necessarily vanish because of an interruption in the use of a drug.
  3. Limit bacteria’s ability to mutate drug-resistance genes. One approach is to use antibiotic cocktails, as microbes rarely develop resistance to multiple antibiotics at once. Slowly building a massive reservoir of antibiotic-resistance genes in the wild is “madness” according to Dr. Raymond. Traces of antibiotics in wastewater, or the use of antibiotics in livestock farming, are doing exactly that. “As an individual you are very unlikely to have acquired an antibiotic resistant microbe from an animal, but it’s highly likely that environmental contamination has helped some of the microbes in your body acquire resistance,” he says.
  4. Low doses don’t work, but short courses might. A greater pool of mutations can give microbes the chance to resist low doses of antibiotics, so lowering the dose doesn’t prevent resistance from evolving. However a shorter, more intense course of treatment might benefit patients without giving the bugs a chance to evolve, he says.
  5. Know your enemy. “If you don’t know what kind of resistance is around among patients or in your hospital, you could give people the wrong drug at the wrong time,” he says. “The more data you have, the better you can design your resistance management programmes. Resistance management programmes should target specific microbes or groups of microbes, rather than resistance in general.”

“Some humility in the face of natural selection can ensure that human creativity keeps pace with evolutionary innovation,” he adds, noting that other disciplines have a broader knowledge of resistance management, but that their input is “not widely appreciated” among microbiologists.

The paper “Five rules for resistance management in the antibiotic apocalypse, a road map for integrated microbial management” has been published in the journal Evolutionary Applications.

Seafloor Alvin Image.

New deep-water microbes have the skills to help fight climate change

Newly-discovered deep-water microbes could help us clean CO2 out of the air.

Seafloor Alvin Image.

View of the seafloor.
Image credits Brett Baker / University of Texas at Austin.

A bunch of microbes collected at around 2,000 metres (6,562 feet) below the surface of the surface of the Gulf of California might have a strong appetite for pollutants — including CO2 and crude oil. The team describing these organisms hopes they can be used to lessen our environmental footprint.

Tiny helpers

“This [discovery] shows the deep oceans contain expansive unexplored biodiversity, and microscopic organisms there are capable of degrading oil and other harmful chemicals,” says lead researcher and marine scientist Brett Baker from the University of Texas at Austin.

The microbes live under water in very harsh conditions. Besides sheer pressure, they also have to endure temperatures of around 200 degrees Celsius (392 degrees Fahrenheit) generated by subterranean vulcanic activity.

With this in mind, the wealth of microbes the team recovered is really impressive. A total of 551 separate genomes were identified in the samples — including 22 that had never been recorded before. Better yet, the bugs were observed chowing down on hydrocarbons (such as methane and butane) for their meals.

“Beneath the ocean floor huge reservoirs of hydrocarbon gases – including methane, propane, butane and others – exist now, and these microbes prevent greenhouse gases from being released into the atmosphere,” Baker explains.

This makes their diet very unusual — and valuable. The microbes could help in cleaning up pollution in the future, if we can find a way to harness or copy their abilities. Another very surprising discovery is how genetically different these organisms are from anything we’ve ever seen before. The 22 newly-discovered species are so unique that they could require us ‘adding’ a new branch on the tree of life.

The findings are still new, and more work will be needed to determine where these lifeforms fit into the larger picture, as well as any of their potential uses.

“The tree of life is something that people have been trying to understand since Darwin came up with the concept over 150 years ago, and it’s still this moving target at the moment,” says Barker.

Recent improvements in DNA sequencing and computer software technology, however, are helping clear the picture. The microbes discovered in this study can improve our understanding of biology as well as – potentially – keep a lid on pollutants in the environment.

Also notable is the craft which collected the microbes — it was the Alvin submersible, the same vehicle that explored the wreck of the Titanic bank in 1986.

The paper “Expansive microbial metabolic versatility and biodiversity in dynamic Guaymas Basin hydrothermal sediments” has been published in the journal Nature Communications.

antimicrobial gloves

Researchers create the first antimicrobial medical examination gloves

antimicrobial gloves

Credit: Pixabay.

At an event in London, British researchers unveiled to the world the very first medical gloves designed to prevent the spread of infection. The team predicts that their product will be a game changer, selling in the billions in the coming years.

The gloves were developed by the UK-based antimicrobial R&D company Chemical Intelligence, with funding from Hartalega Malaysia, the largest producer of nitrile gloves in the world. Chemical Intelligence closely worked with Professor Richard James and Dr. Paul Wight, both at the University of Nottingham.

To ward off infection, the gloves contain an active microorganism-killing substance on their surface. The molecules are inserted into the glove’s material, meaning no additional application of an antimicrobial solution is required.

Tests suggest that 99.99% of any germs that came into contact with the gloves were killed within five minutes.

“These gloves will be a game-changer for the healthcare industry, both public and private. I am delighted that my lifetime’s research into bacteria and antibiotic resistance has directly informed the science behind a practical tool that will have a major impact on medical care in the future,” James said in a statement.

It’s estimated that in the EU alone, 37,000 pre-mature deaths can be attributed to cross-contamination in hospitals, costing the healthcare system 7 billion euros. The standard medical glove has remained virtually unchanged for the last 30 years but James and colleagues hope that their innovation will finally bring a much needed revamp and save many lives in the process across the globe.

It took six years and millions of dollars to develop the first non-leaching antimicrobial medical gloves in the world. According to the researchers, the gloves will be manufactured at a low cost in order to prevent access barriers.

“After years of development, we are delighted to finally release this product to market and truly believe it will make a significant difference in the fight against healthcare associated infections (HAIs). Like Hartalega, we have a passion for innovation and together we are the perfect partners to release this technology,” said RobGrossaid, the founder of Chemical Intelligence UK.

Also this year, American company GloDea introduced the market the very first antimicrobial gloves meant for the foodservice industry. These gloves provide a broad spectrum of antimicrobial performance against a wide range of microorganisms, including MRSA, Escherichia coli, Salmonella, Listeria, Pseudomonas, Candida, Corynebacterium, Klebsiella, etc.

Wort infection cross-section.

Plants learned how to fight microbes even before they moved to dry land

Early plants must’ve been really annoyed with microbes, new research suggests; the findings show that not only do plants’ adaptations against germs date back millions of years, but they’ve maintained these systems up to the present.

Wort infection cross-section.

Microscopy image of a cross-section of a Marchantia polymorpha thallus showing the Phytophthora infection (red) in the upper photosynthetic layer of the liverwort plant.
Image credits Philip Carella.

A team from the University of Cambridge looked to liverworts — a family that branched out from other land plants relatively early — to gain a better understanding of how early plants dealt with pathogens. According to the researchers, the interaction between the two started millions of years ago, at least as early as plants set root on dryland. That legacy persists to this day, keeping our green leafy friends safe from microbial pests.

Live, err, wort

“We know a great deal about microbial infections of modern flowering plants, but until now we haven’t known how distantly related plant lineages dealt with an invasion by an aggressive microbe,” says the paper’s first author Dr. Philip Carella.

“To test this, we first wanted to see if Phytophthora could infect and complete its life cycle in a liverwort.”

He is specifically referring to Phytophthora palmivora. As you, our attractive and perceptive readers might have already guessed, it belongs to the Phytophthora genus, which is a very fine example of convergent evolutionPhytophthora is strikingly similar to fungi in form and function, despite there being virtually no ties between two’s evolutionary history. That being said, Phytophthora uses different metabolic pathways (their ‘engines’ work differently), use cellular walls composed of cellulose (typically associated with plants) where fungi use chitin (more of an animal compound), and there are some significant differences in how they handle genetic material during reproduction. So in a way, they’re like fungi who are more in tune with their ‘plant’ side than their ‘animal’ side.

The other thing you need to know about Phytophthora is that these things have earned their name in spades — and, in ancient Greek, that name literally means “plant destroyer”. Phytophthora, you see, is a genus of impressively voracious, extremely damaging, plant-munching oomycetes (water molds). Phytophthora devastate crops, and have among other things caused the Irish potato famine. Phytophthora palmivora causes diseases in cocoa, oil palms, coconut palms, and rubber trees.

Papaya phytophthora blight.

Phytophthora blight on a papaya fruit.
Image credits Scot Nelson / Wikimedia.

Liverworts (which alongside mosses and hornworts form the phylum Bryophyta) are small, green plants — but they don’t have roots, stems, leaves, or flowers. They are thought to resemble ‘early plants’ because they diverged from all other plant lineages very early on. They’re still poorly understood and crassly under-studied, but you can help address our academic shortcomings online by looking at pictures.

[Read More!] There are many kinds of flora out there; don’t lose face at the botanical get-together with this handy who’s who of the plant world.

Common heritage

The team’s investigation revealed that P. palmivora will try to take over the photosynthesizing tissues of liverworts (the team worked with Marchantia polymorpha) by pushing root-like structures (called ‘hyphae’) through their cellular walls — the end goal being to slurp up all the liquid goodness inside those cells, leaving behind dead, dry husks. The liverwort responds by deploying specialized proteins around these hyphal structures in a bid to contain the threat. According to Dr. Carella, these proteins are similar to those employed by “flowering plants such as tobacco, legumes or Arabidopsis in response to infections by both symbiont and pathogenic microbes.”

This last realization surprised the team. The last known link between liverworts and such plants is a common ancestor that lived over 400 million years ago. What fossil evidence we have from these times suggests that plants were already learning to form symbiotic relationships with filamentous microbes (P. palmivora is one such microbe).

“These findings raise interesting questions about how plants and microbes have interacted and evolved pathogenic and symbiotic relationships. Which mechanisms evolved early in a common ancestor before the plant groups diverged and which evolved independently?”

Because both liverworts and the rest of land plants share this mechanism, lead researcher Dr. Sebastian Schornack says it’s likely early land plants already possed the genes to fight off microbial infections before their evolutionary break-up with liverworts. This would imply that the relationship between filamentous microbes and plants is ancient indeed, likely from before plants moved out of the oceans.

What the team plan on doing next is establishing how it all started: did these pathogens evolve to exploit mechanisms plants and other microbes built to support symbiosis? Or was it conflict first, ‘let’s kinda live together’ later? It’s actually a pretty important question because virtually all our key crops today rely on symbiotic interactions with nitrogen-fixing bacteria to live. Plants, as we know them today, could not exist in the absence of this mutually-beneficial relationship — and by extension neither could we.

“Liverworts are showing great promise as a model plant system and this discovery that they can be colonised by pathogens of flowering plants makes them a valuable model plant to continue research into plant-microbe interactions.”

“Hopefully, this will allow us to establish future crop plants that both benefit from symbionts whilst remaining more resistant to pathogens,” Schornack concludes.

The paper “Phytophthora palmivora establishes tissue-specific intracellular infection structures in the earliest divergent land plant lineage” has been published in the journal Proceedings of the National Academy of Sciences.

Copper.

Copper-coated uniforms for medical staff could help shred bacteria in hospitals

Healthcare professionals might soon be bringing on the bling in the workplace, as UK and Chinese researchers designed copper-covered uniforms to help fight bacteria.

Copper.

Image via PxHere.

Materials scientists from the University of Manchester, working with counterparts from several universities in China, have created a ‘durable and washable, concrete-like’ material made from copper nanoparticles. They’ve also developed a method of bringing this composite to textiles such as cotton or polyester, a world first.

Coppering out

Bacterial infections are a major health issue in hospitals across the world. These tiny prokaryotes spread throughout healthcare facilities on surfaces and clothing, leading to losses both of life and of funds. The issue becomes worse still after you factor in the rise of drug resistance in most strains, which is rendering our once-almighty antibiotics more and more powerless. So we need to look for alternative ways of dealing with them, ones that do not rely on antibiotics.

One increasingly promising set of tools in our fight against disease are precious metals, such as gold and silver, which have excellent antibacterial and antimicrobial properties. However, deploying these on the surfaces and clothing mentioned earlier runs into some pretty obvious problems: first, gold and silver are really expensive — after all, they literally used to be money. Secondly, they don’t lend that well to making practical clothes, especially in a hospital setting.

Enter copper. Less expensive than gold or silver, copper is nevertheless still very good at killing pathogens, which solves problem one. However, up to now, we still didn’t have an adequate answer to issue number two — which is what the team addresses in this paper.

Using a process dubbed ‘Polymer Surface Grafting’, the researchers were successful in tying copper nanoparticles to cotton or polyester using a polymer brush. Cotton and polyester were chosen as a test bed as they’re the most widely used natural fiber and a typical man-made synthetic fabric, respectively.

The materials were brushed over with copper nanoparticles measuring between 1 and 100 nm, which is really small — one nm equals one-millionth of a mm. The metal particles formed a strong, stable chemical bond with the cloth, meaning the metal won’t flake off or be washed away.

“Now that our composite materials present excellent antibacterial properties and durability, it has huge potential for modern medical and healthcare applications,” says lead author Dr Xuqing Liu, from UoM’s School of Materials.

During lab tests, the copper-coated materials easily killed Staphylococcus aureus (S. aureus) and E. coli, two of the most common and infectious bacteria in hospitals, even after being washed 30 times.

The team says their results are very promising, and Dr. Liu adds that “some companies are already showing interest” in developing it further.

“We hope we can commercialise the advanced technology within a couple of years,” he adds. “We have now started to work on reducing cost and making the process even simpler.”

The paper “Durable and Washable Antibacterial Copper Nanoparticles Bridged by Surface Grafting Polymer Brushes on Cotton and Polymeric Materials” has been published in the Journal of Nanomaterials.

The Search for Alien Life: We Have Been Looking in the Wrong Places

SETI Initiative. Source: Traces Online.

Humanity has pondered the existence of alien life for centuries. However, it has been in just the past 100 years or so that modern science has backed some of this thinking. Scientists of the late 1800’s and early 1900’s believed that objects appearing on the surface of Mars were canals constructed by aliens. Particularly, astronomer Percival Lowell believed this concept and promoted it in works such as the book Mars As the Abode of Life (1908).

This belief in the scientific community led to a huge amount of pop culture based around the concept of extraterrestrials. This has resulted in some people even believing in the existence of aliens like the ones in the movies. Who knows? They could be out there. But some wonder how probable their existence is.

With aliens constantly being depicted in entertainment, even after the Martian alien canal hypothesis was busted, scientists considered communicating with otherworldly life forms. The first scientists looking for a close encounter believed the best bet was to use radio waves as the communication medium. The first of such proposed experiments was conducted in 1960 by astronomer Frank Drake.

One of the most eye-opening quotes about extraterrestrial alien life comes from the book Time for the Stars by Alan Lightman. The author states, “Are we alone in the universe? Few questions are more profound… Extraterrestrial contact would forever change the way we view our place in the cosmos” (Lightman 21).

Drake would definitely not be the last scientist to attempt to summon a response from an alien. But this was the first modern example of tests which would now be referred to as part of SETI, the search for extraterrestrial intelligence. In 1980, to bring more of a public interest to SETI, the legendary astrophysicist, astronomer, and astrobiologist Carl Sagan and several others formed The Planetary Society. In more recent years, other programs with goals similar to SETI’s have been established such as METI, messaging extraterrestrial intelligence.

Apart from radio waves, humans have tried other ways of communicating with hypothetical aliens. One example is a plaque which was attached to the Pioneer 10 probe in 1972. This plaque would be a unique kind of “message in a bottle,” except the ocean it was doomed to drift in was far more vast than any sea on Earth. It was inquired of Carl Sagan about sending such a message several months before the scheduled departure of the craft. So Sagan went to work, and assisting him with this undertaking was none other than Frank Drake, the man who had conducted the first modern SETI tests in 1960. The fruit of numerous labors and laborers, the Pioneer 10 plaque that was sent into space depicted a man and a woman and several objects. Through the imagery, the scientists were trying to give any aliens who might see this plaque an idea of what humans are like and where Earth is located.

This could be the first big mistaken researchers are making. They are looking to make contact. They are putting their faith in a sci-fi movie concept. What these scientists are attempting to do is call up and have a conversation with an alien or, better yet, a race of aliens. This is not to say that SETI is pointless, but it might not be the most opportune method for seeking alien life.

Perhaps scientists should strive to discover life in its simpler forms. As Lee Billings of Scientific American states in a recent article, if you were able to travel to another planet it is likely “you would find a planet dominated by microbes rather than charismatic megafauna.” Many scientists are now suggesting microscopic organisms could be more plentiful throughout the cosmos than macroscopic creatures.

Microbes Are a Realistic Form of Alien Life. Source: Joi Ito’s PubPub.

A specific search for such minuscule life forms is not a new practice. Bacteria are, of course, microbes. Astrobiologists like Richard Hoover and Dave McKay have examined certain meteorites. Some of the microscopic structures found embedded in or on the space relics resemble bacteria. They have released their findings in past years. They have admitted that even though the fossilized structures appear to be remnants of bacteria there is still some skepticism as to whether those structures are alien in origin. This is because bacteria from Earth could have been attached to the meteorites once they entered our atmosphere.

So how do scientists narrow down the search for alien life even further? Billings’ piece may give us the best idea available at the moment. He informs his readers that one of oxygen’s properties is that it tends to descend from an atmosphere in the form of mineral oxides. It does not remain in its gaseous phase for long. Because of its nature, in an atmosphere such as Earth’s, the oxygen has to be reinstituted on a regular basis.

Astrobiologists have to accept oxygen may be one of the least familiar elements they come upon when studying potential life-supporting bodies. For example, atmospheric chemist David Catling has said the atmosphere of a world dominated by microscopic life could be largely comprised of methane and carbon dioxide gases. Keeping this in mind, this will hopefully narrow down the most likely planet candidates for life.

DNA strands.

Blood DNA sequencing reveals there’s a lot more microbes living inside you — and we’ve never seen over 99% of them before

A new paper looking at the DNA fragments floating around in human blood reports that there are way more microbes living inside us than we thought — and we’ve never seen most of them before.

DNA strands.

Image credits Colin Behrens.

The idea behind this paper started taking shape as a team led by Stephen Quake, a professor of bioengineering and applied physics, a member of Stanford Bio-X and the paper’s senior author, were looking for a new non-invasive method to determine the risk of rejection in transplant patients. This is traditionally done using a biopsy, which involves a very large needle and quite a bit of ‘ow’.

Needless to say, nobody was very big on the procedure. So Quake’s lab wanted to see if they can work around the issue by looking at the bits of DNA floating around in patients’ blood — what’s known as cell-free DNA. The team expected to find the patient’s DNA, the donor’s DNA, and genetic material from all the bacteria, viruses, and all the other critters that make up our personal microbiome. A spike of donor DNA would, in theory, be one of the first signs of organ rejection.

But what the team didn’t expect to find was the sheer quantity and diversity of microbiome-derived DNA in the blood samples they used.

Bugs galore

“We found the gamut,” says professor Quake. “We found things that are related to things people have seen before, we found things that are divergent, and we found things that are completely novel.”

 

Throughout their project (which spanned several studies), the team gathered samples from 156 heart, lung, and bone marrow transplant recipients, and 32 from pregnant woman — pregnancy also has a huge effect on the immune system, similar to immunosuppressants, although we don’t really know how.

Of all the non-human DNA bits found in these samples, a whopping 99% couldn’t be matched to anything in existing genetic databases. In other words, they came from strains we didn’t even know existed. So the team went to work on characterizing all that genetic material. According to them, the “vast majority” falls into the phylum proteobacteria. The largest single group of viruses identified in this study belong to the torque teno family (TTVs). In fact, Quake says their work has “doubled the number of known viruses in that family” in one fell swoop.

Known torque teno viruses infect either animals or humans, but many of the TTVs the team identified don’t fit in either group.

 

“We’ve now found a whole new class of human-infecting ones that are closer to the animal class than to the previously known human ones, so quite divergent on the evolutionary scale,” Quake adds.

The team believes that we’ve missed all these microbes up to now because narrow studies, by their very nature, miss the bigger picture. Researchers often focus their attention on a few interesting microbes and glance over everything else. Blood samples, by contrast, allowed them to look at everything swimming around inside of us, instead of looking at a few individual pieces. It was this net-cast-wide approach — which the team humorously refer to as a “massive shotgun sequencing” of cell-free DNA — that allowed the team to discover how hugely diverse human microbiomes are.

In the future, the team plans to take a similar look at other animals to see what species their microbiomes harbor.

“There’s all kinds of viruses that jump from other species into humans, a sort of spillover effect, and one of the dreams here is to discover new viruses that might ultimately become human pandemics,” Quake says.

“What this does is it arms infectious disease doctors with a whole set of new bugs to track and see if they’re associated with diseases. That’s going to be a whole other chapter of work for people to do.”

The paper “Numerous uncharacterized and highly divergent microbes which colonize humans are revealed by circulating cell-free DNA” has been published in the journal Proceedings of the National Academy of Sciences.

Credit: Wikipedia.

What is antibiotic resistance: everything you need to know

Antibiotics are medicines that combat infections caused by bacteria. However, due to misuse and overuse of antibiotics, many bacterial strains are developing antibiotic resistance.

antibiotic resistance art

Credit: Wikipedia.

Before Alexander Fleming discovered penicillin in 1928, there was no effective treatment for infections such as pneumonia, gonorrhea or rheumatic fever. Fleming’s discovery kicked off a golden age of antimicrobial research with many pharmaceutical companies developing new drugs that would save countless lives. Some doctors in the 1940s would famously prophesize that antibiotics would finally eradicate the infectious diseases that had plagued humankind throughout history. Almost a hundred years later since Fleming made his milestone discovery not only are bacterial infections still common, the misuse and overuse of antibiotics are threatening to undo all of this medical progress as bacterial strains become resistant. 

Antibiotic resistance: a modern problem that can be traced to ancient times.

Contrary to common belief, human exposure to antibiotics isn’t confined to the modern era. Traces of tetracycline, a broad-spectrum antibiotic, have been found in the skeleton remains from ancient Sudanese Nubia dating from 350-550 CE. Likewise, tetracycline has been found in remains dating from the late Roman period in the Dakhleh Oasis, Egypt. These people must have included tetracycline in their diet — and it was to their good fortune as the rate of infectious diseases documented in Sudanese Nubian populations was low. For thousands of years, Chinese herbalists have been using a variety of plants which contain antimicrobial active components for ancient traditional remedies.

Naturally, the selective pressure imposed by these ancient antimicrobial activities has led to the accumulation of antibiotic resistance genes. But that’s nothing like the scale and intensity of antibiotic resistance we’re seeing today.

What is antibiotic resistance

Antibiotic resistance occurs when an antibiotic is no longer effective at controlling or killing bacterial growth. Bacteria which are ‘resistant’ can multiply in the presence of various therapeutic levels of an antibiotic. Sometimes, increasing the dose of an antibiotic can help tackle a more severe infection but in some instances — and these are becoming more and more frequent — no dose seems to control the bacterial growth. Each year, 25,000 patients from the EU and 63,000 patients from the USA die because of hospital-acquired bacterial infections which are resistant to multidrug-action. The ECDC/EMA Joint Working Group estimated in 2009 that the cost due to multidrug-resistant bacterial infections amounts to EUR 1.5 million in the EU alone. According to a 2013 CDC report titled “Antibiotic Resistance Threats in the United States, antibiotic resistance is responsible for $20 billion in direct health-care costs in the United States.

Antimicrobial resistance threatens to undermine all the immense clinical and public health progress we’ve come to achieve so far. This is a very complex problem that requires concentrated and coordinated efforts of microbiologists, ecologists, health care specialists, educationalists, policy makers, legislative bodies, agricultural and pharmaceutical industry workers, and the public to deal with.

The main challenges in dealing with antibiotic resistance are, on one hand, genetically acquired immunity and, on the other hand, fewer and fewer novel drugs. Since the 1970s, the rate at which new antibiotic classes have been discovered has continued to drop. No novel drug classes have been developed in the last 20 years. Researchers nowadays agree that, at this current rate, humanity is destined to lose the arms race as sooner or later bacteria will acquire resistance to modified versions of currently available antibiotic classes.

How bacteria develop resistance to antibiotics

Schematic by MeMed.

Schematic by MeMed.

Every time a person takes antibiotics, sensitive bacteria are killed, but resistant germs may be left to grow and multiply. In time, these leftover populations can become so strong that antibiotics no longer are effective.

There are several mechanisms bacteria employ to become resistant. Some gain the ability to neutralize the drug before it gets the chance to attack the bacteria. Other bacteria can rapidly pump the antibiotic out or can even change the attack site so the function of the bacteria isn’t affected.

Whenever bacteria survives an antibiotic onslaught, it can acquire resistant through mutation of the genetic material or by ‘borrowing’ pieces of DNA that code for the resistance to antibiotics from other bacteria, like those from livestock. Moreover, the DNA that codes the resistance is grouped in an easily transferable package which enables the germs to become resistant to many antimicrobial agents.

The types of bacterial resistance

  • Intrinsic resistance. Some bacteria are intriguingly resistant to antibiotics, such as those that don’t build a cell wall (penicillin prevents cell-wall building).
  • Acquired resistance. Bacteria can acquire resistance through new genetic change or by transferring DNA from a bacterium that is already resistant. This is the issue we’re having today.

According to the CDC, the following bacterial strains have developed the most resistance such that they’ve been listed as urgent hazards:

  • Clostridium difficile. Causes severe diarrhea, especially in older people and those who have serious illnesses.
  • Enterobacteriaceae. These normally live in the digestive tract but can invade other parts of the body, like the urinary tract, and cause infections.
  • Neisseria gonorrhoeae. Causes gonorrhea, a sexually transmitted infection. In 2016, the WHO said gonorrhea might soon become untreatable. 

 

Why antibiotic resistance is growing

When antibiotics are introduced in a bacterial population, most of the population dies but some resistant bacteria may survive. These resistant bacteria will continue to proliferate despite the presence of the antibiotic. In time, their population will increase until it becomes comprised mainly of resistant bacteria. Credit: ReActGroup.

When antibiotics are introduced in a bacterial population, most of the population dies but some resistant bacteria may survive. These resistant bacteria will continue to proliferate despite the presence of the antibiotic. In time, their population will increase until it becomes comprised mainly of resistant bacteria. Credit: ReActGroup.

There are a number of factors that contribute to this growing health hazard. Among them we can mention:

  • self-medication;
  • hygienic habits such as the use of anti-bacterial soap which research suggests is useless but significantly contributes to the growing problem of antimicrobial resistance;
  • counterfeit drugs, particularly rampant in the developing world;
  • antibiotics for livestock;
  • infections acquired in hospitals and nursing homes, particularly in the developed world;

There’s no surprise in the fact that antibiotic resistance infections correlate with the level of antibiotic consumption. The more antibiotics a population consumes, the faster bacteria will adapt and become resistant. One huge problem is the mindless use of antibiotics. For instance, many patients request their doctors to prescribe antibiotics when there is no need for them, such as in the case of viral infections. Research shows that up to 15 million people in the United States go to the doctor for a sore throat every year. About 70 percent of these patients receive strep throat antibiotics but only 20 percent actually have strep throat, according to the IDSA.

Another problem is compliance with strict drug regimes. To be effective, antibiotics needs to be taken at least over several days and the scheduling needs to be respected on the clock yet many patients fail to follow these instructions.

Things are worse in some countries than others. For instance, in some countries, antibiotics are available without a prescription so the potential for self-medication abuse is huge especially if the patient is not educated about antibiotics. In the absence of a proper diagnosis, suitable antibiotic choice, correct usage, compliance, and treatment efficiency monitoring, self-medicating antibiotics can only exacerbate the mounting resistance problem.

Another issue lies with antibiotics for domestic animals, particularly livestock. Farmers widely use antibiotics to stave off infections but also for promoting growth. Approximately 80 percent of the antibiotics sold in the United States are used in meat and poultry production, and in the vast majority of cases, the antibiotics are used on healthy animals. This practice can lead to the evolution of ‘superbugs’ which can migrate into the environment as people consume meat.

In 2003, an Expert Workshop co-sponsored by the World Health Organization, Food and Agricultural Organization (FDA), and World Animal Health Organization (OIE) concluded “that there is clear evidence of adverse human health consequences due to resistant organisms resulting from non-human usage of antimicrobials.  These consequences include infections that would not have otherwise occurred, increased frequency of treatment failures (in some cases death) and increased severity of infections”

Most recently in 2012, the FDA stated “Misuse and overuse of antimicrobial drugs creates selective evolutionary pressure that enables antimicrobial resistant bacteria to increase in numbers more rapidly than antimicrobial susceptible bacteria and thus increases the opportunity for individuals to become infected by resistant bacteria.”

Solutions to antibiotic resistance

The sad reality today is that there’s not much we can do for patients who don’t respond to antibiotics, which is why mortality rates are so high.

“Antibiotic resistance is rising for many different pathogens that are threats to health,” said CDC Director Tom Frieden, M.D., in a statement. “If we don’t act now, our medicine cabinet will be empty and we won’t have the antibiotics we need to save lives.”

Some researchers have proposed alternatives to antibiotic treatment such as passive immunization or phage therapy but most efforts are directed towards the discovery of new and more efficient antibiotics. Like outlined earlier, however, most of our antibiotics have been isolated in the so-called ‘golden era’ of antibiotic discovery from a limited number of taxonomic groups, mainly from Actinomyces that live in the soil. Some research groups are exploring alternative ecological niches such as the marine environment. Other approaches involve borrowing antimicrobial peptides and compounds from animals and plants, as well as the natural lipopeptides of bacteria and fungi. There is also a potential to find new antibiotics by exploring the microbiota through the metagenomic approach. Finally, some groups are looking design new classes of antibiotics from scratch through complete synthesis.

Preventing antibiotic resistance

Finding new antibiotics, however, will likely not solve our growing antibiotic resistance problem. History has shown that after a new antibiotic therapy is introduced, sooner or later resistance will arise. This approach is destined to fail since bacteria will eventually respond to selective pressure by the emergence of resistance mechanisms.

What we can do, however, is to buy time until someone very clever figures a way to outsmart bacteria for good.

Scandinavian countries, for instance, banned the use of growth-promoting antibiotics in livestock since 2006 and other EU countries have been implementing similar measures. In 2012, the FDA ruled that certain extra-label uses of cephalosporin antimicrobial drugs should be banned from certain livestock.

It is estimated that in half of all cases, antibiotics are prescribed for conditions caused by viruses. Obviously, in such cases the antibiotics are useless and doctors and nurses ought to know better.

Governments have a critical role in combating antibiotic resistance. It’s imperative that robust action is taken both at a national and international level in order to regulate the appropriate use of quality medicines and education about the dangers of overuse. A lot of antibiotic resistance is building up in developing countries where there is little oversight. Governments need to work together to strengthen the health care quality in such places for the good of us all. Not least, the industry needs to move faster and more aggressively to research and develop new antibiotics.

What you can do

  • Don’t take antibiotics for a viral infection like a cold or the flu.
  • Do not save any antibiotics for the next time you get sick. Discard any leftover medication once you have completed your prescribed course of treatment
  • Always take antibiotics only after you’ve consulted with a health care professional. The FDA has a great campaign called “Get Smart: Know When Antibiotics Work”  that offers Web pages, brochures, fact sheets, and other information sources aimed at helping the public learn about preventing antibiotic-resistant infections.
  • Take an antibiotic exactly as the healthcare provider tells you. Do not skip doses.
  • Never pressure your provider to prescribe an antibiotic.
  • Never use antibacterial soap.

Fracking-only bacteria discovered in two separate wells hundreds of miles apart

Fracking may produce more than shale hydrocarbons, say researchers analyzing the genomes of microorganisms living in these wells. Evidence suggests underground sustainable ecosystems are forming due to this practice, populated in part by a never-before-seen bacteria dubbed “Frackibacter”.

Samples of “produced water fluids” collected at the surface of wells in Macellus and Utica shale formations after fracturing. The fluids are orange because they contain large amounts of iron that oxidizes when brought to the surface. By analyzing the genomes of microbes in the water, the researchers are piecing together the existence of microbial communities inside the wells. Image credits Rebecca Daly / Ohio State University.

Ohio State University researchers report finding the new genus along with 30 microbial members in two separate fracturing wells. Even though they are drilled hundreds of miles apart and into different kinds of shale formations, the microbial communities found inside them were nearly identical, they say. And astonishingly, these little bugs seem to create their own self-sustaining ecosystems inside the wells.

By sampling fluids taken from the two wells over a period of 328 days, the researchers reconstructed the genomes of bacteria and archaea (single-celled organisms) living in the shale. Incredibly, both wells showed nearly identical microbial communities. They’re geologically different (one drilled in Utica shale and the other drilled in Marcellus shale,) they’re formed millions of years apart, are worked by two different companies using their own techniques and fluid mixes, and each formation contains different forms of hydrocarbons. Yet one bacterium, Halanaerobium, emerged to dominate communities in both wells.

“We thought we might get some of the same types of bacteria, but the level of similarity was so high it was striking. That suggests that whatever’s happening in these ecosystems is more influenced by the fracturing than the inherent differences in the shale,” said Kelly Wrighton, assistant professor of microbiology and biophysics at Ohio State.

Most of the microbes identified in the wells are familiar. The team suspects they most likely come from the surface ponds that hold the liquid needed to fill the wells, but they’re not 100 percent sure. One new species was identified only in these two points and may very well be unique to hydraulic fracturing sites — Candidatus Frackibacter. In biological nomenclature, “Candidatus” is affixed to an organism whose genome is being studied for the first time without being isolated in a lab culture. “Frackibacter” is short for hydraulic fracturing bacteria, because even biologists need a giggle sometimes.

Frackibacter seems to prosper alongside the microbes we’ve introduced from the surface, forming communities in both of these wells which have been stable for nearly a year now.

“We think that the microbes in each well may form a self-sustaining ecosystem where they provide their own food sources,” Wrighton said.

“Drilling the well and pumping in fracturing fluid creates the ecosystem, but the microbes adapt to their new environment in a way to sustain the system over long periods.”

Produced water fluid being filtered. Image credits Rebecca Daily / Ohio State University.

Where the bugs come from is still unclear — while some are almost guaranteed to come from the ponds, other bacteria and archaea could have been living in the rock before drilling began. Candidatus Frackibacter among them.

Energy companies usually mix their own proprietary recipes for the fluid they use in fracking, but basically they all start with water and add other chemicals in various proportions. Once the fluid reaches the shale, it leaches salt from the rocks becoming briny. The microorganisms that live inside shale deposits naturally endure high temperatures, pressure, and salinity. But this salinity is likely the most dangerous stressor acting on the bugs because the huge osmotic pressure it generates wants to suck the water right out of them. So, they synthesize organic compounds called osmoprotectants to keep themselves from bursting.

When they die, the osmoprotectants are released into the water and other microbes feed on or use them to protect themselves. In that way, salinity forced the microbes to generate a sustainable food source.

Epifluorescence microscope image of Halanaerobium bacteria cells. Image credits Michael Wilkins / Ohio State University.

They also have to contend with viruses. The researchers found evidence that some bacteria were falling pray to viruses and releasing their osmoprotectants into the water when they died. By examining the genomes of the different microbes, the researchers found that the osmoprotectants were being consumed by Halanaerobium and Candidatus Frackibacter. In turn, these bacteria provided food for other microbes called methanogens, which ultimately produced methane.

To check their findings, the researchers grew these microbes in a lab under similar conditions. They also produced osmoprotectants that were converted to methane, confirming the team’s theory. One implication of the study is that methane produced by microbes living in shale wells could possibly supplement the wells’ energy output. Wrighton and Daly described the amount of methane produced by the microbes as likely minuscule compared to the amount of oil and gas harvested from the shale even a year after initial fracturing. But there is a precedent in the related industry of coal-bed methane of using microbes to increase yield.

“In coal-bed systems they’ve shown that they can facilitate microbial life and increase methane yields,” Wrighton said.

“As the system shifts over time to being less productive, the contribution of biogenic methane could become significantly higher in shale wells. We haven’t gotten to that point yet, but it’s a possibility.”

Co-author Michael Wilkins, assistant professor of earth sciences and microbiology, has used genomics information to grow Candidatus Frackibacter in the lab and is further testing its ability to handle high pressure and salinity.

The full paper “Microbial metabolisms in a 2.5-km-deep ecosystem created by hydraulic fracturing in shales, Nature Microbiology” has been published online in the journal Nature Microbiology.