DailyDirt: NYC Subways Filled With Unknown Species

from the urls-we-dig-up dept

No one would want to lick a handrail on the New York City subway because it's just gross -- and who knows what kind of germs and stuff are living in the urban grime? Well, now we have a better idea. Thousands of samples have been analysed, and the results are published. A city-wide metagenomic profile of NYC could tell us demographic data and confirm census polls, and a map of the data is available online. Follow a few of the links below for a bit more info.

• A biological study of the NYC subway system has mapped and identified (where possible) the DNA found on handrails, turnstiles, kiosks and other places commonly touched by gazillions of people all the time. They found at least 637 known species of bacteria -- as well as viruses, fungi, microscopic animals... and a bunch of DNA (48% of all their samples) that hasn't been identified yet. [url]
• Specimens of anthrax and bubonic plague were also found in NYC subway stations, as well as drug-resistant bacteria. Human DNA made it into the top five most abundant species in NYC subways, after insects and microbes. [url]
• This DNA study of a "healthy" ecosystem highlights just how little we actually know about the species all around us. It may be time to start sequencing the cockroach genome so we know what will still be alive when humans aren't around anymore. [url]

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Filed Under: anthrax, bacteria, biology, bubonic plague, cockroaches, dna, ecosystem, humans, microbes, nyc subway, species

DailyDirt: Killing Those Tiny Germs

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The overuse of antibiotics may be leading us into the "post-antibiotic era" where we'll face numerous bacteria that are resistant to our most advanced drugs. We may need to develop different strategies for identifying antibiotics or try various phage therapies to fend off antibiotic-resistant superbugs. Here are just a few links on finding new antibiotics and using bacteriophages in medicine.

• If we really met the end of antibiotics without any medicines to fight bacterial infections, it would be horrible. If you think Ebola is scary, just read up on MRSA and KPC-Oxa 48. [url]
• Tweaking antibiotic drugs can still produce some variants that may extend the usefulness of these pharmaceuticals by several years. A chemically-modified vancomycin has been discovered with 10-100 times the potency of the native compound. [url]
• The strategy of looking for new antibiotics in natural products has provided diminishing returns as researchers discovered they were finding the same compounds again and again, but new ways to genetically identify microbes could help refine the screening process and avoid redundant targets. Compiling a database of known genes could help identify potentially new antibiotics by highlighting the strains that might be more fruitful for novel drug targets. [url]
• Viruses are not evil. Bacteriophages actually keep us healthy by infecting and killing off disease-causing bacteria. Phage therapy could be a viable alternative to using antibiotics, but using viruses to fight off infections is not a widely used procedure in Western medicine (yet). [url]

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Filed Under: antibiotics, bacteria, bacteriophages, biotech, drug discovery, health, kpc-oxa 48, medicine, microbes, mrsa, phage therapy, pharmaceuticals, superbugs, vancomycin, virus

DailyDirt: Storing Energy In Organic Molecules

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Petroleum products are a pretty convenient way to store energy. It's just unfortunate that burning the stuff releases carbon dioxide into the atmosphere. Biofuels could be a solution, but relying on natural biological processes can be difficult to scale up -- especially if we expect biofuels to try to match up with the current energy demands. Researchers are working on ways to modify biology or circumvent it with chemical engineering to make some carbon neutral hydrocarbon fuels in large quantities. Here are a few possible examples.

• A copper catalyst system can produce ethanol (and acetate) from carbon monoxide at room temperature and pressure -- without any kind of fermentation. This copper-based system relies on an electrochemical cell and could be a environmentally-friendly way to produce a non-toxic, renewable fuel. [url]
• Scientists have played with Escherichia coli bacteria that can generate propane gas. The process needs a lot more work to become a practical way to produce propane as a fuel, but a bioreactor to make propane could be viable in a decade or so. (Maybe.) [url]
• Some species of bacteria have been found that can consume pure electricity for food. These naturally-occurring microorganisms usually live near hydrothermal vents on the seafloor, but if they can feed on electrons directly (instead of soluble bits of iron), then they might be able to store energy in biomolecules for us and turn electricity into convenient biofuels. [url]

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Filed Under: bacteria, biofuel, biotech, carbon dioxide, electricity, energy, ethanol, extremophiles, fuel, hydrocarbons, petroleum, propane

DailyDirt: Fighting Off Teeny Tiny Threats...

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The population of superbugs that are resistant to antibiotic drugs is a growing concern. If we run out of effective medicines to fight off bacterial infections, it won't be pretty. Fortunately, we might have a few more tricks up our sleeves, and hopefully, these new tactics will be tested and ready by the time our current line of antibiotics stop working. Here are just a few links on how we might save ourselves.

• Bacteriophages are viruses that can infect bacteria, and phage therapy could use these viruses to combat all kinds of disease-causing microbes. Using viruses to fight bacterial infections has been widely used in Russia and other parts of eastern Europe, but engineering viruses is not quite a mature field (yet). [url]
• Attacking the cell membranes of bacteria could be an effective approach to killing off antibiotic-resistant bacteria. If new drugs can selectively break down bacterial membranes, then they won't even need to enter the cells.. and no resistance can be developed. [url]
• Plastics that prevent the attachment of biofilms on their surfaces could be useful in eliminating bacterial infections from common medical devices. These materials prevent bacterial growth by resisting bacterial attachment at the earliest stages, so catheters and other medical tools coated in these polymers could put an end to a large number of hospital infections. [url]

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Filed Under: antibiotics, bacteria, bacteriophages, biofilm, drug-resistant, health, infection, microbes, phage therapy, plastic

DailyDirt: Teeny Tiny Threats

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Bacteria are all around us. They outnumber us vastly, and fortunately, nature has created a balance such that we seem to be able to coexist with these tiny organisms (for the most part). However, there are some disease-causing bacteria that are pretty nasty and deadly, so we were pretty lucky to discover antibiotics like penicillin. But the process of evolution is rendering our antibiotic medicines useless against a growing population of bacteria. Here are just a few informative links on these superbugs.

• Carbapenem-resistant Enterobacteriaceae (CRE) -- also known as "nightmare bacteria" -- are resistant to the most effective antibiotics we have currently. Simple bacteria can exchange genetic information more easily than other organisms, and drug-resistance may be spreading among microbes -- in hospitals. [url]
• An imported batch of squid has been discovered with antibiotic-resistant microbes... in squid sold for human consumption. The bacteria found were not disease-causing, but this is the first time a carbapenem-resistant bacteria has been detected in the US/Canadian food supply. [url]
• Antibiotic resistance isn't actually a new thing. Ancient bacteria found in an isolated cave in New Mexico exhibited antibiotic resistance to multiple drugs that are currently used in medicine. Other ancient microbes revived from permafrost in the Yukon have also shown to be resistant to a bunch of common antibiotics. [url]

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Filed Under: ancient bacteria, antibiotic resistance, bacteria, carbapenem-resistant enterobacteriaceae, cre, microbes, nightmare bacteria, superbugs

DailyDirt: Is It Safe To Eat That?

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The global food supply chain is significantly more complicated than it was a few generations ago. Some of it is due to technological progress, but sometimes it's due to greed and/or pollution. Eliminating waste and making food processes as efficient as possible sounds like a admirable goal, but the food products created at the end of the day should be appetizing... and, more importantly, safe to eat. If you're not too squeamish, check out these links on food that might churn your stomach.

• Fermented sausages (aka fuet) can be delicious, but what if the bacteria used to make them came from baby poop? Spanish scientists collected some diapers and isolated some Lactobacillus and Bifidobacterium samples from the fecal matter, and then they made some yummy (and healthier!?) sausages with the microbes. [url]
• Gutter oil is created from animal fats and cooking oil waste (collected from sewer drains), and the resulting recycled cooking oil -- along with toxins and carcinogens -- can end up in small restaurants and food trucks in China. The gutter oil industry has reportedly existed for over a decade, and there are estimates that as much as 10% of the cooking oil sold in China is gutter oil. [url]
• French beekeepers were wondering why their honey was a strange blue-green color that looked really unnatural. The likely culprit for the blue-green honey was processing waste that came from an M&M chocolate factory producing bright red, blue, green, yellow and brown candy shells. The resulting honey didn't taste much different, but it wasn't a product that could be sold. [url]

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Filed Under: bacteria, cooking oil, feces, fermented, food, food waste, fuet, gutter oil, honey, m&ms, scandal, toxic
Companies: mars

DailyDirt: Nature Abhors A Vacuum

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Studies have shown that spore-forming bacteria can survive in space under certain conditions, so it doesn't seem so implausible that life -- as we know it -- has accomplished interplanetary travel successfully. Extremophiles living in unexpected places also seems to suggest mounting evidence that life exists on other worlds, even though we have no direct proof of extraterrestrial beings (yet). Here are just a few links related to the growing field of astrobiology.

• NASA microbiologists have classified a new genus (not just a species) of bacteria that can survive in the clean rooms designed to prevent spacecraft from contaminating the rest of the solar system with terrestrial organisms. The bacterium Tersicoccus phoenicis was first found in 2007 in a clean room made for the Mars lander Phoenix, and it's been seen again in another clean room 4,000 km away that housed the ESA's Herschel space telescope. [url]
• When the universe was just 15 million years old, the 'Goldilocks' conditions for supporting life might have existed nearly everywhere -- 10 billion years before life on Earth likely began. No one is actually certain if planets even existed when the universe was that young, but if there were, liquid water and nice ambient temperatures were probably not that hard to find. [url]
• The asteroid that killed off all the dinosaurs about 65 million years ago hit with such force that rocks from Earth could have been ejected out of our atmosphere -- to travel as far as Saturn. Rocks from our planet could have carried life to Mars, Venus, Jupiter and Saturn (as well as the moons of those planets), so if we ever find life elsewhere in our solar system, it might have come from Earth. [url]
• Biomolecules may have formed on asteroids when our sun was much younger and warmer than it is now. The 'Goldilocks' zone for our sun may have included the asteroid belt between Mars and Jupiter, but our sun has cooled with age and the asteroid belt isn't a very likely place to find liquid water anymore. [url]

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Filed Under: asteroids, astrobiology, bacteria, et, extraterrestrial, extraterrestrial life, extremophile, life, microbe, planets, seti, space, tersicoccus phoenicis
Companies: esa, nasa

DailyDirt: Replacing Exercise With A Pill

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Some people really enjoy exercising. Some people really don't. And some people have physical limitations that restrict the amount or kinds of exercise they can do. If there were a pill that could provide some of the benefits of exercising, plenty of folks would take it. Not surprisingly, a lot of research is looking at how exercise affects the body -- and some projects might lead to a pharmaceutical solution for couch potatoes. Here are just a few examples.

• Drug candidate SR9009 sounds like a pill from The Jetsons that helps you lose weight and build muscle -- without exercising. Mice treated with this drug showed increased metabolic activity in skeletal muscle and improved athletic endurance for running. [url]
• Different colonies of intestinal bacteria may spur obesity or prevent it. Studies of lab rodent fecal transplants suggest that some kinds of bacteria can help keep fat mice lean when eating a low-fat, high-fiber diet. [url]
• Regular exercise may help boost autophagy processes in the body that clear out surplus proteins and other cellular detritus -- potentially leading to some anti-aging benefits. Researchers are just beginning to learn more about autophagy mechanisms (and maybe someday we'll get the benefits without the exercise). [url]

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Filed Under: anti-aging, autophagy, bacteria, drugs, exercise, health, medicine, pharmaceuticals, sr9009

DailyDirt: Creative Ways To Eat Less

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A pretty concerning statistic for Americans is that 17% of kids in the US are obese. The solutions to reduce that figure range from getting kids to eat better school lunches to eliminating various kinds of advertising aimed at getting kids to equate food with fun. There are a few other crazy ideas to keep people from getting fat, without trying to eat less or exercise more. Here are just a sampling of such suggestions.

• There's a chance that the bacteria in our intestines have some influence on obesity. From a preliminary study, morbidly obese people were found to have different bacterial communities in their intestines, but it's not clear if the different flora are a cause (or a result) of obesity. If there is a causal relationship, maybe there will be an effective treatment that involves cultivating different intestinal microbes. [url]
• "The Parasite Diet" isn't a new idea. At the turn of the 20th century, some people used tapeworms to lose weight (before modern medicine convinced people this was a very bad idea). But genetically modified tapeworms that are benign to people could be a reality someday. [url]
• Freakonomics has yet another podcast on obesity called "100 Ways to Fight Obesity" that covers some interesting proposals to prevent overweight adults and children. Some suggestions, such as smelling a vial of vomit to curb an appetite, are not so pleasant -- and not really guaranteed to work that well, either. [url]

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Filed Under: bacteria, diets, eating, flora, food, obesity, tapeworm

DailyDirt: Life Abhors A Vacuum

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Biologists continue to find signs of life in some of the most remote places on Earth. A variety of organisms seem to be able to thrive under harsh conditions that are similar to extra-terrestrial places elsewhere in our solar system. So finding these extremophiles could point us towards good places to find alien life forms on other planets or moons or asteroids... Here are just a few more examples of some really tough microorganisms.

• Evidence of life in a subglacial lake in Antarctica has been found, and it could mean that bacteria are much more widespread than we previously thought. Researchers still need to verify this discovery and make sure they're not looking at bacterial contamination from other sources. [url]
• Frost flowers are salty ice crystals that form on calm ocean surfaces, and arctic sea meadows of these flowers may become more common with climate change near the north/south poles. About a million bacteria live in the few milliliters of frozen saltwater of a frost flower, and studying these cells could teach us more about how hardy some extremophile organisms can be. [url]
• Bacteria living below the ocean and at the ocean surface have it easy compared to bacteria that live 6 miles above sea level in the troposphere. Microorganisms could play a role in cloud formation, and there is a lot we don't know about how life survives in different parts of the atmosphere. [url]

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Filed Under: bacteria, biology, extremophiles, frost flowers, life, microorganisms, troposphere