Boing Boing 

Watching the climate-cholera connection from orbit

Dr. Kiki Sanford on how scientists are predicting outbreaks from an unusual new vantage point.

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NYT jumps on our smelly old 'I don't use soap' bandwagon

splash

Sean Bonner writing for Boing Boing, 2011: "I haven't used soap or shampoo in a year, and it's awesome: a personal experiment." NYT, 2014: "My No-Soap, No-Shampoo, Bacteria-Rich Hygiene Experiment."

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Life is hard in Antarctica

Antarctica's Organic Lake is 8 degrees Fahrenheit, but the water doesn't freeze, thanks to a heavy concentration of salt. But wait, it gets more awesome. Despite the cold and the salt, Organic Lake is also home to a diverse array of life.

Microbes and health: The debate continues

Last week, I linked you to a piece pointing out that three New York Times op-ed pieces linking bacterial exposure (or lack thereof) to autism, celiac disease, and allergies were all written by the same guy, Moises Velasquez-Manoff. His ideas are interesting, but there's also good reason to be skeptical. If you want to get a better idea of the arguments for and against Velasquez-Manoff's thesis, I'd recommend checking out this post at the Knight Science Journalism Tracker, which links to several critical stories and to Velasquez-Manoff's response to them.

Antibiotic resistance: Watch a documentary tonight, join in a live chat tomorrow

Tonight at 10:00 Eastern/9:00 Central, PBS Frontline will air a documentary about the growing threat of antibiotic-resistant bacteria. I got a chance to see a preview of the show, and it's definitely interesting, including details I wasn't previously aware of, despite having written about this topic before. Particularly interesting: An emphasis on naturally occurring gene transfer between different species of bacteria, which is allowing antibiotic resistance to spread at an alarmingly quick rate. I had also not realized that antibiotic-resistant bacteria probably kill more Americans every year than AIDS — "probably", because nobody is required to actually track and report this stuff. Your local hospital could be in the midst of a serious outbreak of antibiotic-resistant bacteria and, unless they choose to voluntarily release that information, you might never know.

Whether or not you get a chance to watch the documentary tonight, we hope you'll join us here tomorrow for a live chat session with the producers and a doctor who specializes in treating patients with antibiotic-resistant infections. That starts at noon Eastern/11:00 central, and will be moderated by either me or Rob. We've got some questions we're looking forward to addressing with the panel, and we hope you'll bring in some great questions, too. The first half of the chat will focus on the documentary. The second half will be aimed more at a practical understanding of what you can actually do to protect yourself, your family, and your community.

Gut microbes may control your brain

At The Verge, Carrie Arnold writes about a scientist who thinks that our intestinal bacteria could have an influence on mental health. It's not proven, but it's not a totally crazy idea, either, and there's some good evidence supporting the connection. The catch: Even if what's happening in your gut affects what is happening in your head, there might not be much we can do change the mental health outcomes.

From the front lines in the fight against antibiotic-resistant bacteria

Bacteria are becoming resistant to one of the last classes of antibiotics available to treat them, writes Maryn McKenna at Nature. Carbapenem-resistant Enterobacteriaceae are a family of lung, blood, and bladder infections that can turn horribly deadly. Meanwhile, at Scientific American, Charles Q. Choi writes about other scientists looking for ways to turn bacteria against one another, unleashing predatory microbes that can destroy drug-resistant bacteria.

Working with your microbiome to produce better-scented breath

Our great, collective, ongoing realization that wiping out all the bacteria in our bodies may not actually be a great idea marches on. At Scientific American, Deborah Franklin writes about chronic halitosis — the sort of bad breath that doesn't go away with a simple brushing — and scientists' efforts to cure it by encouraging the growth of some mouth bacteria, instead of pouring Listerine on everything and letting God sort it out.

A beautiful bacterium

David Goodsell of the Scripps Research Institute made this lovely watercolor illustration of a cell of Mycoplasma mycoides. This bacterium is the cause of a deadly respiratory disease that affects cattle and other cud-chewing animals.

If you've ever read much about zoonoses — diseases that pass from animals to humans — then you know that the domestication of livestock played a huge role in introducing many diseases to people. Living in close proximity to the animals we ate provided ample opportunities for those animals' diseases to jump over to us. What's interesting about Mycoplasma mycoides is that it represents a disease of animals that seems to have its origins in domestication, as well.

In 2012, scientists found evidence that suggests domesticating livestock — a process that resulted in closer living conditions for the animals and in animals from one herd being moved to other herds they likely wouldn't have otherwise had contact with — helped Mycoplasma mycoides evolve and spread. Today, different species of Mycoplasma mycoides cause a range of diseases that can kill between 10 and 70 percent of the cows they infect.

Goodsell's illustration is an attempt to show all the different parts of the bacterial cell, in the shapes, sizes, locations, and concentrations that those parts take in the real world. If you go to his site, you can see a legend explaining what everything is.

How animals pass disease to humans

Given the ongoing outbreak of H7N9 flu in China (and, now, also Taiwan), this is a good time to listen to a fascinating podcast discussion with David Quammen. Quammen recently published a FANTASTIC book, Spillover, about zoonoses — the diseases that humans contract from animals. This includes bird flus like H7N9. It also includes AIDS and a whole host of familiar viruses and bacteria. Bonus: Scary disease girl Maryn McKenna has a cameo in the podcast, discussing the way news media (in China and the US) are covering H7N9 and what you can do to better understand what's happening.

We are all star stuff

How scientists study the fossils of ancient bacteria to find clues to a 2.6-million-year-old supernovae. Jennifer Ouellette explains how the the bacteria incorporated elements from an exploding star into their bodies, and how those elements can still be found today.

A spaceship that tastes like Grape-Nuts

This morning, Marketplace Tech Report had a story on a new cellulose-based building material that could be made by genetically engineered bacteria — altered versions of the bacteria that naturally make stuff like kombucha. This tech sounds like it's got a long way to go from laboratory to the real world, but if they can perfect the process and make it large enough quantities, what you'd end up with a strong, inexpensive goop that could be used to build everything from medical dressings, to digital paper, to spaceships. Yes, you could theoretically use this stuff to make rocket casings, according to R. Malcolm Brown, Jr., a professor of cell biology at UT Austin. And if you can build a rocket from this stuff, you could also break the same material back down into an edible, high-fiber foodstuff.

Lake Vostok bacteria: It's something new. No, it's not. Yes, it is, maybe.

Let's just play this safe and assume that, until more samples have been collected and detailed DNA analysis has been done, the real answer to the question, "Is bacteria found in Antarctica's Lake Vostok actually new to science or just contamination from the drilling?" is "We don't really know." This is a great example of why making scientific pronouncements from the field, before you've had time to do the really in-depth analysis that goes into writing a peer-reviewed research paper, can be problematic. Right now, you've got different camps of researchers making totally contradictory claims. Who is right is, so far, anybody's guess.

"New" bacteria from Lake Vostok is not actually new (or from Lake Vostok)

"You can say anything you want in a press release". Sadly, that sentiment is too true. Turns out, recent reports of the discovery of previously unknown bacteria in samples hauled up from the waters of Antarctica's frozen Lake Vostok have turned out to be premature. The bacteria turned out to be contaminants carried by the drilling and collection apparatus. At Scientific American, Elizabeth Howell talks about this flub in the context of other stories where scientists bypassed peer review and announced findings to the newspapers first.

Scientists discover life in Antarctica

“It appears that there lies a large wetland ecosystem under Antarctica’s ice sheet, with an active microbiology.” — There's some really exciting news coming from the land at the bottom of the world.

How bad research gets published (and promoted)

In 2010, a group of scientists claimed to have found bacteria that could build its DNA using arsenic, instead of the phosphorous used by the rest of Earth's life forms. Within days, the research behind "arsenic life" was under serious scrutiny and we now know that it was totally wrong. But the work was peer-reviewed. It was sponsored by NASA. How do so many experts make such a big mistake? Dan Vergano at USA Today has an excellent article looking at just that — and it includes the peer review comments that helped the arsenic life paper get published. Though normally secret, Vergano got a hold of them through a Freedom of Information Act request.

The future of fuel has gone to sh*%.

Everybody poops, including panda bears. (See about 0:35 in the above video for evidence.) But panda poop could turn out to be quite a bit more important than your average animal excrement. That's because scientists are "mining" it for bacteria that could help make better biofuel.

The key problem with biofuel today is that the stuff that's actually economical to produce — i.e., corn ethanol — isn't really that great for the environment. Corn farming uses a lot of fertilizer, water, and herbicide. Using corn that was previously grown for food to make fuel, instead, can lead to deforestation as people clear land to make up for the lost food farming. Some models of carbon dioxide emissions suggest that, by the time you factor in things like fossil-fuel derived fertilizers and the deforestation, a gallon of corn ethanol might not be any better for climate change than a gallon of gasoline. Not all the models agree on that. But even if corn ethanol produces fewer carbon emissions than gas, you still have to deal with the fact that growing nutrient-hungry corn on the same patch of ground over and over and over is really bad for local soil and water quality.

Cellulosic ethanol could be a much better alternative — particularly cellulosic ethanol made from native, perennial plants that don't require heavy inputs to thrive and actually improve the health of the land they're grown on. The problem: Converting those plants into fuel is, so far, a lot more expensive. Cellulose — the plant fiber that makes up things like stalks of bamboo and tall prairie grasses — is tough stuff and hard to break down.

That's where panda poop comes in. Pandas process tons of cellulose every day, right in their guts. Maybe the bacteria that work for them could work for us, too.

Read more about this research at Chemical and Engineering News

Viruses to the rescue

Technology Review's list of 35 Innovators Under 35 includes Timothy Lu, an MIT researcher who is engineering viruses designed to seek out and destroy biofilms — bacterial colonies that stick together on a surface, like bits of pear suspended in the world's most disgusting jell-o salad. Biofilms have been implicated in human disease, especially chronic infections like those that can happen in the urinary tract and inner ear. But the first place Lu's biofilm-eating viruses will likely be put to work is cleaning out ducts in industrial HVAC systems. (Via Carl Zimmer)

Bacteriogoraphs of famous scientists in petri dishes

NewImage

Zachary Copfer is a microbiologist and artist who creates portraits of his favorite scientists from living bacterial emulsions in petri dishes. I find what he wrote here to be inspiring:

When I was an undergraduate perusing a degree in Biology, I found myself utterly mesmerized by what I was learning. Each day’s lecture brought to my attention new insights into the complex systems at work in the world around me. The more I learned, the more mystified I became. Science grew into a way for me to revel in the beauty of the universe. I began to better understand and appreciate my place among all of the other particles floating in space. After obtaining my bachelors degree, I began working as a microbiologist in a commercial lab setting. Quickly I began to lose sight of all that I had found romantic about science. Shortly after this disinfatuation of science, I began an adventure into the field of photography. Photography developed into my new method of inquiry. Everything that I had missed about science I rediscovered in photography. For me, the two seemingly disparate fields of study served the same purpose, a way to explore my connection to everything else around me. As a former microbiologist recently turned visual artist, I seek to create work that is less of an intersection of art and science and more of a genuine fusion of the two.
"Bacteria Portraits, Bacteriogoraphy" (via Smithsonian)

Previously: "Photosensitive bacteria art"

You are your bellybutton lint

Last January, at the Science Online conference, I noticed that there was a research group collecting swabs taken from the bellybuttons of scientists, science bloggers, and science journalists. That culture above? It's made from the bellybutton of Anton Zuiker, one of the organizers of that conference.

Beyond personalized petri dishes, what is the point of all this? Turns out, the goal is to learn more about the bacteria that lives on us. Some of the data from analyzing all those bellybutton samples is starting to come back, and it's turning up some interesting facts about the tiny ecological niches on our tummys.

About 18 months ago, researcher in the laboratory of Dr. Dunn, a North Carolina State University professor, came up with an idea to explore the ecology and evolution of daily life and wanted to find a spot on the body that could provide an understanding of the natural skin microbiome. They needed a place that was infrequently disturbed, avoided the scrubbing of daily wash and was common to all humans. There was no better choice than the bellybutton. Dunn and his clan of navel gazers then invited people from two conferences, 60 in total, to swab their bellybuttons and provide him with the samples, which he took back to his lab and cultured. The next several months were spent not only growing the bacteria, but also typing them to identify the species.

The first set of data is in review, but the results suggest that the bellybutton offers far more to our understanding of life and our journey through it. From these 60 people, Dr. Dunn identified close to 1,400 species of bacteria. From these, a number were predictable, such as the ever-prominent Staphylococcus epidermidis and the corynebacteria, both of which give off that "eau de germs" scent when we don't wash frequently. But others, such as those found on volunteer Carl Zimmer, were completely unexpected, such as species that are found only in the ocean or the soil or in faraway lands.

...The navel bacteria were related to where the person has lived over the course of their lifetime. The tiny anatomical vestibule was actually a museum of lifetime experiences.

Read the rest of this story by microbiologist Jason Tetro at Huffington Post.

Learn more about the Bellybutton Biodiversity Project

What a chronic ear infection looks like

These are images from the inside of two human ears. The ear on the top doesn't get chronic infections. The ear on the bottom does. The difference seems to be the presence of a biofilm—a little colony of bacteria or other microorganisms that build up in a thin layer.

Biofilms happen all over the place in nature. That slime that covers the surface of rocks at the bottom of a river or lake? That's a biofilm. The slick, green coating on the underside of a boat when you pull it out of the water? That's a biofilm, too. And so is the plaque that builds up on your teeth.

In the case of ears, though, biofilms might explain why it's so difficult to treat chronic ear infections—biofilms are not easily killed off by antibiotics. The image above, showing a biofilm-coated ear drum, was captured using a new imaging device that produces pictures from reflected light, the same way ultrasound makes images from reflected sound waves. It's part of a research paper that presents evidence about the role of biofilms in ear infection and long-term hearing loss.

Check out Scientific American for more information

Via Bora Zivkovic

Exploring ancient water

I love it when news lines up almost perfectly with our editorial calendar. Next week, I've got a Science Question from a Toddler feature lined up that will explain how scientists can date reserves of water, and what makes ancient water special.

This week, in Antarctica, a team of Russian scientists made contact with some very ancient water. Yesterday, they drilled through the last of a more than 12,000-foot ice cover and into Lake Vostok, a reserve of liquid water that hasn't had contact with the outside world in 15-34 million years.

These researchers are looking for extremophile bacteria—semi-alien Earthlings that have evolved separately from the rest of their terrestrial kin. Bryan Walsh at Time.com explains:

The hope is that some form of new microbial life might exist within the waters of the lake, which remain liquid despite the cold thanks to heat generated by the pressure of all that ice and geothermal energy rising from the planet’s core. The environment of Lake Vostok is similar to that found on Jupiter’s icy moon of Europa. If life can survive in Lake Vostok, it might just be able to survive on another planetary body.

It’s still going to take the Russian scientists some time to actually take samples from the lake—with the Antarctic winter on its way, they’ll need to leave Vostok Station soon. And there are environmental concerns that the drilling process could contaminate the lake, which is pristine. The researchers used more than 66 tons (60 metric tons) of lubricants and antifreeze in the drilling process—chemicals that would have polluted Lake Vostok had they leaked through the ice, and contaminated any samples. The good news is that contamination seems to have been avoided: the scientists plugged the bottom of the bore hole with Freon, an inert fluid, and drilled the final distance to the lake surface using a heated drill tip instead of a motorized drill that needed chemical lubricants. When the lake was breached, water flowed up the bore hole before freezing and forming an icy plug.

The world, as mapped by frequency of cholera cases

This really fascinating image comes from a Scientific American guest blog post about the appendix. What does the appendix have to do with cholera? Turns out, the more we study the appendix, the more it appears that this organ—once thought to be useless—is actually a storage system that allows your gut to repopulate itself with beneficial bacteria following a bout with a dramatic, gut-wrenching such as cholera.

This theory makes a lot of sense, but it hasn't been proven yet. The blog post, written by Rob Dunn, tells the story of a couple of studies that seem to add further support to the theory. In one, 11% of people with an appendix had a recurrence of Clostridium difficile infection, while 48% of those without an appendix had a recurrence.

Grendell’s results do not prove Parker is right. Science does not work that way. More tests, even true experiments, need to be done. Maybe there was something else that differed between individuals with and without their appendixes. Maybe the result only applies to the mostly white population Winthrop hospital serves. Maybe the immune system plays a more important or different role than Parker envisions. These “maybes” are part of what make science beautiful — the idea that each question, each test, and each day, lead to more questions. Every good question is a road that goes on forever, diverging and bounding forward, sometimes quickly, other times more slowly, as new paths emerge and some of the old ones run straight into brick walls.

Where does this leave us? In your body is an organ that appears to be/may be/could be helping out the bacteria in your life so they can, in turn, help keep you alive. If you do not have your appendix anymore, you may be at an increased risk of recurrence and even death when confronted with a pathogen like C. diff., cholera or any of a wild kingdom of other pathogens. This possibility raises the question of what to do if your appendix (or your child’s appendix) becomes inflamed. First things first, you should seek medical attention. As for what the treatment should be, while appendicitis can be deadly, recent studies suggest some, but not the majority, of cases of appendicitis can be resolved using antibiotics, though the topic is an active area of research and little is known about the prognosis for individuals treated with antibiotics for appendicitis later in life7. Might there, some day, be solutions other than surgery and antibiotics, solutions that aim at restoring the sanctuary of the appendix? Maybe. Until then, doctors keep cutting infected appendixes out. When they do, when they hold them up, they hold up a symbol — a somewhat gross, pinky-finger-sized symbol –both of our complex relationship with other species and of how little we know.

Instant holiday diet plan

Reduce your consumption of turkey this Thanksgiving by simply reading Maryn McKenna's report on drug-resistant staph bacteria infecting the U.S. meat supply.

How yogurt can alter gene expression

Scientists don't actually know how the bacteria in yogurt and other fermented foods help humans digest food easier. But a recent study hit on a possible explanation. Turns out, some probiotics seem to be capable of altering gene expression in our native gut flora.

Jeffrey Gordon, a microbiologist at Washington University in St. Louis, and his team gave a commercially-available probiotic yogurt containing five strains of bacteria to healthy adult volunteers and administered the same five strains to mice that harbored a subset of genetically-characterized human gut microbes. The yogurt bacteria did not significantly alter population structure in any of the entrenched gut microbes, in humans or mice—a result that is not surprising, according to Mills. “To assume that you could eat a yogurt and numerically challenge what’s in your gut is kind of like dumping a gallon of Kool-Aid in your swimming pool and expecting it to change color,” he said.

But RNA sequencing of the human gut microbes in the mice revealed that the probiotic bacteria changed the expression of gut microbe genes encoding key metabolic enzymes, such as those involved in the catabolism of sugars called xylooligosaccharides, which are found in many fruits and vegetables. Mass spectrometry of metabolites in urine, which result from the ramped up metabolic processes in the probiotic-fed mice, confirmed the alterations, and when the researchers ran similar analyses on gut microbes from the human yogurt eaters, they found upregulation of the same genes.

This study won't be the final word on the subject of how probiotics work. It needs to be replicated and, even then, there are still a lot of questions that need answering. But it does represent an interesting peek inside an interaction between our bodies and other life forms. Cool stuff!

Scientists simulate Europa

Researchers at the Universidad de Buenos Aires recreated conditions found on the surface of Jupiter's moon Europa in the lab, and then proved that some Earth organisms are capable of surviving in that extreme environment. At least, for three hours. It's one experiment in a growing body of work aimed at proving that Earth could seed other planets with life.