Dr. Kiki Sanford on how scientists are predicting outbreaks from an unusual new vantage point.Read the rest
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." Read the rest
Read the rest
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.
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.
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.
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"
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
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.
Via Bora Zivkovic
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.
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.
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!