WBEZ | bacteria http://www.wbez.org/tags/bacteria Latest from WBEZ Chicago Public Radio en Clever Apes: A world of bugs http://www.wbez.org/blog/clever-apes/2012-02-22/clever-apes-world-bugs-96637 <img typeof="foaf:Image" src="http://llnw.wbez.org/blog/photo/2012-February/2012-02-22/Underwater sampling.jpg" alt="" /><p><p><img alt="A scientist samples the bottom of the Pacific Ocean, part of a global census of " class="caption" height="450" src="http://llnw.wbez.org/blog/insert-image/2012-February/2012-02-22/Underwater sampling.jpg" title="A scientist samples the bottom of the Pacific Ocean, part of a global census of microbes. (Courtesy of Argonne National Lab)" width="600"></p><p>Microbes are by far the most abundant life form on the planet. The numbers are so big, they’re almost comical: maybe <a href="http://www.pnas.org/content/95/12/6578.full.pdf+html?sid=46290cc2-454b-4f78-8a1f-6d40b692e10d">five million trillion trillion bacteria on earth</a>, and that’s conservative. And yet we know shockingly little about who’s living where, and what they do.</p><p>So, big deal, right? We’ve gotten along this far without a phone book for the hordes of germs in almost every nook and cranny on the globe. But consider some of the very practical things bacteria do for us. They break down stuff in the soil, without which we couldn’t grow crops. They are a carbon spigot, releasing or trapping greenhouse gasses that contribute to climate change. They even <a href="http://www.scientificamerican.com/article.cfm?id=gulf-oil-eating-microbes-slide-show">eat oil spills</a>. That’s not to mention everything the bugs that <a href="http://www.wbez.org/blog/clever-apes/2012-01-23/clever-apes-another-gut-check-95760">live in and on our bodies </a>do for our digestion, metabolism and immune system.</p><p>Now the <a href="http://www.google.com/url?sa=t&amp;rct=j&amp;q=&amp;esrc=s&amp;source=web&amp;cd=1&amp;ved=0CCwQFjAA&amp;url=http%3A%2F%2Fwww.earthmicrobiome.org%2F&amp;ei=_qhFT8T9Ha7MsQKQt83CDw&amp;usg=AFQjCNGfbEVeT_VlkeubEK-QcNpIp8Wucw">Earth Microbiome Project </a>is out to catalog microbial life all over the planet – it’s billed as the largest microbiology study ever undertaken. Scientists at Argonne National Laboratory are taking much of the lead. They are collecting samples from basically everywhere: the arctic tundra, the deep ocean, a farm in Ohio, the hind legs of a lizard, the inside of a kid’s aquarium.</p><p>They also have samples from <a href="http://www.facebook.com/photo.php?fbid=283433271723536&amp;set=a.266678816732315.61506.260248800708650&amp;type=1&amp;theater">my cell phone, and my left shoe</a>. Last weekend, at the annual meeting of the <a href="http://www.google.com/url?sa=t&amp;rct=j&amp;q=&amp;esrc=s&amp;source=web&amp;cd=1&amp;ved=0CEcQFjAA&amp;url=http%3A%2F%2Fwww.aaas.org%2F&amp;ei=malFT_PAA6qKsAKKpoHEDw&amp;usg=AFQjCNF2TmSKtn3_NU20wh7uJAsOC7HYVg">American Association for the Advancement of Science</a> in Vancouver, Canada, Argonne scientists Jack Gilbert and others briefed the press on the project. In a PR masterstroke, they distributed swabs to all the reporters and had us swab our phones and shoes. They then rushed the specimens back to Argonne, where they’re rapidly sequencing the genes. Any day now, they’ll be publishing the results on <a href="http://www.google.com/url?sa=t&amp;rct=j&amp;q=&amp;esrc=s&amp;source=web&amp;cd=4&amp;ved=0CEQQFjAD&amp;url=http%3A%2F%2Fwww.facebook.com%2FHomeMicrobiome&amp;ei=6q9FT7z0HszyggfI-9yLBA&amp;usg=AFQjCNG_UTzJ7QGpLe8lCPXzp9m_H1NWsQ">Facebook</a>. As soon as I know what kind of filth I’m carrying around on my touchscreen and shoe sole, I’ll post it here.</p><p>(I talked over these issues on WBEZ’s new show, <a href="http://www.wbez.org/afternoonshift">The Afternoon Shift with Steve Edwards. </a>You can hear the conversation by clicking the “listen” link above, or by subscribing to our <a href="http://itunes.apple.com/us/podcast/wbezs-clever-apes/id379051174">podcast</a>.)</p><p>A fuller picture of earth’s microbial life could have some very concrete benefits for us. Gilbert says by understanding the soil bacteria on farmland, we might be able to put together a kind of microbial weather report, predicting what will grow well there under which conditions. We might also be able to come up with better climate change models, and even change the course of climate change, by figuring out where microbes are big players in either producing or trapping greenhouse gasses. We might someday be able to predict where and when to expect a particularly high load of bad bugs, like tropical diseases or flu. And we might even be able to make better decisions about when to wipe out all the microbial life somewhere (99.9 percent of which is benign, or even beneficial) by, say, sanitizing your hands, sterilizing a hospital room or <a href="http://www.wbez.org/blog/clever-apes/2012-01-17/clever-apes-24-gut-feelings-95602">taking an antibiotic</a>, or when to leave well enough alone.</p><p>We’ll have more on the microbial civilization that lives on my iPhone and my Doc Martens in coming days, along with a whole other fascinating element of this microbiology bonanza: the <a href="http://scistarter.com/project/562-Home%20Microbiome%20Study">Home Microbiome Study</a>. You can find out how you might enroll in the study, and learn how your microbial profile matches up with your house’s.</p><p>Don’t forget to subscribe to our <a href="http://feeds.feedburner.com/CleverApesPodcast" target="_blank" title="http://feeds.feedburner.com/CleverApesPodcast">podcast</a>, follow us on&nbsp;<a href="http://twitter.com/#%21/cleverapes" target="_blank" title="http://twitter.com/#!/cleverapes">Twitter</a>, and find us on&nbsp;<a href="http://www.facebook.com/pages/Clever-Apes-on-WBEZ/118246851551412" target="_blank" title="http://www.facebook.com/pages/Clever-Apes-on-WBEZ/118246851551412">Facebook</a>.</p></p> Wed, 22 Feb 2012 23:09:00 -0600 http://www.wbez.org/blog/clever-apes/2012-02-22/clever-apes-world-bugs-96637 Clever Apes: Another gut check http://www.wbez.org/blog/clever-apes/2012-01-23/clever-apes-another-gut-check-95760 <img typeof="foaf:Image" src="http://llnw.wbez.org/blog/photo/2012-January/2012-01-24/breast cancer_flickr_ginko lev.jpg" alt="" /><p><p><img alt="Spotted on the wall at Rush's digestive diseases lab. (WBEZ/Gabriel Spitzer)" class="caption" src="http://llnw.wbez.org/blog/insert-image/2012-January/2012-01-23/Stool sample.jpg" style="width: 500px; height: 444px;" title="Spotted on the wall at Rush's digestive diseases lab. (WBEZ/Gabriel Spitzer)"></p><p>So we just finished explaining how <a href="http://www.wbez.org/blog/clever-apes/2012-01-17/clever-apes-24-gut-feelings-95602">the gut is our second brain</a>. How to top that? How about this: Your gut is its own planet.</p><p>The human intestine hosts an entire civilization of microorganisms – about 100 trillion by most estimates. That’s many times more than there are cells in your body. You may think you’re the center of your own universe, but in a sense you’re just a walking ecosystem for this teeming population of bugs.</p><p>The good news is, most of them are beneficial to us. Our intestinal flora help us digest food, excrete waste and even train our immune system. That is kind of old news, but only recently have scientists begun to uncover just how central a role our microscopic gut workforce plays in our overall health.</p><p>Here is one surprising connection – or rather, hypothesized connection: The gut flora <a href="http://www.physorg.com/news175953178.html">may have a hand in breast cancer risk. </a><a href="http://rush.photobooks.com/directory/profile.asp?dbase=main&amp;setsize=10&amp;last=mutlu&amp;Submit=Search%21&amp;pict_id=0005920">Dr. Ece Mutlu</a> of Rush University Medical Center is investigating this possibility. Click the “Listen to this story” button above to hear our interview with her.</p><p>It goes something like this: As the bacteria go through their little lives, eating and excreting, they produce many different compounds. Certain bugs are involved with hormones, specifically estrogen (listen to the interview to hear how Dr. Mutlu started thinking about this hint: it involves <a href="http://www.ncbi.nlm.nih.gov/pubmed/11351429">sewage treatment plants</a>). Some bacteria break down estrogen, some activate it. Depending on what food we eat, we might encourage the growth of some bacteria or suppress others. That in turn could lead to higher levels of estrogen exposure, which is known to increase the risk of certain kinds of cancers (at least in some people).</p><p>This is still in the early stages of study. But it’s a hallmark of the new ways in which researchers are thinking about the gut flora. Science in general is good at identifying correlations (say, diet and cancer risk), but often less good at teasing out the mechanism behind it – the reason why some environmental factor influences a disease or condition. The gut bacteria are becoming prime candidates to make a lot of those links.</p><p>I, for one, am becoming a bit fanatic about this subject, so expect more down the line. Meanwhile, don’t forget to subscribe to our <a href="http://feeds.feedburner.com/CleverApesPodcast" target="_blank" title="http://feeds.feedburner.com/CleverApesPodcast">podcast</a> (so you won’t miss out on cool interviews like Dr. Mutlu), follow us on&nbsp;<a href="http://twitter.com/#%21/cleverapes" target="_blank" title="http://twitter.com/#!/cleverapes">Twitter</a>, and find us on&nbsp;<a href="http://www.facebook.com/pages/Clever-Apes-on-WBEZ/118246851551412" target="_blank" title="http://www.facebook.com/pages/Clever-Apes-on-WBEZ/118246851551412">Facebook</a>.</p></p> Mon, 23 Jan 2012 23:17:00 -0600 http://www.wbez.org/blog/clever-apes/2012-01-23/clever-apes-another-gut-check-95760 Feds okay Chicago River cleanup http://www.wbez.org/story/feds-okay-chicago-river-cleanup-93801 <img typeof="foaf:Image" src="http://llnw.wbez.org/story/photo/2011-May/2011-05-03/Chi River.jpg" alt="" /><p><p>After months of back and forth, the federal Environmental Protection Agency has approved Illinois' new water quality standards for several Chicago area waterways.&nbsp; For more than a year, the EPA has encouraged Illinois to make the Chicago and Calumet Rivers clean enough to swim in.</p><p>Former Mayor Richard Daley responded to federal regulators by telling them to "go swim in the Potomac."&nbsp;</p><p>Chicago is one of the few big cities in the country that doesn't disinfect sewage before discharging it. But this past May, the EPA's encouragement became a demand. After overcoming political opposition from local water officials, the Illinois government was forced to change its quality standards. Local water officials will now have to disinfect water discharged into the river system.</p><p>The approved standards will apply to the North and South Branches of the Chicago River, the North Shore Channel, the Cal-Sag Channel and the Little Calumet River.</p><p>An EPA official says the new standards will transform the Chicago River from a sewage canal to a recreational and economic asset.</p></p> Mon, 07 Nov 2011 13:28:00 -0600 http://www.wbez.org/story/feds-okay-chicago-river-cleanup-93801 Organic poultry farms have fewer drug-resistant bacteria, study finds http://www.wbez.org/story/2011-08-10/organic-poultry-farms-have-fewer-drug-resistant-bacteria-study-finds-90508 <img typeof="foaf:Image" src="http://llnw.wbez.org/npr_story/photo/2011-August/2011-08-12/organic chickens_Flickr_WBUR.jpg" alt="" /><p><p>Proponents of organic meat often make the case that it's inherently better for people's health and the environment than meat raised by conventional farming methods. But the actual impacts of organic production can be tough for scientists to prove.</p><p>A <a href="http://ehp03.niehs.nih.gov/article/fetchArticle.action?articleURI=info%3Adoi%2F10.1289%2Fehp.1003350">study</a> out today in <em>Environmental Health Perspectives</em> adds some weight to the argument that organic poultry, at least, may reduce one type of health risk. A team of scientists from the University of Maryland and other universities found that large-scale organic poultry farms — which are not allowed to use antibiotics to prevent disease in the animals — had significantly lower levels of one group of drug-resistant bacteria than their conventional counterparts.</p><p></p><p>The study comes at a time when antibiotic use in industrial livestock production is under heavy fire from the public health community. Farmers who raise food-producing animals use about <a href="http://www.wired.com/wiredscience/2010/12/news-break-fda-estimate-us-livestock-get-29-million-pounds-of-antibiotics-per-year/">29 million pounds</a> of antibiotics each year, according to the Food and Drug Administration, and the latest <em>Salmonella</em> outbreak in ground turkey turned out <a href="http://www.npr.org/blogs/health/2011/08/06/139019030/salmonella-outbreak-reignites-debate-over-antibiotics-in-food-supply?ps=sh_sthdl">to be caused</a> by a strain resistant to several antibiotics.</p><p>Bacteria resistant to antibiotics can make their way to humans through the meat itself and the environment — like waterways contaminated with runoff. If humans ingest those bacteria or are exposed to them other ways and get sick, there aren't many options for treating them.</p><p>Several European countries have already banned the prophylactic or preventative use of antibiotics for exactly this reason, and some studies there have shown that once farmers reduce antibiotic use, those resistant microbes mostly go away.</p><p>But that's been difficult to study in the U.S., since the majority of farmers still use antibiotics pretty indiscriminately. So <a href="http://www.sph.umd.edu/miaeh/people/index.cfm">Amy Sapkota</a>, an assistant professor of environmental health sciences at the University of Maryland and lead author of the study, decided to look at 10 mid-Atlantic farms that had just adopted organic practices. She measured the change in levels of <em>enterococci</em> bacteria against 10 mid-Atlantic conventional farms. <em>Enterococci </em>can show up in poultry litter, feed, and water. The researchers tested their resistance to 17 different types of antibiotic drugs.</p><p>"We were surprised to see such dramatic differences in the levels of antibiotic-resistant bacteria in the very first flock at these organic farms," Sapkota tells Shots.</p><p>For one common antibiotic, erythromycin, 67 percent of an <em>Enterococcus </em>bacterium from conventional poultry farms were found to be resistant, while 18 percent were resistant at the organic farms. But Sapkota notes that organic farms usually still have "reservoirs" of resistant bacteria that can linger in the soil or the packed dirt floor of the poultry houses, so they may never be completely free of the bugs.</p><p>But Sapkota's work does not mean organic poultry eaters get a free pass when it comes to food safety. No chicken is completely free of <a href="http://www.npr.org/blogs/health/2011/06/08/137055474/mixed-results-on-foodborne-illness-cast-shadow-on-daily-menu">pathogens</a>, and consumers still need to take all the precautions they normally would when preparing poultry: Cook it well and beware of cross-contamination on the cutting board. <div class="fullattribution">Copyright 2011 National Public Radio. <img src="http://metrics.npr.org/b/ss/nprapidev/5/1313159176?&gn=Organic+Poultry+Farms+Have+Fewer+Drug-Resistant+Bacteria%2C+Study+Finds&ev=event2&ch=103537970&h1=antibiotics,food+safety,Public+Health,Infectious+Disease,Shots+-+Health+Blog,Health,Your+Health,Food,Home+Page+Top+Stories,News&c3=D%3Dgn&v3=D%3Dgn&c4=139386917&c7=1128&v7=D%3Dc7&c18=1128&v18=D%3Dc18&c19=20110810&v19=D%3Dc19&c20=1&v20=D%3Dc20&c31=133650740,133490675,133188449,126568156,103537970&v31=D%3Dc31&c45=MDA0OTc2MjAwMDEyNjk0NDE4OTI2NmUwNQ001"/></div></p></p> Wed, 10 Aug 2011 13:02:00 -0500 http://www.wbez.org/story/2011-08-10/organic-poultry-farms-have-fewer-drug-resistant-bacteria-study-finds-90508 Gut Bacteria Know Secrets About Your Future http://www.wbez.org/story/2011-06-10/gut-bacteria-know-secrets-about-your-future-87773 <img typeof="foaf:Image" src="http://llnw.wbez.org/npr_story/photo/2011-June/2011-06-13/rod-shaped_bacterium.jpg" alt="" /><p><p>You have a hundred trillion of these guys in you right now. Before you were born, you had hardly any.</p><p>Back then, you were floating in amniotic fluid, protected, sanitized. Bacteria kept their distance. Until you slipped down that birth canal, you were pretty much spic-and-span.</p><p>Then came your birthday, and all of a sudden, you were invaded. From the delivery, from the doctor's hands, from the first meal at your mother's breast, from your older sister who kisses you (or, if no one's looking, spits on you), from everyone, from everywhere came an army of bacteria that moved in and stayed.</p><p>Right now, in your mouth, in your gut, on your skin, you are carrying about 10 times more bacteria cells than human cells. If you swallow antibiotics and kill a lot of them, a few weeks later, the same bacteria come bounding back. They're staying.</p><p>"We are, in essence, only 10 percent human," Dr. Roy Sleator, lecturer at Cork Institute of Technology in Ireland, told <a href="http://www.telegraph.co.uk/health/healthpicturegalleries/8523602/Meet-some-of-the-bacteria-that-make-up-90-per-cent-of-the-living-cells-in-your-body.html?image=3"><em>The Daily Telegraph</em></a>. "The rest is pure microbe."</p><p></p><p><strong>Mostly Microbe</strong></p><p>What are bacteria doing in you? For you? Against you?</p><p>They look, yes, a little alien. This image of hairy lozenges cruising through an intestine are Escherichia coli (E. coli, for short), the bacteria now making people sick all over Europe. Bacteria also come in all kinds of shapes, strings, spheres, oblongs. But they aren't all bad guys. In fact, without them, we wouldn't survive very long. We need them to digest food, to produce vitamins. We use them to fight off the bad bacteria. In spite of what you're reading in the papers this week, they are more helpers than hurters.</p><p>Now comes the big (and double) surprise.</p><p>First (<a href="http://www.npr.org/templates/story/story.php?storyId=95900616">I wrote about this a few years ago</a>), scientists discovered that people around the world can have different communities of bacteria in our intestines. If we are hotels, we seem to attract very different guests. So as adults, we become identified with certain bacteria. Which has consequences.</p><p>I, for example, might have a lot of bacteria in me that are great at digesting oats. You? Your bacteria may not care much for oats. What happens if both of us have a giant bowl of Cheerios for breakfast?</p><p>I gain weight. You make more frequent trips to the rest room (and stay skinny). The bacteria in your gut may make you susceptible to certain diseases, to obesity, or they may make you less susceptible. Bacteria matter.</p><p>So why do different people attract different bacteria as they grow up? Here comes the second surprise.</p><p>Scientists assumed it must be cultural. Babies born in northern Alaska presumably drink milk from moms who eat fish, who live in cold, snowy places, have dogs as pets and attract one mix of bacteria.</p><p>Indian babies, on the other hand, have mothers who eat rice, potatoes, spices, have different pets, birds maybe, and create a different mix of bacteria. Different worlds produce different environments. That makes sense, no?</p><p>But — along come Peer Bork, Manimozhiyan Arumugam and Jeroen Raes from the European Molecular Biology Laboratory in Heidelberg, Germany. They took a look at stool samples (aren't you glad you didn't become a biologist?) from a small group of Europeans and read similar studies from Japan and America and, startlingly, found that gut bacteria in humans don't reflect local cultures. Not at all. Instead, <a href="http://www.embl.de/aboutus/communication_outreach/media_relations/2011/110420_Heidelberg/">said Peer Bork</a>:</p><p><blockquote></p><p>We found that the combination of microbes in the human intestine isn't random. Our gut flora can settle into three different types of community — three different ecosystems, if you like.</p><p></blockquote></p><p>And weirder still, food, diet, culture don't seem to matter. Nor do age, gender or nationality. So if we look at a bunch of Alaskans and a bunch of Indians, it now seems their gut bacteria <em>will not look that different</em>. What's more, all three "gut types" will show up in both groups. As <a href="http://blogs.discovermagazine.com/notrocketscience/">blogger Ed Yong</a> puts it, "In gut bacteria, we are united."</p><p>The scientists don't know how to explain this finding. It's so startling.</p><p>Maybe further studies will change the result. After all, these subjects all come from rich countries (where packaged food and imported food may dramatically reduce the range of what people eat). Perhaps the pattern will change when they check stools in central Africa or Borneo. Plus, the initial data sample was small, just 39 people. But they've now looked at an extra 85 people from Denmark and 154 in America and the pattern is still there.</p><p>Here's a possibility: It may turn out that when you take your first drink from your mother's breast, the earliest bacteria set up shop and decide who gets to follow. In other words, instead of humans choosing their bacteria, the bacteria choose each other. A Daniel Boone bacterium arrives in your gut, builds some kind of barrier, and like a bouncer at a night club, only lets its "friends" in.</p><p>The mystery deepens: Why only three types? Nobody knows yet. Gut bacteria may turn out to be like blood types. We know there are A people and O people and B people. Now there may be Gut Type A, B and C people.</p><p>And if this turns out to be true, we may be able to go to the doctor, get our "gut profile" and discover that because of the population inside, we are slightly more likely to get fat or get ulcers, or hormone problems, or autism (yup, there's <a href="http://www.ncbi.nlm.nih.gov/pubmed/12173102">a study</a> about that), or at least get a little peek into our probabilistic future. While tentative, this science is telling us that each of us is a package composed of Mommy's genes, Daddy's genes and the bacterial genes that have moved in and stayed. We have a genome and we also have a "microbiome." And the microbiome is a whole new window into who we are and are going to be.</p><p><hr /></p><p><em>For more information on gut bacteria studies, check</em> <em>Ed Yong's posts</em> <em>at his blog</em> <a href="http://blogs.discovermagazine.com/notrocketscience/2011/01/31/gut-bacteria-steer-the-development-of-the-young-brain/">Not Exactly Rocket Science</a> <em>and Carl Zimmer's <a href="http://www.nytimes.com/2011/04/21/science/21gut.html">recent stories</a></em> <em>at the New York Times and at his blog</em>, <a href="http://blogs.discovermagazine.com/loom/">The Loom.</a></p><p><strong> </strong></p><p><strong> </strong> <div class="fullattribution">Copyright 2011 National Public Radio. To see more, visit <a href="http://www.npr.org/">http://www.npr.org/</a>.<img src="http://metrics.npr.org/b/ss/nprapidev/5/1307981634?&gn=Gut+Bacteria+Know+Secrets+About+Your+Future&ev=event2&ch=5500502&h1=Krulwich+Wonders%E2%80%A6,Brain+Candy,Humans,Health,Opinion,Environment,Science,Home+Page+Top+Stories&c3=D%3Dgn&v3=D%3Dgn&c4=137084528&c7=1057&v7=D%3Dc7&c18=1057&v18=D%3Dc18&c19=20110610&v19=D%3Dc19&c20=1&v20=D%3Dc20&c31=5500502&v31=D%3Dc31&c45=MDA0OTc2MjAwMDEyNjk0NDE4OTI2NmUwNQ001"/></div></p></p> Fri, 10 Jun 2011 11:46:00 -0500 http://www.wbez.org/story/2011-06-10/gut-bacteria-know-secrets-about-your-future-87773