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Human-engineered microbes are workhorses of the pharmaceutical and chemical industries, churning out biofuels, drugs, and many other products. But they can cause big problems if they become contaminated by other microbes or viruses or escape into the environment. Now, a new type of microbe that can survive only on artificial nutrients promises better security against such mishaps. The strategy, described in two papers in this week's issue of Nature, might ultimately be used to control genetically engineered plants or other organisms released into the wild to create products or clean up pollution.

But when Sokol did a comparative DNA analysis of diseased sections of intestine surgically removed from the patients, he observed a relative depletion of just one common bacterium, Faecalibacterium prausnitzii. Rather than "bad" microbes prompting disease, he wondered, could a single "good" microbe prevent disease?

Gut microbes-the collection of bacteria and other organisms that inhabit our intestines-have been shown to play a role in a wide variety of conditions from asthma to obesity. But researchers still don't know precisely how they contribute to obesity. To gain a better understanding, a team led by physiologist Mirko Trajkovski from the University of Geneva in Switzerland has been following up on any leads he can to learn about the link between these microbes and metabolism. Trajkovski knew from past research that getting rid of some gut bacteria in mice makes them less able to maintain their internal body temperature in the cold. He wondered whether there might be a connection between gut microbes, external temperature, and weight control.

This interrupted case study for the flipped classroom introduces the human microbiome from the perspective of one of its occupants, Heidi Helicobacter (Helicobacter pylori).  Heidi lives in the gut of Kristen, a college student, and discusses her fellow microbial inhabitants, functions of these various microbes, and alludes to factors that can disrupt the healthy human microbiome. Students prepare for class by viewing several brief videos and then discuss in class whether Kristen should undergo a fecal microbiota transplant to treat her Clostridium difficile infection.  A lab component has students model, using colored beads, how antibiotics can act as a selective agent for drug-resistant microbes such as C. difficile. The case concludes with Kristen about to give birth to a new baby several years later.  Students listen in as Kristen's microbes discuss the formation of the new baby's microbiome. The case has been used successfully in a general biology class and could easily be adapted for a microbiology, human physiology, ecology, or evolution course.

The groundwater is cold, deep and twice as salty as seawater, but the water streaming out of Blood Falls, which teems with microbes, tells us that it is unlikely to be lifeless. "The fact that the [water] contains metabolically active micro-organisms that appear to be suited to life in a dark, cold brine supports the idea that life should persist throughout the subsurface," says Mikucki. If so, those microbes could be fuelling life in the Southern Ocean. By breaking down iron-containing rocks they might be dumping as much as 170 million kilograms of iron into the ocean each year, according to the researchers' estimates, helping to explain why marine productivity is seasonally very high near to the coast.

Microbes 2,500 meters below the seafloor in Japan are most closely related to bacterial groups that thrive in forest soils on land, suggesting that they might be descendants of ones that survived when their terrestrial habitat was flooded 20 million years ago

3:45 video, From the microbes in our stomachs to the ones on our teeth, we are homes to millions of unique and diverse communities which help our bodies function. Jessica Green and Karen Guillemin emphasize the importance of understanding the many organisms that make up each and every organism.

A microbe that causes malaria tricks mosquitos into helping it spread, a new study finds. The microbe is a parasite that leaves a chemical behind in the blood of the people or other animals that it infects. Mosquitoes are drawn to scent of blood hosting this chemical. It entices them to slurp up some of the infected meal. Then voila! The parasites get airlifted from their old host to new ones. And so malaria spreads.

Sonnenburg, his wife Erica, and the graduate student Samuel Smits confirmed this idea in a recent experiment. The researchers started with mice that had been raised in sterile bubbles and then loaded with identical collections of gut microbes. They then fed these mice a high-fiber diet, before randomly switching half of them to low-fiber chow for seven weeks. Predictably, the fall in fiber caused upheavals in the rodents' guts. In the low-fiber group, the numbers of 60 percent of the local microbe species fell dramatically, and some remained low even after the mice returned to high-fiber meals. Those seven low-fiber weeks left lingering scars on the animals' microbiomes.

Dubilier is hardly alone in her plight. A heaping teaspoon of soil or a shot of ocean water may contain as many as one million bacterial species. Many of them are potential gold mines of chemicals and metabolites with medicinal, engineering, and energy applications. But when researchers have tried to culture these microbes in the lab, only a minority of cells form colonies. Clearly, nutrients, a carbon source, and time are usually not enough to coax bacteria isolated from the wild to grow in a laboratory setting. So what's the missing ingredient?

 Students must consider the role of rumen bacteria and how genetic modification may alter the potential of these bacteria. The case engages students in learning basic principles of bacterial genetics and biotechnology as they consider how microbes and microbial processes impact the environment. The case could also be used in an introductory genetics or biotechnology course.

Behold the microscopic jungle in and around you: tiny organisms living on your cheeks, under your sofa and in the soil in your backyard. We have an adversarial relationship with these microbes -- we sanitize, exterminate and disinfect them -- but according to microbiologist Anne Madden, they're sources of new technologies and medicines waiting to be discovered. These microscopic alchemists aren't gross, Madden says -- they're the future.

The next time you look in a mirror, think about this: In many ways you're more microbe than human. There are 10 times more cells from microorganisms like bacteria and fungi in and on our bodies than there are human cells. But these tiny compatriots are invisible to the naked eye. So we asked artist Ben Arthur to give us a guided tour of the rich universe of the human microbiome.

In short, you have an aura, except it isn't made of purplish light; it's your personal cloud of dead skin cells, fungus and many, many microbes. And researchers are learning to be able to identify you by it.

Microbiome cloud story 4:12

Inflammation may help you fight off invading microbes, but it can also kill you, leading to insufficient blood flow and even organ failure. A new study shows that some cancer drugs may be able to quell the excessive inflammation that occurs in conditions such as sepsis, which is responsible for more than 250,000 deaths in the United States each year.

4:30 video When life emerged on Earth about 4 billion years ago, the earliest microbes had a set of basic genes that succeeded in keeping them alive. In the age of humans and other large organisms, there are a lot more genes to go around. Where did all of those new genes come from? Carl Zimmer examines the mutation and multiplication of genes.

Using bacteriophages to deliver a specific CRISPR/Cas system into antibiotic-resistant bacteria can sensitize the microbes to the drugs, according to a study published this week (May 18) in PNAS.

When researchers tested wastewater before and after treatment at a Milwaukee-area treatment plant, they found that two drugs-the anti-epileptic carbamazepine and antibiotic ofloxacin-came out at higher concentrations than they went in. The study suggests the microbes that clean our water may also piece some pharmaceuticals back together.

If thinking about the billions of bacteria taking up residence in and on your body gives you the willies, you probably won't find it comforting that humans are also full of viruses. These maligned microbes are actually intertwined in the very fibers of our being-about 8 percent of our genetic material is made up of absorbed forms of retroviruses, the viral family to which HIV, the pathogen that causes AIDS, belongs.