gut microbes influence behavior

TheScientist | Gut microbes acquired early in life can impact brain development in mice and subsequent behavior, such as decreasing physical activity and increasing anxiety, according to a study published this week in the Proceedings of the National Academy of Sciences.

"This paper opens the door to new studies in at least two directions," Yale University microbiologist Andrew Goodman, who was not involved in the research, told The Scientist in an email. "First, determining how differences between complete host-associated microbial communities lead to differences in behavior, and second, exploring the contributions of microbes during specific developmental periods in the host."

Gut microbiota often colonize their hosts early in life, either during pregnancy or following birth, and play an integral role in the health of developing organisms. Previous research has shown that the bacteria affect the development of liver function, the protection epithelial cells afford underlying digestive tissue, gut regulation and the growth of new capillary blood vessels. But this is the first time gut flora have been linked to brain development and behavior.

Harmful microbial infections, on the other hand, have been linked to neurodevelopmental disorders, including autism and schizophrenia. And rodents infected by microbial pathogens before and after birth demonstrated behavioral abnormalities, such as anxiety-like behavior and impaired cognitive function, leading Rochellys Diaz Heijtz, a neurobiologist at the Karolinska Institute in Sweden, and her colleagues to wonder if the gut's normal microbial residents may similarly influence brain development.

The researchers tested exploratory activity in germ-free mice and mice with normal gut microbiota by tracking their movements across open space. They also tested anxiety of the two groups in two classic rodent behavioral tests -- the light-dark box and the elevated maze. Spending more time in lit areas and along unwalled, elevated maze portions equated to less anxiety.

Germ-free mice appeared to be more exploratory than mice with normal microbiota, venturing farther and to more areas of the space provided. Germ-free mice also spent more time in the light and engaged in riskier behavior in the maze, indicating they suffered from less anxiety than their microbe-filled counterparts.

The team then infected germ-free mice with normal gut microbiota when they were born to test whether the gut flora could alter the mice's activity and anxiety levels. Sure enough, the newly infected mice spent less time exploring and engaging in risky behavior, like the normal mice in the initial experiments. The results further supported the argument that the microorganisms can affect brain and behavior when introduced early enough in development.

"These microorganisms communicate in a systemic fashion to the developmental programming of a new individual and can influence fundamental aspects of behavior," said Diaz Heijtz. "We should start to consider the possibility that the microbiome and/or its composition may contribute to psychiatric problems."

bacteria farming amoeba

Wired | Colonies of a bizarre microbial goo have been found practicing agriculture at a scale tinier than any seen before.

Animals such as ants, snails and beetles are known to farm fungus. But the slime mold’s bacterial-farming trick takes it into a whole new realm..

“If you can pack your food source with you, it’s a serious advantage,” said molecular biologist Debra Brock of Rice University, co-author of the slime-mold study, published Jan. 19 in Nature.

Dictyostelium discoideum, the best-known of a group of creatures called slime molds, spends part of its life as a single-celled amoeba feeding on bacteria that grow in decomposing leaves on forest floors.

When food is short, hundreds of thousands of amoebas come together, fusing into a single entity. It may crawl off as a slug in search of richer pastures, then form a stalk topped by a “fruiting body” that bursts to disperse a few lucky amoebas-turned-spores. Or it may form the stalk right away, without crawling.

It’s been thought that slime molds simply scavenge, eating bacteria they like and oozing out the rest. In laboratories, researchers “cure” slime molds of their bacteria by allowing them to purge themselves on Petri dishes. But Brock, who studies how slime-mold cells communicate and self-organize, kept finding bacteria in the fruiting bodies of some slime molds and not others.

When grown in the lab, the unusual fruiting bodies grew both the slime mold and the bacteria.

“The typical response to finding two species in a culture is, ‘Ick, I don’t want this!’” said evolutionary biologist Kevin Foster of Oxford University, who wasn’t involved in the study. “[Brock's team] had the insight to realize this was more than a simple contamination, that something else was going on here.” Fist tap Dale.

yeast nasty...,

LiveScience | It doesn't take much to get the fungus that causes thrush and other infections in the mood. New research suggests that in addition to chemical signals from its own species, the yeast, called Candida albicans, also gets turned on by the so-called pheromones sent out by other species.

And when turned on, this yeast isn't selective. If cells of the opposite sex aren't around, then it mates with same-sex partners, according to Richard Bennett, one of the study researchers and an assistant professor at Brown University in Rhode Island.

This type of fungus is a natural inhabitant of our bodies, particularly our guts, but, given the opportunity, the yeast can also cause harmful infections, ranging from a superficial thrush infection in the mouth to potentially lethal blood infections among those with weakened immune systems.

C. albicans cells come in two forms: white and opaque, names derived from the appearance of their colonies. Opaque cells are the reproductive ones. They produce a pheromone that prompts other opaque cells to turn on genes associated with mating. In the presence of this pheromone, the opaque cells also put out long projections that search for another cell with which to fuse (the yeast equivalent of sex), according to Bennett.

The white cells do not reproduce, but they also respond to the pheromone, which activates an entirely different set of genes. They become sticky, and start to glom together and to surfaces, such as a catheter, forming what is known as a biofilm. This is a common route to harmful infections.

The researchers synthesized a variety of pheromones produced by this species and a variety of other fungal species, and found that the white and opaque cells were not picky about a trigger for their responses. The normal opaque cell pheromone is a string of 13 amino acids, which are organic compounds.

“In some of the pheromones eight of 13 residues were different,” Bennett said. “That’s why we were so surprised with these pheromones. We didn’t expect them to work because they look so different.”

It is not unusual for one species to respond to pheromones from another, however, it is unusual for that response to lead to productive mating, he said.

C. albicans' lax standards may mean that it could respond to other signals from its environment, including signals directly from the host. The next step, Bennett said, is to figure out how these findings fit in with disease.

The research was published online today (Jan. 24) by the journal Proceedings of the National Academy of Sciences. Fist tap Nana.

do bacteria have intelligence?

WeirdAsianNews | This is done within the framework of laying puzzles, akin to Sudoko-style grids, which present simple rules to the bacteria, which are able to establish their own unique traffic schemes within the grids.

The ability to solve logical problems clearly suggests the possibility that they can be trained.

The research team, headed by Ryo Taniuchi, conducted an experiment involving 16 kinds of bacteria aligned in a cage with colors and identical numbers. Each colony contained similar genetic characteristics, depending on what type of cell it held within the puzzle box.

“…We are interested in the advantages that recombination (the swapping of large blocks of genetic information) could have played during the advent of life. We are investigating both the benefits that recombination gives for the creation of new genetic diversity and the protection that recombination provides against the accumulation of deleterious mutations…,” said Taniuchi.

The bacteria respond to one of four colors to solve the problem by utilizing a class of enzymes capable of DNA recombination. These enzymes transmit messages about the location and color of undifferentiated bacteria in the remaining cells of the grid.

The genetic information stored in these “messages” prevents the bacteria from differentiating and becoming the same color as the bacteria-transmitters. Thus, scientists can observe the pattern as undifferentiated bacteria determine what color path to take to solve the problem.

The question remains:

Why are scientists in Japan harvesting intelligent bacteria?

Perhaps it involves the search for knowledge concerning very rich, very complex population-level behavior, such as that found in an ant colony?

So watch out for that moldy bread you may have forgotten to throw out.

Just to be on the safe side, the next time you come across a slice, salute it out of respect. Fist tap Big Don.

ideas of the microbiome and the virome...,

Sciencemag | Humans have been doing battle with bacteria since the 1800s, thwarting disease with antibiotics, vaccines, and good hygiene with mixed success. But in 2000, Nobel laureate Joshua Lederberg called for an end to the “We good; they evil” thinking that has fueled our war against microbes. “We should think of each host and its parasites as a superorganism with the respective genomes yoked into a chimera of sorts,” he wrote in Science in 2000.

His comments were prescient. This past decade has seen a shift in how we see the microbes and viruses in and on our bodies. There is increasing acceptance that they are us, and for good reason. Nine in 10 of the cells in the body are microbial. In the gut alone, as many as 1000 species bring to the body 100 times as many genes as our own DNA carries. A few microbes make us sick, but most are commensal and just call the human body home. Collectively, they are known as the human microbiome. Likewise, some viruses take up residence in the body, creating a virome whose influence on health and disease is just beginning to be studied.

Their genes and ours make up a metagenome that keeps the body functioning. This past decade we've begun to see how microbial genes affect how much energy we absorb from our foods and how microbes and viruses help to prime the immune system. Viewing the human and its microbial and viral components as intimately intertwined has broad implications. As one immunologist put it, such a shift “is not dissimilar philosophically from the recognition that the Earth is not the center of the solar system.”

This appreciation has dawned gradually, as part of a growing recognition of the key role microbes play in the world. Microbiologists sequencing DNA from soil, seawater, and other environments have discovered vast numbers of previously undetected species. Other genomics research has brought to light incredible intimacies between microbes and their hosts—such as a bacterium called Buchnera and the aphids inside which it lives. A study in 2000 found that each organism has what the other lacks, creating a metabolic interdependency.

One of the first inklings that microbiologists were missing out on the body's microbial world came in 1999, when David Relman of Stanford University in Palo Alto, California, and colleagues found that previous studies of bacteria cultured from human gums had seriously undercounted the diversity there. Turning to samples taken from the gut and from stools, the researchers identified 395 types of bacteria, two-thirds of them new to science.

In 2006, Steven Gill of the University at Buffalo in New York and colleagues did a metagenomics study of the gut, analyzing all the genes they could find in the 78 million bases sequenced. They found metabolic genes that complemented the human genome, including ones that break down dietary fiber, amino acids, or drugs, and others that produce methane or vitamins. This and a more comprehensive survey in 2010 by Jun Wang of BGI-Shenzhen in China and colleagues provided support for the concept of the microbe-human superorganism, with a vast genetic repertoire. Now, large-scale studies have surveyed the microflora in the gut, skin, mouth, nose, and female urogenital tract. The Human Microbiome Project has sequenced 500 relevant microbial genomes out of a planned 3000.

Some of these microbes may play important roles in metabolic processes. In 2004, a team led by Jeffrey Gordon of Washington University School of Medicine in St. Louis, Missouri, found that germ-free mice gained weight after they were supplied with gut bacteria—evidence that these bacteria helped the body harvest more energy from digested foods. Later studies showed that both obese mice and obese people harbored fewer Bacteroidetes bacteria than their normal-weight counterparts.

The microbiome is also proving critical in many aspects of health. The immune system needs it to develop properly. What's more, to protect themselves inside the body, commensal bacteria can interact with immune cell receptors or even induce the production of certain immune system cells. One abundant gut bacterium, Faecalibacterium prausnitzii, proved to have anti-inflammatory properties, and its abundance seems to help protect against the recurrence of Crohn's disease. Likewise, Sarkis Mazmanian of the California Institute of Technology in Pasadena showed that the human symbiont Bacteroides fragilis kept mice from getting colitis. And inserting bacteria isolated from healthy guts restored the microbial communities, curing chronic diarrhea in a patient infected with Clostridium difficile.

Herbert Virgin of Washington University School of Medicine finds a similar role for the virome. In mice, his team found that dormant herpesviruses revved up the immune system just enough to make the mice less susceptible to certain bacterial infections.

The ideas of a microbiome and a virome didn't even exist a decade ago. But now researchers have reason to hope they may one day manipulate the body's viral and microbial inhabitants to improve health and fight sickness.

bacterium in soil enhances learning decreases anxiety

Video - mycobacterium vaccae light installation.

Sage | Turning off the TV and computer and spending some time outdoors may not only be good for your health, it may also make you smarter, according to research presented at the 110th General Meeting of the American Society for Microbiology in San Diego by associate professor of biology at The Sage Colleges, Dorothy Matthews. Matthews conducted the research, entitled Effect of Mycobacterium vaccae on Learning, with her colleague, associate professor of psychology and biology, Susan Jenks.

Matthews became intrigued by mycobacterium vaccae, a bacterium commonly found in soil, several years ago after a study indicated that mice injected with a heat-killed version of the bacterium resulted in increased levels of serotonin and reduced levels of anxiety. Serotonin levels, which elevate mood and reduce anxiety, are associated with learning and Matthews was intrigued by the possibility that the bacterium could have an effect on learning in mice and that's exactly what the researchers found.

Mice exposed to the bacteria by nibbling on enticing tidbits of peanut butter snacks laced with the live bacterium were able to negotiate through a maze twice as fast as those in the control group and exhibited a reduction in anxiety behaviors as well.

The mice exhibited a profound increase in learning, according to the study. Even weeks after the mice stopped snacking on the live bacterium, they were still able to impress the researches with their newly learned skills. Three weeks later, the effect seemed to taper off, although since mice live on average for about 2 years, the effects were still impressive. Fist tap Dale.

the shadow biosphere

Video - Felisa Simon Wolf discusses her work at Mono Lake.

WaPo | the discovery opens the door to that possibility and to the related existence of a theorized "shadow biosphere" on Earth - life evolved from a different common ancestor from all we've known so far.

"Our findings are a reminder that life-as-we-know-it could be much more flexible than we generally assume or can imagine," said Felisa Wolfe-Simon, 33, the biochemist who led the effort.

Prompted by debate about the possible existence of a shadow biosphere, Wolfe-Simon set out specifically to see whether microbes that lived in California's briny, arsenic-filled Mono Lake naturally used arsenic instead of phosphorus for basic cellular functions, or were able to replace the phosphorus with arsenic.

She took mud from the lake into the lab and began growing bacteria in Petri dishes. She fed them sugars and vitamins but replaced phosphate salt with arsenic until the surviving bacteria could grow without needing the phosphates at all.

Her research found that some of the bacteria had arsenic embedded into their DNA, RNA and other basic underpinnings.

"If something here on Earth can do something so unexpected - that breaks the unity of biochemistry - what else can life do that we haven't seen yet?" said Wolfe-Simon, a NASA Astrobiology Research Fellow and member of the National Astrobiology Institute team at Arizona State University.

"This is different from anything we've seen before," said Mary Voytek, senior scientist for NASA's program in astrobiology, the arm of the agency involved specifically in the search for life beyond Earth and for how life began here.

"These bugs haven't just replaced one useful element with another; they have the arsenic in the basic building blocks of their makeup," she said. "We don't know if the arsenic replaced phosphorus or if it was there from the very beginning - in which case it would strongly suggest the existence of a shadow biosphere."

Theoretical physicist and cosmologist Paul Davies, director of the Beyond Center at Arizona State and a prolific writer, is a co-author on the new Science paper. He had been thinking about the idea of a shadow biosphere for a decade and had written a paper on it in 2005. Two years later University of Colorado at Boulder philosopher and astrobiologist Carol Cleland also published on the subject. Both asked why nobody was looking for life with different origins on Earth, and Cleland coined the phrase "shadow biosphere."

At a Beyond Center conference four years ago, Wolfe-Simon, then in her late 20s, proposed a way to search for a possible shadow biosphere, and it involved Mono Lake and its arsenic.

"We were kicking vague ideas around, but she had a very specific proposal and then went out and executed it," Davies said. "It defies logic to think she found the only example of this kind of unusual life. Quite clearly, this is the tip of a huge iceberg."

bacterial communities trump game theory

Video - Game Theory explained.

ScienceDaily | When it comes to gambling, many people rely on game theory, a branch of applied mathematics that attempts to measure the choices of others to inform their own decisions. It's used in economics, politics, medicine -- and, of course, Las Vegas. But recent findings from a Tel Aviv University researcher suggest that we may put ourselves on the winning side if we look to bacteria instead.

According to Prof. Eshel Ben-Jacob of Tel Aviv University's School of Physics and Astronomy, current game theory can't account for bacteria's natural decision-making abilities -- it's just too simplistic. Understanding bacteria's reactions to stressful and hazardous conditions may improve decision-making processes in any human arena from everyday life to political elections.

In a recent article published in the Proceedings of the National Academy of Science (PNAS), Prof. Ben-Jacob and his fellow researchers outline how decisions made by communities of bacteria trump game theory. "When human beings make a decision," he says, "they think they're being rational. We now understand that they're influenced by superfluous 'noise,' such as their cognitive state and the influence of others." Bacteria, he explains, are both simpler and more sophisticated -- they can more effectively control this superfluous noise and make group decisions that contribute to the well-being of the entire bacterial colony.

Looking out for the whole
Bacteria live in complex colonies that can be 100 times as numerous as the population of Earth. Under stressful circumstances, bacteria have demonstrated a capacity to assess the noisy and stressful environment around them, filter out what's relevant and what's not, and make decisions that ensure the survival of the colony as a whole.

For example, one bacterial response to starvation or poisoning is that a fraction of the cells "sporulate," enclosing their DNA in a capsule or spore as the mother cell dies. This, says Prof. Ben-Jacob, ensures the survival of the colony -- when the threat is removed, the spores can germinate and the colony grows again.

During this process, the bacteria "choose" whether or not to enter a state called "competence," in which bacteria change their membranes to more easily absorb substances from their neighboring, dying cells. As a result, they recover more quickly when the stress is gone. According to Prof. Ben-Jacob, it's a difficult choice -- in fact, a gamble. The decision to go into a state of competence only pays off if most of the cells decide to sporulate.

Indeed, observations show that only about 10% of cells decide to go into competence. So why don't all bacteria attempt to save themselves? Bacteria don't hide their intentions from their peers in the colony, he explains -- they don't lie or prevaricate, but communicate their intentions by sending chemical messages among themselves. Individual bacteria weigh their decisions carefully, taking into account the stress they are facing, the situation of their peers, the statistics of how many cells are sporulating and how many are choosing competence.

different poop, same gut

The Scientist | For physicians and researchers alike, fecal transplants present an opportunity to gain insight into disease.

Most people might find the idea of having another person's feces injected into their intestine hard to stomach, but for those with intractable gastrointestinal problems, another person's bodily waste is all that's standing between a lifetime of severe illness and a full recovery.
Image: siteflight via stock.xchng

This therapy -- known as fecal transplants, bacteriotherapy, or human probiotic infusions -- has taken to the limelight in recent years, not only because its gross factor makes for great headlines, but in great part because of the growing epidemic of a particularly toxic strain of Clostridium difficile that has been plaguing hospitals across the U.S. for the past decade and affecting more than a quarter of a million Americans per year.

By producing sturdy spores that can linger in the intestinal tract even after repeated antibiotic treatment, C. difficile can continually give rise to new toxin-producing colonies that wreak havoc on the colon. But these colonies prove no match for fecal transplants, which boast a cure rate of up to 95 percent.

At the heart of these transplants are the trillions of microbes that inhabit the gut and have a profound impact on the host's biology -- for better or worse. As Australian gastroenterologist, Thomas Borody, jokingly puts it, "we are 10 percent human, 90 percent poo."

gut bugs affect mating

The Scientist | Differences in diet alter the composition of microbiota in Drosophila, which appears to in turn influence mate preferences -- and drive speciation. Drosophila seem to prefer to mate with other Drosophila raised on the same diet as a result of the bacteria that live in their guts, according to a study published this week in Proceedings of the National Academy of Sciences (PNAS).

These apparent mate preferences, which arose after just one generation, suggest that an organism's microbiota can facilitate rapid evolution and speciation.

"It's an interesting paper," said Patty Gowaty of the University of California, Los Angeles, who did not participate in the study. "The thought that these gut bacteria could be associated with the reproductive outcomes for individuals is fascinating."

"There's a lot of emerging research these days about the physiological effects of microbiota, and changes in microbiota in response to environmental conditions," added evolutionary geneticist Paul Hohenlohe of Oregon State University, who was also not involved in the research. "This study ties that into mating preference, too."

Twenty years ago, Diane Dodd of Yale University raised Drosophila melanogaster on different media for more than 25 generations and found that those raised on starch media were more likely to mate with other starch-raised flies, while those raised on maltose were more likely to mate with maltose-raised flies.

"Nobody understood the mechanism for this, but they understood it was important because mating preference is an early stage of sexual isolation and speciation," said microbiologist Eugene Rosenberg, a professor emeritus at Tel Aviv University in Israel and coauthor of the PNAS paper. "And nothing is more fundamental to evolution than the origin of species."

genetic engineering of space travelers

Video - Twilight Zone Episode Third From the Sun

LiveScience | NASA's human spaceflight program might take some giant leaps forward if the agency embraces genetic engineering techniques more fully, according to genomics pioneer J. Craig Venter.

The biologist, who established the J. Craig Venter Institute that created the world's first synthetic organism earlier this year, told a crowd here Saturday (Oct. 30) that human space exploration could benefit from more genetic screening and genetic engineering. Such efforts could help better identify individuals most suited for long space missions, as well as make space travel safer and more efficient, he said.

"I think this could change the shape of what NASA does, if you make the commitment to do it," said Venter, who led a team that decoded the human genome a decade ago. Venter spoke to a group of scientists and engineers who gathered at NASA's Ames Research Center for two different meetings: a synthetic biology workshop put on by NASA, and Space Manufacturing 14: Critical Technologies for Space Settlement, organized by the nonprofit Space Studies Institute.

Astronauts with the right (genetic) stuff

Genetics techniques could come in extremely handy during NASA's astronaut selection process, Venter said. The space agency could screen candidates for certain genes that help make good spaceflyers — once those genes are identified, he added.

Genes that encode robust bone regeneration, for example, would be a plus, helping astronauts on long spaceflights battle the bone loss that is typically a major side effect of living in microgravity. Also a plus for any prospective astronaut: genes that code for rapid repair of DNA, which can be damaged by the high radiation levels in space.

Genetic screening would be a natural extension of what NASA already does — it would just add a level of precision, according to Venter.

"NASA's been doing genetic selection for a long time," he said. "You just don't call it that."

Last summer, the agency chose just nine astronaut candidates — out of a pool of 3,500 — for its rigorous astronaut training program based on a series of established spaceflight requirements and in-depth interviews.

A new microbiome
At some point down the road, NASA could also take advantage of genetic engineering techniques to make long space journeys more efficient and easier on astronauts, Venter said.

As an example, he cited the human microbiome, the teeming mass of microbes that live on and inside every one of us. Every human body hosts about 100 trillion microbes — meaning the bugs outnumber our own cells by a factor of at least 10 to one.

While humans only have about 20,000 genes, our microbiome boasts a collective 10 million or so, Venter said. These microbes provide a lot of services, from helping us digest our food to keeping our immune system's inflammation response from going overboard.

With some tailoring, the microbiome could help us out even more, according to Venter.

"Why not come up with a synthetic microbiome?" he asked.

Theoretically, scientists could engineer gut microbes that help astronauts take up nutrients more efficiently. A synthetic microbiome could also eliminate some pathogens, such as certain bacteria that can cause dental disease. Other tweaks could improve astronauts' living conditions, and perhaps their ability to get along with each other in close quarters.

Body odor is primarily caused by microbes, Venter said. A synthetic microbiome could get rid of the offenders, as well as many gut microbes responsible for excessive sulfur or methane production. Fist tap Nana.

the mystery of conductive bacterial nanowires

PNAS | Bacterial nanowires are extracellular appendages that may facilitate electron transport between and among diverse species, including the metal-reducing bacteria, Shewanella oneidensis MR-1. Although several biological assays have provided results consistent with bacterial nanowire conductivity, until now researchers had not found direct evidence of electron transport along nanowires. Mohamed El-Naggar et al. used nanofabricated electrodes and conducting probe atomic force microscopy to measure electron transport along individual S. oneidensis MR-1 nanowires. The researchers found that the bacterial nanowires were electrically conductive along micron length scales, and estimate that the nanowires’ current capacity is sufficient to discharge the cell’s respiratory electrons to terminal electron receptors during extracellular electron transport. Bacterial mutants deficient in genes necessary for electron transport produced appendages that were morphologically consistent with wild type nanowires, but were nonconductive. The study suggests that bacteria, the oldest organisms on the planet, may use integrated circuitry for energy distribution, a hypothesis that challenges traditional understanding of extracellular electron transport in microbial communities, according to the authors. — J.M.

delhi belly buckwild?

Video - Weird little agitprop video about NDM-1.

WaPo | The origin of the microbes is politically sensitive. The Indian government has condemned the reports saying the bugs arose in that country, arguing that the tale was concocted by Western pharmaceutical companies and others to discredit India's burgeoning medical tourism industry, which is attracting more than 450,000 patients a year and could generate annual revenues of $2.4 billion by 2012, according to some estimates.

"They say it's found in patients who visit India and Pakistan," said India's health minister, Ghulam Nabi Azad. "It was nowhere mentioned if the bacteria are found even before those persons visited India."

The resistance gene - NDM-1 stands for New Delhi metallo-B-lactamase 1 - was first identified in 2008 in bacteria in a Swedish patient who had been hospitalized in New Delhi. The gene produces an enzyme that destroys most antibiotics, including so-called carbopenems, which are usually used in last-ditch efforts to save patients whose infections fail to respond to standard antibiotics.

"We really are already running out of antibiotics," said Richard Wenzel, an infectious-disease specialist at Virginia Commonwealth University and former president of the International Society for Infectious Diseases. "It's potentially very, very worrisome."

Urinary tract infections, pneumonia and other common ailments caused by germs that carry a new gene with the power to destroy antibiotics are intensifying fears of a fresh generation of so-called superbugs.

The gene, NDM-1, which is apparently widespread in parts of India, has been identified in just three U.S. patients, all of whom had received treatment in India and recovered. But the gene's ability to affect different bacteria and make them resistant to many medications marks a worrying development in the fight against infectious diseases, which can mutate to defeat humans' antibiotic arsenal.

"The problem thus far seems fairly small, but the potential is enormous. This is in some ways our worst nightmare," said Brad Spellberg, an infectious-disease specialist at LA Biomed (the Los Angeles Biomedical Research Institute at Harbor-UCLA Medical Center) and author of "Rising Plague," a book about antibiotic resistance. "You take very common bacteria that live in all of us and can travel from person to person, and you introduce into it some of the nastiest antibiotic-resistance mechanisms there are."

The bacteria, which include previously unseen strains of E. coli and other common pathogens, appear to have evolved in India, where poor sanitation combines with cheap, widely available antibiotics to create a fertile environment for breeding new microorganisms.

The infections were then carried to the United States, Britain and more than a half-dozen other countries, often through "medical tourism," which involves foreigners seeking less expensive, more easily accessible surgery overseas.

"We need to be vigilant about this," said Arjun Srinivasan, a medical epidemiologist at the Centers for Disease Control and Prevention, which has been monitoring the spread of the microbes. "This should not be a call to panic, but it should be a call to action. There are effective strategies we can take that will prevent the spread of these organisms."

Experts fear the germs will follow the path of other multi-drug-resistant bugs and become a common scourge in medical centers and perhaps even among otherwise healthy people.

"It's an acute example of how bacteria can outwit people," said Stuart Levy, a professor of molecular biology at Tufts University School of Medicine and president of the Alliance for Prudent Use of Antibiotics.

globe-spanning underground bacterial networks

NatGeo | Though the calling card of the horseshoe-shaped Cave of Crystals may be its massive mineral formations, some of its biggest surprises are literally microscopic.

In 2008 a team of scientists, including New Mexico Tech's Boston, investigated the cave and found microbial life living in tiny air pockets in the crystals.

In December 2009 Boston returned to the cave with another team. From pools of water that hadn't been present during her first trip, the scientists collected bacteria as well as viruses that prey on the bacteria—something that was suspected but had not been confirmed on the first expedition.

Viruses, after all, are among the "primary predators of bacteria," explained Danielle Winget, a biologist at the University of British Columbia, in the new documentary.

Sure enough, the team found as many as 200 million viruses in a single drop of Cave of Crystals water.

But the virus finding was perhaps not the expedition's most surprising microbial discovery. Analysis of bacterial DNA from the Cave of Crystals showed that the tiny life-forms are related to microbes living in other extreme environments around the world, including caves in South Africa and Australia as well as hydrothermal vents (video).

"We're picking up these patterns of similarities in places that are geographically widely separated," Boston said.

That similarity and separation adds up to a mystery, according to Curtis Suttle, a biologist at University of British Columbia and a member of the 2009 Cave of Crystals expedition.

"We don't really understand how it is that the organisms in a hydrothermal vent in Greece or a deep gold mine in South Africa are related to organisms that we find in a subsurface cave" at Naica, Suttle said.

"It's hard to imagine some kind of underground [network] connecting South Africa with Mexico."

Alien Underworlds

As mind-boggling as the idea of a possibly globe-spanning, underground bacterial network may be, some scientists see potential links between the Cave of Crystals and even farther-flung hot spots—for example, extreme environments on Mars and other worlds.

Though Martian geology might be more static overall than Earth's, "there may be residual pockets of geothermal activity that could provide a zone where water could be liquid and where chemically reduced gases from below can percolate up and act as a nutrient source," as in the Cave of Crystals, Boston said.

(See "Mars Has Cave Networks, New Photos Suggest.")

Poirier, the Ontario astrophysicist, agreed.

"For Mars, our best bet of finding life is to look underground," Poirier said. "So there are a lot of parallels between humans exploring subterranean caves looking for microbes and Martian exploration in the future."

If the caves on Mars are anything like the caverns beneath Naica mountain, she said, future Martian explorers will have to be trained to ignore the strange sights surrounding them.

"When you're in the caves, you're overwhelmed by the [harsh] conditions, but you're also overwhelmed by the beauty, and it's really hard to maintain your focus," she said.

Even if scalding water submerges that beauty tomorrow, Boston said, the caves' scientific potential should live on, thanks to the multitude of samples already collected.

"My usual rule of thumb is for every hour you spend in the field, you spend at least a thousand hours on analysis," Boston said. "So we've got our hands full."

immune response feeds parasite

Video - Original Star Trek Day of the Dove Conclusion

The Scientist | Salmonella is able to out compete resident gut microbes by deriving energy from the immune response that is supposed to combat the pathogen, according to a study published this week in Nature.

"It was a surprise," said microbiologist Samuel Miller of the University of Washington, who was not involved in the research. "[Salmonella] is using [the host immune response] to its own advantage."

It's an "interesting story," added Brett Finlay of the University of British Columbia, who also did not participate in the study, in an email -- "a real twist on pathogenic mechanisms."

Salmonella enterica (specifically, serotype Typhimurium) is a gut parasite known to cause diarrhea and intestinal inflammation. The inflammatory response is part of a multipronged host immune response aimed at eliminating the bacteria, but recent studies have suggested that inflammation does just the opposite -- enhances Salmonella growth and transmission.

"use value" economics in the microcosmos

The Scientist | Microorganisms living in deep sea hydrothermal vents can grow off of energy derived from one of the simplest forms of anaerobic respiration ever described, according to a study published this week in Nature.

The reaction -- in which a chemical called formate is broken down into hydrogen and carbon dioxide -- was previously thought to be too energy poor to support the growth of even the smallest organisms. Finding single-celled microbes from Domain Arcahaea that can glean energy from it may point the way towards efficient hydrogen fuel production while providing clues as to how our planet's earliest inhabitants survived the harsh environment of a young Earth.

Formate is the simplest carboxylate anion, consisting of just one carbon, one hydrogen, and two oxygen atoms, and is an important player in fermentation reactions and anaerobic digestion. Some microbes are known to convert formate to methane and CO2 to produce energy, but the conversion of formate into hydrogen and CO2 wasn't thought to release enough energy to support microbial growth.

The problem, it seemed, was that the accumulation of hydrogen inhibits the reaction from continuing to occur. But in special circumstances, this may not be the case. In 2008, for example, Stams and his colleagues showed that in microbial communities where methanogens -- archaea that produce methane as a byproduct of metabolism -- live in partnership with fermentative bacteria that convert formate to hydrogen and CO2, the methanogens consume the hydrogen product of the reaction, allowing the reaction to continue. In doing so, enough energy is generated to support the growth of the bacteria.

The new study provides the first evidence that a microbe can derive energy from this conversion without the help of any partners. Sung Gyun Kang of the Korea Ocean Research and Development Institute and his colleagues were sequencing the genome of a strain of the deep-sea hydrothermal vent archaea Thermococcus onnurineus when they noticed it contained many copies of formate dehydrogenases and hydrogenases thought to be involved in formate conversion reactions.

bacteria and climate change - invisible carbon pumps

The Economist | UNDERSTANDING how the oceans absorb carbon dioxide is crucial to understanding the role of that gas in the climate. It is rather worrying, then, that something profound may be missing from that understanding. But if Jiao Nianzhi of Xiamen University in China is right, it is. For he suggests there is a lot of carbon floating in the oceans that has not previously been noticed. It is in the form of what is known as refractory dissolved organic matter and it has been put there by a hitherto little-regarded group of creatures called aerobic anoxygenic photoheterotrophic bacteria (AAPB). If Dr Jiao is right, a whole new “sink” for carbon dioxide from the atmosphere has been discovered. Fist tap ProfGeo.

what is the role of bacteria in carcinogenesis?

Video - growth hormones and carcinogenesis.

JNCI | Radiation, chemicals, heredity, and viruses have all been linked to cancer. Although bacteria seem to be unlikely contributors to cancer, experts continue to look into their role in carcinogenesis.

In his book, Can Bacteria Cause Cancer?, David Hess, Ph.D., a professor and chair of the Department of Science and Technology Studies at Renesselear Polytechnic Institute, Albany, suggests that bacterial theories of cancer development have been largely overlooked.

Helicobacter pylori was isolated from the human stomach for the first time in 1982. The bacterium can cause stomach ulcers, and those who are infected are more likely to develop stomach cancer. Some health organizations estimate that more than one half of the world is infected with the organism.

The H. pylori–stomach cancer link is one of the few accepted connections between cancer and bacteria. However, Hess argues that bacterial theories related to cancer may not have been given proper consideration.

“I am not a microbiologist and I don’t claim that there is an established relationship, but I can offer an historical perspective on the issue,” Hess said in an interview. “I think it is fair to say that the older attempts to find a single bacterial agent represent a rejected program. However, with emerging linkages between H. pylori and cancer, the research field may be reopening.

“If you look back in the history of science, a number of chronic diseases have been linked to bacteria, so it is not entirely unreasonable to wonder if the long history of clinical findings of bacteria associated with tumor samples or the blood of cancer patients suggests an overlooked pathogenic role.”

Hess added that bacterial advocates were largely ignored because emerging trends favored today’s conventional therapies and because of the extreme nature of some bacterial theories.

“There is good evidence that the bacterial theories and therapies were pushed aside by the emerging trends in support of the chemotherapy and radiation therapy,” said Hess. “There was also evidence that advocates overstated their case by claiming that a single, pleomorphic bacterium caused all cancers.”

However, with the acceptance of H. pylori as a cause of stomach cancer, more doctors and researchers are studying other cancer and bacteria connections.

virus behind cancer, ms?

The Scientist | After uncovering HPV's role in cancer, Harald zur Hausen is investigating another virus-disease relationship. Nobel Laureate Harald zur Hausen has a hunch, and he's gathering the data to support it.

For the past decade, zur Hausen and Ethel-Michelle de Villiers, his scientific partner and wife, are studying a little-known, single-stranded DNA virus -- Torque teno virus (TTV). Preliminary evidence is suggesting it may be an indirect cause or co-factor in certain multi-factorial diseases, including cancer and autoimmune diseases.

Addressing 675 young scientists at last month's 60th Meeting of the Nobel Laureates in Lindau, Germany, zur Hausen presented new findings on TTV. He and de Villiers have identified viral proteins that resemble certain MS auto-antigens in brain lesions of patients with multiple sclerosis. He's also found segments of TTV genomes in many cancer cell lines, including leukemia and Hodgkin's lymphoma lines, with no similar patterns in normal human tissues. He's found relatively high levels of complete TTV sequences in gastrointestinal, breast, lung cancers, as well as in samples of leukemia and myeloma. But the virus is also present at high levels in normal tissues.

Still, in TTV-infected tissues and cell lines, zur Hausen and de Villiers have found evidence of genomic rearrangements, and have linked a specific small region of TTV in cancer cells to truncated host cell genes. Given that studies have also linked TTV to immunosuppression and immunomodulation, chronic inflammation, prevention of apoptosis, and chromosomal aberrations, they suggest that TTV may act as an indirect carcinogen. Unlike human papillomavirus (HPV), which has a direct oncogenic effect on cells, TTV alone may not trigger disease -- but when combined with host factors such as higher levels of pro-inflammatory cytokines, and other diseases such as malaria, that recipe could create problems.

gut sex

The Scientist | Jo Handelsman discusses a paper that found gut microbiota can influence sexual fitness in an invasive pest.

The Mediterranean fruit fly is one of the most damaging agricultural pests in the world. A common strategy to reduce its population consists of releasing sterilized industrially grown flies out into the wild in the hopes that they will steal females from virile males. It turns out, however, that the sterilized males are not as lucky in getting the attention of the ladies. A recent paper—selected by F1000 Faculty Member Jo Handelsman, a microbiologist at Yale—has a surprising explanation for the altered males’ inability to attract females: their gut microbiota ( ISME J , 4:28-37, 2010).

TS: Why would intestinal microbes affect the sexual performance of an organism?

JH: We know that the gut microbiota of many organisms controls the most surprising breadths of activities and physiology. In humans we’re finding that gut microbiota affects obesity, and sleep cycles perhaps, heart disease, diabetes, and all sorts of things that we never connected with microbial function before. The gut is emerging as perhaps the most important organ on the body for regulating health and disease, and that’s mainly through the functions of the bacteria that live there. I guess it shouldn’t be surprising that bacteria may also affect sexual behavior and performance.

TS: Is this the first link between gut microbes and sexual behavior?

JH: As far as I know, yes.