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Old 05-27-2012, 10:57 AM   #62
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Dear Germaphobes.... You've already lost... The human body is now composed of more bacteria cells than human cells. We are legion....

Bacteria ‘R’ Us

Emerging research shows that bacteria have powers to engineer the environment, to communicate and to affect human well-being. They may even think.

Today’s revelation in the journal Science that researchers have found a bacterium in California’s Mono Lake that can thrive on arsenic — usually implicated in killing life, not sustaining it — is quickly revolutionizing our conception of what is life and where it might be found. To help in deciphering the direct contribution bacteria make to human life, we’re reposting this story which originally debuted on Oct. 18.

A few scientists noticed in the late 1960s that the marine bacteria Vibrio fischeri appeared to coordinate among themselves the production of chemicals that produced bioluminescence, waiting until a certain number of them were in the neighborhood before firing up their light-making machinery. This behavior was eventually dubbed “quorum sensing.” It was one of the first in what has turned out to be a long list of ways in which bacteria talk to each other and to other organisms.

Some populations of V. fischeri put this skill to a remarkable use: They live in the light-sensing organs of the bobtail squid. This squid, a charming nocturnal denizen of shallow Hawaiian waters, relies on V. fischeri to calculate the light shining from above and emit exactly the same amount of light downward, masking the squid from being seen by predators swimming beneath them.

For their lighting services, V. fischeri get a protected environment rich in essential nutrients. Each dawn, the squid evict all their V. fischeri to prevent overpopulation. During the day, the bacteria recolonize the light-sensing organ and detect a fresh quorum, once again ready to camouflage the squid by night.

This tale of bobtail squid would be just another mildly jaw-dropping story in a natural world full of marvels if it weren’t a portal into an unsuspected realm that has profound consequences for human beings. Regardless of the scale at which we explore the biosphere — whether we delve into the global ocean or the internal seas of individual organisms — bacteria are now known to be larger players than humans ever imagined.

Strictly by the numbers, the vast majority — estimated by many scientists at 90 percent — of the cells in what you think of as your body are actually bacteria, not human cells. The number of bacterial species in the human gut is estimated to be about 40,000, according to Daniel Frank and Norman Pace, writing in the January 2008 Current Opinion in Gastroenterology. The total number of individual bacterial cells in the gut is projected to be on the order of 100 trillion, according to Xing Yang and colleagues at the Shanghai Center for Bioinformation Technology, reporting in the June 2009 issue of PLoS One, a peer-reviewed online science journal. Xing calculated a ballpark figure for the number of unique bacterial genes in a human gut at about 9 million.
In fact, most of the life on the planet is probably composed of bacteria.
They have been found making a living in Cretaceous-era sediments below the bottom of the ocean and in ice-covered Antarctic lakes, inside volcanoes, miles high in the atmosphere, teeming in the oceans — and within every other life-form on Earth.

These facts by themselves may trigger existential shock: People are partly made of pond scum. But beyond that psychic trauma, a new and astonishing vista unfolds. In a series of recent findings, researchers describe bacteria that communicate in sophisticated ways, take concerted action, influence human physiology, alter human thinking and work together to bioengineer the environment. These findings may foreshadow new medical procedures that encourage bacterial participation in human health. They clearly set out a new understanding of the way in which life has developed on Earth to date, and of the power microbes have to regulate both the global environment and the internal environment of the human beings they inhabit and influence so profoundly.

There’s such ferment afoot in microbiology today that even the classification of the primary domains of life and the relationships among those domains are subjects of disagreement. For the purposes of this article, we’ll focus on the fundamental difference between two major types of life-forms: those that have a cell wall but few or no internal subdivisions, and those that possess cells containing a nucleus, mitochondria, chloroplasts and other smaller substructures, or organelles. The former life-forms — often termed prokaryotes — include bacteria and the most ancient of Earth’s life-forms, the archaea. (Until the 1970s, archaea and bacteria were classed together, but the chemistry of archaean cell walls and other features are quite different from bacteria, enabling them to live in extreme environments such as Yellowstone’s mud pots and hyperacidic mine tailings.) Everything but archaea and bacteria, from plants and animals to fungi and malaria parasites, is classified as a eukaryote.


Bacteria can live solitary lives, of course, but they prefer to aggregate in biofilms, also known as “slime cities.” Biofilms usually form on a surface, whether it’s the inner lining of the intestines or inside water pipes or on your teeth. In these close-knit colonies, bacteria coordinate group production of a slimy translucent coating and fibers called “curli” and “pili” that attach the colony to something else. Biofilms can harbor multiple types of bacteria as well as fungi and protists (microscopic eukaryotes). A complex vascular system for transporting nutrients and chemical signals through a biofilm may also develop. As Tim Friend described in his book The Third Domain, explorers diving to the wreck of the Titanic found these features in “rusticles” — draped colonies of microbes — feeding on the iron in the Titanic‘s hull and skeleton, more than 2 miles under the surface.

The abilities of bacteria are interesting to understand in their own right, and knowing how bacteria function in the biosphere may lead to new sources of energy or ways to degrade toxic chemicals, for example. But emerging evidence on the role of bacteria in human physiology brings the wonder and promise — and the hazards of misunderstanding them — up close and personal.

Because in a very real sense, bacteria are us.

In 2007, the National Institutes of Health began an ambitious program called the Human Microbiome Project, which aims to take a census of all the microorganisms that normally live in and on the human body. Most of these live in the digestive tract, but researchers have also discovered unique populations adapted to the inside of the elbow and the back of the knee. Even the left and right hands have their own distinct biota, and the microbiomes of men and women differ. The import of this distribution of microorganisms is unclear, but its existence reinforces the notion that humans should start thinking of themselves as ecosystems, rather than discrete individuals.
As of early 2010, the Human Microbiome Project had collected samples of microbial DNA from about 300 people and had sequenced or prepared to sequence the genomes of about 500 bacterial strains from these samples. Fifteen studies of microbial involvement in human disease have been funded. “These sorts of trials take time,” says Microbiome Project program director Susan Garges, so clinical treatments based on the research from the project could be years off unless, she says, “in the shorter term, specific microorganisms are associated with a disease state.” In that case, protocols for clinical diagnosis and treatment might be accelerated.

But the microbiome project is not just about disease-causing microbes such as E. coli and Staphylococcus strains. Many of the organisms it is identifying are responsible for regulating the digestive tract and keeping humans healthy in a variety of ways.

The human gut is filled with large numbers of a wide variety of bacteria; clearly those that cause disease must rank high on the priority list of those to be studied, but the picture emerging from new research is that pathogens and beneficial bacteria are not necessarily mutually exclusive organisms. A microbe’s effects on the human body can depend on conditions. And if you approach the human body as an ecosystem, some researchers are finding, it may be possible to tune that system and prevent many diseases — from acute infections to chronic debilitating conditions — and even to foster mental health, through bacteria.

Recent research has shown that gut microbes control or influence nutrient supply to the human host, the development of mature intestinal cells and blood vessels, the stimulation and maturation of the immune system, and blood levels of lipids such as cholesterol. They are, therefore, intimately involved in the bodily functions that tend to be out of kilter in modern society: metabolism, cardiovascular processes and defense against disease. Many researchers are coming to view such diseases as manifestations of imbalance in the ecology of the microbes inhabiting the human body. If further evidence bears this out, medicine is about to undergo a profound paradigm shift, and medical treatment could regularly involve kindness to microbes.

Still, in practice, the medical notion of friendly microbes has yet to extend much past the idea that eating yogurt is good for you. For most doctors and medical microbiologists, microbes are enemies in a permanent war. Medicine certainly has good reason to view microbes as dangerous, since the germ theory of disease and the subsequent development of antibiotics are two of medical science’s greatest accomplishments.

But there’s a problem: The paradigm isn’t working very well anymore. Not only are bacteria becoming antibiotic-resistant, but antibiotics are creating other problems. Approximately 25 percent of people treated with antibiotics for an infection develop diarrhea. Moreover, people who contract infections just by being hospitalized are at risk of developing chronic infections in the form of biofilms. These not only gum up the works of devices such as IV tubes, stents and catheters, but also protect their constituent microbes from antibiotics.

In addition to antibiotic-resistant E. coli and Salmonella that often spread through our food supply, common pathogens that make doctors’ blood run cold include Pseudomonas aeruginosa and Clostridium difficile. P. aeruginosa is responsible for about 40 percent of all fatalities from hospital-acquired infections. C. difficile is the culprit in at least a quarter of diarrhea cases caused by antibiotics. A 2007 study by the Los Angeles County Department of Public Health found that mortality rates from C. difficile infections in the United States quadrupled between 1999 and 2004. C. difficile will invade an antibiotic-cleansed colon and “poke holes in it,” says Vincent Young, a gastrointestinal infection specialist at the University of Michigan. Some people in this situation rush to the bathroom 20 times a day. “It’s not just an inconvenience,” Young says.

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