Bacteria and ways to detect

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Innovative Techniques Identify Thousands of New Bacteria

One gram of soil -- the weight of a little packet of low-calorie sweetener -- can contain as many as 10,000 species unknown to science, says Dr. Handelsman, a professor of plant pathology at the University of Wisconsin.

For more than a decade, Dr. Handelsman had tantalizing glimpses of an elusive microscopic world she could not enter. When she put samples of soil under the microscope, she saw countless species of organisms she couldn't identify.

But efforts to isolate and grow these microbes in the lab failed, and she couldn't learn much about them. Except for one thing: Genetic and statistical analyses revealed that these unknown organisms must make up 99.9% of all the microbes in the soil.

Now, for the first time, she and her colleagues, along with several other research groups working independently, are learning to extract the DNA of these mysterious creatures and clone it.

They are finding that the microbes differ so profoundly from known bacteria that they could represent entirely new kingdoms of life -- as different from other bacteria as animals are from plants. That means that the proteins produced by these creatures could have properties unlike any other such substances known.

Most current antibiotics come from microbes in the soil. They include streptomycin, the first treatment for tuberculosis, and vancomycin, currently the drug of last resort for the toughest infections.

By now, however, conventional bacteria have been largely "mined out": Most of their useful properties have already been exploited. Researchers say that studies of the palette of novel biological agents Handelsman and others are discovering could lead to a new wave of medicines, anticancer drugs, insecticides and industrial enzymes, many radically different from those already in use.

The research builds on earlier studies of exotic microbes that live in boiling pools in Yellowstone National Park, at steaming volcanic vents on the sea floor, and in other forbidding locales.

These so-called extremophiles -- named for their affinity for extreme environments -- were crucial in the development of one of molecular biology's most useful tools, a method of extracting and studying DNA called polymerase chain reaction, or PCR.

In a report in mid-November at the annual New Horizons in Science briefing in Tempe, Ariz., Handelsman said she and her colleagues at Wisconsin have already identified several new antibiotics from soil microbes, at least one of which is also proving to be a powerful pesticide.

And in California, F. DeLong and his colleagues at the Monterey Bay Aquarium have found a distinctive light-sensitive protein that could have applications in optical computers. They expect these to be only the first of many more such discoveries from a field of research known as metagenomics, or environmental genomics.

Dazzling Variety

The field has led, among other things, to a new view of biological diversity. The dazzling variety of tropical rain forests, it turns out, is dwarfed by the unseen diversity in the microbial world.

To take one example, a single gram of sediment on the ocean floor contains 1 billion organisms, says one of the field's pioneers, biologist Norman R. Pace of the University of Colorado.

Dig down about one-third of a mile to an even more forbidding environment, and the sediment still contains about 10 million microbes per gram.

The microbes in that 500-meter-thick layer of ocean floor make up 10% to 20% of all the biological matter on earth, Pace says. They include uncounted numbers of species unknown to science.

Even human intestines -- an environment most people consider pretty familiar -- are home to perhaps 10,000 kinds of microbes. "I've been blown away by the diversity there," says Pace, whose work was recognized in October with a MacArthur Foundation Fellowship.

Indeed, one of the surprises in the decoding of the human genome was that it contains more than 200 genes that come from bacteria. Microbes not only keep us alive; in some small part, we are made of them.

Pace is looking at how these largely unknown microbes might play a role in Crohn's disease, an inflammation of the small intestine. He has found that the makeup of the mixed "community" of microbes in the intestines changes in people with the disease.

A similar thing might happen with tuberculosis, Pace says, leading him to wonder whether some diseases might be caused not by a single dangerous microbe but by a change in the microbial community -- an ecological imbalance inside the human body.

Handelsman and R. Rondon, formerly of the University of Wisconsin and now at Ohio State University, have done most of their work with soil obtained from a University of Wisconsin research station 15 minutes from their lab.

They devised a technique for isolating long pieces of DNA from soil, something that other researchers had assured them could not be done. Because soil is full of contaminants that can interfere with the finicky chemicals used to isolate DNA, it was a trial-and-error process -- and in the beginning, it was mostly error.

Rondon's persistence paid off, however, and the researchers learned to extract strings of DNA from soil long enough to contain 50 to 80 genes. Some of this DNA came from known organisms, of course, but most of it came from the vast profusion of unknown organisms that couldn't be grown in the lab. "This sent shivers down our spines, because it was the first glimpse we had of the uncultured world," Handelsman says.

Business Week December 3, 2001 pages 61-62

DR. MERCOLA'S COMMENT:

Keep your eyes peeled on this one folks. The reason it made Business Week is because of the potential for producing new antibiotics. However, the traditional paradigm, as usual, is way off here.

They are completely missing that this technology could lead to one of the most useful developments in the history of medicine. It could potentially even dwarf the Human Genome Project.

The key here is that the tools now apparently exist to start classifying the thousands of anaerobic bacteria that are growing in our gut.

Many natural medicine experts, and I am one of them, are strongly convinced that physical healing starts by controlling the balance of bacteria in the gut.

My approach to achieving that is to use the eating plan which optimizes the environment for the maintenance and sustaining of the best organisms to grow there.

Additionally, I use the highest potency good bacteria in the world to help repopulate the colon.

I hope to make this product available in the next two months. I am still in the process of negotiating arrangements for how this will happen with the product's manufacturer.