By David N. Leff

There are more bacteria on, or in, a single human body than there are human beings on earth. (We now number more than 6 billion.) What's more, the total population of these indigenous microbes per individual person is estimated to equal the trillions of cells in that human body.

A single gram (0.035 ounce) of feces contains about 10 billion microbes. That figures, given that the human intestinal tract is more densely populated with the greatest variety of people-friendly microorganisms than any other organ. Certainly, the best known of these myriad bacterial lodgers is Escherichia coli - the boon of biologists and the bane of contaminated-hamburger consumers.

Yet, except for such occasional infectious bacteria, surprisingly little is known about the lifestyles of the benign bugs that dwell in the gut throughout every person's life from birth. The interfaces between people and the complex colonies of microbes that flourish in our gastrointestinal tract is an age-old mystery. Now, that black box is being pried open by new laboratory techniques, notably gene chips and lasers.

A report in today's Science, dated Feb. 2, 2001, takes an educated look inside that box. The paper is titled: "Molecular analysis of commensal host-microbial relationships in the intestine." Its senior author is molecular biologist Jeffrey Gordon, who heads the department of molecular biology and pharmacology at Washington University School of Medicine in St. Louis.

"We live in a world predominated by microbes," Gordon told BioWorld Today. "These organisms have co-evolved with their mammalian hosts over millions of years. During this time, they have been forced to become master physiologic chemists. They have had to develop strategies for satisfying their own nutritional needs - and various needs of their hosts. We wanted to figure out some of the lessons that they have learned about us, and how they contribute to our health."

Are Gut Bacteria Freeloaders? No Way!

Gordon's article in Science reveals that microorganisms in the gut influence the expression of a number of mouse genes that are important to intestinal development and function. He pointed out, "These bacteria don't simply sit and wait to be fed by the nutrients people consume. Instead, they actively shape our biology, so they can establish and maintain homes for themselves."

To train their sights on a single representative microorganism in a defined in vivo environment, the co-authors began their study by raising a population of gnotobiotic - germ-free - mice. To do so, they took advantage of the fact that fetuses in gestation are essentially sterilized of contact with microorganisms. These come on board as they begin to acquire organisms during the birthing process, via the vagina, which harbors varieties of germs. To preserve the pristine state of their future mouse-model colony, the team delivered perinatal mice via sterile Caesarian section, directly into sterile plastic isolators, and fed them autoclaved chow.

Once their high-purity animals reached 7 to 15 weeks of age, they were inoculated with cultures of a benign bacterium - Bacteroides thetaiotaomicron - a prominent member of the normal micoflora that inhabits the small intestines of healthy humans and mice. Then, using DNA microarrays and laser capture microdissection, the co-authors examined the effect of the bacterium on intestinal functions. The microchips allowed the scientists to monitor expression of thousands of genes at once.

"We did not have a preconceived notion of how many intestinal functions are influenced by gut microbes," observed the Science paper's first author, molecular biologist Lora Hooper. "Gene chips," she told BioWorld Today, "allowed us to survey, in a relatively unbiased way, the effects of that common gut microbe on more than 20,000 mouse genes."

Entry of B. theta into the germ-free intestine activated several murine genes involved in absorption and metabolism of sugars and fats. Other genes, they found, control the integrity of the cellular mucosal barrier that lines the intestine, and separate humans as well as mice from dangerous organisms and ingested substances. Still other genes influenced by the bacterium regulate how potentially toxic compounds are metabolized, how blood vessels are formed and how the gut matures during the postnatal period. "B. theta normally colonizes the distal small intestine - the ileum - during the suckling-weaning transition, a time of rapid and pronounced maturation of the gut," Gordon explained.

"Shortly after birth," he noted, "resident microbes begin to educate the gut's immune system, signaling that they are safe, normal partners that do not merit a robust immune response to bacterial antigens. As well as preventing adverse reactions to normal bacteria," he went on, "this educational process may help ensure that we folks don't react poorly to certain antigens that we ingest."

"We were amazed," Hooper said, "at the breadth of normal intestinal function affected by a single microbe." To understand which gut cells were responsible for these results, the co-authors applied laser capture dissection, a technology that can carve out a particular cell from a tissue sample, and measure its gene expression.

For example, the team determined that certain populations of cells lining the gut responded to B. theta by increasing its production of three proteins: colipase, which helps break down fats; a small proline-rich protein, which seems to help fortify the intestinal barrier; and angiogenin-3, which stimulates blood-vessel formation.

Can Gut Bug Effects Vary With Individual?

"One of our findings," Gordon pointed out, "is that microbes are able to regulate intestinal genes involved in breaking down foods into simpler units that can be absorbed. This raises the question," he went on, "of whether there are variations in the types of intestinal microbes between individual humans, and how such differences affect our nutritional status, our health and our predisposition to certain diseases."

In the future, the co-authors aim to learn more about how normal bacteria develop an effective working relationship with their human hosts. "We would like to exploit the strategies developed by our microbes over the course of several million years," Gordon concluded, "to help identify new therapies for promoting health, and for treating diseases that occur outside, or even inside, our gastrointestinal tract."