Mention the phrase "diverse ecosystem," and it conjures images of tropical rainforests and endangered coral reefs.
It also describes the human colon.
A new study from the Stanford University School of Medicine reveals in greater detail than ever before the full extent of the bacterial community inhabiting the human bowel - 10 times more diverse than previous research had suggested. The technology that yielded this result offers the potential for much more accurate assessments of people's complex internal ecosystems, as well as more-sophisticated monitoring of the degree to which they are affected by, for example, antibiotics. The study will be published online Nov. 18 in the journal Public Library of Science-Biology .
The prospect of swallowing an antibiotic takes on a new meaning when you consider that for each human cell in your own body, there are roughly 10 single-celled microbes, most of which live in our digestive tracts. In sheer numbers, the mammalian colon harbors one of the densest microbial communities found on Earth. Estimates of the number of distinct kinds of bacteria in the human colon, based on the older technique of detecting lower-gut-dwelling organisms by growing them in petri dishes, have ranged upwards of 500. But these estimates have been hampered by huge numerical disparities between more abundant vs. rarer bacterial varieties, rendering the latter essentially undetectable (not to mention that only some varieties of organisms thrive in culture while others perish).
David Relman, MD, professor of medicine and of microbiology and immunology, and his associates used a technique know as pyrosequencing, developed outside of Stanford, to get a more complete count of the different varieties of bacteria colonizing the human colon, including myriad strains that exist in small numbers. Pyrosequencing has been used before to assess the richness of bacterial ecosystems in marine environments and soil, Relman said. "But this was one of the first times it has been employed to look inward at the ecosystems within our own bodies," he said.
It turns out that the colon is even more multicultural than had been imagined. In the new study, the investigators found at least 5,600 separate species or strains by looking at variations in DNA sequences that code for a molecule universal among all living cells. Pyrosequencing generates extremely large numbers of small DNA "tags" copied from the genes of organisms being examined.
"The new gene-sequencing technology lets us check far more 'bacterial ID cards' than the older methods did," said Les Dethlefsen, PhD, a postdoctoral researcher in the Relman laboratory who is the first author of the study. This, in turn, makes possible more-precise assessments of the effect of a disturbance in the lower-gut ecosystem - say, through the administration of broad-spectrum antibiotics - Dethlefsen said.
By and large, intestinal microbes just mind their own business, subsisting on complex carbohydrates impervious to our own digestive enzymes. But they also perform numerous critical functions of benefit to us, from fine-tuning our immune systems to producing nutrients such as vitamin K. Importantly, by occupying intestinal real estate and devouring its useless-to-us, tasty-to-them contents, friendly gut organisms prevent pathogens from taking over, much as a house filled with legal residents deters squatters.
The researchers tested the effects of a commonly used antibiotic, known for its mild digestive-tract side-effect profile, and were able to show that it had a measurable and pronounced effect on gut microbes. Fortunately, an approximately normal balance appears to be restored within a matter of weeks.