For each of the three research subjects, the researchers analyzed samples from six different anatomical sites inside the large intestine as well as a stool sample.
Eckburg and his team determined more than 13,000 sequences of 16S rRNA. Most of what they identified included the usual suspects in the intestinal flora, but there were surprises. Nearly two-thirds of the bacteria they identified were novel, meaning that they had no genetic close neighbors in the existing databases that store sequence information about all known species.
"We thought we would find new ones, but it was a bit surprising to see such a large percentage that had remained unidentified," said Eckburg. "Despite this large effort, we are still not approaching the point of complete coverage of the intestinal community in any one individual - much less the complete coverage of all human intestinal communities." In contrast, the investigators found very limited diversity within the archaea, microbes that look a lot like bacteria but are genetically and biochemically as different from bacteria as bacteria are from humans.
The team also used the samples to examine how microbial communities differ among locations within the intestine as well as among different people.
"We were surprised at the degree to which an individual determines the particular picture of microbial diversity that we see," said Relman. "Variation between individuals had been suspected, but our data proved to be a dramatic confirmation of this belief."
An interesting corollary of this finding is that the ability to create a comprehensive census of the microbes living inside a person could have implications for human forensics. Unlike people's genetic makeup, their endogenous microbial communities