Harmful Bacteria Live In Healthy Bodies Without Causing Disease

Scientists working on a huge project that has mapped all the different microbes that live in and on a healthy human body have made a number of remarkable discoveries, including the fact that harmful bacteria can live in healthy bodies and co-exist with their host and other microbes without causing disease.
This week sees the publication of several papers from the Human Microbiome Project (HMP), including two in Nature and two in PLoS ONE.
The Microbiome
The microbiome is the sum of all the microbes that colonize the body: it comprises trillions of microorganisms that outnumber human cells by 10 to 1. The microbes inhabit every nook and cranny of the body, and most of the time the relationship is a friendly one, because they help digest food, strengthen the immune system and fight off dangerous pathogens.
Colorado University (CU)-Boulder Associate Professor Rob Knight of the BioFrontiers Institute is co-author on the two Nature papers. He told the press that the microbiome may only make up 1 to 3% of human body mass, but it plays a key role in human health.
One of the fascinating features of the microbiome is that different body sites have different communites of microorganisms that are as different from each other as the differences between microbial communities in oceans and deserts.
Knight said:
"By better understanding this microbial variation we can begin searching for genetic biomarkers for disease."
Another of the curious features the HMP has discovered is that even healthy people carry low levels of harmful bacteria, but as long as the body remains healthy, they don't cause disease, they just coexist alongside beneficial microbes. 
Knight said we now need to find out why: what happens to cause pathogens to become deadly?
The Human Microbiome Project (HMP)
The Human Microbiome Project (HMP) Consortium is a collaborative group of over 200 researchers from 80 research centers that is organized and funded by the National Institutes of Health (NIH) in the United States. The project has been going since 2007.
Many scientists now regard human bodies as "supra-organisms", collections of communities made up of human and microbial cells coexisting in a whole that is more than the sum of its parts.
The idea behind the HMP is that because the microbiome is more varied than the genome, and easier to modify, it gives a more logical starting point for individually tailoring treatments, the goal of personalized medicine.
Knight said the HMP has sampled the microbiome of many people, to "get a better idea of variability, and how microbes work together in complex communities".
In 2009, a team from CU-Boulder and the Washington University School of Medicine in St. Louis, led by Knight, published the first atlas of bacterial diversity across the human body in a paper in Science.
For that study they took swab samples from 27 sites on the bodies of 9 volunteers and found that we human beings have personal bacterial communities that vary widely over our bodies: the ones on our forehead have a different signature to the ones on our feet, and to the ones in our navels and the ones in our noses.
New Way of Investigating the Microbiome
For the recently published 2012 studies, HMP researchers sampled the microbiomes of 242 healthy Americans: collecting tissue at three different times from 15 body sites in 129 males and from 18 sites in 113 females. The sites included the skin, nose, mouth, elbows, and lower intestines.