Landmark microbiome study surprises and redefines health

Considering that our microbes outnumber our human cells ten to one, it was about time for the first major study of our microbiomes. The results were beyond what researchers had imagined.
Written by Laura Shin, Contributor on

After a long, hot shower with lots of antibacterial soap, it probably feels like you're scrubbed clean.

But a new five-year federal study shows that you'll never be free of the many bacteria, yeasts, viruses and amoebas that live and die on your body -- and that they are much more diverse than we ever imagined.

The $170 million Human Microbiome Project, which comprised 200 scientists at 80 institutions and has been compared to the Human Genome project, has sequenced the genes of the bacterial zoo on almost 250 healthy individuals. (The microbiome is this collection of microbes on the human body and their genes.)

The researchers discovered that a single human body can contain as many as a thousand types of bacteria -- more than they had expected. The number of microbes on our bodies can outnumber the cells that make us human by ten to one, and they outnumber our genes by even more. In a 200-pound person, the microbiome can weigh two to six pounds.

Additionally, the microbiome on each body differs from that of the next person's -- and they sometimes even contain disease-causing bacteria that don't actually make people sick.

The results, published in two studies in Nature and 12 studies in PLoS journals, are expected to transform research on human health and disease.

The study

Six hundred subjects began the tests to determine whether they were healthy enough to be included in the study. They were inspected for disease in the nose, skin, mouth, gastrointestinal tract and, for the women, vagina. Half had to be dismissed for not being completely healthy, and 80% of those accepted had to first be treated for cavities or gum disease.

With 242 completely healthy subjects, The New York Times reports, "the investigators collected stool samples and saliva, and scraped the subjects’ gums and teeth and nostrils and their palates and tonsils and throats. They took samples from the crook of the elbow and the folds of the ear. In all, women were sampled in 18 places, including three sites in the vagina, and men in 15."

They then took samples of each subject three times during the course of the study to see whether the bacterial makeup of their bodies was stable. All told, they ended up with 11,174 samples.

Looking for a specific gene, 16S rRNA, that is a marker for bacteria, the researchers were able to sequence the bacterial DNA and uncover each microbiome's unique genes.

Changing conceptions of the bacteria on our bodies

Prior to this project, the bacteria in the microbiome have not been much studied.

While it was known that our microbiomes begin to form as we pass through the birth canal (which means that babies born by Caesaran have different microbes), they were exceedingly difficult to study: Since they live on the body and in body cavities, it was hard to culture them in a lab. Even if they did grow there, they behaved differently because the environment was so different. The Human Microbiome Project was possible only because of advances in gene sequencing technology that allowed the researchers to see which bacteria were present.

Because this study was conducted on healthy subjects, researchers can establish criteria for a healthy microbiome. While they hoped to establish a "core microbiome" that showed what types of bacteria would always exist in, say, the mouth or the large intestine, they found instead that while each person has different microbes in each of those areas, those microbes will still perform the same functions.

"You can think about it like jobs in a city," Curtis Huttenhower, a computational biologist at the Harvard School of Public Health who workedon the study, told The Los Angeles Times. "If you go to two different cities, both will have banks and transportation and lawyers, but the specific people performing those tasks might be very different."

The results also surprised in other ways: The "healthy" subjects sometimes had disease-causing bacteria on their bodies. For instance, Staphylococcus aureus, the most common cause of staph infections, was detected in the noses of 29% of the volunteers, and on the skin of 4% of them.  The researchers found about 100 of these kinds of disease-causing bacteria.


Even if the researchers found that there was no "core microbiome" in various places on the body, the work can still help establish criteria for a healthy microbiome, which can then be used to see how antibiotics disturb a person's microbiome and how long it takes for the microbiome to recover.

The data will also show how the microbiome is related to disease. With a picture of a healthy microbiome, scientists can look at the microbes of the sick and determine whether their microbiomes are contributing to any diseases they have.

Some studies have already shown that the state of a persons's microbiome is linked to conditions such as inflammatory bowel disease, ulcerative colitis and Crohn's disease. But there is some indication that they may also have a connection to diseases such as diabetes, asthma, heart disease, obesity, rheumatoid arthritis, psoriasis and colorectal cancer.

Over time, researchers may be able to develop treatments that right a disturbed microbiome. For instance, a person could be fed "corrective" bacteria.

Already, some studies have shown success with such treatments, like fecal transplants (previously covered here), in which patients who have the bacteria Clostridium difficile in their large intestine receive a transplant of stool from someone with a healthy gut; limited studies have shown success with this method, which researchers surmise re-populates the diseased gut with healthy bacteria.

Related on SmartPlanet:

via: first Nature story, second Nature story, New York Times, Los Angeles TimesE! Science News

photo: National Human Genome Research Institute (NHGRI), part of the National Institutes of Health (NIH)

This post was originally published on Smartplanet.com

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