NATURE | LETTER
Dynamics and associations of microbial community types across the human body
Tao Ding & Patrick D. Schloss
AffiliationsContributionsCorresponding author
Nature 509, 357–360 (15 May 2014) doi:10.1038/nature13178
Received 02 September 2013 Accepted 20 February 2014 Published online 16 April 2014
A primary goal of the Human Microbiome Project (HMP) was to provide a reference collection of 16S ribosomal RNA gene sequences collected from sites across the human body that would allow microbiologists to better associate changes in the microbiome with changes in health1. The HMP Consortium has reported the structure and function of the human microbiome in 300 healthy adults at 18 body sites from a single time point2, 3. Using additional data collected over the course of 12–18?months, we used Dirichlet multinomial mixture models4 to partition the data into community types for each body site and made three important observations. First, there were strong associations between whether individuals had been breastfed as an infant, their gender, and their level of education with their community types at several body sites. Second, although the specific taxonomic compositions of the oral and gut microbiomes were different, the community types observed at these sites were predictive of each other. Finally, over the course of the sampling period, the community types from sites within the oral cavity were the least stable, whereas those in the vagina and gut were the most stable. Our results demonstrate that even with the considerable intra- and interpersonal variation in the human microbiome, this variation can be partitioned into community types that are predictive of each other and are probably the result of life-history characteristics. Understanding the diversity of community types and the mechanisms that result in an individual having a particular type or changing types, will allow us to use their community types to assess disease risk and to personalize therapies.
April 16, 2014
Scientists re-define what's healthy in newest analysis for Human Microbiome Project
As scientists catalog the trillions of bacteria found in every nook and cranny of the human body, a new look by the University of Michigan shows wide variation in the types of bacteria found in healthy people.
Based on their findings in today's Nature, there is no single healthy microbiome. Rather each person harbors a unique and varied collection of bacteria that's the result of life history as well their interactions with the environment, diet and medication use.
"Understanding the diversity of community types and the mechanisms that result in an individual having a particular type or changing types will allow us to use their community type to assess disease risk and to personalize their medical care," says lead study author Patrick D. Schloss, Ph.D., associate professor of microbiology and immunology at the U-M Medical School.
Additional findings reveal bacteria can be grouped into community types that are predictive of each other.
"What was unexpected was that it was possible to predict the type of community a person had in their gastrointestinal track based on the community in their mouth," Schloss explains. "This was possible even though the types of bacteria are very different in the two sites."
The Human Microbiome Project is the movement to understand how changes in the microbiome are associated with changes in health.
More than 200 scientists in the HMP consortium spent five years analyzing samples from nearly 300 healthy adults. The samples came from 18 different places on their bodies, including their mouths, noses, guts, behind each ear and inside each elbow.
Schloss and co-author Tao Ding, Ph.D, revealed it is possible to associate a limited amount of data from the subjects with their community type.
Whether a person was breastfed was associated with their gut community type, level of education was associated with the vaginal community type, and one's gender affected several body types as well.
For the study, U-M researchers were not able to associate any of the changes in community type with changes in health.
"What our data shows is that just because a person's microbiome is different doesn't make it unhealthy," says Schloss. "It demonstrates there's more to learn about the factors that cause one's microbiome to change."
Understanding why community types change will be useful in developing therapies that can alter one's community type using pre- and probiotics, fecal transplants or antibiotics.
Explore further: Microbes in the gut help determine risk of tumors
More information: "Dynamics and associations of microbial community types across the human body," Nature, 10.1038/nature13178
Journal reference: Nature
Provided by University of Michigan Health System