Variation In Bacterial Populations From Person To Person Surprises Researchers
The study, which was led by the University of Colorado at Boulder (CU-Boulder) and was published on 5th November in Science Express, the online version of the magazine, showed that humans are home to "personalized" communities of bacteria that vary widely from one part of the body to another.
Senior author Rob Knight, who is an assistant professor in CU-Boulder's chemistry and biochemistry department, told the media that:
"This is the most complete view we have yet of the microbial side of ourselves, one that our group and others will be adding to over the coming years."
He said they were aiming to find out what was normal for a healthy person so they could provide a baseline for people with diseases, but:
"One of the biggest surprises was how much variation there was from person to person in a healthy group of subjects," he added.
Each of us carries an estimated 100 trillion "friendly" microbes on and inside our bodies. These are necessary for all aspects of our wellbeing, from supporting the resistance of unwanted pathogens to helping us digest certain essential foods.
For the study, Knight and other colleagues from CU-Boulder and the Washington University School of Medicine in St. Louis, recruited 9 healthy volunteers who were willing to allow samples to be taken four times over a 3 month period from 27 specific sites on their bodies, including head hair, ear canals, nostrils, mouth, lower intestine, forehead, armpits, forearms, palms, index fingers, navel, backs of knees and the soles of the feet (18 of the sites were on different parts of the skin).
The swabs were usually taken an hour or two after showering.
The researchers analyzed the microbial colonies using the latest generation of parallel DNA sequencers and computerized tools developed at CU- Boulder.
Knight said they analyzed the DNA directly from the swabs, thus bypassing the need for lab-culturing, amplified specific RNA genes using PCR, and then sequenced them with high-capacity DNA sequencers.
(PCR stands for polymerase chain reaction, a method that is now common in lab-based DNA tests, for instance there is a PCR test for identifying the 2009 H1N1 swine flu strain).
During the PCR stage, they "tagged" each specific microbial RNA gene with a sample-specific DNA "barcode" from which they could tell which site on which person it came from.
Using this barcode system, which they developed themselves, Knight and colleagues found it allowed them to pool hundreds of samples for sequencing runs, thus reducing the cost and time taken to do the work.
The results showed that certain skin sites, hair, nostrils, and ear canals had the highest range of variability within individuals over time, and was about the same as that in the human lower intestine. The skin sites were the: forearms, palms, index fingers, backs of the knees and soles of the feet.
The armpits and soles of the feet showed some similarities, perhaps because they are dark and moist environments, suggested co-author Noah Fierer, an assistant professor in CU-Boulder's ecology and evolutionary biology department.
The site with the least variation in diversity over time in one person and across persons was the mouth cavity.
The researchers also found that one type of bacteria dominated head sites such as head hair, forehead, external nose and external ear, and another type dominated the trunk and the legs.
Fierer said they now have a number of interesting questions, such as:
"Why do healthy people have such different microbial communities? Do we each have distinct microbial signatures at birth, or do they evolve as we age?"
"And how much do they matter? We just don't know yet," he added.
First author Elizabeth K Costello, who has just taken up a postdoctoral position at Stanford University, said analyzing the human bacterial communities was like charting the growth of newborn babies:
"Just as babies are tracked for weight and height as they grow to see where they fall in relation to normal ranges, we'd like to be able to find out if there are normal ranges of microbial communities for humans that could be tracked over time."
The researchers also experimented with moving the microbial communities from one site to another.
For example, they disinfected the forearms and foreheads of some of the volunteers and seeded both sites with samples of bacteria taken from the tongue. The tongue bacteria lasted longer on the forearms than on the foreheads.
Costello explained that:
"As some others have speculated, it may be that drier areas of the skin like forearms make generally more hospitable landing pads for bacteria."
There was no difference in the ease with which a disinfected forehead or forearm could be colonized with a person's own or someone else's "transplated" bacteria, they said.
The researchers concluded that:
"These results indicate that our microbiota, although personalized, varies systematically across body habitats and time: Such trends may ultimately reveal how microbiome changes cause or prevent disease."
Knight said understanding the variation in human microbial communities was important for future research:
"If we can better understand this variation, we may be able to begin searching for genetic biomarkers for disease," explained Knight.
"Bacterial Community Variation in Human Body Habitats Across Space and Time."
Elizabeth K. Costello, Christian L. Lauber, Micah Hamady, Noah Fierer, Jeffrey I. Gordon, and Rob Knight.
Science Express, Published online 5 November 2009.
Source: University of Colorado at Boulder.
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