Atlas of Bacterial Diversity Charts Microbe Variability in Humans

An atlas of bacterial diversity across the human body charts wide variations in microbe populations that live in different regions of the human body.

A study showed that humans carry "personalized” communities of bacteria that vary widely from foreheads and feet to noses and navels. The scientists found wide variability in bacterial communities from person to person in the study, which included nine healthy volunteers and targeted 27 specific sites on the body.

Subjects were sampled four times each over a three-month period, typically one or two hours after taking a shower. Microbial DNA was then isolated directly from swabs used for sampling each body site, eliminating the standard culturing step. Specific bacterial RNA genes present in the DNA were then amplified using the polymerase chain reaction (PCR) and the genes were then sequenced with high-capacity DNA sequencers.

The specific bacterial RNA genes amplified from each sample were tagged during the PCR step with a sample-specific DNA barcode. This allowed the team to pool hundreds of samples together prior to a single sequencing run, reducing the cost and increasing the speed of the work.

The team of scientists, mostly from the University of Colorado at Boulder (CU-Boulder; USA), analyzed microbial communities in places such as hair on the head, ear canals, nostrils, mouth, lower intestine, and 18 different skin sites ranging from foreheads and armpits, forearms, palms, index fingers, navels, the back of the knees, and the soles of the feet. The latest generation of massively parallel DNA sequencers and new computational tools developed at CU-Boulder were used for the study.

"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,” said Bob Knight, assistant professor in CU-Boulder's chemistry and biochemistry department. "The goal is to find out what is normal for a healthy person, which will provide a baseline for further studies to look at people with diseased states. One of the biggest surprises was how much variation there was from person to person in a healthy group of subjects.”

There are an estimated 100 trillion microbes residing on and within each human being that are thought to collectively endow us with the essential traits we rely on for a variety of functions, including the proper development of our immune systems, efficient digestion of key foods and resistance to invasion by lurking microbial pathogens.

The CU-Boulder researchers reported that it might someday be possible to identify sites on the human body that would be amenable to microbial community transplants with either natural or engineered microbial systems that would be beneficial to the health of the host.

The study appeared in the November 6, 2009, issue of the journal Science Express, the online form of the journal Science.

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University of Colorado at Boulder