A University of Colorado at Boulder team has developed the first atlas of bacterial diversity across the human body, charting wide variations in microbe populations that live in different regions of the body and which aid us in physiological functions that contribute to our health.
The study showed humans carry "personalized" communities of bacteria around that vary widely from our foreheads and feet to our noses and navels, said CU-Boulder's Rob Knight, senior author on the paper published in the Nov. 6 issue of Science Express. The researchers found unexpectedly wide variability in bacterial communities from person to person in the study, which included nine healthy volunteers and which targeted 27 specific sites on the body.
"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 Knight an 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."
Co-authors on the Science Express study, the online version of the journal Science, included CU-Boulder's Elizabeth Costello, Christian Lauber, Micah Hamady and Noah Fierer, as well as Jeffrey Gordon from the Washington University School of Medicine in St. Louis.
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 team looked high and low, analyzing 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 team used the latest generation of massively parallel DNA sequencers and new computational tools developed at CU-Boulder.
The study subjects were sampled four times each over a three-month period, typically after showering an hour or two earlier. 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 a technique known as PCR and the genes were then sequenced with high-capacity DNA sequencers, said Knight.
The specific bacterial RNA genes amplified from each sample, which were obtained from each body site of each individual, were "tagged" during the PCR step with a sample-specific DNA barcode developed by Knight's group. 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.
Specific skin sites, as well as hair, nostril and ear canal sites, had the highest levels of variability within individuals over time and were roughly on a par with the human lower intestine, according to the study. The highest diversity skin sites were the forearms, palm, index finger, back of the knee and sole of the foot. The armpits and soles of the feet showed some similarities, perhaps because they are dark and moist environments, said Fierer.