Humans host melting pot of ‘personal’ bacteria

U. COLORADO (US)—People carry “personalized” communities of bacteria around that vary widely from our foreheads and feet to our noses and navels, says chemistry professor Rob Knight. He’s part of a research team that has developed the first atlas of bacterial diversity across the human body.

The researchers found unexpectedly 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. Knight is senior author on the paper published in the Nov. 6 issue of Science Express.

“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,” says Knight, an assistant professor in the University of Colorado at 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 researchers 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, says 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 from dark and moist environments, says study coauthor Noah Fierer.

The mouth cavity showed the least variation in diversity both within individuals and between people, according to the study. The team also found the skin “head group”—which included forehead, external nose, external ear, and hair—was dominated by one type of bacteria, while sites on the trunk and legs were dominated by a different group.

“We have an immense number of questions to answer,” says Fierer, an assistant professor in CU-Boulder’s ecology and evolutionary biology department. “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.”

Elizabeth Costello, the first author on the paper who recently accepted a postdoctoral position at Stanford University, likened the analysis of human bacterial communities to charting the growth of newborns. “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.”

In an intriguing microbial community “transplant” experiment, the team disinfected the forearms and foreheads of some test subjects, then “inoculated” both sites with bacterial communities harvested from the tongue. The tongue bacteria persisted longer on the forearms than foreheads, suggesting some bacterial populations more strongly prefer sebaceous, or oily sites.

“As some others have speculated, it may be that drier areas of the skin like forearms make generally more hospitable landing pads for bacteria,” Costello notes. The team did not find any significant difference in how easily a person’s forehead or forearm could be colonized by his or her own “transplanted” microbes as opposed to those of other people.

“These patterns suggest that the search for microbial factors associated with disease, although difficult to ascertain due to the high intrinsic levels of variability among healthy individuals, may be achieved using broad profiling techniques such as those employed here,” the authors wrote in Science Express.

Previous microbial studies of healthy individuals have generally focused on individual body habitats including the lower intestine, skin and mouth. The new study builds on a 2008 CU study on hand bacteria indicating that while more than 4,200 species of bacteria resided on 102 human hands, only about five species were shared by all 51 participants. The 2008 study also showed women had a greater diversity of bacteria on their palms than men.

Knight says understanding the variation in human microbial communities holds promise for future clinical research. “If we can better understand this variation, we may be able to begin searching for genetic biomarkers for disease,” he adds.

The researchers says 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 research was funded by the Howard Hughes Medical Institute, the National Institutes of Health, the Bill and Melinda Gates Foundation, and the Crohn’s and Colitis Foundation of America. Jeffrey Gordon from the Washington University School of Medicine in St. Louis was one of the study’s coauthors.

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