As human beings have evolved during the past 6 million years, our resident microbes also have evolved into different species to adapt to different conditions throughout the body, according to research from Duke University. For example, the researchers found that a group of streptococci bacteria in the oral cavity diverged fairly recently, as the palate, tongue, throat, tonsils, gums, and plaque all house their own species of bacteria. According to the university, these findings could help researchers determine how different genes allow microbes to adapt to one place or another and could lead to new therapies that shape the microbiome.
"Over the last decade, there has been significant interest in developing probiotics and transplants of beneficial bacteria to treat a wide variety of health issues," said Lawrence A. David, PhD, senior author of the study and assistant professor of molecular genetics and microbiology at the Duke University School of Medicine. "Our analysis gives us a window into how different bacteria adapt and evolve so that we can more effectively predict which implanted species will survive to make an impact on disease."
Scientists typically learn about the microbiome by sampling a few million bacteria from an area of the body and sequencing them to count which bacteria belong to each species. Then, they compare these counts and generate values that tell them the relative abundance of each type of bacteria. However, relative abundance data requires statistical methods that account for how shifts in one species might affect another. Justin Silverman, an MD-PhD student in David’s laboratory, found a mathematical tool used by geologists, called the PhILR transform, that could be adapted to study the relative amounts of bacteria in the microbiome.
Using data from the Human Microbiome Project, the new technique combines the sequencing counts for each species with information on their position on the bacterial family tree. The resulting statistical framework starts with a common ancestor at the top and subsequent generations suspended underneath, like a mobile over a baby’s crib, connected by a series of crossbars. By looking at how these crossbars tilt and sway with the weight of the various species dangling from their tips, the researchers could assess how microbial communities grew and evolved in different body sites.
"This technique unlocks a tremendous toolbox of statistical methods that wouldn’t have worked before, but that can now be used to analyze microbiome data," Silverman said.
The study, "A Phylogenetic Transform Enhances Analysis of Compositional Microbiota Data," (https://elifesciences.org/content/6/e21887) was published by eLife.
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