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   Microbes evolved to colonize different parts of the human body   
      
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   Microbes evolved to colonize different parts of the human body    
      
   Geology software used to measure relative abundance of bugs    
   Date:    
   March 20, 2017    
   Source:    
   Duke University    
   Summary:    
   Microbes have evolved over millions of years to live in and on all parts of   
   the human body. Scientists have created new ways to reconstruct how this   
   evolution unfolded, using mathematical tools originally developed for   
   geologists. They identified    
   microbes that diverged into new species as they colonized one area of the body   
   after another. The research could prompt new theories and treatments to manage   
   our bacterial ecology and improve our personal health.    
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   FULL STORY    
      
   Duke scientists have identified microbes that diverged into new species to   
   specialized in colonizing one area after another of the human body. The new   
   analysis used mathematical tools originally developed for geologists.    
   Credit: Jonathan Fuller, Duke University    
   As the human species evolved over the last six million years, our resident   
   microbes did the same, adapting to vastly different conditions on our skin and   
   in our mouths, noses, genitalia and guts.    
      
      
   A team of Duke University scientists has tracked how this microbial evolution   
   unfolded, using mathematical tools originally developed for geologists.    
      
   The scientists identified microbes that diverged into new species as they   
   colonized one area of the body after another. Their study provides a new way   
   of looking at complicated microbial data to tease out the evolution of   
   bacteria associated with our    
   bodies.    
      
   The research, published in the open access journal eLife, could prompt new   
   theories and treatments for managing these bacterial communities, collectively   
   known as the human microbiome, to improve our personal health.    
      
   "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, Ph.D., senior author of the study and   
   assistant professor of    
   molecular genetics and microbiology at 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."    
      
   Only recently have scientists begun to appreciate just how much our health   
   depends on the trillions of bacteria that call our bodies home. We now know   
   that these bacteria help digest the food we eat, boost our brain function, and   
   regulate our immune    
   systems. But figuring out how our bacteria -- which by some accounts outnumber   
   our own cells by ten to one -- evolved to live with each other and with us has   
   proven particularly challenging.    
      
      
   Scientists typically glean information on the microbiome by sampling a few   
   million bacteria -- say, from the gut or tonsils -- and sequencing them to   
   count which bacteria belong to each species. Then they compare those counts,   
   generating values that tell    
   them the relative abundance of each type of bug. But relative abundance data   
   requires statistical methods that take into account how shifts in one species   
   might affect another.    
      
   Justin Silverman, an MD-PhD student in the David laboratory, searched the   
   literature for possible workarounds, and found one in an unlikely place -- the   
   field of geology. To make sense of the relative amounts of different elements   
   like calcium and    
   aluminum found in rocks, geologists had devised a mathematical tool called the   
   PhILR transform. Silverman adapted this tool to study the relative amounts of   
   bacteria found in the microbiome.    
      
   The new technique combined the sequencing counts for each species with   
   information on their position on the bacterial family tree. The resulting   
   statistical framework looks like a mobile you might find hanging over a baby's   
   crib, with a common ancestor    
   at the top and all the subsequent generations suspended underneath, connected   
   by a series of cross-bars. By looking at how these cross-bars tilted and   
   swayed with the weight of the various species dangling from their tips,   
   Silverman and his colleagues    
   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.    
      
   Silverman used this framework to look at data from the Human Microbiome   
   Project and found that different microbes have evolved to adapt to   
   environments like our skin and mouth. For example, they discovered a group of   
   streptococci bacteria that diverged    
   fairly recently in different regions in the oral cavity. Our palate, tongue,   
   throat, tonsils, gums -- even the plaque on our teeth -- each house their own   
   species of bacteria. Such findings could help researchers determine how   
   different genes allow    
   microbes to adapt to one place or another, and could one day lead to new   
   therapies that shape the microbiome.    
      
   The researchers believe their technique could be applied in practically any   
   situation where high-throughput technologies are used to measure the   
   composition of a sample, from the genetic makeup of a tumor to the strains of   
   an influenza virus.    
      
      
   Story Source:    
      
   Materials provided by Duke University. Original written by Marla Vacek   
   Broadfoot. Note: Content may be edited for style and length.    
      
   Journal Reference:    
      
   Justin D Silverman, Alex D Washburne, Sayan Mukherjee, Lawrence A David. A   
   phylogenetic transform enhances analysis of compositional microbiota data.   
   eLife, 2017; 6 DOI: 10.7554/eLife.21887    
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   Duke University. "Microbes evolved to colonize different parts of the human   
   body: Geology software used to measure relative abundance of bugs."   
   ScienceDaily. ScienceDaily, 20 March 2017. .    
      
        
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