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2017-03-28 19:33:52 UTC
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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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
Cite This Page:
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APA
Chicago
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. <www.sciencedaily.com/releases/2017/03/170320143839.htm>.
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https://www.sciencedaily.com/releases/2017/03/170320143839.htm
ScienceDaily
Your source for the latest research news
Science News from research organizations
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.
Share:
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
Cite This Page:
MLA
APA
Chicago
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. <www.sciencedaily.com/releases/2017/03/170320143839.htm>.
Recommended Articles
The Evolving Human Microbiome
GenomeWeb, 2010
Humans as Host
GenomeWeb, 2011
Metagenomic Techniques Can Profile Individual Microbe Strains
GenomeWeb, 2016
Gene Co-variance Approach Shows Promise for Identifying, Assembling Microbial Genomes from Metagenomic Sequences
GenomeWeb, 2014
Study Highlights Diversity, Dynamics of Human Vaginal Microbiome
GenomeWeb, 2012
Gut Bacteria and Obesity: How Strong a Link?
MedPage Today, 2016
Gut Bacteria Linked to Anti-PD-1 Response
Charles Bankhead, MedPage Today, 2017
Physician Pay and the Value of a Hug
MedPage Today, 2016
Patient Goals Should Figure Prominently in Tx Discussions
MedPage Today, 2016
Drug-Resistant Gonorrhea Finally Gets Attention
MedPage Today, 2017
Powered by TrendMD
Toggle navigationMenu FullA-AA+SD
Free Subscriptions
Get the latest science news with ScienceDaily's free email newsletters, updated daily and weekly. Or view hourly updated newsfeeds in your RSS reader:
Email Newsletters
RSS Feeds
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Keep up to date with the latest news from ScienceDaily via social networks:
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Mobile Apps
Get the latest news from ScienceDaily via our free mobile apps, available for download on the following platforms:
iPhone/iPad
Android
Have Feedback?
Tell us what you think of ScienceDaily -- we welcome both positive and negative comments. Have any problems using the site? Questions?
Leave Feedback
Contact Us
About This Site | Editorial Staff | Awards & Reviews | Contribute | Advertise | Privacy Policy | Terms of Use
Copyright 2016 ScienceDaily or by third parties, where indicated. All rights controlled by their respective owners.
Content on this website is for information only. It is not intended to provide medical or other professional advice.
Views expressed here do not necessarily reflect those of ScienceDaily, its staff, its contributors, or its partners.
https://www.sciencedaily.com/releases/2017/03/170320143839.htm