Featured Research

from universities, journals, and other organizations

Evolution on the inside track: How viruses in gut bacteria change over time

Date:
July 26, 2013
Source:
Perelman School of Medicine at the University of Pennsylvania
Summary:
The digestive tract is home to a vast colony of bacteria, as well as the myriad viruses that prey upon them. Because the bacteria species vary from person to person, so does this viral population, the virome. By closely analyzing the virome of one individual over two-and-a-half years, researchers have uncovered new insights on the virome can change and evolve -- and why the virome of one person can vary so greatly from that of another.

Phylogenetic tree of microphages detected in PNAS study and other studies. The four microphage contigs with the highest substitution rates observed in the PNAS study are shown in large black lettering. The scale bar indicates the proportion of amino acid substitutions within the 919 amino acid major coat protein, which was aligned to make the tree.
Credit: Frederick Bushman, PhD, Perelman School of Medicine, University of Pennsylvania; PNAS

Humans are far more than merely the sum total of all the cells that form the organs and tissues. The digestive tract is also home to a vast colony of bacteria of all varieties, as well as the myriad viruses that prey upon them. Because the types of bacteria carried inside the body vary from person to person, so does this viral population, known as the virome.

Related Articles


By closely following and analyzing the virome of one individual over two-and-a-half years, researchers from the Perelman School of Medicine at the University of Pennsylvania, led by professor of Microbiology Frederic D. Bushman, Ph.D., have uncovered some important new insights on how a viral population can change and evolve -- and why the virome of one person can vary so greatly from that of another. The evolution and variety of the virome can affect susceptibility and resistance to disease among individuals, along with variable effectiveness of drugs.

Their work was published in the Proceedings of the National Academy of Sciences.

Most of the virome consists of bacteriophages, viruses that infect bacteria rather than directly attacking their human hosts. However, the changes that bacteriophages wreak upon bacteria can also ultimately affect humans.

"Bacterial viruses are predators on bacteria, so they mold their populations," says Bushman. "Bacterial viruses also transport genes for toxins, virulence factors that modify the phenotype of their bacterial host." In this way, an innocent, benign bacterium living inside the body can be transformed by an invading virus into a dangerous threat.

At 16 time points over 884 days, Bushman and his team collected stool samples from a healthy male subject and extracted viral particles using several methods. They then isolated and analyzed DNA contigs (contiguous sequences) using ultra-deep genome sequencing .

"We assembled raw sequence data to yield complete and partial genomes and analyzed how they changed over two and a half years," Bushman explains. The result was the longest, most extensive picture of the workings of the human virome yet obtained.

The researchers found that while approximately 80 percent of the viral types identified remained mostly unchanged over the course of the study, certain viral species changed so substantially over time that, as Bushman notes, "You could say we observed speciation events."

This was particularly true in the Microviridae group, which are bacteriophages with single-stranded circular DNA genomes. Several genetic mechanisms drove the changes, including substitution of base chemicals; diversity-generating retroelements, in which reverse transcriptase enzymes introduce mutations into the genome; and CRISPRs (Clustered Regularly Interspaced Short Palindromic Repeats), in which pieces of the DNA sequences of bacteriophages are incorporated as spacers in the genomes of bacteria.

Such rapid evolution of the virome was perhaps the most surprising finding for the research team. Bushman notes that "different people have quite different bacteria in their guts, so the viral predators on those bacteria are also different. However, another reason people are so different from each other in terms of their virome, emphasized in this paper, is that some of the viruses, once inside a person, are changing really fast. So some of the viral community diversifies and becomes unique within each individual."

Since humans acquire the bacterial population -- and its accompanying virome -- after birth from food and other environmental factors, it's logical that the microbial population living within each of us would differ from person to person. But this work, say the researchers, demonstrates that another major explanatory factor is the constant evolution of the virome within the body. That fact has important implications for the ways in which susceptibility and resistance to disease can differ among individuals, as well as the effectiveness of various drugs and other treatments.

The research was supported by Human Microbiome Roadmap Demonstration Project (UH2DK083981) the Penn Genome Frontiers Institute, and the University of Pennsylvania Center for AIDS Research (CFAR; P30 Al 045008).

Samuel Minot, Alexandra Bryson, Christel Chehoud, Gary D. Wu, James D. Lewis, all from Penn, are co-authors.


Story Source:

The above story is based on materials provided by Perelman School of Medicine at the University of Pennsylvania. Note: Materials may be edited for content and length.


Journal Reference:

  1. S. Minot, A. Bryson, C. Chehoud, G. D. Wu, J. D. Lewis, F. D. Bushman. Rapid evolution of the human gut virome. Proceedings of the National Academy of Sciences, 2013; 110 (30): 12450 DOI: 10.1073/pnas.1300833110

Cite This Page:

Perelman School of Medicine at the University of Pennsylvania. "Evolution on the inside track: How viruses in gut bacteria change over time." ScienceDaily. ScienceDaily, 26 July 2013. <www.sciencedaily.com/releases/2013/07/130726191528.htm>.
Perelman School of Medicine at the University of Pennsylvania. (2013, July 26). Evolution on the inside track: How viruses in gut bacteria change over time. ScienceDaily. Retrieved October 25, 2014 from www.sciencedaily.com/releases/2013/07/130726191528.htm
Perelman School of Medicine at the University of Pennsylvania. "Evolution on the inside track: How viruses in gut bacteria change over time." ScienceDaily. www.sciencedaily.com/releases/2013/07/130726191528.htm (accessed October 25, 2014).

Share This



More Plants & Animals News

Saturday, October 25, 2014

Featured Research

from universities, journals, and other organizations


Featured Videos

from AP, Reuters, AFP, and other news services

Deep Sea 'mushroom' Could Be Early Branch on Tree of Life

Deep Sea 'mushroom' Could Be Early Branch on Tree of Life

Reuters - Innovations Video Online (Oct. 24, 2014) Miniature deep sea animals discovered off the Australian coast almost three decades ago are puzzling scientists, who say the organisms have proved impossible to categorise. Academics at the Natural History of Denmark have appealed to the world scientific community for help, saying that further information on Dendrogramma enigmatica and Dendrogramma discoides could answer key evolutionary questions. Jim Drury has more. Video provided by Reuters
Powered by NewsLook.com
Black Bear Cub Goes Sunday Shopping

Black Bear Cub Goes Sunday Shopping

Reuters - Light News Video Online (Oct. 23, 2014) Price check on honey? Bear cub startles Oregon drugstore shoppers. Rough Cut (no reporter narration). Video provided by Reuters
Powered by NewsLook.com
Dances With Wolves in China's Wild West

Dances With Wolves in China's Wild West

AFP (Oct. 23, 2014) One man is on a mission to boost the population of wolves in China's violence-wracked far west. The animal - symbol of the Uighur minority there - is under threat with a massive human resettlement program in the region. Duration: 00:41 Video provided by AFP
Powered by NewsLook.com
Breakfast Debate: To Eat Or Not To Eat?

Breakfast Debate: To Eat Or Not To Eat?

Newsy (Oct. 23, 2014) Conflicting studies published in the same week re-ignited the debate over whether we should be eating breakfast. Video provided by Newsy
Powered by NewsLook.com

Search ScienceDaily

Number of stories in archives: 140,361

Find with keyword(s):
Enter a keyword or phrase to search ScienceDaily for related topics and research stories.

Save/Print:
Share:

Breaking News:

Strange & Offbeat Stories


Plants & Animals

Earth & Climate

Fossils & Ruins

In Other News

... from NewsDaily.com

Science News

Health News

Environment News

Technology News



Save/Print:
Share:

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:

Get Social & Mobile


Keep up to date with the latest news from ScienceDaily via social networks and mobile apps:

Have Feedback?


Tell us what you think of ScienceDaily -- we welcome both positive and negative comments. Have any problems using the site? Questions?
Mobile: iPhone Android Web
Follow: Facebook Twitter Google+
Subscribe: RSS Feeds Email Newsletters
Latest Headlines Health & Medicine Mind & Brain Space & Time Matter & Energy Computers & Math Plants & Animals Earth & Climate Fossils & Ruins