Featured Research

from universities, journals, and other organizations

Previously 'hidden diversity' of mouth bacteria revealed in study

Date:
June 23, 2014
Source:
Marine Biological Laboratory
Summary:
A new computational method for analyzing bacterial communities has uncovered closely related, previously indistinguishable bacteria living in different parts of the human mouth. The technique provides high taxonomic resolution of bacterial communities and has the capacity to improve the understanding of microbial communities in health and disease.

An important step in understanding the role of oral bacteria in health and disease is to discover how many different kinds live in the mouths of healthy people, and exactly where in the mouth they normally live.
Credit: dimj / Fotolia

A new computational method for analyzing bacterial communities has uncovered closely related, previously indistinguishable bacteria living in different parts of the human mouth. The technique, developed by Marine Biological Laboratory (MBL) scientists, provides high taxonomic resolution of bacterial communities and has the capacity to improve the understanding of microbial communities in health and disease. The study will be published in PNAS Online Early Edition.

Related Articles


An important step in understanding the role of oral bacteria in health and disease is to discover how many different kinds live in the mouths of healthy people, and exactly where in the mouth they normally live.

Using a novel computational method called oligotyping, developed by MBL Assistant Research Scientist A. Murat Eren, scientists analyzed gene sequence data from nine sites in the oral cavity. The data was provided by The Human Microbiome Project (HMP), an effort of the National Institutes of Health that produced a census of bacterial populations from 18 body sites in more than 200 healthy individuals. DNA in these samples was sequenced from the gene in bacteria that encodes ribosomal RNA, called the 16S rRNA gene, or 16S.

To this point, an understanding of the biomedical significance of HMP data has been hindered by limited taxonomic resolution. "Different species of bacteria can have very similar 16S gene sequences, sometimes differing by only a single DNA base in the region that was sequenced, and errors in DNA sequencing can also create differences of one or a few DNA bases," says the study's co-author Jessica Mark Welch, an Assistant Research Scientist at the MBL.

While the HMP data set has been used to identify bacteria broadly, to genus-level groups, it has never been used to identify bacteria more precisely, to the species level. "This genus-level grouping meant that many bacteria with similar DNA, but very different roles in the human microbiome, were lumped together, limiting the usefulness of the data," says Mark Welch.

Using oligotyping, Eren, Mark Welch and their colleagues Gary Borisy of the Forsyth Institute and Susan Huse of Brown University re-analyzed the HMP 16S gene data from dental plaque, saliva, and the surfaces of the tongue, cheek, gums, hard palate, tonsils, and throat. They found closely related, but distinct, bacteria living on the tongue, on the gums, and in plaque. For example, bacteria in saliva and in hard palate, tonsils, and throat resembled the tongue bacteria, while bacteria on the cheek were similar to bacteria on the gums. Bacteria from plaque below the gum-line also were detected on the tonsils, suggesting that the tonsils provide an oxygen-free environment where these bacteria can grow and come into contact with the human immune system.

Oligotyping detected kinds of bacteria that differed by as little as a single DNA base in the sequence tag. These differences in the 16S gene did not change the properties of the bacteria, but acted as markers for larger changes elsewhere in the bacterial genome which, the researchers believe, lead to different bacterial properties that make the bacteria prefer one part of the mouth over another.

"These distinct bacteria were present in the data all along, but were indistinguishable because they were so similar to each other -- hidden in plain sight, and revealed by oligotyping," says Mark Welch. "This method offers a better understanding of the distribution of precisely defined taxa within the mouth, and demonstrates a level of ecological and functional biodiversity not previously recognized. The ability to extract maximum information from sequencing data opens up new possibilities for the analysis of the dynamics of the human oral microbiome."

Eren has applied the oligotyping method to improve taxonomic resolution in other bacterial communities, including those from wastewater, from marine sponges, and from ocean water. The researchers say the technique has the capacity to analyze entire microbiomes, discriminate between closely related but distinct taxa and, in combination with habitat analysis, provide deeper insights into the microbial communities in health and disease. "The diversity of naturally occurring bacteria continues to impress us, and our study demonstrates that a comprehensive understanding in microbial ecology through marker genes requires our attention to subtle nucleotide variations," says Eren. "I anticipate that the ecologically important information oligotyping helped us recover from the human oral microbiome will intrigue other investigators to take a second look from their microbiome data sets."


Story Source:

The above story is based on materials provided by Marine Biological Laboratory. The original article was written by Gina Hebert. Note: Materials may be edited for content and length.


Journal Reference:

  1. Eren AM, Borisy GG, Huse SM, Mark Welch JL. Oligotyping analysis of the human oral microbiome. PNAS, June 2014 DOI: 10.1073/pnas.1409644111

Cite This Page:

Marine Biological Laboratory. "Previously 'hidden diversity' of mouth bacteria revealed in study." ScienceDaily. ScienceDaily, 23 June 2014. <www.sciencedaily.com/releases/2014/06/140623154759.htm>.
Marine Biological Laboratory. (2014, June 23). Previously 'hidden diversity' of mouth bacteria revealed in study. ScienceDaily. Retrieved December 18, 2014 from www.sciencedaily.com/releases/2014/06/140623154759.htm
Marine Biological Laboratory. "Previously 'hidden diversity' of mouth bacteria revealed in study." ScienceDaily. www.sciencedaily.com/releases/2014/06/140623154759.htm (accessed December 18, 2014).

Share This


More From ScienceDaily



More Plants & Animals News

Thursday, December 18, 2014

Featured Research

from universities, journals, and other organizations


Featured Videos

from AP, Reuters, AFP, and other news services

When You Lose Weight, This Is Where The Fat Goes

When You Lose Weight, This Is Where The Fat Goes

Newsy (Dec. 17, 2014) Can fat disappear into thin air? New research finds that during weight loss, over 80 percent of a person's fat molecules escape through the lungs. Video provided by Newsy
Powered by NewsLook.com
The Hottest Food Trends for 2015

The Hottest Food Trends for 2015

Buzz60 (Dec. 17, 2014) Urbanspoon predicts whicg food trends will dominate the culinary scene in 2015. Mara Montalbano (@maramontalbano) has the story. Video provided by Buzz60
Powered by NewsLook.com
Rover Finds More Clues About Possible Life On Mars

Rover Finds More Clues About Possible Life On Mars

Newsy (Dec. 17, 2014) NASA's Curiosity rover detected methane on Mars and organic compounds on the surface, but it doesn't quite prove there was life ... yet. Video provided by Newsy
Powered by NewsLook.com
Ivory Trade Boom Swamps Law Efforts

Ivory Trade Boom Swamps Law Efforts

Reuters - Business Video Online (Dec. 17, 2014) Demand for ivory has claimed the lives of tens of thousands of African elephants and now a conservation report says the illegal trade is overwhelming efforts to enforce the law. Amy Pollock reports. Video provided by Reuters
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