(Press-News.org) MBL, WOODS HOLE, MA—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 the week of June 23-27, 2014.
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."
The results of the oligotyping analysis of the human oral microbiome, the first investigation of its kind, are published in the June 23-27, 2014, online Early Edition of Proceedings of the National Academy of Sciences by Eren, Mark Welch, Gary Borisy (The Forsyth Institute, formerly at the MBL), and Susan Huse (Brown University, formerly at the MBL). The team's research was supported was supported by a G. Unger Vetlesen Foundation, National Institutes of Health (NIH), National Institute of Dental and Craniofacial Research Grant, and NIH Human Microbiome Project Demonstration Project Award.
Eren AM, Borisy GG, Huse SM, Mark Welch JL. Oligotyping analysis of the human oral microbiome. PNAS Early Edition, published online June 23-27, 2014, doi: 10.1073/pnas.1409644111.
The Marine Biological Laboratory (MBL) is dedicated to scientific discovery and improving the human condition through research and education in biology, biomedicine, and environmental science. Founded in Woods Hole, Massachusetts, in 1888, the MBL is a private, nonprofit institution and an affiliate of the University of Chicago.
New analysis reveals previously 'hidden diversity' of mouth bacteria
Groundbreaking method could provide insight into a variety of microbial communities
ELSE PRESS RELEASES FROM THIS DATE:
Computational technique provides new insight into oral microbiome
CAMBRIDGE, Mass., June 23, 2014—Scientists have applied a new technique to comprehensively analyze the human oral microbiome—providing greater knowledge of the diversity of the bacteria in the mouth. For the first-time, scientists can provide high-resolution bacterial classification at the sub-species level. This work will enable researchers to more closely examine the role of bacterial communities in health and disease. The study, "Oligotyping analysis of the human oral microbiome," will be published in the Proceedings of the National Academy of Sciences and available ...
Delivering drugs on cue
June 23, Boston -- Current drug-delivery systems used to administer chemotherapy to cancer patients typically release a constant dose of the drug over time - but a new study challenges this "slow and steady" approach and offers a novel way to locally deliver the drugs "on demand," as reported in the Proceedings of the National Academy of Sciences (PNAS). Led by David J. Mooney, Ph.D., a Core Faculty member at Harvard's Wyss Institute for Biologically Inspired Engineering and the Robert P. Pinkas Family Professor of Bioengineering at the Harvard School of Engineering ...
Bone loss persists 2 years after weight loss surgery
CHICAGO, IL — A new study shows that for at least two years after bariatric surgery, patients continue to lose bone, even after their weight stabilizes. The results—in patients undergoing gastric bypass, the most common type of weight loss surgery—were presented Monday at the joint meeting of the International Society of Endocrinology and the Endocrine Society: ICE/ENDO 2014 in Chicago. "The long-term consequences of this substantial bone loss are unclear, but it might put them at increased risk of fracture, or breaking a bone," said Elaine Yu, MD, MSc, the study's principal ...
A disease of mistaken identity
The symptoms of Cushing disease are unmistakable to those who suffer from it – excessive weight gain, acne, distinct colored stretch marks on the abdomen, thighs and armpits, and a lump, or fat deposit, on the back of the neck. Yet the disorder often goes misdiagnosed. To help combat misdiagnosis, Saleh Aldasouqi, an associate professor in the College of Human Medicine at Michigan State University, is drawing more attention to the rare disease through a case study, which followed a young patient displaying classic, yet more pronounced signs of the condition. Caused ...
Date labeling confusion contributes to food waste
Date labeling variations on food products contribute to confusion and misunderstanding in the marketplace regarding how the dates on labels relate to food quality and safety, according to a scientific review paper in the July issue of Comprehensive Reviews in Food Science and Food Safety. This confusion and misunderstanding along with different regulatory date labeling frameworks, may detract from limited regulatory resources, cause financial loss, and contribute to significant food waste. In the United States, the United States Department of Agriculture Economic Research ...
Understanding the ocean's role in Greenland glacier melt
The Greenland Ice Sheet is a 1.7 million-square-kilometer, 2-mile thick layer of ice that covers Greenland. Its fate is inextricably linked to our global climate system. In the last 40 years, ice loss from the Greenland Ice Sheet increased four-fold contributing to one-quarter of global sea level rise. Some of the increased melting at the surface of the ice sheet is due to a warmer atmosphere, but the ocean's role in driving ice loss largely remains a mystery. Research by scientists at Woods Hole Oceanographic Institution (WHOI) and the Univ. of Oregon sheds new light ...
Protecting and connecting the Flathead National Forest
A new report from the Wildlife Conservation Society (WCS) calls for completing the legacy of Wilderness lands on the Flathead National Forest in Montana. The report identifies important, secure habitats and landscape connections for five species—bull trout, westslope cutthroat trout, grizzly bears, wolverines, and mountain goats. These iconic species are vulnerable to loss of secure habitat from industrial land uses and/or climate change. Located in northwest Montana adjacent to Glacier National Park, the 2.4 million-acre Flathead Forest is a strategic part of the stunning ...
Ferroelectric switching seen in biological tissues
Measurements taken at the molecular scale have for the first time confirmed a key property that could improve our knowledge of how the heart and lungs function. University of Washington researchers have shown that a favorable electrical property is present in a type of protein found in organs that repeatedly stretch and retract, such as the lungs, heart and arteries. These findings are the first that clearly track this phenomenon, called ferroelectricity, occurring at the molecular level in biological tissues. The researchers published their findings online June 23 ...
Grinding away at history using 'forensic' paleontology and archeology
Tulsa, Ok. – The Society for Sedimentary Geology (SEPM) announces an unusual paper in their journal PALAIOS that combines 'forensic' paleontology and archeology to identify origins of the millstones commonly used in the 1800's. While all millstones were used similarly, millstones quarried in France were more highly valued than similar stones quarried in Ohio, USA. Over four years the scientific team located millstones by visiting historical localities in Ohio, then studied them and identified unique characteristics between the coveted French buhr and the locally sourced ...
By any stretch
After their hectic experience of delivery, newborns are almost immediately stretched out on a measuring board to assess their length. Medical staff, reluctant to cause infants discomfort, are tasked with measuring their length, because it serves as an indispensable marker of growth, health and development. But the inaccuracy and unreliability of current measurement methods restrict their use, so routine measurements are often not performed. Now Tel Aviv University researchers have taken a 21st century approach to the problem, using new software that harnesses computer ...
LAST 30 PRESS RELEASES:
Study finds senescent immune cells promote lung tumor growth
Study examines benefits and obstacles of library data storytelling
Cost of living crisis set to cut UK lives short and significantly widen wealth-health gap
Flawed body of research indicates true ‘long COVID’ risk likely exaggerated
Wealthier kids in UK may have experienced steepest fall in mental health during pandemic
Stem cell therapy can safely slow progression of relapsing-remitting MS
NASA’s Interstellar Mapping and Acceleration Probe passes system integration review
National Science Foundation taps Worcester Polytechnic Institute fire protection expertise and resources for the Wildfire Interdisciplinary Research Center
Doctor and pharmacist revamp standard processes for ordering and documenting mifepristone use
Screening for adverse childhood experience can improve trauma-informed care, though time constraints and limited referral resources present challenges
Understanding parents’ care expectations for a child with gastroenteritis could prevent after-hours care requests
Learning collaborative promotes mifepristone education and utilization training in federally qualified health centers
Men who trust their doctors, receive adequate time and general information about prostate cancer screening are more likely to have productive discussions
Study identifies patient and clinician-level characteristics associated with sexual history screening administration
Researchers identify important strategies for diabetes care and quality improvements in the primary care setting
Attentiveness to resting leg cramps may afford greater insight into advancing age and declining health
Staffing challenges and general time constraints may harm primary care teams’ ability to implement quality improvement efforts
Primary care investigators, clinicians, patients and community members reflect on NAPCRG’s 50 years of leadership and service
September/October Annals of Family Medicine 2023 tip sheet
Combination radiation with immunotherapy shows promise against “cold” breast cancer tumors
A new AI model has been developed to improve accuracy of breast cancer tumor removal
Finding the balance: Opioids and pain control after surgery
UC Irvine scientists reveal what fuels wildfires in Sierra Nevada Mountains
US Department of Energy Office of Science awards $115M for High Rigidity Spectrometer project at FRIB
Algorithm would predict disease relapses
Exercise-mimicking drug sheds weight, boosts muscle activity in mice
Did life exist on Mars? Other planets? With AI's help, we may know soon
Wind energy projects in North America are more likely to be opposed by white, wealthy communities
Naming and shaming can be effective to get countries to act on climate
Scientists develop method of identifying life on other worlds[Press-News.org] New analysis reveals previously 'hidden diversity' of mouth bacteria
Groundbreaking method could provide insight into a variety of microbial communities