|Scientists Launch First Comprehensive Database
of Human Oral Microbiome
Scientists know more today than ever before about the microbes
that inhabit our mouths. They know so much, in fact, that gathering
all of the relevant bits of information into one place when designing
experiments can be a labor-intensive job in itself. Now, grantees
of the National Institute of Dental and Craniofacial Research (NIDCR),
part of the National Institutes of Health, and their international
colleagues intend to solve this problem with the launch of the
first comprehensive database of the oral microbiome, or the approximately
600 distinct microorganisms currently known to live in the mouth.
The free online compendium is called the Human Oral Microbiome
Database (HOMD). The database goes live today as the digital equivalent
of an Oxford dictionary of oral microorganisms, providing detailed
biological entries for each species and an extensive catalogue
of the thousands of genes that these microbes express. The site
is located at http://www.homd.org and
is overseen by scientists at The Forsyth Institute in Boston and
King's College London in England.
"The HOMD fills a critical research need," said NIDCR
director Lawrence Tabak, D.D.S., Ph.D. "The oral microbiome
is extremely rich in data, and HOMD becomes the essential search
engine for scientists to view and retrieve this information, generate
novel hypotheses, make computational discoveries, and ultimately
develop more biologically sound therapies to control oral diseases."
According to Floyd Dewhirst, D.D.S., Ph.D., a leader of the project
and a scientist at The Forsyth Institute, HOMD also introduces
the first comprehensive nomenclature system to bring order to the
naming of uncultured or previously unnamed oral microbes. The standardized
numbering system helps to eliminate the Babel of confusing names
and uninformative database designations that have frustrated scientists
and sometimes hindered their research.
The database also categorizes each microbe by its 16S rRNA sequence,
a distinctive fingerprint of genetic information that scientists
have used for the past two decades to identify microorganisms.
This sequence information allows the microbes to be placed in a
family tree that shows how they are related to one another. For
those organisms whose DNA has been sequenced, HOMD provides online
tools to view and analyze all of their genes and proteins. Each
category of information in the database is interlinked, readily
searchable, appropriately annotated, and will be frequently updated
to remain current.
Dewhirst noted that although HOMD has officially opened to scientists,
the database remains an ongoing project. "We've already assembled
a great deal of useful information for the research community,
but we will continue to expand and refine the database for the
next several years," said Dewhirst. "I can see the
Human Oral Microbiome Database serving as a valuable model for
other microbiome databases now and in the years to come."
Informally called "biology's next revolution," microbiome
studies have opened a needed window into the complex microbial
communities that occupy most parts of the human body. These studies
will define how microbes contribute to sustaining health and, when
their community dynamics are perturbed, play a role in common chronic
disease, such as tooth decay and periodontal disease in the mouth.
In December 2007, NIH launched the Human Microbiome Project that
initially will sequence all of the genes, or genomes, of 600 representative
microorganisms sampled from microbial communities in the mouth,
skin, digestive tract, nose, and female urogenital tract. Additional
studies are either under way or under development.
Among those already well under way is a NIDCR-supported project
to compile a full catalogue of the complete genomes of all oral
microbes. It has generated a tremendous amount of data and, coupled
with the decades of more traditional studies of oral bacteria,
the need for a comprehensive, user-friendly database has become
"The oral microbiome is currently better understood than
those of other sites in the body, such as the intestine," said
Dr. Bruce Paster, Ph.D., also at The Forsyth Institute and another
project scientist. "Since oral microorganisms appear in infections
throughout the human body, the HOMD database certainly will be
useful to physicians. Likewise, microbiologists in industry will
find HOMD helpful because oral microbes sometimes contaminate food
or the drug manufacturing process."
The National Institute of Dental and Craniofacial Research (NIDCR)
is the Nation's leading funder of research on oral, dental, and
The National Institutes of Health (NIH) — The Nation's
Medical Research Agency — includes 27 Institutes and
Centers and is a component of the U.S. Department of Health and
Human Services. It is the primary federal agency for conducting
and supporting basic, clinical and translational medical research,
and it investigates the causes, treatments, and cures for both
common and rare diseases. For more information about NIH and
its programs, visit www.nih.gov.