The human mouth is home to a complex community of microorganisms, including bacteria, fungi, and viruses, collectively known as the oral microbiome. To understand these microscopic residents, scientists require organized systems to classify and study them. This need led to the development of specialized resources, and the Human Oral Microbiome Database (HOMD) stands as a principal, web-accessible repository for this scientific field.
The Purpose and Creation of the Database
The primary goal of the Human Oral Microbiome Database is to provide the scientific community with a comprehensive resource for studying oral microbes. Before its existence, information was scattered, and many microbes were known only by vague clone numbers, making collaborative research difficult. A major challenge was that a large percentage of oral bacteria had not been formally named or grown in a lab, existing primarily as genetic sequence data.
To address this, researchers at the Forsyth Institute, with significant funding from the National Institute of Dental and Craniofacial Research (NIDCR), developed the HOMD. The project’s aim was to establish a stable and standardized classification system. By creating a common reference point, the database allows researchers from anywhere in the world to work with the same information, preventing confusion and streamlining the study of oral health and disease.
Cataloging Oral Microbes
The core of the HOMD is its detailed catalog of information, which is primarily divided into two types: taxonomic and genomic. The database organizes each microbe into a hierarchy of genus and species. It assigns a unique identifier, the Human Oral Taxon (HOT) ID, to every distinct microbial entry, whether it’s a well-known species or a newly identified strain. This numbering system acts as a stable reference, linking all associated data to a single, traceable entity.
Beyond classification, the database stores vast amounts of genomic information. This includes the full genetic blueprints, or genomes, for hundreds of oral microbes. These genomes are sourced from various research efforts, including the Human Microbiome Project, and are regularly updated as new sequences become available. The database also provides annotations, which are notes that describe the functions of specific genes.
The HOMD connects this taxonomic and genomic data to the microbes’ roles within the oral environment. It compiles information from scientific literature, linking specific bacteria to their typical locations in the mouth, such as on the tongue or below the gumline. This information also extends to their association with health or disease, noting whether a microbe is commonly found in a healthy mouth or if it is linked to conditions like dental caries (cavities) or periodontal (gum) disease.
Applications in Scientific Research
The HOMD directly impacts how scientists investigate oral health. Researchers can use the database to identify unknown bacteria they have collected from a patient’s mouth. By sequencing a part of the microbe’s DNA, typically the 16S rRNA gene, they can compare it against the HOMD’s curated library to find a match.
This capability allows for large-scale comparative studies. For instance, a research team can analyze the microbial communities of individuals with periodontitis and compare them to those of healthy individuals. By identifying which bacteria are more abundant in the disease group, they can form hypotheses about the causes of gum disease and develop targeted treatments.
The database also supports research connecting oral health to overall systemic health. Studies have shown that bacteria originating in the mouth can enter the bloodstream and may be associated with other conditions, including cardiovascular disease and diabetes. The HOMD provides the foundational data needed to explore these links, allowing scientists to track specific oral microbes and investigate their potential impact on other parts of the body.
Navigating the Database Tools
The HOMD website offers several tools designed to make its vast collection of data accessible. One of the primary functions is the “Taxon Search,” which allows a user to look up information on a specific microbe by its name or its unique HOT ID. This feature provides a direct path to a dedicated page for that microbe, containing all its curated taxonomic, genomic, and clinical information.
Another powerful tool available is a “BLAST search.” BLAST is an algorithm that functions like a search engine for genetic data. A scientist can take a DNA sequence obtained from their own lab sample, paste it into the search tool, and the HOMD will scan its entire library to find the closest genetic matches. This allows for the rapid identification of microbes from environmental or clinical samples.
These tools collectively empower the scientific community to leverage the database effectively. The user interface is designed to present complex information in an organized manner. The availability of these tools ensures that the HOMD is not just a static repository but a dynamic workspace for advancing oral microbiome research.