image: The Human Oral Microbiome Database comprises genomic analysis of known types of bacteria common to the human oral cavity.
Credit: Tsute George Chen/ADA Forsyth Institute
Somerville, Mass., 07/09/2025 – The human oral microbiome, a diverse community of microorganisms in the mouth, performs many key physiological functions that can benefit or harm the human host, depending on its state.
Scientists at the ADA Forsyth Institute (AFI), a world-class leader in oral health research and innovation, have curated information on the oral microbiome for over two decades through the Human Oral Microbiome Database (HOMD). A recent update to the database includes a greatly expanded set of whole-genome sequences, reflecting a significant advancement in taxonomy of bacterial species and the study of microbial states in disease and health.
“The latest version of the Human Oral Microbiome Database represents the new era of genomic information,” said AFI Professor Jessica Mark Welch, Ph.D. “The large breadth of data we curated helps the entire scientific community study the oral microbiome.”
Version 4 of the database introduces 44 new human oral taxa, bringing the total taxa identified to 834, including 523 primarily oral species and 22 primarily nasal species. The researchers also deleted taxa revealed to be redundant by whole-genome sequencing.
Among oral taxa identified in the HOMD, 49% are named, 21% are unnamed but cultivated, and 29% are known only as uncultivated phylotypes.
The update provides an unprecedented level of genomic detail that enables researchers to study the oral microbiome with greater precision and depth. By resolving redundancies and expanding the catalog of species, the updated HOMD opens new pathways for exploring microbial contributions to both oral and systemic health that were not previously accessible.
Whole-genome sequencing allows the scientific community to access detailed information about bacteria in the oral cavity. Scientists can use the updated HOMD to ask and answer questions about topics such as the makeup of the oral microbiome in states of health or disease, the habitat preferences and functions of certain microbes, or the effects of interactions between species.
“You must look at all the species, and what they are doing together, to understand how bacteria interact with the human host in the oral environment,” said ADA Forsyth Associate Investigator Tsute Chen, Ph.D. “Mapping to the whole genome allows us to gain the full picture of which genes are expressed and which may be virulence genes, then the scientific community can more fully understand a disease mechanism.”
The HOMD has been accessible online since 2008. The database evolved from earlier projects driven by AFI scientists Floyd Dewhirst, Ph.D., Bruce Paster, Ph.D., and Dr. Chen. The HOMD was the first human body-site specific microbiome database, part of the National Institutes of Health’s Human Microbiome Project which started in 2007. The HOMD has been recognized by all major dental and oral health research institutes worldwide and has been cited by over 5,500 scientific publications and textbooks and have impacted many disciplines well beyond oral health.
Additional collaborators (all from ADA Forsyth unless otherwise noted): Kathryn Kauffman (University at Buffalo), Andrew Voorhis (Marine Biological Laboratory), Susan Yost, Susan Weir, Tina Yaskell, and William G. Wade (King’s College London).
Funding:
This work was funded by the NIH NIDCR R01DE016937.
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About the ADA Forsyth Institute
The ADA Forsyth Institute was founded in 1910 as the Forsyth Dental Infirmary for Children (later, the Forsyth Institute), to provide dental care to the disadvantaged children of Boston. While continuing to serve children in need, yet recognizing the ultimate goal is to prevent dental disease, the Institute in 1915 began to focus on scientific research and is today the world’s leader in oral health research. In October of 2023, the Institute joined with the American Dental Association to form the ADA Forsyth Institute, a 501(c)(3) entity dedicated to improving people’s oral and overall health and powering the profession of dentistry through cutting-edge basic research, creative translational science, innovative clinical technologies, and global public health outreach. Consistent with the Institute’s founding mission, the ADA ForsythKids mobile dental program continues to serve children in need.
About the American Dental Association
The not-for-profit ADA is the nation's largest dental association, representing 159,000 dentist members. The premier source of oral health information, the ADA has advocated for the public's health and promoted the art and science of dentistry since 1859. The ADA's state-of-the-art research facilities develop and test dental products and materials that have advanced the practice of dentistry and made the patient experience more positive. The ADA Seal of Acceptance long has been a valuable and respected guide to consumer dental care products. The Journal of the American Dental Association (JADA), published monthly, is the ADA's flagship publication and the best-read scientific journal in dentistry. For more information about the ADA, visit ADA.org. For more information on oral health, including prevention, care and treatment of dental disease, visit the ADA's consumer website MouthHealthy.org.
Method of Research
Data/statistical analysis
Subject of Research
Cells