updated 5-12-14, All 50 States and 87 countries! IADR presentations, Next generation sequencing analysis with HOMIM probes, 37 peer-reviewed publications. High-throughput Oral Bacterial Detection and Identification
Since February 2008, the Human Microbial Identification Microarray core (MIM) at The Forsyth Institute, now in Cambridge, Massachusetts, has provided a specialized service for the rapid determination of bacterial profiles of clinical samples from the human oral cavity, esophagus and lung. Since 1986, Dr. Bruce Paster and Dr. Floyd Dewhirst used molecular analyses based on 16S rRNA sequencing to identify over 600 predominant bacterial species in the oral cavity. About 35% of these species has not yet been cultivated (for details, see Dewhirst et. al and the Human Oral Microbiome Database, HOMD). Using this information, they developed for their own research the Human Oral Microbe Identification Microarray, known as HOMIM, which allows for the simultaneous detection of about 300 of the most prevalent oral bacterial species, including those that have not yet been cultivated. HOMIM is recognized as a valuable research tool by many investigators from academic and private national and international institutions, government, and industry. Resulting from these studies have been 37 peer-reviewed publications, 6 reviews describing HOMIM, and many presentations at national and international meetings. Under development are microarrays that target bacterial species from the human gastrointestinal tract and the macaque oral cavity.
Next Generation HOMIM will be released soon! These new analyses, called HOMINGS (Human Oral Microbe Identification using Next Generation Sequencing), will provide a higher throughput using the MiSeq (Illumina) platform with in silico 16S rRDNA probe analysis for species-level identification. We are in the final stages of validation of the system--at present, we can determine over 600 oral taxa at the species-level. Those taxa that cannot be resolved at the species level will be identified at the genus level. Percent frequency of each taxon is presented in an excel spreadsheet. Data can be simultaneously analyzed with traditional bioinformatics, e.g., QIIME. Supporting data will be presented at the 2014 IADR in Cape Town. The new website for HOMINGS is presently under construction, but feel free to contact Dr. Paster for details.
Utility of HOMIM (and HOMINGS)
- To determine and compare bacterial associations in oral health and disease, including different types of periodontitis, caries, gingivitis, ventilator-associated pneumonia, endodontic and odontogenic lesions, abscesses, and halitosis
- To determine the efficacy of therapies, e.g., mouth rinses, antibiotic treatment, scaling and root planing, and laser or periodontal surgery
- To determine the progression of oral diseases
- To determine those patients at risk for periodontitis and other oral diseases
- To determine potential biomarkers for non-oral, systemic diseases, e.g., Crohn's Disease and pancreatic cancer
HOMIM has been used to rapidly produce preliminary data for grants, to obtain data for student projects or theses, and to analyze precious, archived frozen samples (e.g., saliva).
HOMIM service procedure
Investigators submit DNA isolated from clinical samples (see Sample Preparation) and receive via email data analyses in the form of excel spread sheets. However, due to the varied nature of projects, in-depth statistical analyses are not generally provided. For registered users, data can be also accessed online through a dedicated website. In addition, data are cumulative, so analyses of old data can be potentially compared with new data.
Time frame for HOMIM analyses
Our present processing capacity for HOMIM analysis is approximately 60 samples per week, but may take longer depending upon the position in the queue.
At this time, HOMIMs are to be used only for research endeavors and cannot be used for diagnostic purposes.
To learn more about this service including potential collaboration, please contact Dr. Paster at firstname.lastname@example.org or 617-892-8288.
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