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Human Oral Microbe Identification using Next Generation Sequencing


HOMINGS utilized the speed and efficiency of next generation sequencing combined with the refinement of bacterial species-level identification based on 16S rDNA comparisons. HOMINGS replaced the earlier, microarray-based technology HOMIM (The Human Oral Microbe Identification Microarray). Although HOMINGS and HOMIM are no longer available, potential collaborations are still possible using newer NGS pipelines that focus on 16S rRNA gene sequencing of the V1-V3 regions (contact Dr. Bruce Paster, bpaster@forsyth.org). Consequently, the information presented here represents a legacy website, which illustrates the utility of HOMINGS and its validation as compared to current technologies.


Features of HOMINGS

  • Species-level identification of nearly 600 oral bacterial taxa
  • Genus-level identification of remaining sequences for 129 genera

  • High-throughput Illumina sequencing
  • In silico 16S rDNA probe analysis
  • Rapid—computationally-efficient
  • User-friendly dataset, e.g., relative abundance
  • Traditional bioinformatics compatible, e.g., QIIME

History of HOMIM and HOMINGS

Beginning February 2008, HOMIM provided the scientific community a rapid means for oral bacterial identification in clinical samples. Developed from the research of Dr. Bruce Paster and Dr. Floyd Dewhirst, HOMIM allowed for the simultaneous detection of about 270 of the most prevalent, cultivated and not-yet-cultivated oral bacterial species. HOMIM was recognized as a valuable research tool by over 120 investigators or teams from academic and private national and international institutions, government, and industry. Resulting from these studies there are 59 peer-reviewed publications, 8 reviews describing HOMIM, and over 50 presentations at national and international meetings. Since the end of 2014, the sequence-based method HOMINGS continued in that tradition, as many collaborators used this methodology (see Testimonials) with 27 peer-reviewed publications and 2 reviews.


Utility of HOMINGS

As with HOMIM, many types of microbiome studies have been performed including the following:

  • Determined and compared bacterial associations in oral health and disease, including different types of periodontitis, caries, gingivitis, ventilator-associated pneumonia, endodontic and odontogenic lesions, abscesses, and halitosis
  • Determined the efficacy of therapies/treatments, e.g., mouth rinses, antibiotic treatment, scaling and root planing, and laser or periodontal surgery
  • Determined the progression of oral diseases
  • Determined those patients at risk for periodontitis and other oral diseases
  • Determined potential biomarkers for non-oral, systemic diseases, e.g., Crohn's Disease and pancreatic cancer

HOMIM/HOMINGS have had over 15,000 visits from more than 10,000 unique visitors from all 50 US States and 87 countries.