title: Concordance of HOMIM and HOMINGS technologies in the microbiome analysis of clinical samples.
abstract: BACKGROUND
  Over 700 bacterial species reside in human oral cavity, many of which are associated with local or distant site infections. Extensive characterization of the oral microbiome depends on the technologies used to determine the presence and proportions of specific bacterial species in various oral sites.
  
  
  OBJECTIVE
  The objective of this study was to compare the microbial composition of dental plaque at baseline using Human Oral Microbe Identification Microarray (HOMIM) and Human Oral Microbe Identification using Next Generation Sequencing (HOMINGS) technologies, which are based on 16S rRNA.
  
  
  METHODS
  Dental plaque samples were collected from 96 patients at baseline prior to a dental procedure involving manipulation of gingival tissues. The samples were surveyed for 293 and 597 oral bacterial species via HOMIM and HOMINGS, respectively, based on 16S rRNA gene sequences. We determined the concordance between the two technologies for common species. Genus level analysis was performed using HOMINGS-specific genus identification capabilities.
  
  
  RESULTS
  HOMINGS detected twice the number of species in the same dental plaque samples compared to HOMIM. For the species detected by both HOMIM and HOMINGS, there was no difference in relative proportions of overall bacterial composition at the species, genus or phylum levels. Additionally, there was no difference in relative proportion for total species per patient between the two technologies.
  
  
  CONCLUSIONS
  HOMINGS significantly expanded oral bacterial species identification compared to HOMIM. The genus and species probes, combined in HOMINGS, provided a more comprehensive representation of oral bacterial community, critical for future characterization of oral microbes in distant site infections.
authors.affiliation: Department of Oral Medicine, Cannon Research Center, Carolinas Health Care System, Charlotte, NC, USA; jean-luc.mougeot@carolinashealthcare.org.
authors.forename: Jean-Luc C
authors.initials: JL
authors.lastname: Mougeot
authors.affiliation: Department of Oral Medicine, Cannon Research Center, Carolinas Health Care System, Charlotte, NC, USA.
authors.forename: Craig B
authors.initials: CB
authors.lastname: Stevens
authors.affiliation: The Forsyth Institute, Cambridge, MA, USA.
authors.forename: Sean L
authors.initials: SL
authors.lastname: Cotton
authors.affiliation: Department of Oral Medicine, Cannon Research Center, Carolinas Health Care System, Charlotte, NC, USA.
authors.forename: Darla S
authors.initials: DS
authors.lastname: Morton
authors.affiliation: The Forsyth Institute, Cambridge, MA, USA.
authors.forename: Keerthana
authors.initials: K
authors.lastname: Krishnan
authors.affiliation: Department of Oral Medicine, Cannon Research Center, Carolinas Health Care System, Charlotte, NC, USA.
authors.forename: Michael T
authors.initials: MT
authors.lastname: Brennan
authors.affiliation: Department of Oral Medicine, Cannon Research Center, Carolinas Health Care System, Charlotte, NC, USA.
authors.forename: Peter B
authors.initials: PB
authors.lastname: Lockhart
authors.affiliation: The Forsyth Institute, Cambridge, MA, USA.
authors.forename: Bruce J
authors.initials: BJ
authors.lastname: Paster
authors.affiliation: Department of Oral Medicine, Cannon Research Center, Carolinas Health Care System, Charlotte, NC, USA; farah.mougeot@carolinashealthcare.org;
authors.forename: Farah K
authors.initials: FK
authors.lastname: Bahrani Mougeot
keywords: HOMIM; HOMINGS; MiSeq; ProbeSeq; dental plaque; oral microbiome