Concordance of HOMIM and HOMINGS technologies in the microbiome analysis of clinical samples
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 variou...
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| Format: | Article |
| Language: | English |
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Taylor & Francis Group
2016-04-01
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| Series: | Journal of Oral Microbiology |
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| Online Access: | http://www.journaloforalmicrobiology.net/index.php/jom/article/view/30379/45939 |
| _version_ | 1819157407532580864 |
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| author | Jean-Luc C. Mougeot Craig B. Stevens Sean L. Cotton Darla S. Morton Keerthana Krishnan Michael T. Brennan Peter B. Lockhart Bruce J. Paster Farah K. Bahrani Mougeot |
| author_facet | Jean-Luc C. Mougeot Craig B. Stevens Sean L. Cotton Darla S. Morton Keerthana Krishnan Michael T. Brennan Peter B. Lockhart Bruce J. Paster Farah K. Bahrani Mougeot |
| author_sort | Jean-Luc C. Mougeot |
| collection | DOAJ |
| description | 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. Conclusion: 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. |
| first_indexed | 2024-12-22T16:08:17Z |
| format | Article |
| id | doaj.art-7c3f508bc00d49aba72e44512e063f6b |
| institution | Directory Open Access Journal |
| issn | 2000-2297 |
| language | English |
| last_indexed | 2024-12-22T16:08:17Z |
| publishDate | 2016-04-01 |
| publisher | Taylor & Francis Group |
| record_format | Article |
| series | Journal of Oral Microbiology |
| spelling | doaj.art-7c3f508bc00d49aba72e44512e063f6b2022-12-21T18:20:32ZengTaylor & Francis GroupJournal of Oral Microbiology2000-22972016-04-01801910.3402/jom.v8.3037930379Concordance of HOMIM and HOMINGS technologies in the microbiome analysis of clinical samplesJean-Luc C. Mougeot0Craig B. Stevens1Sean L. Cotton2Darla S. Morton3Keerthana Krishnan4Michael T. Brennan5Peter B. Lockhart6Bruce J. Paster7Farah K. Bahrani Mougeot8 Department of Oral Medicine, Cannon Research Center, Carolinas Health Care System, Charlotte, NC, USA Department of Oral Medicine, Cannon Research Center, Carolinas Health Care System, Charlotte, NC, USA The Forsyth Institute, Cambridge, MA, USA Department of Oral Medicine, Cannon Research Center, Carolinas Health Care System, Charlotte, NC, USA The Forsyth Institute, Cambridge, MA, USA Department of Oral Medicine, Cannon Research Center, Carolinas Health Care System, Charlotte, NC, USA Department of Oral Medicine, Cannon Research Center, Carolinas Health Care System, Charlotte, NC, USA The Forsyth Institute, Cambridge, MA, USA Department of Oral Medicine, Cannon Research Center, Carolinas Health Care System, Charlotte, NC, USABackground: 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. Conclusion: 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.http://www.journaloforalmicrobiology.net/index.php/jom/article/view/30379/45939HOMINGSHOMIMMiSeqProbeSeqdental plaqueoral microbiome |
| spellingShingle | Jean-Luc C. Mougeot Craig B. Stevens Sean L. Cotton Darla S. Morton Keerthana Krishnan Michael T. Brennan Peter B. Lockhart Bruce J. Paster Farah K. Bahrani Mougeot Concordance of HOMIM and HOMINGS technologies in the microbiome analysis of clinical samples Journal of Oral Microbiology HOMINGS HOMIM MiSeq ProbeSeq dental plaque oral microbiome |
| title | Concordance of HOMIM and HOMINGS technologies in the microbiome analysis of clinical samples |
| title_full | Concordance of HOMIM and HOMINGS technologies in the microbiome analysis of clinical samples |
| title_fullStr | Concordance of HOMIM and HOMINGS technologies in the microbiome analysis of clinical samples |
| title_full_unstemmed | Concordance of HOMIM and HOMINGS technologies in the microbiome analysis of clinical samples |
| title_short | Concordance of HOMIM and HOMINGS technologies in the microbiome analysis of clinical samples |
| title_sort | concordance of homim and homings technologies in the microbiome analysis of clinical samples |
| topic | HOMINGS HOMIM MiSeq ProbeSeq dental plaque oral microbiome |
| url | http://www.journaloforalmicrobiology.net/index.php/jom/article/view/30379/45939 |
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