BACKGROUND

HOMIM was developed as a high throughput technology to examine complex oral microbial diversity in a single hybridization, i.e., simultaneous detection of about 300 predominant oral bacterial species, including the not-yet-cultivated phylotypes. HOMIMs are used extensively in ongoing studies at The Forsyth Institute (9 PIs) and in other collaborative studies with national and international academic institutions (more than 70 investigative teams), government including NIH (6 investigative teams), and industry (12 companies).  As a result of some of these studies, there are now 25 peer-reviewed publications, 4 reviews describing HOMIM, and since 2009, 43 national and international abstracts or presentations.  

HOMIM-associated, peer-reviewed publications (25)

Alt-Holland A, Murphy CM, Powers A, Kublin CL, Jeong YN, DiMattia M, Pham L, Park A, Finkelman M, Lombard M, Hanley JB, Paster BJ, Kugel G. Comprehensive analysis of aerobic and anaerobic bacteria found on dental bib clips at hygiene clinic. Compendium Cont Ed Dent; 2013;34:S1-12 (in press).

Xin B, Luo A, Qin J, Paster BJ, Xu Y, Li Y, Yang D. Microbial diversity in the oral cavity of healthy Chinese Han children. Oral Dis; 2013; 19: 401-405. PMID: 23034082.

Holgerson PL, Vestman NR, Claesson R, Ohman C, Domellöf M, Tanner AC, Hernell O, Johansson I. Oral microbial profile discriminates breatfed from formula-fed infants. J Pediatr Gastroenterol Nutr. 2013. 56:127-36. PMID:22955450.

Ames N, Sulima P, Ngo T, Barb J, Munson PJ, Paster BJ, Hart TC. A characterization of the oral microbiome in allogeneic stem cell transplant patients. PloSOne; 2012;7(10):e47628. PMID:23144704.

Rudney JD, Chen R, Lenton P, Li J, Li Y, Jones RS, Reilly C, Fok AS, Aparicio C. A reproducible oral microcosm biofilm model for testing dental materials. J Appl Microbiol; 2012; 113:1540-53. PMID:22925110.

Shaddox LM, Huang H, Tong L, Hou W, Harrison PL, Aukhil I, Walker CB, Klepac-Ceraj, V, Paster BJ. Microbiological characterization in children with aggressive periodontitis. J Dent Res; 2012; 91:927-933. PMID:22863892.

Tanner ACR, Sonis AL, Lif Holgerson P, Starr JR, Nunez Y, Kressirer CA, Paster BJ, Johansson I. White spot lesion and gingivitis microbiota in orthodontic patients. J Dent Res; 2012; 91:853-858. PMID:22837552.

Dang AT, Cotton S, Sankaran-Walters S, Li C-S, Lee C-YM, Dandekar S, Paster BJ, George MD. Evidence of an increased pathogenic footprint in the lingual microbiome of HIV infected patients. BMC Microbiology; 2012;12:153. PMID:22838383.

Filkins LM, Hampton TH, Gifford AH, Gross MJ, Hogan DA, Sogin ML, Morrison HG, Paster BJ, O’Toole GA. The prevalence of streptococci and increased polymicrobial diversity associated with cystic fibrosis patient stability. J Bacteriol; 2012;194:4709-4717. PMID:22753064.

Luo A, Paster BJ, Xin B, Yang D. Microbial profiles in saliva from children with and without caries in mixed dentition. Oral Dis 2012;18:595-601. doi: 10.1111/j.1601-0825.2012.01915.x. PMID:22458262.

Torlakovic L, Klepac-Ceraj V, Øgaard B, Cotton SL, Paster BJ, Olsen I. Microbial community succession on developing lesions on human enamel. J Oral Microbiol 2012;4: doi: 10.3402/jom.v4i0.16125. PMID:22432048.

Colombo APV, Bennet S, Cotton SL, Goodson JM, Kent R, Haffajee AD, Socransky SS, Hasturk H, van Dyke TE, Dewhirst FE, Paster BJ. Impact of periodontal therapy on the subgingival microbiota of severe periodontitis: Comparison between good responders and “Refractory” subjects by the Human Oral Microbe Identification Microarray (HOMIM). J Periodontol 2012;83:1279-1287. PMID:22324467.

Sizova MV, Hohmann T, Hazen A, Paster BJ, Halem SR, Murphy CM, Panikov NS, Epstein SS. New approaches for isolation of previously uncultivated species. Appl Environ Microbiol 2012;78:194-203. PMID:22057871.

Farrell JJ, Zhang L, Zhou H, Chia D, Elashoff D, Akin D, Paster BJ, Joshipura K, Wong DT. Variations of oral microbiota are associated with pancreatic diseases including pancreatic cancer. GUT 2012;61:582-588. PMID:21994333.

Docktor MJ, Paster BJ, Abramowicz S, Ingram J, Wang YE, Correll M, Jiang H, Cotton SL, Kokaras AS, Bousvaros A. Alterations in diversity of the oral microbiome in pediatric inflammatory bowel disease. Inflammatory Bowel Dis 2012;18:935–942. PMID:21987382.

Albandar JM, Khattab R, Monem F, Barbuto SM, Paster BJ. The subgingival microbiota of Papillon-Lefèvre Syndrome.  J Periodontol 2011;82:902-908. doi:10.1902/jop.2011.110450. PMID:22141356.

Duran-Pinedo AE, Paster B, Teles R, Frias-Lopez J. Correlation network analysis applied to complex biofilm communities. PloS One 2011;6(12):e28438. doi: 10.1371/journal.pone.0028438. PMID:22163302.

Ahn JY, Yang LY, Paster BJ, Ganly I, Morris L, Pei ZH, Hayes RB. Oral microbiome profiles: 16S rRNA pyrosequencing and microarray assay comparison. PloS One 2011;6(7):e22788. PMID:21829515.

Tanner ACR, Kent RL Jr, Lif Holgerson P, Hughes CV, Loo CY, Kanasi E, Chalmers NI, Johansson I. Microbiota of severe early childhood caries before and after therapy. J Dent Res 2011;90:1298-1305.

Lif Holgerson P, Harnevik L, Hernell O, Tanner ACR, Johansson I.  Mode of birth delivery affects oral microbiota in infants.  J  Dent Res 2011;90:1183-1188.

Olson et al. Use of 16S ribosomal RNA gene analyses to characterize the bacterial signature associated with poor oral health in West Virginia.  BMC Oral Health 2011;11:7.

Asikainen et al. Specified bacterial species in gingival crevicular fluid predict diversity of unattached subgingival microbiota. PloS One 2010;5(10):e13589.

Colombo et al.  Comparisons of subgingival microbial profiles of refractory periodontitis, severe periodontitis and periodontal health using the human oral microbe identification microarray.  J Periodontol 2009;80:1421-1432.

Preza et al. Microarray analysis of the microflora of root caries in elderly. Eur J Clin Microbiol Infect Dis 2009;28:509-517.

Preza et al. Diversity and site-specificity of the oral microflora in the elderly.  Eur J Clin Microbiol Infect Dis 2009;28:1033-1040.

HOMIM-associated reviews

Teles R, Teles F, Frias-Lopez J, Paster B, Haffajee A.  Lessons learned and unlearned in periodontal microbiology. Periodontol 2000;2013;62:95-162.

Paster BJ, Dewhirst FE. Molecular microbial diagnosis. Periodontol 2000 2009;51:38-44.

Olsen el al. Cultivated and not-yet-cultivated bacteria in oral biofilms. Microb Ecol Hlth Dis 2009;21:65-71.

Paster et al. The breadth of bacterial diversity in the human periodontal pocket and other oral sites. Periodontol 2000 2006;42:80-87.

Background publications

Dewhirst et al. The human oral microbiome. J Bacteriol 2010;192:5002-5017.

Aas et al. Defining the normal bacterial flora of the oral cavity. J Clin Microbiol 2005;43:5721-5732.

Paster et al. Bacterial diversity in human subgingival plaque. J Bacteriol 2001;183:3770-3783.

HOMIM-associated abstracts/presentations (44 since 2009)

Cotton SL, Klepac-Ceraj V, Murphy CM, Kokaras AS, Paster BJ. Species Level Determination of High-throughput Sequencing Data using HOMIM Probes. J Dent Res (AADR) 2013;92:3828

Paster BJ, Murphy CM, Martin L, Kokaras AS, Klepac-Ceraj V, Cugini M, Patel M, Sherzai H., Roberts C, Nguyen DH, Aleksandrova V, Pratten JR, Bradshaw DJ, Hasturk H. The Microbiome of Maxillary Dentures. J Dent Res (AADR) 2013;92:1382.

Belstrøm D, Fiehn NE, Poulsen K, Reinholdt J, Kirkby N, Nielsen CH, Klepac-Ceraj V, Paster BJ, Cotton S, Kokaras AS, Holmstrup P. Bacterial profile of saliva in oral health. J Dent Res (AADR) 2013;92:1364.

Heller D, Custodio W, Helmerhorst EJ, Paster BJ, Siqueira WL, Oppenheim FG. Synchrony of Protein and Microbial Attachment in Early Dental Integuments.  J Dent Res (AADR) 2013;92:1744.

Alt-Holland A, Murphy CM, Srinivasan S, Lucier R, Kublin CL, Fong JM, Goldfein J, Baker DL, Park A, Finkelman M, Kawai T, Paster BJ, Kugel G. Patient Napkin Holders – Is There Potential Risk For Cross-Contamination? J Dent Res (AADR) 2013;92: 3403.

Fine DH, Furgang D, Tischio-Bereski D, Fairlie K, Markowitz K, Mckiernan M, Curro V, Paster BJ, Dewhirst F.  Aa Induced Localized Aggressive Periodontitis in Children.  J Dent Res (AADR) 2013;92:2983.

Chalmers NI, Paster BJ, Barb J, Uzel G, Munson P, Holland S, Moutsopoulos N. Neutrophil Recruitment Deficiencies Result in Distinctive Periodontal Biofilm Microbiota. J Dent Res (AADR) 2013;92:3832.

Li Y, Saxena D, Chen Z, Phelan J, Norman RG, Li YH, Corby PM, Kokaras AS, Dewhirst F, Paster BJ, Malamud D. HIV Infection And HAART Affect Salivary Microbial Colonization And Diversity. J Dent Res (AADR) 2013;92:3780.

Mehta NM, Pichoff D, McAdam A, Paster B, Priebe GP.Microbiome Identification Using A Culture-Independent Molecular Technique In Mechanically Ventilated Children - New Insights. Crit Care Med. 2012; 40 Supplement S:U55.

Docktor M, Wang Y, Abramowicz S, et al.  Disease Activity Is Associated With Increased Bacterial Diversity in Inflammatory Bowel Disease. Inflammatory Bowel Diseases 2012; 18 Supplement 1: S63.

Yu L, Hou B, Paster BJ. Comparative study of microorganisms in dental plaque from caries-active and caries-free volunteers. Caries Res 2012;46:280.

Torlakovic L, Klepac-Ceraj V, Ogaard B, Cotton SL, Paster BJ, Olsen I.
Microbiology of white spot lesions--New insights. Congress 2012 European Orthodontic Society, Santiago de Compostella, Spain.  June  20, 2012

Waters C, Motlagh HM, Wilson A, Paster B, Thomas JG.   Unmasking the contribution of oral flora to the biofilm accretion-endotrach microbiota during mechanical ventilation using 16S microarray detection. 112th ASM General Meeting, June 16-19, 2012, San Francisco.

Aspiras M, Strate J, Ward M, Barros S, Barrow D, Moss K, Beck J, Offenbacher S. Salivary metabolomic profiles discriminate between periodontal health and disease. J Dent Res (IADR) 2012; 91:3238.

Teles F, Patel M, Teles R, Paster BJ, Socransky S. A targeted approach to identify relevant uncultivated/unrecognized periodontal taxa. J Dent Res (IADR) 2012; 91:315.

Heller et al. Early colonization of in vivo acquired enamel pellicle using a microarray approach. J Dent Res (IADR) 2012; 91:247.

Asikainen SE, Dogan B, Turgut Z, Bodur A, Tacoy G, Granstrom E, Paster BJ, Oscarsson J. Characteristic subgingival microbiota in periodontitis patients with acute coronary syndrome. J Dent Res (IADR) 2012; 91:3005.

Tanner et al. Scardovia wiggsiae in White Spot Lesions of orthodontic patients. J Dent Res (IADR) 2012; 91:3119.

Rudney J, Chen R, Jones R, Fok A, Aparicio C. A reproducible oral microcosm biofilm model for testing dental materials. J Dent Res (AADR) 2012;91:1339.

Albandar et al. Periodontal treatment outcome and microbioloogical findings in prepubertal periodontitis. J Dent Res (AADR) 2012;91:561.

Boisvert et al. Oral Microbial biomarkers in Crohn’s Disease in children. J Dent Res (AADR) 2012;91:931.

Murphy et al. Differences of subgingival microbiota between young and elder rhesus macaques. J Dent Res (AADR) 2012;91:397.

Torlakovic et al. Microbial community succession on developing lesions on human enamel. J Dent Res (AADR) 2012;91:696.

Chalmers et al. Periodontal biofilm microbiota of patients with Leukocyte Adhesion Deficiency Type 1. J Dent Res (AADR) 2012;91:1484.

Kokaras et al. Effect of periodontal therapy on subgingival taxa identified using HOMIM. J Dent Res (AADR) 2012;91:401.

Teles F, Teles R, Patel M, Guinan E, Paster BJ, Socransky S. Search for microbial markers of oral cancer in Fanconi Anemia. J Dent Res (AADR) 2012;91:121.

Huang H, Tong L, Hou W, Aukhil I, Walker C, Paster BJ, Shaddox L. Comprehensive Microbiological Characterization in Children with Localized Aggressive Periodontitis. J Dent Res (AADR) 2012;91:748.

Romani Vestman et al. Oral microbiota in breastfed and formula fed infants. J Dent Res 2011;90:239. Now published.

Tanner et al. Microbiota of severe early childhood caries by microarray and PCR. J Dent Res 2011;90:240. Now published.

Ahn et al. Oral microbiome profiles: 16S rRNA pyrosequencing and microarray assay comparison. J Dent Res 2011;90:416. Now published.

Furgang et al. Microbiology of LAP Bone Loss: Preliminary Findings. J Dent Res 2011;90:440.

Yang & Luo. The microflora profiles in saliva from the isolated population. J Dent Res 2011;90:3482. Now published.

Khullar et al. Bacteria associated with osteonecrosis of the jaw in West Africa. J Dent Res 2011;90:3521.

Murphy et al. The macaque oral microbiome is different from that of humans. J Dent Res 2011;90:3522.

Docktor et al. The oral microbiome in children with Inflammatory Bowel Disease. North American Soc. Pediatric Gastroenterol, Hepatol. Nut. Ann. Meeting, October 21-24, 2010, New Orleans, LA. Now published.

Kokaras et al.  Effect of periodontal therapy on subgingival taxa identified using HOMIM. J Dent Res 2010;89: #383.

Yaskell et al.  Post-treatment changes in subgingival species using checkerboard and HOMIM. J Dent Res 2010;89: #384.

Colombo et al.  Subgingival microbiota of refractory periodontitis determined by microarray (HOMIM). J Dent Res 2009;88: #232. See publication in J Periodontol

Albandar et al. Molecular analysis of Papillon-Lefèvre Syndrome periodontitis subgingival microbiota.  J Dent Res 2009;88: #1373. In press.

Cotton et al. Subgingival taxa in periodontal health and disease using HOMIM. J Dent Res 2009;88: #1378.

Yaskell et al. Comparison of checkerboard and HOMIM for detecting subgingival species. J Dent Res 2009;88: #1379.

Preza et al. Microarray analysis of bacteria in root caries. J Dent Res 2009;88: #3086. Now published

Zhang et al. Multiple salivary biomarkers for pancreatic cancer detection. J Dent Res 2009;88: #3399. Now published.

Uraz et al. Microbial microarray analysis of gingival crevicular fluid in periodontitis. Europerio 6; 6th Congress of the European Federation of Periodontology, June 4-6, 2009, Stockholm, Sweden. Now published.