Background Publications Establishing Oral Microbiome Expertise

In a recent review from NIH ("A review of 10 years of human microbiome research activities at the US National Institutes of Health, Fiscal Years 2007-2016"), two of our papers were considered as pioneering studies that helped lay the foundation for microbiome research and inform the development of the Human Microbiome Project (HMP) program.
Aas JA, Paster BJ, Stokes LN, Olsen I, Dewhirst FE. Defining the normal bacterial flora of the oral cavity. J Clin Microbiol. 2005;43(11):5721-32. Epub 2005/11/08. doi: 10.1128/JCM.43.11.5721-5732.2005. PubMed PMID: 16272510; PMCID: PMC1287824. Cited 1,615 times - Web of Science.
Paster BJ, Boches SK, Galvin JL, Ericson RE, Lau CN, Levanos VA, et al. Bacterial diversity in human subgingival plaque. J Bacteriol. 2001;183(12):3770-83. Epub 2001/05/24. doi: 10.1128/JB.183.12.3770-3783.2001. PubMed PMID: 11371542; PMCID: PMC95255. Cited 1,350 times.
The ensuing establishment of the Human Oral Microbiome Database (HOMD) was also noted in that same review as a major resource for the field.
Dewhirst FE, Chen T, Izard J, Paster BJ, Tanner AC, Yu WH, et al. The human oral microbiome. J Bacteriol. 2010;192(19):5002-17. Epub 2010/07/27. doi: 10.1128/JB.00542-10. PubMed PMID: 20656903; PMCID: PMC2944498. Cited 1,396 times.

Publications Using Taxonomy Assignment Algorithms for FOMC

  1. Escapa IF, Huang Y, Chen T, Lin M, Kokaras A, Dewhirst FE, et al. Construction of habitat-specific training sets to achieve species-level assignment in 16S rRNA gene datasets. Microbiome. 2020;8(1):65. Epub 2020/05/18. doi: 10.1186/s40168-020-00841-w. PMID: 32414415; PMCID: PMC7291764.
  2. Baraniya D, Chen T, Nahar A, Alakwaa F, Hill J, Tellez M, et al. Supragingival mycobiome and inter-kingdom interactions in dental caries. J Oral Microbiol. 2020;12(1):1729305. Epub 2020/03/12. doi: 10.1080/20002297.2020.1729305. PMID: 32158514; PMCID: PMC7048226.
  3. Baraniya D, Naginyte M, Chen T, Albandar JM, Chialastri SM, Devine DA, et al. Modeling Normal and Dysbiotic Subgingival Microbiomes: Effect of Nutrients. J Dent Res. 2020;99(6):695-702. Epub 2020/01/31. doi: 10.1177/0022034520902452. PMID: 31999932; PMCID: PMC7243421.
  4. Acharya A, Chen T, Chan Y, Watt RM, Jin L, Mattheos N. Species-Level Salivary Microbial Indicators of Well-Resolved Periodontitis: A Preliminary Investigation. Front Cell Infect Microbiol. 2019;9:347. Epub 2019/11/05. doi: 10.3389/fcimb.2019.00347. PMID: 31681625; PMCID: PMC6797555.
  5. Al-Hebshi NN, Baraniya D, Chen T, Hill J, Puri S, Tellez M, et al. Metagenome sequencing-based strain-level and functional characterization of supragingival microbiome associated with dental caries in children. J Oral Microbiol. 2019;11(1):1557986. Epub 2019/01/24. doi: 10.1080/20002297.2018.1557986. PMID: 30671194; PMCID: PMC6327923.
  6. Al-Kamel A, Baraniya D, Al-Hajj WA, Halboub E, Abdulrab S, Chen T, et al. Subgingival microbiome of experimental gingivitis: shifts associated with the use of chlorhexidine and N-acetyl cysteine mouthwashes. J Oral Microbiol. 2019;11(1):1608141. Epub 2019/07/06. doi: 10.1080/20002297.2019.1608141. PMID: 31275528; PMCID: PMC6598494.
  7. Del Castillo E, Meier R, Chung M, Koestler DC, Chen T, Paster BJ, et al. The Microbiomes of Pancreatic and Duodenum Tissue Overlap and Are Highly Subject Specific but Differ between Pancreatic Cancer and Noncancer Subjects. Cancer Epidemiol Biomarkers Prev. 2019;28(2):370-83. Epub 2018/10/31. doi: 10.1158/1055-9965.EPI-18-0542. PMID: 30373903; PMCID: PMC6363867.
  8. Stashenko P, Yost S, Choi Y, Danciu T, Chen T, Yoganathan S, et al. The Oral Mouse Microbiome Promotes Tumorigenesis in Oral Squamous Cell Carcinoma. mSystems. 2019;4(4). Epub 2019/08/08. doi: 10.1128/mSystems.00323-19. PMID: 31387932; PMCID: PMC6687944.
  9. Bruserud O, Siddiqui H, Marthinussen MC, Chen T, Jonsson R, Oftedal BE, et al. Oral microbiota in autoimmune polyendocrine syndrome type 1. J Oral Microbiol. 2018;10(1):1442986. Epub 2018/03/06. doi: 10.1080/20002297.2018.1442986. PMID: 29503707; PMCID: PMC5827717.
  10. Escapa IF, Chen T, Huang Y, Gajare P, Dewhirst FE, Lemon KP. New Insights into Human Nostril Microbiome from the Expanded Human Oral Microbiome Database (eHOMD): a Resource for the Microbiome of the Human Aerodigestive Tract. mSystems. 2018;3(6). Epub 2018/12/12. doi: 10.1128/mSystems.00187-18. PMID: 30534599; PMCID: PMC6280432.
  11. Kressirer CA, Chen T, Lake Harriman K, Frias-Lopez J, Dewhirst FE, Tavares MA, et al. Functional profiles of coronal and dentin caries in children. J Oral Microbiol. 2018;10(1):1495976. Epub 2018/07/24. doi: 10.1080/20002297.2018.1495976. PMID: 30034639; PMCID: PMC6052428.
  12. Perera M, Al-Hebshi NN, Perera I, Ipe D, Ulett GC, Speicher DJ, et al. Inflammatory Bacteriome and Oral Squamous Cell Carcinoma. J Dent Res. 2018;97(6):725-32. Epub 2018/04/10. doi: 10.1177/0022034518767118. PMID: 29630846.
  13. Adams SE, Arnold D, Murphy B, Carroll P, Green AK, Smith AM, et al. A randomised clinical study to determine the effect of a toothpaste containing enzymes and proteins on plaque oral microbiome ecology. Sci Rep. 2017;7:43344. Epub 2017/02/28. doi: 10.1038/srep43344. PMID: 28240240; PMCID: PMC5327414.
  14. Al-Hebshi NN, Alharbi FA, Mahri M, Chen T. Differences in the Bacteriome of Smokeless Tobacco Products with Different Oral Carcinogenicity: Compositional and Predicted Functional Analysis. Genes (Basel). 2017;8(4). Epub 2017/03/24. doi: 10.3390/genes8040106. PMID: 28333122; PMCID: PMC5406853.
  15. Perera M, Al-Hebshi NN, Perera I, Ipe D, Ulett GC, Speicher DJ, et al. A dysbiotic mycobiome dominated by Candida albicans is identified within oral squamous-cell carcinomas. J Oral Microbiol. 2017;9(1):1385369. Epub 2017/11/21. doi: 10.1080/20002297.2017.1385369. PMID: 29152157; PMCID: PMC5678454.
  16. Ribeiro AA, Azcarate-Peril MA, Cadenas MB, Butz N, Paster BJ, Chen T, et al. The oral bacterial microbiome of occlusal surfaces in children and its association with diet and caries. PLoS One. 2017;12(7):e0180621. Epub 2017/07/06. doi: 10.1371/journal.pone.0180621. PMID: 28678838; PMCID: PMC5498058.
  17. Al-Hebshi NN, Abdulhaq A, Albarrag A, Basode VK, Chen T. Species-level core oral bacteriome identified by 16S rRNA pyrosequencing in a healthy young Arab population. J Oral Microbiol. 2016;8:31444. Epub 2016/05/20. doi: 10.3402/jom.v8.31444. PMID: 27193835; PMCID: PMC4871898.
  18. Siddiqui H, Chen T, Aliko A, Mydel PM, Jonsson R, Olsen I. Microbiological and bioinformatics analysis of primary Sjogren's syndrome patients with normal salivation. J Oral Microbiol. 2016;8:31119. Epub 2016/10/23. doi: 10.3402/jom.v8.31119. PMID: 27770517; PMCID: PMC5075221.
  19. Al-Hebshi NN, Nasher AT, Idris AM, Chen T. Robust species taxonomy assignment algorithm for 16S rRNA NGS reads: application to oral carcinoma samples. J Oral Microbiol. 2015;7:28934. Epub 2015/10/02. doi: 10.3402/jom.v7.28934. PMID: 26426306; PMCID: PMC4590409.
  20. Romani Vestman N, Chen T, Lif Holgerson P, Ohman C, Johansson I. Oral Microbiota Shift after 12-Week Supplementation with Lactobacillus reuteri DSM 17938 and PTA 5289; A Randomized Control Trial. PLoS One. 2015;10(5):e0125812. Epub 2015/05/07. doi: 10.1371/journal.pone.0125812. PMID: 25946126; PMCID: PMC4422650.

Publications using HOMINGS and HOMIM

HOMIM's were used extensively in microbiome studies at The Forsyth Institute (9 PIs) and in other collaborative studies with national and international academic institutions (more than 120 investigative teams), government including NIH (6 investigative teams), and industry (12 companies). As a result of many of these studies, there were 61 peer-reviewed publications (most recently in 2019), 8 reviews describing HOMIM, and since 2009, over 50 national and international abstracts or presentations. HOMINGS, the HOMIM replacement, was also utilized by many investigators or teams. As of May 2021, there were 33 peer-reviewed, HOMINGS-associated publications and 3 HOMINGS-associated reviews. In addition, there have been over 20 abstracts/presentations at national and international meetings.

HOMINGS-associated, Peer-reviewed Publications

  1. Qudeimat MA, Alyahya A, Karched M, Behbehani J, Salako NO. Dental plaque microbiota profiles of children with caries-free and caries-active dentition. 2021 Jan;104:103539. doi: 10.1016/j.jdent.2020.103539. Epub 2020 Nov 25. PMID: 33248211.
  2. de Brito LCN, Doolittle-Hall J, Lee CT, Moss K, Bambirra Junior W, Tavares WLF, et al. The apical root canal system microbial communities determined by next-generation sequencing. Sci Rep. 2020;10(1):10932. Epub 2020/07/04. doi: 10.1038/s41598-020-67828-3. PMID: 32616783; PMCID: PMC7331743.
  3. Mougeot JC, Beckman MF, Stevens CB, Almon KG, Morton DS, Von Bultzingslowen I, et al. Lasting Gammaproteobacteria profile changes characterized hematological cancer patients who developed oral mucositis following conditioning therapy. J Oral Microbiol. 2020;12(1):1761135. Epub 2020/06/17. doi: 10.1080/20002297.2020.1761135. PMID: 32537095; PMCID: PMC7269028.
  4. Papapanou PN, Park H, Cheng B, Kokaras A, Paster B, Burkett S, et al. Subgingival microbiome and clinical periodontal status in an elderly cohort: The WHICAP ancillary study of oral health. J Periodontol. 2020. Epub 2020/06/14. doi: 10.1002/JPER.20-0194. PMID: 32533776.
  5. Damgaard C, Danielsen AK, Enevold C, Massarenti L, Nielsen CH, Holmstrup P, et al. Porphyromonas gingivalis in saliva associates with chronic and aggressive periodontitis. J Oral Microbiol. 2019;11(1):1653123. Epub 2019/09/07. doi: 10.1080/20002297.2019.1653123. PMID: 31489129; PMCID: PMC6713147.
  6. Harris-Ricardo J, Fang L, Herrera-Herrera A, Fortich-Mesa N, Olier-Castillo D, Cavanzo-Rojas D, et al. Bacterial profile of the supragingival dental biofilm in children with deciduous and early mixed dentition using next generation sequencing (HOMINGS) technique. Enferm Infecc Microbiol Clin. 2019;37(7):448-53. Epub 2018/12/14. doi: 10.1016/j.eimc.2018.10.019. PMID: 30545671.
  7. Mitwalli H, Mourao MDA, Dennison J, Yaman P, Paster BJ, Fontana M. Effect of Silver Diamine Fluoride Treatment on Microbial Profiles of Plaque Biofilms from Root/Cervical Caries Lesions. Caries Res. 2019;53(5):555-66. Epub 2019/05/29. doi: 10.1159/000499578. PMID: 31137026.
  8. Mougeot JC, Stevens CB, Almon KG, Paster BJ, Lalla RV, Brennan MT, et al. Caries-associated oral microbiome in head and neck cancer radiation patients: a longitudinal study. J Oral Microbiol. 2019;11(1):1586421. Epub 2019/03/21. doi: 10.1080/20002297.2019.1586421. PMID: 30891159; PMCID: PMC6419625.
  9. Nascimento MM, Alvarez AJ, Huang X, Browngardt C, Jenkins R, Sinhoreti MC, et al. Metabolic Profile of Supragingival Plaque Exposed to Arginine and Fluoride. J Dent Res. 2019;98(11):1245-52. Epub 2019/08/28. doi: 10.1177/0022034519869906. PMID: 31454264; PMCID: PMC6755720.
  10. Ortiz S, Herrman E, Lyashenko C, Purcell A, Raslan K, et al. Sex-specific differences in the salivary microbiome of caries-active children. J Oral Microbiol. 2019 11:1653124. doi: 10.1080/20002297.2019.1653124. eCollection 2019. PMID: 31497256.
  11. Palmer RJ, Cotton SL, Kokaras AS, Gardner P, Grisius M, Pelayo E, et al. Analysis of oral bacterial communities: comparison of HOMINGS with a tree-based approach implemented in QIIME. J Oral Microbiol. 2019;11(1):1586413. Epub 2019/04/17. doi: 10.1080/20002297.2019.1586413. PMID: 30988892; PMCID: PMC6450576.
  12. Belstrøm D, Grande MA, Sembler-Moller ML, Kirkby N, Cotton SL, Paster BJ, et al. Influence of periodontal treatment on subgingival and salivary microbiotas. J Periodontol. 2018;89(5):531-9. Epub 2018/03/10. doi: 10.1002/JPER.17-0377. PMID: 29520798.
  13. Belstrøm D, Sembler-Moller ML, Grande MA, Kirkby N, Cotton SL, Paster BJ, et al. Impact of Oral Hygiene Discontinuation on Supragingival and Salivary Microbiomes. JDR Clin Trans Res. 2018;3(1):57-64. Epub 2018/04/18. doi: 10.1177/2380084417723625. PMID: 29662960; PMCID: PMC5896869.
  14. Colombo APV, Paster BJ, Grimaldi G, Lourenco TGB, Teva A, Campos-Neto A, et al. Clinical and microbiological parameters of naturally occurring periodontitis in the non-human primate Macaca mulatta. J Oral Microbiol. 2017;9(1):1403843. Epub 2018/05/29. doi: 10.1080/20002297.2017.1403843. PMID: 29805776; PMCID: PMC5963701.
  15. Eriksson L, Lif Holgerson P, Esberg A, Johansson I. Microbial Complexes and Caries in 17-Year-Olds with and without Streptococcus mutans. J Dent Res. 2018;97(3):275-82. Epub 2017/09/21. doi: 10.1177/0022034517731758. PMID: 28930642.
  16. Velsko IM, Shaddox LM. Consistent and reproducible long-term in vitro growth of health and disease-associated oral subgingival biofilms. BMC Microbiol. 2018;18(1):70. Epub 2018/07/13. doi: 10.1186/s12866-018-1212-x. PMID: 29996764; PMCID: PMC6042318.
  17. Zheng Y, Zhang M, Li J, Li Y, Teng F, Jiang H, et al. Comparative Analysis of the Microbial Profiles in Supragingival Plaque Samples Obtained From Twins With Discordant Caries Phenotypes and Their Mothers. Front Cell Infect Microbiol. 2018;8:361. Epub 2018/11/22. doi: 10.3389/fcimb.2018.00361. PMID: 30460203; PMCID: PMC6232758.
  18. Belstrøm D, Holmstrup P, Fiehn NE, Kirkby N, Kokaras A, Paster BJ, Bardow A. Salivary microbiota in individuals with different levels of caries experience. J Oral Microbiol. 2017 Jan 23;9(1):1270614. doi: 10.1080/20002297.2016.1270614. PMID: 28326153; PMCID: PMC5328370.
  19. Belstrøm D, Sembler-Moller ML, Grande MA, Kirkby N, Cotton SL, Paster BJ, et al. Microbial profile comparisons of saliva, pooled and site-specific subgingival samples in periodontitis patients. PLoS One. 2017;12(8):e0182992. Epub 2017/08/12. doi: 10.1371/journal.pone.0182992. PMID: 28800622; PMCID: PMC5553731.
  20. Eriksson L, Lif Holgerson P, Johansson I. Saliva and tooth biofilm bacterial microbiota in adolescents in a low caries community. Sci Rep. 2017;7(1):5861. Epub 2017/07/21. doi: 10.1038/s41598-017-06221-z. PMID: 28724921; PMCID: PMC5517611.
  21. Keller MK, Kressirer CA, Belstrøm D, Twetman S, Tanner ACR. Oral microbial profiles of individuals with different levels of sugar intake. J Oral Microbiol. 2017;9(1):1355207. Epub 2017/08/26. doi: 10.1080/20002297.2017.1355207. PMID: 28839520; PMCID: PMC5560414.
  22. Mougeot JC, Stevens CB, Paster BJ, Brennan MT, Lockhart PB, Mougeot FK. Porphyromonas gingivalis is the most abundant species detected in coronary and femoral arteries. J Oral Microbiol. 2017;9(1):1281562. Epub 2017/03/23. doi: 10.1080/20002297.2017.1281562. PMID: 28326156; PMCID: PMC5328378.
  23. Richards VP, Alvarez AJ, Luce AR, Bedenbaugh M, Mitchell ML, Burne RA, et al. Microbiomes of Site-Specific Dental Plaques from Children with Different Caries Status. Infect Immun. 2017;85(8). Epub 2017/05/17. doi: 10.1128/IAI.00106-17. PMID: 28507066; PMCID: PMC5520424.
  24. Sanz-Martin I, Doolittle-Hall J, Teles RP, Patel M, Belibasakis GN, Hammerle CHF, et al. Exploring the microbiome of healthy and diseased peri-implant sites using Illumina sequencing. J Clin Periodontol. 2017;44(12):1274-84. Epub 2017/08/03. doi: 10.1111/jcpe.12788. PMID: 28766745; PMCID: PMC7209775.
  25. Timby N, Domellof M, Holgerson PL, West CE, Lonnerdal B, Hernell O, et al. Oral Microbiota in Infants Fed a Formula Supplemented with Bovine Milk Fat Globule Membranes - A Randomized Controlled Trial. PLoS One. 2017;12(1):e0169831. Epub 2017/01/19. doi: 10.1371/journal.pone.0169831. PMID: 28099499; PMCID: PMC5242539.
  26. Belstrøm D, Holmstrup P, Bardow A, Kokaras A, Fiehn NE, Paster BJ. Comparative analysis of bacterial profiles in unstimulated and stimulated saliva samples. J Oral Microbiol. 2016;8:30112. Epub 2016/03/19. doi: 10.3402/jom.v8.30112. PMID: 26987356; PMCID: PMC4796727.
  27. Belstrøm D, Holmstrup P, Bardow A, Kokaras A, Fiehn NE, Paster BJ. Temporal Stability of the Salivary Microbiota in Oral Health. PLoS One. 2016;11(1):e0147472. Epub 2016/01/23. doi: 10.1371/journal.pone.0147472. PMID: 26799067; PMCID: PMC4723053.
  28. Belstrøm D, Holmstrup P, Fiehn NE, Rosing K, Bardow A, Paster BJ, et al. Bacterial composition in whole saliva from patients with severe hyposalivation--a case-control study. Oral Dis. 2016;22(4):330-7. Epub 2016/01/30. doi: 10.1111/odi.12452. PMID: 26824889.
  29. Belstrøm D, Paster BJ, Fiehn NE, Bardow A, Holmstrup P. Salivary bacterial fingerprints of established oral disease revealed by the Human Oral Microbe Identification using Next Generation Sequencing (HOMINGS) technique. J Oral Microbiol. 2016;8:30170. Epub 2016/01/20. doi: 10.3402/jom.v8.30170. PMID: 26782357; PMCID: PMC4717152.
  30. McIntyre MK, Peacock TJ, Akers KS, Burmeister DM. Initial Characterization of the Pig Skin Bacteriome and Its Effect on In Vitro Models of Wound Healing. PLoS One. 2016;11(11):e0166176. Epub 2016/11/09. doi: 10.1371/journal.pone.0166176. PMID: 27824921; PMCID: PMC5100914.
  31. Mougeot JL, Stevens CB, Cotton SL, Morton DS, Krishnan K, Brennan MT, et al. Concordance of HOMIM and HOMINGS technologies in the microbiome analysis of clinical samples. J Oral Microbiol. 2016;8:30379. Epub 2016/04/12. doi: 10.3402/jom.v8.30379. PMID: 27065347; PMCID: PMC4827145.
  32. Gomes BP, Berber VB, Kokaras AS, Chen T, Paster BJ. Microbiomes of Endodontic-Periodontal Lesions before and after Chemomechanical Preparation. J Endod. 2015;41(12):1975-84. Epub 2015/11/02. doi: 10.1016/j.joen.2015.08.022. PMID: 26521147; PMCID: PMC7061340.
  33. Rudney JD, Jagtap PD, Reilly CS, Chen R, Markowski TW, Higgins L, et al. Protein relative abundance patterns associated with sucrose-induced dysbiosis are conserved across taxonomically diverse oral microcosm biofilm models of dental caries. Microbiome. 2015;3:69. Epub 2015/12/20. doi: 10.1186/s40168-015-0136-z. PMID: 26684897; PMCID: PMC4684605.

HOMINGS-associated Reviews

  1. Robledo-Sierra J, Ben-Amy DP, Varoni E, Bavarian R, Simonsen JL, Paster BJ, et al. World Workshop on Oral Medicine VII: Targeting the oral microbiome Part 2: Current knowledge on malignant and potentially malignant oral disorders. Oral Dis. 2019;25 Suppl 1:28-48. Epub 2019/05/30. doi: 10.1111/odi.13107. PMID: 31140694.
  2. Krishnan K, Chen T, Paster BJ. A practical guide to the oral microbiome and its relation to health and disease. Oral Dis. 2017;23(3):276-86. Epub 2016/05/25. doi: 10.1111/odi.12509. PMID: 27219464; PMCID: PMC5122475.
  3. Duran-Pinedo AE, Frias-Lopez J. Beyond microbial community composition: functional activities of the oral microbiome in health and disease. Microbes Infect. 2015;17(7):505-16. Epub 2015/04/12. doi: 10.1016/j.micinf.2015.03.014. PMID: 25862077; PMCID: PMC4495649.

HOMIM-associated, Peer-reviewed Publications

  1. Cui X, Liu J, Xiao W, Chu Y, Ouyang X. Subgingival microbiome in Chinese patients with generalized aggressive periodontitis compared to healthy controls. Arch Oral Biol. 2019;101:92-9. Epub 2019/03/26. doi: 10.1016/j.archoralbio.2019.02.012. PMID: 30909081.
  2. Inui T, Palmer RJ, Jr., Shah N, Li W, Cisar JO, Wu CD. Effect of mechanically stimulated saliva on initial human dental biofilm formation. Sci Rep. 2019;9(1):11805. Epub 2019/08/16. doi: 10.1038/s41598-019-48211-3. PMID: 31413280; PMCID: PMC6694102.
  3. Bassir SH, Chase I, Paster BJ, Gordon LB, Kleinman ME, Kieran MW, et al. Microbiome at sites of gingival recession in children with Hutchinson-Gilford progeria syndrome. J Periodontol. 2018;89(6):635-44. Epub 2018/03/10. doi: 10.1002/JPER.17-0351. PMID: 29520806; PMCID: PMC6041179.
  4. Grauballe MB, Belstrøm D, Ostergaard JA, Paster BJ, Schou S, Flyvbjerg A, et al. Ligature-associated bacterial profiles are linked to type 2 diabetes mellitus in a rat model and influenced by antibody treatment against TNF-alpha or RAGE. Clin Exp Dent Res. 2017;3(1):25-31. Epub 2017/03/28. doi: 10.1002/cre2.54. PMID: 28344834; PMCID: PMC5347912.
  5. Palmer RJ, Jr., Shah N, Valm A, Paster B, Dewhirst F, Inui T, et al. Interbacterial Adhesion Networks within Early Oral Biofilms of Single Human Hosts. Appl Environ Microbiol. 2017;83(11). Epub 2017/03/28. doi: 10.1128/AEM.00407-17. PMID: 28341674; PMCID: PMC5440702.
  6. ElSalhy M, Soderling E, Honkala E, Fontana M, Flannagan S, Kokaras A, et al. Salivary microbiota and caries occurrence in Mutans Streptococci-positive school children. Eur J Paediatr Dent. 2016;17(3):188-92. Epub 2016/10/21. PMID: 27759406.
  7. George N, Flamiatos E, Kawasaki K, Kim N, Carriere C, Phan B, et al. Oral microbiota species in acute apical endodontic abscesses. J Oral Microbiol. 2016;8:30989. Epub 2016/03/18. doi: 10.3402/jom.v8.30989. PMID: 26983837; PMCID: PMC4794734.
  8. Heller D, Helmerhorst EJ, Gower AC, Siqueira WL, Paster BJ, Oppenheim FG. Microbial Diversity in the Early In Vivo-Formed Dental Biofilm. Appl Environ Microbiol. 2016;82(6):1881-8. Epub 2016/01/10. doi: 10.1128/AEM.03984-15. PMID: 26746720; PMCID: PMC4784052.
  9. Marchesan J, Jiao Y, Schaff RA, Hao J, Morelli T, Kinney JS, et al. TLR4, NOD1 and NOD2 mediate immune recognition of putative newly identified periodontal pathogens. Mol Oral Microbiol. 2016;31(3):243-58. Epub 2015/07/16. doi: 10.1111/omi.12116. PMID: 26177212; PMCID: PMC4713362.
  10. Paes Batista da Silva A, Barros SP, Moss K, Preisser J, Marchesan JT, Ward M, et al. Microbial Profiling in Experimentally Induced Biofilm Overgrowth Among Patients With Various Periodontal States. J Periodontol. 2016;87(1):27-35. Epub 2015/10/03. doi: 10.1902/jop.2015.150328. PMID: 26430927.
  11. Romanos GE, Biltucci MT, Kokaras A, Paster BJ. Bacterial Composition at the Implant-Abutment Connection under Loading in vivo. Clin Implant Dent Relat Res. 2016;18(1):138-45. Epub 2014/09/10. doi: 10.1111/cid.12270. PMID: 25195711.
  12. Belstrøm D, Fiehn NE, Nielsen CH, Klepac-Ceraj V, Paster BJ, Twetman S, et al. Differentiation of salivary bacterial profiles of subjects with periodontitis and dental caries. J Oral Microbiol. 2015;7:27429. Epub 2015/04/10. doi: 10.3402/jom.v7.27429. PMID: 25854857; PMCID: PMC4390560.
  13. Elabdeen HR, Mustafa M, Hasturk H, Klepac-Ceraj V, Ali RW, Paster BJ, et al. Subgingival microbial profiles of Sudanese patients with aggressive periodontitis. J Periodontal Res. 2015;50(5):674-82. Epub 2014/12/10. doi: 10.1111/jre.12250. PMID: 25487558; PMCID: PMC4646740.
  14. Lif Holgerson P, Ohman C, Ronnlund A, Johansson I. Maturation of Oral Microbiota in Children with or without Dental Caries. PLoS One. 2015;10(5):e0128534. Epub 2015/05/29. doi: 10.1371/journal.pone.0128534. PMID: 26020247; PMCID: PMC4447273.
  15. Lin SW, Freedman ND, Shi J, Gail MH, Vogtmann E, Yu G, et al. Beta-diversity metrics of the upper digestive tract microbiome are associated with body mass index. Obesity (Silver Spring). 2015;23(4):862-9. Epub 2015/03/11. doi: 10.1002/oby.21020. PMID: 25755147; PMCID: PMC4380747.
  16. Ma C, Chen F, Zhang Y, Sun X, Tong P, Si Y, et al. Comparison of oral microbial profiles between children with severe early childhood caries and caries-free children using the human oral microbe identification microarray. PLoS One. 2015;10(3):e0122075. Epub 2015/03/31. doi: 10.1371/journal.pone.0122075. PMID: 25821962; PMCID: PMC4378984.
  17. Moutsopoulos NM, Chalmers NI, Barb JJ, Abusleme L, Greenwell-Wild T, Dutzan N, et al. Subgingival microbial communities in Leukocyte Adhesion Deficiency and their relationship with local immunopathology. PLoS Pathog. 2015;11(3):e1004698. Epub 2015/03/06. doi: 10.1371/journal.ppat.1004698. PMID: 25741691; PMCID: PMC4351202.
  18. Seoudi N, Bergmeier LA, Drobniewski F, Paster B, Fortune F. The oral mucosal and salivary microbial community of Behcet's syndrome and recurrent aphthous stomatitis. J Oral Microbiol. 2015;7:27150. Epub 2015/06/04. doi: 10.3402/jom.v7.27150. PMID: 26037240; PMCID: PMC4452653.
  19. Soderling E, ElSalhy M, Honkala E, Fontana M, Flannagan S, Eckert G, et al. Effects of short-term xylitol gum chewing on the oral microbiome. Clin Oral Investig. 2015;19(2):237-44. Epub 2014/03/26. doi: 10.1007/s00784-014-1229-y. PMID: 24663814.
  20. Toiviainen A, Jalasvuori H, Lahti E, Gursoy U, Salminen S, Fontana M, et al. Impact of orally administered lozenges with Lactobacillus rhamnosus GG and Bifidobacterium animalis subsp. lactis BB-12 on the number of salivary mutans streptococci, amount of plaque, gingival inflammation and the oral microbiome in healthy adults. Clin Oral Investig. 2015;19(1):77-83. Epub 2014/03/19. doi: 10.1007/s00784-014-1221-6. PMID: 24638207; PMCID: PMC4286650.
  21. Vogtmann E, Flores R, Yu G, Freedman ND, Shi J, Gail MH, et al. Association between tobacco use and the upper gastrointestinal microbiome among Chinese men. Cancer Causes Control. 2015;26(4):581-8. Epub 2015/02/24. doi: 10.1007/s10552-015-0535-2. PMID: 25701246; PMCID: PMC4852095.
  22. Belstrøm D, Fiehn NE, Nielsen CH, Holmstrup P, Kirkby N, Klepac-Ceraj V, et al. Altered bacterial profiles in saliva from adults with caries lesions: a case-cohort study. Caries Res. 2014;48(5):368-75. Epub 2014/03/20. doi: 10.1159/000357502. PMID: 24643218.
  23. Belstrøm D, Fiehn NE, Nielsen CH, Kirkby N, Twetman S, Klepac-Ceraj V, et al. Differences in bacterial saliva profile between periodontitis patients and a control cohort. J Clin Periodontol. 2014;41(2):104-12. Epub 2013/12/07. doi: 10.1111/jcpe.12190. PMID: 24303924.
  24. Belstrøm D, Holmstrup P, Nielsen CH, Kirkby N, Twetman S, Heitmann BL, et al. Bacterial profiles of saliva in relation to diet, lifestyle factors, and socioeconomic status. J Oral Microbiol. 2014;6. Epub 2014/04/26. doi: 10.3402/jom.v6.23609. PMID: 24765243; PMCID: PMC3974179.
  25. Gilbert K, Joseph R, Vo A, Patel T, Chaudhry S, Nguyen U, Trevor A et al. Children with severe early childhood caries: streptococci genetic strains within carious and white spot lesions. J Oral Microbiol. 2014 Oct 29;6. doi: 10.3402/jom.v6.25805. PMID: 25405004; PMCID: PMC4216391.
  26. Goncalves PF, Klepac-Ceraj V, Huang H, Paster BJ, Aukhil I, Wallet SM, et al. Correlation of Aggregatibacter actinomycetemcomitans detection with clinical/immunoinflammatory profile of localized aggressive periodontitis using a 16S rRNA microarray method: a cross-sectional study. PLoS One. 2013;8(12):e85066. Epub 2014/01/01. doi: 10.1371/journal.pone.0085066. PMID: 24376864; PMCID: PMC3871691.
  27. Li Y, Saxena D, Chen Z, Liu G, Abrams WR, Phelan JA, et al. HIV infection and microbial diversity in saliva. J Clin Microbiol. 2014;52(5):1400-11. Epub 2014/02/14. doi: 10.1128/JCM.02954-13. PMID: 24523469; PMCID: PMC3993673.
  28. Lourenco TG, Heller D, Silva-Boghossian CM, Cotton SL, Paster BJ, Colombo AP. Microbial signature profiles of periodontally healthy and diseased patients. J Clin Periodontol. 2014;41(11):1027-36. Epub 2014/08/21. doi: 10.1111/jcpe.12302. PMID: 25139407; PMCID: PMC4213353.
  29. Nascimento MM, Browngardt C, Xiaohui X, Klepac-Ceraj V, Paster BJ, Burne RA. The effect of arginine on oral biofilm communities. Mol Oral Microbiol. 2014;29(1):45-54. Epub 2013/12/03. doi: 10.1111/omi.12044. PMID: 24289808; PMCID: PMC7003997.
  30. Reilly C, Rasmussen K, Selberg T, Stevens J, Jones RS. Biofilm community diversity after exposure to 0.4% stannous fluoride gels. J Appl Microbiol. 2014;117(6):1798-809. Epub 2014/09/30. doi: 10.1111/jam.12655. PMID: 25263195; PMCID: PMC4664451.
  31. Yu G, Dye BA, Gail MH, Shi J, Klepac-Ceraj V, Paster BJ, et al. The association between the upper digestive tract microbiota by HOMIM and oral health in a population-based study in Linxian, China. BMC Public Health. 2014;14:1110. Epub 2014/10/29. doi: 10.1186/1471-2458-14-1110. PMID: 25348940; PMCID: PMC4223728.
  32. Yu G, Gail MH, Shi J, Klepac-Ceraj V, Paster BJ, Dye BA, et al. Association between upper digestive tract microbiota and cancer-predisposing states in the esophagus and stomach. Cancer Epidemiol Biomarkers Prev. 2014;23(5):735-41. Epub 2014/04/05. doi: 10.1158/1055-9965.EPI-13-0855. PMID: 24700175; PMCID: PMC4011942.
  33. Alt-Holland A, Murphy CM, Powers A, Kublin CL, Jeong YN, DiMattia M, et al. Comprehensive analysis of aerobic and anaerobic bacteria found on dental bib clips. Compend Contin Educ Dent. 2013;34(4 Suppl):1-12. Epub 2013/04/01. PMID: 25280353.
  34. Aspiras MB, Barros SP, Moss KL, Barrow DA, Phillips ST, Mendoza L, et al. Clinical and subclinical effects of power brushing following experimental induction of biofilm overgrowth in subjects representing a spectrum of periodontal disease. J Clin Periodontol. 2013;40(12):1118-25. Epub 2013/11/07. doi: 10.1111/jcpe.12161. PMID: 24192073.
  35. Fine DH, Markowitz K, Fairlie K, Tischio-Bereski D, Ferrendiz J, Furgang D, et al. A consortium of Aggregatibacter actinomycetemcomitans, Streptococcus parasanguinis, and Filifactor alocis is present in sites prior to bone loss in a longitudinal study of localized aggressive periodontitis. J Clin Microbiol. 2013;51(9):2850-61. Epub 2013/06/21. doi: 10.1128/JCM.00729-13. PMID: 23784124; PMCID: PMC3754677.
  36. Holgerson PL, Vestman NR, Claesson R, Ohman C, Domellof M, Tanner AC, et al. Oral microbial profile discriminates breast-fed from formula-fed infants. J Pediatr Gastroenterol Nutr. 2013;56(2):127-36. Epub 2012/09/08. doi: 10.1097/MPG.0b013e31826f2bc6. PMID: 22955450; PMCID: PMC3548038.
  37. Torlakovic L, Paster BJ, Ogaard B, Olsen I. Changes in the supragingival microbiota surrounding brackets of upper central incisors during orthodontic treatment. Acta Odontol Scand. 2013;71(6):1547-54. Epub 2013/11/05. doi: 10.3109/00016357.2013.776107. PMID: 24180590.
  38. Xin BC, Luo AH, Qin J, Paster BJ, Xu YL, Li YL, et al. Microbial diversity in the oral cavity of healthy Chinese Han children. Oral Dis. 2013;19(4):401-5. Epub 2012/10/05. doi: 10.1111/odi.12018. PMID: 23034082.
  39. Albandar JM, Khattab R, Monem F, Barbuto SM, Paster BJ. The subgingival microbiota of Papillon-Lefevre syndrome. J Periodontol. 2012;83(7):902-8. Epub 2011/12/07. doi: 10.1902/jop.2011.110450. PMID: 22141356.
  40. Ames NJ, Sulima P, Ngo T, Barb J, Munson PJ, Paster BJ, et al. A characterization of the oral microbiome in allogeneic stem cell transplant patients. PLoS One. 2012;7(10):e47628. Epub 2012/11/13. doi: 10.1371/journal.pone.0047628. PMID: 23144704; PMCID: PMC3483166.
  41. Colombo AP, Bennet S, Cotton SL, Goodson JM, Kent R, Haffajee AD, et al. Impact of periodontal therapy on the subgingival microbiota of severe periodontitis: comparison between good responders and individuals with refractory periodontitis using the human oral microbe identification microarray. J Periodontol. 2012;83(10):1279-87. Epub 2012/02/14. doi: 10.1902/jop.2012.110566. PMID: 22324467; PMCID: PMC3971922.
  42. Dang AT, Cotton S, Sankaran-Walters S, Li CS, Lee CY, Dandekar S, et al. Evidence of an increased pathogenic footprint in the lingual microbiome of untreated HIV infected patients. BMC Microbiol. 2012;12:153. Epub 2012/07/31. doi: 10.1186/1471-2180-12-153. PMID: 22838383; PMCID: PMC3438044.
  43. Docktor MJ, Paster BJ, Abramowicz S, Ingram J, Wang YE, Correll M, et al. Alterations in diversity of the oral microbiome in pediatric inflammatory bowel disease. Inflamm Bowel Dis. 2012;18(5):935-42. Epub 2011/10/12. doi: 10.1002/ibd.21874. PMID: 21987382; PMCID: PMC4208308.
  44. Farrell JJ, Zhang L, Zhou H, Chia D, Elashoff D, Akin D, et al. Variations of oral microbiota are associated with pancreatic diseases including pancreatic cancer. Gut. 2012;61(4):582-8. Epub 2011/10/14. doi: 10.1136/gutjnl-2011-300784. PMID: 21994333; PMCID: PMC3705763.
  45. Filkins LM, Hampton TH, Gifford AH, Gross MJ, Hogan DA, Sogin ML, et al. Prevalence of streptococci and increased polymicrobial diversity associated with cystic fibrosis patient stability. J Bacteriol. 2012;194(17):4709-17. Epub 2012/07/04. doi: 10.1128/JB.00566-12. PMID: 22753064; PMCID: PMC3415522.
  46. Luo AH, Yang DQ, Xin BC, Paster BJ, Qin J. Microbial profiles in saliva from children with and without caries in mixed dentition. Oral Dis. 2012;18(6):595-601. Epub 2012/03/31. doi: 10.1111/j.1601-0825.2012.01915.x. PMID: 22458262.
  47. Palmer EA, Nielsen T, Peirano P, Nguyen AT, Vo A, Nguyen A, Jackson S, Finlayson T, et al. Children with severe early childhood caries: pilot study examining mutans streptococci genotypic strains after full-mouth caries restorative therapy. Pediatr Dent. 2012 34(2):e1-10. PubMed: 22583870; PMCID: PMC3828076.
  48. Rudney JD, Chen R, Lenton P, Li J, Li Y, Jones RS, et al. A reproducible oral microcosm biofilm model for testing dental materials. J Appl Microbiol. 2012;113(6):1540-53. Epub 2012/08/29. doi: 10.1111/j.1365-2672.2012.05439.x. PMID: 22925110; PMCID: PMC3501590.
  49. Shaddox LM, Huang H, Lin T, Hou W, Harrison PL, Aukhil I, et al. Microbiological characterization in children with aggressive periodontitis. J Dent Res. 2012;91(10):927-33. Epub 2012/08/07. doi: 10.1177/0022034512456039. PMID: 22863892; PMCID: PMC3446830.
  50. Sizova MV, Hohmann T, Hazen A, Paster BJ, Halem SR, Murphy CM, et al. New approaches for isolation of previously uncultivated oral bacteria. Appl Environ Microbiol. 2012;78(1):194-203. Epub 2011/11/08. doi: 10.1128/AEM.06813-11. PMID: 22057871; PMCID: PMC3255620.
  51. Tanner AC, Sonis AL, Lif Holgerson P, Starr JR, Nunez Y, Kressirer CA, et al. White-spot lesions and gingivitis microbiotas in orthodontic patients. J Dent Res. 2012;91(9):853-8. Epub 2012/07/28. doi: 10.1177/0022034512455031. PMID: 22837552; PMCID: PMC3420397.
  52. Torlakovic L, Klepac-Ceraj V, Ogaard B, Cotton SL, Paster BJ, Olsen I. Microbial community succession on developing lesions on human enamel. J Oral Microbiol. 2012;4. Epub 2012/03/21. doi: 10.3402/jom.v4i0.16125. PMID: 22432048; PMCID: PMC3307376.
  53. Ahn J, Yang L, Paster BJ, Ganly I, Morris L, Pei Z, et al. Oral microbiome profiles: 16S rRNA pyrosequencing and microarray assay comparison. PLoS One. 2011;6(7):e22788. Epub 2011/08/11. doi: 10.1371/journal.pone.0022788. PMID: 21829515; PMCID: PMC3146496.
  54. Duran-Pinedo AE, Paster B, Teles R, Frias-Lopez J. Correlation network analysis applied to complex biofilm communities. PLoS One. 2011;6(12):e28438. Epub 2011/12/14. doi: 10.1371/journal.pone.0028438. PMID: 22163302; PMCID: PMC3233593.
  55. Lif Holgerson P, Harnevik L, Hernell O, Tanner AC, Johansson I. Mode of birth delivery affects oral microbiota in infants. J Dent Res. 2011;90(10):1183-8. Epub 2011/08/11. doi: 10.1177/0022034511418973. PMID: 21828355; PMCID: PMC3173012.
  56. Olson JC, Cuff CF, Lukomski S, Lukomska E, Canizales Y, Wu B, 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. Epub 2011/03/03. doi: 10.1186/1472-6831-11-7. PMID: 21362199; PMCID: PMC3061962.
  57. Tanner AC, Kent RL, Jr., Holgerson PL, Hughes CV, Loo CY, Kanasi E, et al. Microbiota of severe early childhood caries before and after therapy. J Dent Res. 2011;90(11):1298-305. Epub 2011/08/27. doi: 10.1177/0022034511421201. PMID: 21868693; PMCID: PMC3188461.
  58. Asikainen S, Dogan B, Turgut Z, Paster BJ, Bodur A, Oscarsson J. Specified species in gingival crevicular fluid predict bacterial diversity. PLoS One. 2010;5(10):e13589. Epub 2010/11/05. doi: 10.1371/journal.pone.0013589. PMID: 21049043; PMCID: PMC2963608.
  59. Colombo AP, Boches SK, Cotton SL, Goodson JM, Kent R, Haffajee AD, 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(9):1421-32. Epub 2009/09/03. doi: 10.1902/jop.2009.090185. PMID: 19722792; PMCID: PMC3627366.
  60. Preza D, Olsen I, Willumsen T, Boches SK, Cotton SL, Grinde B, et al. Microarray analysis of the microflora of root caries in elderly. Eur J Clin Microbiol Infect Dis. 2009;28(5):509-17. Epub 2008/11/29. doi: 10.1007/s10096-008-0662-8. PMID: 19039610; PMCID: PMC2713778.
  61. Preza D, Olsen I, Willumsen T, Grinde B, Paster BJ. Diversity and site-specificity of the oral microflora in the elderly. Eur J Clin Microbiol Infect Dis. 2009;28(9):1033-40. Epub 2009/04/18. doi: 10.1007/s10096-009-0743-3. PMID: 19373498; PMCID: PMC2821189.

HOMIM-associated Reviews

  1. Duran-Pinedo AE, Frias-Lopez J. Beyond microbial community composition: functional activities of the oral microbiome in health and disease. Microbes Infect. 2015;17(7):505-16. Epub 2015/04/12. doi: 10.1016/j.micinf.2015.03.014. PMID: 25862077; PMCID: PMC4495649.
  2. Wang L, Ganly I. The oral microbiome and oral cancer. Clin Lab Med. 2014;34(4):711-9. Epub 2014/12/03. doi: 10.1016/j.cll.2014.08.004. PMID: 25439271.
  3. Yoshizawa JM, Schafer CA, Schafer JJ, Farrell JJ, Paster BJ, Wong DT. Salivary biomarkers: toward future clinical and diagnostic utilities. Clin Microbiol Rev. 2013;26(4):781-91. Epub 2013/10/05. doi: 10.1128/CMR.00021-13. PMID: 24092855; PMCID: PMC3811231.
  4. Teles R, Teles F, Frias-Lopez J, Paster B, Haffajee A. Lessons learned and unlearned in periodontal microbiology. Periodontol 2000. 2013;62(1):95-162. Epub 2013/04/12. doi: 10.1111/prd.12010. PMID: 23574465; PMCID: PMC3912758.
  5. Ahn J, Chen CY, Hayes RB. Oral microbiome and oral and gastrointestinal cancer risk. Cancer Causes Control. 2012;23(3):399-404. Epub 2012/01/25. doi: 10.1007/s10552-011-9892-7. PMID: 22271008; PMCID: PMC3767140.
  6. Paster BJ, Dewhirst FE. Molecular microbial diagnosis. Periodontol 2000. 2009;51:38-44. Epub 2009/11/03. doi: 10.1111/j.1600-0757.2009.00316.x. PMID: 19878468; PMCID: PMC3070264.
  7. Olsen I, Preza D, Aas JA, Paster BJ. Cultivated and not-yet-cultivated bacteria in oral biofilms. Microb Ecol Hlth Dis 2009;21:65-71.
  8. Paster BJ, Olsen I, Aas JA, Dewhirst FE. The breadth of bacterial diversity in the human periodontal pocket and other oral sites. Periodontol 2000. 2006;42:80-7. Epub 2006/08/26. doi: 10.1111/j.1600-0757.2006.00174.x. PMID: 16930307.
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