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; PubMed Central 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; PubMed Central 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; PubMed Central 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. PubMed 32414415; PubMed Central 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. PubMed 32158514; PubMed Central 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. PubMed 31999932; PubMed Central 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. PubMed 31681625; PubMed Central 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. PubMed 30671194; PubMed Central 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. PubMed 31275528; PubMed Central 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. PubMed 30373903; PubMed Central 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. PubMed 31387932; PubMed Central 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. PubMed 29503707; PubMed Central 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. PubMed 30534599; PubMed Central 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. PubMed 30034639; PubMed Central 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. PubMed 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. PubMed 28240240; PubMed Central 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. PubMed 28333122; PubMed Central 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. PubMed 29152157; PubMed Central 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. PubMed 28678838; PubMed Central 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. PubMed 27193835; PubMed Central 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. PubMed 27770517; PubMed Central 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. PubMed 26426306; PubMed Central 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. PubMed 25946126; PubMed Central 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 60 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 September 2020, there were 32 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 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. PubMed 32616783; PubMed Central PMCID: PMC7331743.
2.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. PubMed 32537095; PubMed Central PMCID: PMC7269028.
3.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. PubMed 32533776.
4.Qudeimat MA, Alyahya A, Karched M, Behbehani J, Salako NO. Dental plaque microbiota profiles of children with caries-free and caries-active dentition. J Dent. 2020 Nov 25:103539. doi: 10.1016/j.jdent.2020.103539. Epub ahead of print. PMID: 33248211.
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. PubMed 31489129; PubMed Central 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. PubMed 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. PubMed 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. PubMed 30891159; PubMed Central 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. PubMed 31454264; PubMed Central PMCID: PMC6755720.
10.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. PubMed 30988892; PubMed Central PMCID: PMC6450576.
11.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. PubMed 29520798.
12.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. PubMed 29662960; PubMed Central PMCID: PMC5896869.
13.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. PubMed 29805776; PubMed Central PMCID: PMC5963701.
14.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. PubMed 28930642.
15.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. PubMed 29996764; PubMed Central PMCID: PMC6042318.
16.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. PubMed 30460203; PubMed Central PMCID: PMC6232758.
17.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.
18.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. PubMed 28800622; PubMed Central PMCID: PMC5553731.
19.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. PubMed 28724921; PubMed Central PMCID: PMC5517611.
20.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. PubMed 28839520; PubMed Central PMCID: PMC5560414.
21.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. PubMed 28326156; PubMed Central PMCID: PMC5328378.
22.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. PubMed 28507066; PubMed Central PMCID: PMC5520424.
23.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. PubMed 28766745; PubMed Central PMCID: PMC7209775.
24.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. PubMed 28099499; PubMed Central PMCID: PMC5242539.
25.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. PubMed 26987356; PubMed Central PMCID: PMC4796727.
26.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. PubMed 26799067; PubMed Central PMCID: PMC4723053.
27.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. PubMed 26824889.
28.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. PubMed 26782357; PubMed Central PMCID: PMC4717152.
29.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. PubMed 27824921; PubMed Central PMCID: PMC5100914.
30.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. PubMed 27065347; PubMed Central PMCID: PMC4827145.
31.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. PubMed 26521147; PubMed Central PMCID: PMC7061340.
32.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. PubMed 26684897; PubMed Central 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. PubMed 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. PubMed 27219464; PubMed Central 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. PubMed 25862077; PubMed Central 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. PubMed 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. PubMed PMID: 31413280; PubMed Central 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. PubMed PMID: 29520806; PubMed Central 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. PubMed PMID: 28344834; PubMed Central 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. PubMed PMID: 28341674; PubMed Central 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. PubMed 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. PubMed PMID: 26983837; PubMed Central 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. PubMed PMID: 26746720; PubMed Central 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. PubMed PMID: 26177212; PubMed Central 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. PubMed 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. PubMed 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. PubMed PMID: 25854857; PubMed Central 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. PubMed PMID: 25487558; PubMed Central 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. PubMed PMID: 26020247; PubMed Central 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. PubMed PMID: 25755147; PubMed Central 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. PubMed PMID: 25821962; PubMed Central 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. PubMed PMID: 25741691; PubMed Central 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. PubMed PMID: 26037240; PubMed Central 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. PubMed 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. PubMed PMID: 24638207; PubMed Central 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. PubMed PMID: 25701246; PubMed Central 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. PubMed 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. PubMed 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. PubMed PMID: 24765243; PubMed Central PMCID: PMC3974179.
25.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. PubMed PMID: 24376864; PubMed Central PMCID: PMC3871691.
26.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. PubMed PMID: 24523469; PubMed Central PMCID: PMC3993673.
27.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. PubMed PMID: 25139407; PubMed Central PMCID: PMC4213353.
28.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. PubMed PMID: 24289808; PubMed Central PMCID: PMC7003997.
29.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. PubMed PMID: 25263195; PubMed Central PMCID: PMC4664451.
30.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. PubMed PMID: 25348940; PubMed Central PMCID: PMC4223728.
31.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. PubMed PMID: 24700175; PubMed Central PMCID: PMC4011942.
32.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. PubMed PMID: 25280353.
33.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. PubMed PMID: 24192073.
34.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. PubMed PMID: 23784124; PubMed Central PMCID: PMC3754677.
35.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. PubMed PMID: 22955450; PubMed Central PMCID: PMC3548038.
36.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. PubMed PMID: 24180590.
37.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. PubMed PMID: 23034082.
38.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. PubMed PMID: 22141356.
39.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. PubMed PMID: 23144704; PubMed Central PMCID: PMC3483166.
40.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. PubMed PMID: 22324467; PubMed Central PMCID: PMC3971922.
41.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. PubMed PMID: 22838383; PubMed Central PMCID: PMC3438044.
42.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. PubMed PMID: 21987382; PubMed Central PMCID: PMC4208308.
43.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. PubMed PMID: 21994333; PubMed Central PMCID: PMC3705763.
44.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. PubMed PMID: 22753064; PubMed Central PMCID: PMC3415522.
45.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. PubMed PMID: 22458262.
46.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. PubMed PMID: 22925110; PubMed Central PMCID: PMC3501590.
47.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. PubMed PMID: 22863892; PubMed Central PMCID: PMC3446830.
48.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. PubMed PMID: 22057871; PubMed Central PMCID: PMC3255620.
49.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. PubMed PMID: 22837552; PubMed Central PMCID: PMC3420397.
50.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. PubMed PMID: 22432048; PubMed Central PMCID: PMC3307376.
51.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. PubMed PMID: 21829515; PubMed Central PMCID: PMC3146496.
52.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. PubMed PMID: 22163302; PubMed Central PMCID: PMC3233593.
53.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. PubMed PMID: 21828355; PubMed Central PMCID: PMC3173012.
54.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. PubMed PMID: 21362199; PubMed Central PMCID: PMC3061962.
55.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. PubMed PMID: 21868693; PubMed Central PMCID: PMC3188461.
56.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. PubMed PMID: 21049043; PubMed Central PMCID: PMC2963608.
57.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. PubMed PMID: 19722792; PubMed Central PMCID: PMC3627366.
58.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. PubMed PMID: 19039610; PubMed Central PMCID: PMC2713778.
59.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. PubMed PMID: 19373498; PubMed Central 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. PubMed PMID: 25862077; PubMed Central 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. PubMed 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. PubMed PMID: 24092855; PubMed Central 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. PubMed PMID: 23574465; PubMed Central 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. PubMed PMID: 22271008; PubMed Central 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. PubMed PMID: 19878468; PubMed Central 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. PubMed PMID: 16930307.
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