Publications
If you use eHOMD please cite the publications below:
General Usage
- F. Escapa, I., Huang, Y., Chen, T., Lin, M., Kokaras, A., Dewhirst F.E., Lemon, K.P. (2020) Construction of habitat-specific training sets to achieve species-level assignment in 16S rRNA gene datasets. Microbiome 8, 65. Online Open Access https://doi.org/10.1186/s40168-020-00841-w
- Isabel Fernández Escapa, Tsute Chen, Yanmei Huang, Prasad Gajare, Floyd E Dewhirst, and Katherine P Lemon. (2018) New insights into human nostril microbiome from the expanded Human Oral Microbiome Database (eHOMD): a resource for species-level identification of microbiome data from the aerodigestive tract. DOI: 10.1128/mSystems.00187-18. Online Open Access: https://msystems.asm.org/content/3/6/e00187-18
- Chen, T., Yu, W-H, Izard, J., Baranova, O.V., Lakshmanan, A., Dewhirst, F.E. (2010) The Human Oral Microbiome Database: a web accessible resource for investigating oral microbe taxonomic and genomic information. Database, Vol. 2010, Article ID baq013, doi: 10.1093/database/baq013. Online Open Access: https://academic.oup.com/database/article/doi/10.1093/database/baq013/405450
- Dewhirst, F.E., Chen, T., Izard, J, Paster, B.J., Tanner, A.C.R., Yu, W.-H., Lakshmanan, A., Wade, W.G. (2010) The Human Oral Microbiome. J. Bacteriol. 192: 5002-5017. Online Open Access: http://jb.asm.org/cgi/content/full/192/19/5002
Pangenomes
- Torres-Morales J, Giacomini JJ, Chen T, Voorhis A, Kauffman KM, Dewhirst FE, Borisy GG, Mark Welch JL.2026.Pangenomes of the human oral microbiome. Microbiol Resour Announc15:e00261-26. https://doi.org/10.1128/mra.00261-26
- McLean, A. R., Torres-Morales, J., Dewhirst, F. E., Borisy, G. G., & Mark Welch, J. L. (2022). Site-tropism of streptococci in the oral microbiome. Molecular Oral Microbiology, 37, 229–243. https://doi.org/10.1111/omi.12387
- Torres-Morales, J., Mark Welch, J. L., Dewhirst, F. E., & Borisy, G. G. (2023). Site-specialization of human oral Gemella species. Journal of Oral Microbiology, 15(1). https://doi.org/10.1080/20002297.2023.2225261
- Giacomini JJ, Torres-Morales J, Dewhirst FE,Borisy GG, Mark Welch JL,2023.Site Specialization of Human Oral Veillonella Species. Microbiol Spectr11:e04042-22. https://doi.org/10.1128/spectrum.04042-22
- Giacomini JJ, Torres-Morales J, Tang J, Dewhirst FE, Borisy GG, Mark Welch JL.2024.Spatial ecology of Haemophilus and Aggregatibacter in the human oral cavity. Microbiol Spectr12:e04017-23. https://doi.org/10.1128/spectrum.04017-23
- Giacomini JJ, Torres-Morales J, Dewhirst FE, Borisy GG, Mark Welch JL.2025.Spatial ecology of the Neisseriaceae family in the human oral cavity. Microbiol Spectr13:e03275-24. https://doi.org/10.1128/spectrum.03275-24
- Giacomini JJ, Torres-Morales J, Dewhirst FE, Borisy GG, Mark Welch JL.2026.Spatial ecology of the Capnocytophaga genus in the human oral cavity. Microbiol Spectr14:e03626-25. https://doi.org/10.1128/spectrum.03626-25
- Julian Torres-Morales, Floyd E. Dewhirst, Kathryn M. Kauffman, Jessica L. Mark Welch, Gary G. Borisy. bioRxiv 2026.06.02.729646; doi: https://doi.org/10.64898/2026.06.02.729646
Phage and Virus Resources
- Matrishin, C.B., Haase, E.M., Dewhirst, F.E. et al. Phages are unrecognized players in the ecology of the oral pathogen Porphyromonas gingivalis. Microbiome 11, 161 (2023). https://doi.org/10.1186/s40168-023-01607-w
- Cole B. Matrishin, Elaine M. Haase, Ashley K. Miles, Stephanie Steimer, Dam Soh, Matthew Smardz, Patricia I. Diaz, Kathryn M. Kauffman. bioRxiv 2026.08.04.741601; doi: https://doi.org/10.64898/2026.08.04.741601
Abundance and Prevalence Information
- Jessica L. Mark Welch, Floyd E. Dewhirst, Gary G. Borisy. 2019. Biogeography of the Oral Microbiome: The Site-Specialist Hypothesis. Annual Review of Microbiology 73:335-358. https://doi.org/10.1146/annurev-micro-090817-062503
- A.M. Eren, G.G. Borisy, S.M. Huse, & J.L. Mark Welch, Oligotyping analysis of the human oral microbiome, Proc. Natl. Acad. Sci. U.S.A. 111 (28) E2875-E2884, https://doi.org/10.1073/pnas.1409644111 (2014).
