Headshot photo of Jonathon L. Baker, Ph.D.<span class="profile__pronouns"> (he/him)</span>

Jonathon L. Baker, Ph.D. (he/him)

  • Assistant Professor of Department of Oral Rehabilitation & Integrative Biosciences, School of Dentistry


Jonathon Baker, PhD, joined the Department of Oral Rehabilitation & Biosciences at OHSU in 2023. The research in Dr. Baker’s laboratory leverages emerging technologies in bioinformatics and molecular biology to answer fundamental questions regarding the ecology, physiology, and pathogenesis of the human oral microbiome.  The oral microbiome is the collection of microorganisms that live in the human oral cavity, and includes bacteria, viruses, archaea, and microeukaryotes such as fungi. These microbes have a major impact on human health, with extremely prevalent and costly oral diseases such as dental caries, periodontal disease, and oral cancers being caused mainly by the bacteria and viruses present in the mouth. In addition to oral diseases, there are increasing lines of evidence linking the oral microbiota to a myriad of extra-oral and systemic diseases, such obesity, diabetes, cardiovascular disease, inflammatory bowel disease, nonalcoholic fatty liver disease, rheumatoid arthritis, colorectal cancers, and Alzheimer’s Disease. 

Originally from Rochester, NY, Dr. Baker has a PhD in Microbiology & Immunology from the University of Rochester School of Medicine & Dentistry and a BS in biology from SUNY Geneseo. Prior to joining the faculty at OHSU, Baker conducted research in the Genomic Medicine Group at the J. Craig Venter Institute, the Department of Pediatrics at the UC San Diego School of Medicine, the Department of Oral Biology at the UCLA School of Dentistry and in the Vaccine Research and Early Development group at Pfizer, Inc.


Selected publications

  • Baker, J.L., Mark Welch, J.L., Kauffman, K., McLean, J.S., He, X.  The oral microbiome: diversity, biogeography and human health. Nature Reviews Microbiology. 2023 September 12
  • Baker, J.L.  Illuminating the oral microbiome and its host interactions: recent advancements in omics and bioinformatics technologies in the context of oral microbiome research. FEMS Microbiology Reviews. 2023 September 4
  • Baker, J.L. Using nanopore sequencing to obtain complete genomes from saliva samples. mSystems.. 2022 Aug 22:e0049122. 
  • Baker, J.L.  Complete genomes of clade G6 Saccharibacteria suggest a divergent ecological niche and lifestyle. mSphere.2021 Aug 11; e00530-21.
  • Baker, J.L., Bor, B., Agnello, M., Shi, W., He, X.  Ecology of the oral microbiome: beyond bacteria.  Trends in Microbiology.. 2017 May; 25(5): 362-374. 
  • Baker, J.L., Tang, X., LaBonte, S., Uranga, C., Edlund, A. mucG, mucH, and mucI modulate production of mutanocyclin and reutericyclins in Streptococcus mutans B04Sm5. Journal of Bacteriology. 2022 April 11
  • Baker, J.L., Hendrickson, E.L., Tang, X., Lux, R., He, X., Edlund, A., McLean, J.S., Shi, W.  Klebsiella and Providencia emerge as lone survivors following long-term starvation of the oral microbiota. PNAS.. 2019 April 23; 116(17):8499-8504
  • Tinder, E.L., Faustoferri, R.C., Buckley, A.A., Quivey, Jr., R.G., Baker, J.L.  Analysis of the Streptococcus mutans proteome during acid and oxidative stress reveals modules of co-expression and an expanded role for the TreR transcriptional regulator.mSystems. 2022 March 15


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