Jonathon Baker, Ph.D.

Matthew Barbisan and Mingzhe Guo did a great job presenting some of their research in our lab at OHSU School of Dentistry Research Day 2026! #microbiology #dentistry

Today at the OHSU School of Dentistry AI in Research Symposium, I presented that AI is a major driver of advances in third-generation sequencing technologies (e.g., Nanopore and PacBio). Our lab is using Nanopore sequencing to study DNA/RNA modifications in oral bacteria.

There were 3 main sources of 6mA: 1) at GATC via DpnII (motif/genes known; PMID 39624001) 2) at CGANNNNNNNTCY via HsdM (characterized in other species, but not S. mutans, novel recognition motif) 3) at the novel motif CTGNAG via a currently unknown gene Preprint soon

Epigenomics and epitranscriptomics, the next revolution enabled by third-generation sequencing. Our lab used nanopore sequencing to characterize the epigenome of the model pathogen Streptococcus mutans UA159 at single-nucleotide resolution, revealing 3 types of methylation.

New publication! In this intra-departmental collaboration, we report phenotypic and genotypic differences between species of oral Corynebacteria. #microbiology #dentistry journals.asm.org/doi/10.1128/sp…

Very pleased to share that our recent article in Nature Communications was selected for the Editor's Highlights, which aims to showcase the 50 best papers recently published in the area of #microbiology & infectious diseases! @JWVeening @vincentdebakker nature.com/collections/je…

fasR (spv0647) is a transcriptional regulator, a ∆fasR strain grew poorly at higher temperature (mimicking fever), reduced unsaturated fatty acids, and reduced expression of fabM, fakB3, and bioY-all involved in fatty acid synthesis and/or utilization.

New Publication! In collaboration with Jan-Willem Veening at Univ. de Lausanne, we used multi-omics to examine the response of Streptococcus pneumoniae to infection-mimicking conditions, discovering a novel regulator of membrane fatty acid composition. nature.com/articles/s4146…

Her research was also just accepted for publication at @JournalSpectrum !

Molly Burnside from our lab did an amazing job presenting her research on Corynebacterium at the 2025 @ASMicrobiology Conference on Biofilms. Molly is applying to PhD programs this fall, and she is going to have a huge amount of success wherever she decides to go! #Microbiology

With my colleague Dr. Jens Kreth representing OHSU and the USA at what was a fantastic conference! #microbiology #dentistry #immunology

After spending 7 months earlier this year visiting our lab at OHSU on a scholarship, Dr. Felipe Farias da Silva recently presented his work with us at the 2025 meeting of the Brazilian Society of Dental Research. Way to go Felipe! #microbiology #dentistry

This summer, we hosted Sadie Drucker (Scripps Coll.) and Michelle Lee (Oregon State Univ.), through our NIH-funded DORS program. They did an amazing job, and Sadie won Best Poster at the OHSU Summer Internship Symposium! We wish them the best on the next step in their careers!

Microbiology faculty welcoming incoming OHSU President, Dr. Shereef Elnahal, at a celebration for the Knight family’s $2B donation to our university to fight cancer. #microbiology

The Baker Lab at OHSU, Summer 2025. 🦠🔬🧫🧪 #microbiology

Reposting the link as the above one only allowed a limited number of views journals.asm.org/doi/10.1128/ms…

The viral component of the microbiome has been understudied compared to the bacterial component, despite playing a crucial role in both microbial ecology and human health. We also discovered 478 novel species-level viruses.

New publication! We examined the viruses present in the human oral microbiome of children with severe cavities versus healthy teeth and there was a significant difference in the diversity of viruses present in the groups! #microbiology #dentistry journals.asm.org/eprint/FDPZ4EA…

Excited to see this out! We identified a novel regulator of fatty acid composition in S. pneumoniae (among a lot of other cool stuff in the paper)!

The Baker Lab at OHSU, Spring 2025. 🧬🔬🧫🦠 #microbiology