Jonathon L. Baker, Ph.D.
@jonbakerlab.bsky.social
Using Microbiology and Bioinformatics to discover how the bacteria that live in our mouth impact health and disease. Assistant Professor at Oregon Health & Science University. Tweets my own. jonbakerlab.github.io
OHSU published an article about my lab's research! #microbiology #dentistry #bioinformatics news.ohsu.edu/2026/05/05/o...
OHSU scientist targets bacteria with precision
Jonathon Baker, Ph.D., uses advanced sequencing to develop treatments for oral infections.
news.ohsu.edu
J. Craig Venter (1946-2026) Polarizing, but an absolute science rock star who drove some of the most significant scientific accomplishments in my lifetime. Forever grateful and proud to have had the privilege of 5 formative years learning #bioinformatics while working for @jcv.bsky.social
New preprint! Using cutting edge epigenomics, we comprehensively identified DNA methylation in the model oral pathogen Streptococcus mutans UA159 and uncovered its three distinct sources. #microbiology #dentistry www.biorxiv.org/content/10.6...
biorxiv.org
Congratulations to our NIH R25 DORS Intern, Sadie Drucker, who presented her research this week at the International Association for Dental Research conference in San Diego, and is a Finalist for the Cariology Research Group Student Research Award! Way to go Sadie! #microbiology #dentistry
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!
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 and RNA modifications in oral bacteria. #microbiology #dentistry
Completely agree!
Antimicrobial resistance #AMR@antimicrobial.bsky.social · 5mo agoIt is time for the dental profession to take a more active role in national action plans against #AMR and to engage systematically in antibiotic stewardship. AMR is a shared challenge that requires dentistry to make a clear contribution to stewardship efforts. www.cidrap.umn.edu/antimicrobia...
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. #microbiology
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/...
Comparative characterization reveals conserved and divergent ecological traits of oral corynebacteria | Microbiology Spectrum
Oral corynebacteria contribute to the structural and ecological stability of supragingival communities. Yet, their species-level functions remain poorly defined. By isolating and characterizing new st...
journals.asm.org
Very pleased to share that our recent article with @veeninglab.com in @natcomms.nature.com was selected for the Editor's Highlights, which aims to showcase the 50 best papers recently published in the area of #microbiology & infectious diseases! www.nature.com/collections/...
Microbiology and infectious diseases
This page highlights recent articles on all aspects of bacteriology, mycology, parasitology and virology, covering the biology of pathogens, host-pathogen ...
nature.com
Great opportunity in a fantastic lab!
Jeff McLean@jeffmclean.bsky.social · 8mo agoA Postdoctoral opportunity in the McLean Lab, funded by an NIH T90 training grant, is available. This is a competitive opportunity (US citizens/perm residents). Applications due Jan 31st- must begin their fellowship no later than May 31, 2026. see dental.washington.edu/research/tra...
Really cool paper from @vincentdebakker.bsky.social @jonbakerlab.bsky.social now published @natcomms.nature.com #MicroSky www.nature.com/articles/s41...
Multi-omics profiling reveals atypical sugar utilization and a key membrane composition regulator in Streptococcus pneumoniae - Nature Communications
The pathogen Streptococcus pneumoniae can adapt to diverse microenvironments in the human body. Here, De Bakker et al. study these adaptation responses, showing unusual sugar utilization and identifyi...
nature.com
New Publication! In this collaboration with @veeninglab.com at the @unil.bsky.social, we used multi-omics to examine the response of Streptococcus pneumoniae to infection-mimicking growth conditions, discovering a novel regulator of membrane fatty acid composition. www.nature.com/articles/s41...
Multi-omics profiling reveals atypical sugar utilization and a key membrane composition regulator in Streptococcus pneumoniae - Nature Communications
The pathogen Streptococcus pneumoniae can adapt to diverse microenvironments in the human body. Here, De Bakker et al. study these adaptation responses, showing unusual sugar utilization and identifyi...
nature.com
Last week, Molly Burnside from our lab did an amazing job presenting her research on Corynebacterium at the 2025 @asm.org 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 #dentistry
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 @ohsunews.bsky.social 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
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! journals.asm.org/eprint/FDPZ4...
The salivary virome during childhood dental caries | mSphere
Dental caries is the most common chronic infectious disease worldwide and is caused by dysbiosis of the oral microbiome featuring an increased abundance of acid-tolerant, acid-producing, and biofilm-f...
journals.asm.org
If high quality treatment is provided to everyone with bacterial infections + innovative new antibiotics funded ... By 2050: Health costs ⬇️ $97 billion The economy ⬆️ $960 billion Generated health benefits 🟰 $680 billion to countries Return on Investment 🟰 28 to 1 www.cgdev.org/publication/...
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)!
Jan-Willem Veening@veeninglab.com · last yr.Some positive news in troubled times: New preprint by Vincent de Bakker, Xue Liu @jonbakerlab.bsky.social Infection-mimicking conditions+transcriptomics/proteomics/'essentialomics'/lipidomics shows many cool things! www.biorxiv.org/content/10.1...
Congratulations to our high school intern, Daniela, and our Research Assistants, Matthew and Jonah, on publishing their pilot study on the impact of beetroot supplement on an in-vitro microbiome of e-cigarette users! #microbiology #dentistry www.tandfonline.com/doi/full/10....
The effect of Beta vulgaris on an in vitro oral microbiome of electronic cigarette users
Although touted as a safer alternative to cigarette smoking, electronic cigarette usage has been increasingly linked to a myriad of health issues and appears to impact the oral microbiome. Meanwhil...
tandfonline.com
I was interviewed by Business Insider magazine as part of an article about the impact of the oral microbiome on overall human health! #microbiology #dentistry www.businessinsider.com/oral-microbi...
Cleaning your teeth could help you live longer: meet your oral microbiome
You may know that caring for your gut microbiome could help you live longer. But brushing and flossing your teeth is also a potential shortcut to better health.
businessinsider.com
New publication! Our findings reveal that the specificity of several FISH probes is compromised, with cross-species hybridization being more common than previously assumed as more genomic data becomes available. #microbiology onlinelibrary.wiley.com/doi/10.1111/...
Shining Light on Oral Biofilm Fluorescence In Situ Hybridization (FISH): Probing the Accuracy of In Situ Biogeography Studies
The oral biofilm has been instrumental in advancing microbial research and enhancing our understanding of oral health and disease. Recent developments in next-generation sequencing have provided deta...
onlinelibrary.wiley.com
Exciting news! Our very first hire, Jonah Tang, was accepted into and will be joining the Bioinformatics Graduate Program at the University of Oregon! After 1.5 years in the lab, Jonah is already an author on 3 submitted publications and several more that are in preparation. Congratulations Jonah!
Tomorrow, 1:30pm. AADOCR in NYC. Honored to be a speaker alongside @jmarkwelch.bsky.social and @mbio.bsky.social Editor in Chief Marvin Whiteley. #microbiology #dentistry
