Jonathon L. Baker, Ph.D.

There were 3 main sources of 6mA:
1) at GATC via DpnII (motif/genes already 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 and GitHub repo 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.
#microbiology

Nice to see this out! Our group found the tools and suggestions provided here super helpful!

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...

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/...

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 ...

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/...

Great opportunity in a fantastic lab!

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...

Really cool paper from @vincentdebakker.bsky.social @jonbakerlab.bsky.social now published @natcomms.nature.com #MicroSky www.nature.com/articles/s41...

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.

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...

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...

This research was also just accepted for publication at the journal mSpectrum!

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

OHSU was very well represented at the 2025 ASM #Biofilms Conference! #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

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

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...

Reposting the link as the above one only allowed a limited number of views

journals.asm.org/doi/10.1128/...

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. Congratulations to Jonah Tang on his first first-author publication!

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...

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...

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)!

The Baker Lab at OHSU, Spring 2025.

🧬🔬🧫🦠 #microbiology

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...

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....

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.

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...

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...

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/...

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

The Baker Lab was very well represented at OHSU School of Dentistry Research Day!

I’m so proud of my team!
#microbiology
#dentistry

Excited to speak at the University of Colorado School of Medicine this Friday!

#microbiology