Jonathon L. Baker, Ph.D.

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

113 followers135 following249 posts

Jonathon L. Baker, Ph.D.
@jonbakerlab.bsky.social

Oral Microbiology and Immunology 4th Edition is out (ASM Press; ISBN: 978-1-683-67511-2). I wrote Chapter 9: From Bacterial Genetics to Genomics! Many thanks to the Editors for the honor of contributing! #microbiology #dentistry www.wiley.com/en-us/shop/g...

wiley.comOral Microbiology and Immunology, 4th Edition<p><b>The updated reference integrating oral microbiology and immunology for dentistry</b> <p>The study of oral microbiology and immunology has entered a new era, shaped by transformative advances in ...
Jonathon L. Baker, Ph.D.
@jonbakerlab.bsky.social

New publication in collaboration with the Pfeifer Lab at OHSU. We identified commercially available drugs capable of inhibiting GtfC, a critical enzyme for biofilm initiation and cohesion by the pathogen, Streptococcus mutans. #microbiology #dentistry www.nature.com/articles/s41...

nature.comDrug repurposing for glucosyltransferase inhibition for targeted oral biofilm disruption - npj Biofilms and Microbiomesnpj Biofilms and Microbiomes - Drug repurposing for glucosyltransferase inhibition for targeted oral biofilm disruption
Jonathon L. Baker, Ph.D.
@jonbakerlab.bsky.social

Big week for our lab, another publication is out! #dentistry has a strategic position in the fight against AMR, yet is under-leveraged because of shortcomings in policy and education. @antimicrobial.bsky.social @amr-twilight.bsky.social @ulfdahle.bsky.social journals.asm.org/doi/10.1128/...

journals.asm.orgmGem: Dentistry is strategically positioned yet underleveraged in the battle against antimicrobial resistance | mBioAntimicrobial resistance (AMR) is among the most significant global health threats of the 21st century, compromising the effectiveness of antibiotics that underpin modern medicine, surgery, transplant...
Jonathon L. Baker, Ph.D.
@jonbakerlab.bsky.social

Without the ability to create MUFAs, the cells of all 3 species were more susceptible to acid stress and antibiotics. Furthermore, S. mutans had its ability to produce toxins impaired and S. mutans and S. pneumoniae were more susceptible to killing by human neutrophils.

Jonathon L. Baker, Ph.D.
@jonbakerlab.bsky.social

We found methylation in UA159 at: 1️⃣ GATC via DpnII 2️⃣ CGANNNNNNNTCY via HsdM (previously unstudied in S. mutans) 3️⃣ CTGNAG via DnmA—both the gene and motif were discovered in this study Deletion of any of these systems resulted in a complete loss of methylation at the cognate DNA sequence.

Jonathon L. Baker, Ph.D.
@jonbakerlab.bsky.social

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

Jonathon L. Baker, Ph.D.
@jonbakerlab.bsky.social

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

Jonathon L. Baker, Ph.D.
@jonbakerlab.bsky.social

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

Jonathon L. Baker, Ph.D.
@jonbakerlab.bsky.social

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

Jonathon L. Baker, Ph.D.
@jonbakerlab.bsky.social

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

Nature Biotechnology@natbiotech.nature.com

Troubleshooting common errors in assemblies of long-read metagenomes - @merenbey.bsky.social @banfieldlab.bsky.social go.nature.com/44P7nSm

go.nature.comTroubleshooting common errors in assemblies of long-read metagenomes - Nature BiotechnologyLong-read sequence assemblies from metagenomes contain frequent errors.
Jonathon L. Baker, Ph.D.
@jonbakerlab.bsky.social

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/...

journals.asm.orgComparative characterization reveals conserved and divergent ecological traits of oral corynebacteria | Microbiology SpectrumOral 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...
Jonathon L. Baker, Ph.D.
@jonbakerlab.bsky.social

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/...

nature.comMicrobiology and infectious diseasesThis page highlights recent articles on all aspects of bacteriology, mycology, parasitology and virology, covering the biology of pathogens, host-pathogen ...

Jonathon L. Baker, Ph.D. reposted

Jan-Willem Veening
@veeninglab.com

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

nature.comMulti-omics profiling reveals atypical sugar utilization and a key membrane composition regulator in Streptococcus pneumoniae - Nature CommunicationsThe 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...
Jonathon L. Baker, Ph.D.
@jonbakerlab.bsky.social

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.

Jonathon L. Baker, Ph.D.
@jonbakerlab.bsky.social

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

Jonathon L. Baker, Ph.D.
@jonbakerlab.bsky.social

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!

Jonathon L. Baker, Ph.D.
@jonbakerlab.bsky.social

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!

Jonathon L. Baker, Ph.D.
@jonbakerlab.bsky.social

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

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...

biorxiv.orgMulti-omics profiling reveals atypical sugar utilization and identifies a key membrane composition regulator in Streptococcus pneumoniaeThe human body comprises many different microenvironments, each with their own challenges for microorganisms to overcome in order to survive, and possibly cause infection. The human pathogen Streptoco...
Jonathon L. Baker, Ph.D.
@jonbakerlab.bsky.social

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....

tandfonline.comThe effect of Beta vulgaris on an in vitro oral microbiome of electronic cigarette usersAlthough 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...
Jonathon L. Baker, Ph.D.
@jonbakerlab.bsky.social

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...

businessinsider.comCleaning your teeth could help you live longer: meet your oral microbiomeYou 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.
Jonathon L. Baker, Ph.D.
@jonbakerlab.bsky.social

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/...

onlinelibrary.wiley.comShining Light on Oral Biofilm Fluorescence In Situ Hybridization (FISH): Probing the Accuracy of In Situ Biogeography StudiesThe 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...
Jonathon L. Baker, Ph.D.
@jonbakerlab.bsky.social

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!

Jonathon L. Baker, Ph.D.
@jonbakerlab.bsky.social

Happy to share that I was a Finalist for the OHSU 2024 Distinguished Faculty Award in Collaboration! In the last 5 years, collaborated with 83 co-authors from 29 institutions in 9 countries. Congratulations to the other finalists and winner, Dr. Lyndie Foster Page! www.linkedin.com/feed/update/...

linkedin.comOHSU School of Dentistry on LinkedIn: #dentistry #ohsuschoolofdentistry #ohsudentistry #ohsu #ohsuresearchOregon Health &amp; Science University celebrated its 2024 Distinguished Faculty Award winners recently and the OHSU School of Dentistry had a winner and several…
Jonathon L. Baker, Ph.D.
@jonbakerlab.bsky.social

A great week at FOP-UNICAMP! We brainstormed ways to get dentists involved in National Action Plans being implemented to combat antibiotic resistance (AMR), showed how to use sequencing to analyze AMR, and also practiced developing grant proposals with the students 🇳🇴🇧🇷🇺🇸

Jonathon L. Baker, Ph.D.
@jonbakerlab.bsky.social

Last month I hosted the annual Symposium for our RESISFORCE Project here at @OHSUNews. We hosted 25 researchers from 🇳🇴🇧🇷🇮🇳🇨🇦🇯🇵🇺🇸 to share their research and build collaborations to address the global challenge of #AntimicrobialResistance. Thanks to @forskningsradet for funding!