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Jonathon L. Baker, Ph.D.

@jonbakerlab.bsky.social
112 followers 135 following 249 posts

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

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Jonathon L. Baker, Ph.D. @jonbakerlab.bsky.social · 09/08/2026
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.
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Jonathon L. Baker, Ph.D. @jonbakerlab.bsky.social · 30/04/2026
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
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Jonathon L. Baker, Ph.D. @jonbakerlab.bsky.social · 09/04/2026
Importantly, all three methylation systems appear to contribute to pathogenicity, as their loss leads to reduced virulence associated traits.
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Jonathon L. Baker, Ph.D. @jonbakerlab.bsky.social · 09/04/2026
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.
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Jonathon L. Baker, Ph.D. @jonbakerlab.bsky.social · 27/03/2026
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
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Jonathon L. Baker, Ph.D. @jonbakerlab.bsky.social · 06/03/2026
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!
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Jonathon L. Baker, Ph.D. @jonbakerlab.bsky.social · 03/03/2026
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
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Jonathon L. Baker, Ph.D. @jonbakerlab.bsky.social · 07/01/2026
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
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Jonathon L. Baker, Ph.D. @jonbakerlab.bsky.social · 07/01/2026
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
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Jonathon L. Baker, Ph.D. @jonbakerlab.bsky.social · 22/11/2025
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
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Jonathon L. Baker, Ph.D. @jonbakerlab.bsky.social · 14/11/2025
OHSU was very well represented at the 2025 ASM #Biofilms Conference! #microbiology #dentistry
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Jonathon L. Baker, Ph.D. @jonbakerlab.bsky.social · 18/10/2025
With my colleague Dr. Jens Kreth representing OHSU and the USA at what was a fantastic conference! #microbiology #dentistry #immunology
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Jonathon L. Baker, Ph.D. @jonbakerlab.bsky.social · 13/09/2025
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
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Jonathon L. Baker, Ph.D. @jonbakerlab.bsky.social · 21/08/2025
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!
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Jonathon L. Baker, Ph.D. @jonbakerlab.bsky.social · 20/08/2025
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
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Jonathon L. Baker, Ph.D. @jonbakerlab.bsky.social · 16/08/2025
The Baker Lab at OHSU, Summer 2025. 🦠🔬🧫🧪 #microbiology
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Jonathon L. Baker, Ph.D. @jonbakerlab.bsky.social · 28/07/2025
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!
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Jonathon L. Baker, Ph.D. @jonbakerlab.bsky.social · 30/05/2025
The Baker Lab at OHSU, Spring 2025. 🧬🔬🧫🦠 #microbiology
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Jonathon L. Baker, Ph.D. @jonbakerlab.bsky.social · 26/03/2025
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!
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Jonathon L. Baker, Ph.D. @jonbakerlab.bsky.social · 11/03/2025
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
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Jonathon L. Baker, Ph.D. @jonbakerlab.bsky.social · 05/03/2025
The Baker Lab was very well represented at OHSU School of Dentistry Research Day! I’m so proud of my team! #microbiology #dentistry
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Jonathon L. Baker, Ph.D. @jonbakerlab.bsky.social · 18/02/2025
Excited to speak at the University of Colorado School of Medicine this Friday! #microbiology
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Jonathon L. Baker, Ph.D. @jonbakerlab.bsky.social · 24/11/2024
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 🇳🇴🇧🇷🇺🇸
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Jonathon L. Baker, Ph.D. @jonbakerlab.bsky.social · 16/11/2024
First start-to-finish, completely in-house RNA-seq in our lab this month, what a time to be alive.
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Jonathon L. Baker, Ph.D. @jonbakerlab.bsky.social · 05/10/2024
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!
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Jonathon L. Baker, Ph.D. @jonbakerlab.bsky.social · 25/07/2024
Here, we go a step further, and show that across multiple human saliva and nares (i.e., nasal) microbiome communities, certain opportunistic pathogens, such as Klebsiella, significantly increase in abundance during starvation of the community.
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Jonathon L. Baker, Ph.D. @jonbakerlab.bsky.social · 11/07/2024
And then there were 6! The Baker Lab at OHSU, Summer 2024
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Jonathon L. Baker, Ph.D. @jonbakerlab.bsky.social · 07/05/2024
New lab website is live...not the flashiest, but not bad from a guy that didn't know any html as of last Tuesday 🤣 jonbakerlab.github.io
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Jonathon L. Baker, Ph.D. @jonbakerlab.bsky.social · 19/03/2024
Great work by several of my neighbors and collaborators at OHSU, supporting taxonomic reclassification of Fusobacterium nucleatum subspecies into distinct species, and the association of Fn animalis, specifically, with abcesses & disease #microbiology sciencedirect.com/science/articl…
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Jonathon L. Baker, Ph.D. @jonbakerlab.bsky.social · 16/03/2024
Had lots of great engagement at my poster session at @IADR #microbiology #dentistry
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Jonathon L. Baker, Ph.D. @jonbakerlab.bsky.social · 12/03/2024
Rising science all-star Jonah Tang did a great job presenting our research at OHSU School of Dentistry Research Day! 🔬🧫🧬 #microbiology #dentistry
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Jonathon L. Baker, Ph.D. @jonbakerlab.bsky.social · 25/02/2024
We had a great time in Cabo sharing science and learning how to make ceviche at the Mark Wilson Oral Microbiology & Immunology Conference! #microbiology
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Jonathon L. Baker, Ph.D. @jonbakerlab.bsky.social · 20/02/2024
At a time when some academic journals are (rightfully) under fire, I want to acknowledge how much I appreciate the rigor and professionalism I have experienced working with @ASMicrobiology, and I am proud to be receive this award from one of my favorite ASM journals, @mSystemsJ
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Jonathon L. Baker, Ph.D. @jonbakerlab.bsky.social · 10/11/2023
The Baker Lab at Oregon Health & Science University is hiring, both postdocs and research assistants. DM me if you know someone who is interested in learning to apply ‘omics and molecular biology to learn how the #micriobiome impacts our health. #microbiology #bioinformatics
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Jonathon L. Baker, Ph.D. @jonbakerlab.bsky.social · 15/09/2023
Recent advancements in #sequencing, #MassSpectrometry, #bioinformatics, #ComputationalBiology, and #MachineLearning are revolutionizing oral #microbiome research, enabling analysis at an unprecedented scale and level of resolution using 'omics approaches.
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Jonathon L. Baker, Ph.D. @jonbakerlab.bsky.social · 12/09/2023
We also discuss recent advances in our understanding of the microbial etiology of dental caries and periodontal disease, as well as the growing evidence linking the oral #microbiome to a myriad of systemic diseases.
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Jonathon L. Baker, Ph.D. @jonbakerlab.bsky.social · 19/06/2023
No idea what the criteria were, but I’ll take it 😂 #microbiology
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Jonathon L. Baker, Ph.D. @jonbakerlab.bsky.social · 11/04/2023
Since my go-to preprint server doesn't accept review articles, I'm going to post a preprint of my latest review article on my GitHub page: github.com/jonbakerlab/or…
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Jonathon L. Baker, Ph.D. @jonbakerlab.bsky.social · 23/03/2023
Great to catch up with @josealemos and @AbranchesJ from @UFDentistry at @AADOCR #aadocr2023 #microbiology #dentistry Keep an eye out for more great #enterococcus and #streptococcus research coming from their labs soon!
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Jonathon L. Baker, Ph.D. @jonbakerlab.bsky.social · 18/03/2023
Big News! I have accepted a tenure-track faculty position at Oregon Health & Science University! I’ll be opening my lab this summer, and I am very excited for the next chapter! #microbiology #dentistry
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Jonathon L. Baker, Ph.D. @jonbakerlab.bsky.social · 17/11/2022
Perfect talk to kick off World Antimicrobial Awareness Week #WAAW2022 by Babatunde Alli from the lab of @belinda_nicolau showing a disturbing increase in unnecessary prophylactic antibiotic prescriptions for dental procedures at a Canadian hospital. #AntimicrobialResistance
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Jonathon L. Baker, Ph.D. @jonbakerlab.bsky.social · 16/11/2022
Exited to be here in Brazil with @AMRTwilight to guide graduate microbiology and dental students from 5 countries through 3 days of problem-based learning workshops and then give 2 seminars. 🇳🇴 🇺🇸 🇧🇷 🇨🇦 🇮🇳 #microbiology #dentistry
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Jonathon L. Baker, Ph.D. @jonbakerlab.bsky.social · 21/09/2022
Achievement Unlocked: Riding a bike to give seminar in business formal. #oslo
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Jonathon L. Baker, Ph.D. @jonbakerlab.bsky.social · 20/09/2022
Great talk about #streptococcus #quorumsesning and its relationship to #AntimicrobialResistance by @MichaelFederle at #periadr2022 #resispart #microbiology #dentistry
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Jonathon L. Baker, Ph.D. @jonbakerlab.bsky.social · 19/09/2022
Excellent presentation at #periadr2022 by @AMRTwilight Dr. Fernanda Petersen discussing growing concerns about the off-target effects of antibiotics. #microbiology #dentistry #antimicrobialresistance #resispart
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Jonathon L. Baker, Ph.D. @jonbakerlab.bsky.social · 18/09/2022
Session Chairs for #antimicrobialresistance symposium at #periadr 🇧🇷 🇺🇸 #microbiology #dentistry #antibiotics
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Jonathon L. Baker, Ph.D. @jonbakerlab.bsky.social · 16/09/2022
Our #RESISPART booth at #PERIADR2022 Stop by, say hello, and learn about our online course and our project to foster education and collaboration between 🇳🇴 🇺🇸 🇧🇷 🇮🇳🇨🇦 in #biofilm and #AntimicrobialResistance @AMRTwilight @Odontologi_UiO #Microbiology #dentistry
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Jonathon L. Baker, Ph.D. @jonbakerlab.bsky.social · 15/09/2022
Made it to Marseille to Session Chair for #PERIADR
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Jonathon L. Baker, Ph.D. @jonbakerlab.bsky.social · 22/08/2022
We are about to see an explosion in the number of complete bacterial genomes available, which will be particularly useful for determining how taxa that have never been successfully isolated and cultivated impact microbial ecology and human health.
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Jonathon L. Baker, Ph.D. @jonbakerlab.bsky.social · 22/08/2022
From 3 saliva samples, 11 complete bacterial genomes were obtained, with 4 representing the first complete genomes from their respective taxa: 3 species of Saccharibacteria as well as Actinomyces graevenitzii
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