Jonathon L. Baker, Ph.D. @jonbakerlab.bsky.social · 09/08/2026Without 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. 000
Jonathon L. Baker, Ph.D. @jonbakerlab.bsky.social · 30/04/2026J. 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 020
Jonathon L. Baker, Ph.D. @jonbakerlab.bsky.social · 09/04/2026Importantly, all three methylation systems appear to contribute to pathogenicity, as their loss leads to reduced virulence associated traits. 000
Jonathon L. Baker, Ph.D. @jonbakerlab.bsky.social · 09/04/2026We 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. 100
Jonathon L. Baker, Ph.D. @jonbakerlab.bsky.social · 27/03/2026Congratulations 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 120
Jonathon L. Baker, Ph.D. @jonbakerlab.bsky.social · 06/03/2026Matthew Barbisan and Mingzhe Guo did a great job presenting some of their research in our lab at OHSU School of Dentistry Research Day 2026! 010
Jonathon L. Baker, Ph.D. @jonbakerlab.bsky.social · 03/03/2026At 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 181
Jonathon L. Baker, Ph.D. @jonbakerlab.bsky.social · 07/01/2026There 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 010
Jonathon L. Baker, Ph.D. @jonbakerlab.bsky.social · 07/01/2026Epigenomics 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 250
Jonathon L. Baker, Ph.D. @jonbakerlab.bsky.social · 22/11/2025Last 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 210
Jonathon L. Baker, Ph.D. @jonbakerlab.bsky.social · 14/11/2025OHSU was very well represented at the 2025 ASM #Biofilms Conference! #microbiology #dentistry 110
Jonathon L. Baker, Ph.D. @jonbakerlab.bsky.social · 18/10/2025With my colleague Dr. Jens Kreth representing OHSU and the USA at what was a fantastic conference! #microbiology #dentistry #immunology 130
Jonathon L. Baker, Ph.D. @jonbakerlab.bsky.social · 13/09/2025After 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 110
Jonathon L. Baker, Ph.D. @jonbakerlab.bsky.social · 21/08/2025This 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! 000
Jonathon L. Baker, Ph.D. @jonbakerlab.bsky.social · 20/08/2025Microbiology 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 130
Jonathon L. Baker, Ph.D. @jonbakerlab.bsky.social · 16/08/2025The Baker Lab at OHSU, Summer 2025. 🦠🔬🧫🧪 #microbiology 140
Jonathon L. Baker, Ph.D. @jonbakerlab.bsky.social · 28/07/2025The 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! 100
Jonathon L. Baker, Ph.D. @jonbakerlab.bsky.social · 30/05/2025The Baker Lab at OHSU, Spring 2025. 🧬🔬🧫🦠 #microbiology 110
Jonathon L. Baker, Ph.D. @jonbakerlab.bsky.social · 26/03/2025Exciting 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! 040
Jonathon L. Baker, Ph.D. @jonbakerlab.bsky.social · 11/03/2025Tomorrow, 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 021
Jonathon L. Baker, Ph.D. @jonbakerlab.bsky.social · 05/03/2025The Baker Lab was very well represented at OHSU School of Dentistry Research Day! I’m so proud of my team! #microbiology #dentistry 020
Jonathon L. Baker, Ph.D. @jonbakerlab.bsky.social · 18/02/2025Excited to speak at the University of Colorado School of Medicine this Friday! #microbiology 010
Jonathon L. Baker, Ph.D. @jonbakerlab.bsky.social · 24/11/2024A 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 🇳🇴🇧🇷🇺🇸 195
Jonathon L. Baker, Ph.D. @jonbakerlab.bsky.social · 16/11/2024First start-to-finish, completely in-house RNA-seq in our lab this month, what a time to be alive. 040
Jonathon L. Baker, Ph.D. @jonbakerlab.bsky.social · 05/10/2024Last 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! 052
Jonathon L. Baker, Ph.D. @jonbakerlab.bsky.social · 25/07/2024Here, 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. 110
Jonathon L. Baker, Ph.D. @jonbakerlab.bsky.social · 11/07/2024And then there were 6! The Baker Lab at OHSU, Summer 2024 020
Jonathon L. Baker, Ph.D. @jonbakerlab.bsky.social · 07/05/2024New 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 030
Jonathon L. Baker, Ph.D. @jonbakerlab.bsky.social · 19/03/2024Great 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… 030
Jonathon L. Baker, Ph.D. @jonbakerlab.bsky.social · 16/03/2024Had lots of great engagement at my poster session at @IADR #microbiology #dentistry 020
Jonathon L. Baker, Ph.D. @jonbakerlab.bsky.social · 12/03/2024Rising science all-star Jonah Tang did a great job presenting our research at OHSU School of Dentistry Research Day! 🔬🧫🧬 #microbiology #dentistry 020
Jonathon L. Baker, Ph.D. @jonbakerlab.bsky.social · 25/02/2024We had a great time in Cabo sharing science and learning how to make ceviche at the Mark Wilson Oral Microbiology & Immunology Conference! #microbiology 030
Jonathon L. Baker, Ph.D. @jonbakerlab.bsky.social · 20/02/2024At 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 030
Jonathon L. Baker, Ph.D. @jonbakerlab.bsky.social · 10/11/2023The 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 100
Jonathon L. Baker, Ph.D. @jonbakerlab.bsky.social · 15/09/2023Recent 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. 000
Jonathon L. Baker, Ph.D. @jonbakerlab.bsky.social · 12/09/2023We 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. 000
Jonathon L. Baker, Ph.D. @jonbakerlab.bsky.social · 19/06/2023No idea what the criteria were, but I’ll take it 😂 #microbiology 020
Jonathon L. Baker, Ph.D. @jonbakerlab.bsky.social · 11/04/2023Since 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… 020
Jonathon L. Baker, Ph.D. @jonbakerlab.bsky.social · 23/03/2023Great 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! 030
Jonathon L. Baker, Ph.D. @jonbakerlab.bsky.social · 18/03/2023Big 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 030
Jonathon L. Baker, Ph.D. @jonbakerlab.bsky.social · 17/11/2022Perfect 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 030
Jonathon L. Baker, Ph.D. @jonbakerlab.bsky.social · 16/11/2022Exited 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 030
Jonathon L. Baker, Ph.D. @jonbakerlab.bsky.social · 21/09/2022Achievement Unlocked: Riding a bike to give seminar in business formal. #oslo 030
Jonathon L. Baker, Ph.D. @jonbakerlab.bsky.social · 20/09/2022Great talk about #streptococcus #quorumsesning and its relationship to #AntimicrobialResistance by @MichaelFederle at #periadr2022 #resispart #microbiology #dentistry 030
Jonathon L. Baker, Ph.D. @jonbakerlab.bsky.social · 19/09/2022Excellent presentation at #periadr2022 by @AMRTwilight Dr. Fernanda Petersen discussing growing concerns about the off-target effects of antibiotics. #microbiology #dentistry #antimicrobialresistance #resispart 030
Jonathon L. Baker, Ph.D. @jonbakerlab.bsky.social · 18/09/2022Session Chairs for #antimicrobialresistance symposium at #periadr 🇧🇷 🇺🇸 #microbiology #dentistry #antibiotics 030
Jonathon L. Baker, Ph.D. @jonbakerlab.bsky.social · 16/09/2022Our #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 030
Jonathon L. Baker, Ph.D. @jonbakerlab.bsky.social · 15/09/2022Made it to Marseille to Session Chair for #PERIADR 030
Jonathon L. Baker, Ph.D. @jonbakerlab.bsky.social · 22/08/2022We 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. 010
Jonathon L. Baker, Ph.D. @jonbakerlab.bsky.social · 22/08/2022From 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 100