Gavin Thomas (he/him)
@gavinhthomas.bsky.social
Microbiologist @UniofYork. Former EiC of @MicrobioSoc #MicrobioJ. Transporters, Staph, BO & skin microbiome. CSO @morfdb.bsky.social York Knavesmire Harrier & EBOR orienteer.
After a bit of a rough patch my lab's funding situation has taken a significant upturn, so if you're looking for a Postdoc position please keep us in mind...Pseudomonas aeruginosa genetics, regulation, and physiology - with a focus on the cell envelope. Please repost. andrewdarwinlab.org
Microbiology | Andrew Darwin Lab | United States
Andrew Darwin Laboratory website. Academic Microbiology research laboratory at NYU School of Medicine. New York, NY, USA.
andrewdarwinlab.org
Science is rapidly changing - for better and worse - and we hope that this article collection will serve as a reference as we all navigate these new realities. The first article by Dr. Friedrich Götz of @unituebingen.bsky.social is posted and i highly recommend it journals.asm.org/doi/10.1128/...
mSphere Legacy: Fritz about Fritz | mSphere
I began my research career in the late 1970s with my doctoral thesis at LMU Munich under Karl Heinz Schleifer in the Department of Microbiology. At the time, the department was a hotspot for bacterial classification, cell wall structure analysis, staphylococcal physiology, and metabolism. I became particularly interested in the latter areas and studied fructose-1,6-bisphosphate (FBP)-activated L-lactate dehydrogenase in Staphylococcus epidermidis and a highly stable class I FBP aldolase in Staphylococcus aureus (1). I also investigated oxygen consumption mediated by pyruvate oxidase in Lactobacillus plantarum, demonstrating that this bacterium does not require an enzymatic superoxide dismutase because it can use Mn-phosphate/pyrophosphate for superoxide scavenging—an example of the diverse mechanisms that bacteria employ to cope with oxidative stress (2–4). My scientific environment was shaped by the work of Karl-Heinz Schleifer (Technical University of Munich) and Wesley E. Kloos (North Carolina State University) who made foundational contributions to the identification and classification of Staphylococcus species, particularly during the 1970s, when bacterial systematics was undergoing major modernization. The Kloos–Schleifer classification frameworks remained standard references for the identification of staphylococci well into the molecular era (5, 6).
journals.asm.org
Happy to have this collaborative work with Zach Armstrong now out in Angewandte chemie doi.org/10.1002/anie... . We use a linked assay, coupled with fluorescent probes, to analyse mucin active carbohydrate sulfatase kinetics, cellular location, and inhibition.
Fluorogenic Coupled Assays Reveal Catalytic Properties, Inhibition Constants and Cellular Location of Mucin‐Active Carbohydrate Sulfatases
We report plate-based coupled assays to rapidly and quantitatively determine the activity and selectivity of mucin-active carbohydrate sulfatases. This fluorogenic assay further enables inhibitor ide...
doi.org
Great to see Sam's work on PdhD out now in Microbiology! Very cool story showing how subtle metabolic adaptations can give Staph an edge during systemic invasion #microsky www.microbiologyresearch.org/content/jour...
Metabolic reprogramming promotes Staphylococcus aureus serum resistance
Staphylococcus aureus is a leading cause of bloodstream infections causing an estimated 300,000 deaths worldwide. Using a functional genomics approach, our group previously identified that adaptation ...
microbiologyresearch.org
A lipid cue drives the subcellular localization of a self-inserting bacterial transmembrane protein bioRxiv from @ramamurthilab.bsky.social www.biorxiv.org/content/10.6...
biorxiv.org
This is awful to hear, describing how Sean Eddy (HMMER, infernal, pfam, rfam) has been defunded. The letter said his work "had been determined to be of absolutely no value to the US taxpayer, and therefore it was being specifically terminated," www.npr.org/2026/05/21/n...
Researchers say the Trump administration is finding new ways to punish science
Even with federal grants largely restored, scientists say the Trump administration is still preventing those funds from reaching them. The consequences, they say, are already becoming clear.
npr.org
What a kick-off to @pintofscience.uk in York last night! Presenters covered topics on solar panels & biodiversity, sustainable fishing & maths, biomolecules science, and stressed microbes by @gavinhthomas.bsky.social #pint26 #STEM #AVERTproject #BBSRC
New work from @henrikstrahl.bsky.social and coworkers!
bioRxiv Microbiology@biorxiv-microbiol.bsky.social · 3mo agoMembrane-targeting antimicrobials trigger lysis in Bacillus subtilis by disturbing the MreB-dependent regulation of peptidoglycan hydrolases https://www.biorxiv.org/content/10.64898/2026.05.01.722135v1
Reflecting on the passing of J. Craig Venter, who I never met, and was not everyone's cup of tea, but TIGR's work on the first bacterial genome in 1995 has to be the landmark paper in my PhD era and it would not be an exaggeration to say that it has shaped my whole academic career. #lovemicrobiology
Congratulations Lukas on this nice work which we heard about at the Staph GRC last Autumn. More great work from Tübingen @andreaspeschel.bsky.social
Andreas Peschel @andreaspeschel.bsky.social · 3mo agoCommensal bacteria are crucial for microbiome interactions and pathogen exclusion but are often very difficult to tackle genetically. Our new paper describes an intriguing advance: @cmfi.bsky.social @dzif.bsky.social @spp2330.bsky.social www.sciencedirect.com/science/arti...
@gavinhthomas.bsky.social is taking the stage for the Pint of Science Festival! 🍻🔬Join him on May 18th for a fascinating deep dive into the world of microbes and how they handle stress pintofscience.co.uk/event/nature... #outreach #BBSRC
Nature, Numbers, and the Invisible World
Explore the hidden rules that shape our world, from the stress responses of microbes and the molecular machinery of life to the maths behind ecosystems, mo…
pintofscience.co.uk
New paper! We have written a (hopefully) simple primer on microbial energy metabolism - how do bacteria harvest energy from their environment, and how does this impact their behaviour? www.microbiologyresearch.org/content/jour...
Microbial Primer: Bacterial energy metabolism
All cells need energy to perform their functions. This primer introduces energy metabolism in bacteria, with a focus on key pathways and examples from model organisms, while acknowledging that bacteri...
microbiologyresearch.org
Had lots of fun too at the Memb Prot Conf in Birmingham a few days prior, getting to know @chrismulligan.bsky.social, @gavinhthomas.bsky.social, @allistercrow.bsky.social, @renaeryan.bsky.social and catching up Andy Lovering, Jani Bolla, @pstansfeld.bsky.social & @davidroper2.bsky.social of course!
If you’re attending @microbiologysociety.org 2026 keep an eye out for Luke Shipley from the MORF-Bio team. He’ll explain how to explore your microbial data through interactive, visual tools with MORF Genomes. 🎁 And there’s a £100 Amazon voucher up for grabs! If you spot Luke, come and say hello!
Check out the first of our public lectures on AMR run by the YPS - kicked off by the fantastic Prof. Jess Blair from Birmingham. What is a superbug? @jessicamablair.bsky.social @ypsyork.bsky.social @ybri-uoy.bsky.social - two more in the series coming soon! www.youtube.com/watch?v=sFYs...
What is a Superbug? The global threat of antibiotic resistance
YouTube video by Yorkshire Philosophical Society
youtube.com
It is with deep sadness that we share the passing of Professor Jeff Cole. An esteemed academic, Jeffs research on bacterial adaptation to oxygen and nitrosative stress made a lasting impact on the field. He mentored nearly 60 doctoral students, our thoughts are with his family, friends & colleagues
"Nobody will care about your work about sugar metabolism and transporters in Neurospora crassa" Nobody can predict what can happen with your work. www.sciencedirect.com/science/arti...
Fungal-derived cellobiose metabolic pathway fuels T cells to bypass intratumoral glucose competition
Solid tumors harbor immunosuppressive microenvironments that inhibit tumor-infiltrating lymphocytes (TILs) through the voracious consumption of glucos…
sciencedirect.com
How do you react when your favorite microbe is renamed by taxonomists who are completely outside your field—and who ignore the community that actually works with it? Here is our clear answer re the case of Pseudomonas putida KT2440 👉🏻 journals.asm.org/doi/10.1128/...
The disputed identity of Pseudomonas putida KT2440: when taxonomists rename your favorite microbe | mBio
Names matter; they are not mere labels. They operate as anchors of memory, social coordinates, and references of collective identity. When a name becomes established through long-term use and broad ad...
journals.asm.org
Heading down to the Festival of Genomics to tell people about MORF and get the latest on Microbial genomics - give me a DM if you’d like to chat 👍
Proud supervisor moment - these two superstars Reyme Herman and Imran Khan (@imrsankhan.bsky.social) graduated today from @biologyatyork.bsky.social. Both key members of the group in developing our Staphylococcal research & much more.
Interesting new paper on Enterococcus lactis (the species formerly known as Clade B E. faecium) 'The Mannose Phosphotransferase System in Enterococcus lactis Is Essential for Gastrointestinal Colonization' onlinelibrary.wiley.com/doi/abs/10.1...
The Mannose Phosphotransferase System in Enterococcus lactis Is Essential for Gastrointestinal Colonization
Enterococcus lactis, a recently established species that was previously classified as Enterococcus faecium clade B. Given its recent taxonomic classification, studies on this bacterium are scarce, an...
onlinelibrary.wiley.com
Interested in the sugars bacteria use to evade our immune system? We are looking to train a student across microbiology & biochemistry to discover the mechanisms for scavenging & recycling these sugars & and join the thriving glycobiology community in York www.findaphd.com/phds/project...
Breaking the surface of Pseudomonas: elucidation of the biochemical basis of pseudaminic acid transport and catabolism in bacteria (York YBDTP Project) at University of York on FindAPhD.com
PhD Project - Breaking the surface of Pseudomonas: elucidation of the biochemical basis of pseudaminic acid transport and catabolism in bacteria (York YBDTP Project) at University of York, listed on ...
findaphd.com
Our paper on polymyxin interacting with the E. coli outer membrane is out! Simulations by the very talented @dheerajprakaash.bsky.social www.nature.com/articles/s42... To scale outer membrane protein island simulated at coarse-grained resolution with portions refined at all atom resolution.
Polymyxins slow down lateral diffusion of proteins and lipopolysaccharide in the E. coli outer membrane - Communications Biology
Multi-scale molecular dynamics simulations reveal that polymyxins form polymyxin-protein aggregates upon associating with the E. coli outer membrane thereby reducing lateral mobility of outer membrane...
nature.com
Amazing dataset describing the metabolic profiles of 66 E. coli transporter knockouts by @sulheim.bsky.social with Peter Doubleday and @nzamboni.bsky.social. The tool, set up by @lambdapp.bsky.social and Eric Ulrich allows you to explore for yourself. Enjoy! Pre-print here: doi.org/10.1101/2025...
doi.org
Snorre Sulheim@sulheim.bsky.social · 8mo agoDo you think transporters in E. coli contribute to metabolite release? No? Explore the effect of 66 different transporter knockout mutations on the exometabolome dynamics of ~300 metabolites yourself: keio.unil.ch Teaser: Increased proline in ΔputP #microsky #MEvoSky
The deadline for the first of our three fully funded PhD studentships is tomorrow! Determining the role of the dual-function VanT in C. diff vancomycin resistance. Collab with @gavinhthomas.bsky.social and Marjan van der Woude
MRC DiMeN Doctoral Training Partnership: Doubling down: determining the dual function of VanT in C. difficile antibiotic resistance. at University of Sheffield on FindAPhD.com
PhD Project - MRC DiMeN Doctoral Training Partnership: Doubling down: determining the dual function of VanT in C. difficile antibiotic resistance. at University of Sheffield, listed on FindAPhD.com
findaphd.com
#Throwback 🧪 COMMENT | Metabolites are not genes — avoiding the misuse of pathway analysis in metabolomics KS Lee, X Su & T Huan
Metabolites are not genes — avoiding the misuse of pathway analysis in metabolomics - Nature Metabolism
Pathway analysis, originally developed for gene expression data, has been adapted for metabolomics. However, owing to the unique characteristics and constraints of metabolites compared with genes, pathway analysis in metabolomics often yields misleading or nonsensical results.
bit.ly
Very nice work from Simon Heilbronner's lab in Munich, which we heard at the Staph GRC this summer. Plenty more of these kinds of interactions going on in these communities I think. academic.oup.com/ismej/articl...
Competitive fitness of Staphylococcus aureus against nasal commensals depends on biotin biosynthesis and acquisition
Abstract. The human nasal microbiome can serve as a reservoir for pathogens. In particular, the opportunistic pathogen Staphylococcus aureus can be a membe
academic.oup.com
Our sLola consortium is now in BlueSky! Worth following for future updates on our work with IM30 proteins including LiaH, PspA, and VIPP's.
AVERT project@avertproject.bsky.social · 8mo ago‼️Research update - the last-resort 💊antibiotic daptomycin attacks🧫bacteria through two independent mechanisms & IM30 protein LiaH helps remodel membranes under stress. Great work by @henrikstrahl.bsky.social & @jbuttresssci.bsky.social @newcastleuni.bsky.social team #microsky #BBSRC #sLoLa ⬇️
Now properly published at @natcomms.nature.com with few additional experiments incl. demonstration of Daptomycin's ability to depolarise non-growing cells. See the original preprint-thread for a summary of our findings. www.nature.com/articles/s41... #microsky
The last resort antibiotic daptomycin exhibits two independent antibacterial mechanisms of action - Nature Communications
The precise mechanism of action of the antibiotic daptomycin is controversial. Here, Buttress et al. provide evidence for two independent antibacterial mechanisms: membrane depolarisation and inhibiti...
nature.com
Dr Jess Buttress@jbuttresssci.bsky.social · 2y agoSo happy our pre-print on daptomycin mechanism of action is now out! Here, we present three main findings: i) daptomycin does not form large membrane pores in either B. subtilis or S. aureus, (1/3)
