Gavin Thomas (he/him)

Hamilton O. Smith, Who Made a Biotech Breakthrough, Is Dead at 94

www.nytimes.com/2025/12/05/s...

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...

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.

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...

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

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

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.

#Throwback 🧪

COMMENT | Metabolites are not genes — avoiding the misuse of pathway analysis in metabolomics

KS Lee, X Su & T Huan

High-resolution Staphylococcus profiling reveals intra-species diversity in a single skin niche The skin microbiome is dominated by a few key genera, among which Staphylococcus is one of the most well characterized. Recent studies have examined the roles of various Staphylococcus species such as...

Interestingly, some of the Staphylococcus epidermidis that we found in people's underarms do make their own biotin, unlike most of the other axilla Staphs.
www.microbiologyresearch.org/content/jour...

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

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...

Our sLola consortium is now in BlueSky! Worth following for future updates on our work with IM30 proteins including LiaH, PspA, and VIPP's.

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

Delighted that @morfdb.bsky.social will be helping with data sharing and developing new web-based tools for data analysis in this project :-)

Structural basis of isethionate transport by a TRAP transporter from a sulfate-reducing bacterium Newton-Vesty et al. used a megabody fiducial to determine the cryo-EM structure of an isethionate TRAP transporter, revealing the substrate and Na+-binding sites. Transport is dependent on Na+ and the...

Check out our new paper:
🔗 www.cell.com/structure/fu...

We explored how sulfate-reducing bacteria import isethionate, a sulfur-containing molecule found in the environment and produced by microbes in the human gut. We captured a structure of the IseQM TRAP transporter in a substrate-bound state.

Contrast this with the response of a president who was an actual decent human being.

From left to right: Willem, Freya, Jess and Rob. We are standing in front of a wall with a congratulations banner and some left-over Halloween decorations.

Absolutely delighted (and proud) that @freyaallen.bsky.social passed her viva with minor corrections today.

Thanks very much @jessicamablair.bsky.social @robfagan.bsky.social for examining!

A simplified version of Figure 4 from our paper https://doi.org/10.1371/journal.pbio.3002741 describing the evolution of vancomycin resistance in C. difficile. The shows phase contract and fluorescence microscopy images of a wild type and a vancomycin resistant C. difficile. In the fluorescence channel can be seen vancomycin -bodipy binding to the mid-cells of wild type cells but this labelling is absent in the resistant bacteria

1. Characterising the role of the dual-function VanT in C. difficile vancomycin resistance.
A collaboration between our group in @molmicrosheffield.bsky.social and the groups of @gavinhthomas.bsky.social and Marjan van der Woude at the University of York

www.findaphd.com/phds/project...

Really enjoyed giving an evening lecture (‘antibiotics from the abyss’) to the Yorkshire Philosophical Society on Tuesday at Tempest Anderson Hall. The AMR series was organised by @gavinhthomas.bsky.social (lectures 1&2 by @jessicamablair.bsky.social & Martha Clokie) www.ypsyork.org/events/antib...

Excited to share our preprint led by Carlos Voogdt et al

We developed new genetic tools & genome-wide libraries for species of the Bacteroidales order; constructed saturated barcoded transposon libraries in key representatives of three genera.
www.biorxiv.org/content/10.1...

High-resolution Staphylococcus profiling reveals intra-species diversity in a single skin niche The skin microbiome is dominated by a few key genera, among which Staphylococcus is one of the most well characterized. Recent studies have examined the roles of various Staphylococcus species such as...

and Staphylococcus story in this paper....
www.microbiologyresearch.org/content/jour...

All dependent on friends in @universityofhull.bsky.social Michelle Rudden, Holly Wilkinson and Matt Hardman & co., & Unilever colleagues Barry Murphy, Jo Hunt & Rob Cornmell & Yorkies @seanmeaden.bsky.social

Revealing the diversity of commensal corynebacteria from a single human skin site | mSystems This study uncovers the hidden diversity of Corynebacterium, an important yet often overlooked group of bacteria inhabiting human skin. Focusing on the underarm and using advanced sequencing technique...

I'll be writing more about this soon, but Reyme's developed a very cool culturomics workflow to enable us to understand and recreated real microbiomes from the human underarm. Corynebacterium focus in this paper. journals.asm.org/doi/full/10....

Massive congratulations to Reyme Herman who passed his PhD viva today and has two new papers out on his (side project) developing and characterising the York Skin Microbiome collection. Thanks to @webberma.bsky.social & Marjan van der Woude for examining & @unileveruki.bsky.social for support.

How do gut bacteria use sialic acid sugars? - Quadram Institute Dr Andrew Bell explains his fundamental research to understand how gut bacteria use specific sugars known as sialic acids

🆕 We catch up with Dr Andrew Bell to find out about his Quadram Institute Fellowship focused on how gut bacteria use a certain group of sugars called sialic acids 🦠

Now published! www.nature.com/articles/s41...

Very nice collaboration with Hoogenboom ( @ucl.ac.uk ) and Bonev ( @uniofnottingham.bsky.social ) labs.

Comprehensive genetic interaction analysis of the Bacillus subtilis envelope using double-CRISPRi Koo et al. apply genome-scale double-CRISPRi to map cell envelope gene interactions in Bacillus subtilis, revealing >1,000 genetic interactions and uncovering gene networks in envelope biogenesis and ...

Also see the accompanying paper from Carol Gross' lab that used a similar approach for Bacillus subtilis: www.cell.com/cell-systems...

Delighted to see our paper studying the evolution of plasmids over the last 100 years, now out! Years of work by Adrian Cazares, also Nick Thomson @sangerinstitute.bsky.social - this version much improved over the preprint. Final version should be open access, apols.
Thread 1/n

Synthetic lethal TN-seq! #microsky 🦠

Big event today as @morfdb.bsky.social
moves into the Catalyst building at the Uni of York where the team assembles for super productive day.
@ybri-uoy.bsky.social

Nasal Staphylococcus aureus carriage promotes depressive behaviour in mice via sex hormone degradation - Nature Microbiology Nasal colonization by Staphylococcus aureus is linked with depression in a human cohort and shown in a mouse model to cause decreased serotonin and dopamine in the brain.

#NewResearch

Nasal colonisation by S. aureus is linked with depression in a human cohort and shown in a mouse model to cause decreased serotonin and dopamine in the brain

#MicroSky #Depression

www.nature.com/articles/s41...

An RNase III–processed sRNA coordinates sialic acid metabolism of Salmonella enterica during gut colonization | PNAS Sialic acids derived from colonic mucin glycans are crucial nutrients for enteric bacterial pathogens like Salmonella. The uptake and utilization o...

www.pnas.org/doi/10.1073/...

#microsky #sialic acid

STM1128 is a Neu5Ac transporter of the sodium-solute symporter (SSS) superfamily, which @gavinhthomas.bsky.social, Arthur Hosie & I identified 15 years :-)

Really looking forward to sharing our science with Yorkshire Philosophical Society at Tempest Anderson Hall on Oct 14th - thank you to @gavinhthomas.bsky.social for the invite www.ypsyork.org/events/antib...

Julian Davies

Julian Davies was a renowned scientist who made crucial strides in the study of antibiotics & antibiotic resistance. Honor his legacy at the Julian Davies Memorial Symposium on Oct. 10, hosted by the University of British Columbia. Register by Sept. 15 to attend via Zoom or in person! asm.social/2Af

Important work by @robfagan.bsky.social