Gavin Thomas (he/him)

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

Efficient sequence alignment against millions of prokaryotic genomes with LexicMap - Nature Biotechnology LexicMap uses a fixed set of probes to efficiently query gene sequences for fast and low-memory alignment.

Sometimes you meet absolutely incredible bioinfo-magicians.
It was a huge privilege when @shenwei356.bsky.social
joined our group for a year on an @embl.org sabbatical.
While here, he developed a new way of aligning to
millions of bacteria, called LexicMap 1/n
www.nature.com/articles/s41...

Cell surface polysaccharides in the gut microbiota: occurrence, structure and role The gastrointestinal (GI) tract is colonized by trillions of microorganisms living in a symbiotic relationship with the host. Commensal bacteria in the gut engage in cross-talks with epithelial and...

www.tandfonline.com/doi/full/10....

#microsky #microbiome #glycotime

✨ Exciting News ✨I am thrilled to share that I have accepted a position as an Assistant Professor in the Department of Infectious Diseases and Microbiology (IDM), at the University of Pittsburgh School of Public Health!

The phage or the flowers :-)

Very excited to share our work on a novel itaconate transporter in P. aeruignosa! A brilliant team effort by the @gavinhthomas.bsky.social lab. 🎉🎉🎉

Hi Gerrich. I think this is unlikely as the binding protein (IctP) imposes directionality on the system such that this will only function as an uptake system physiologically. I would look to other C4-dicarboxylate transporters like DctA for this (which could be evolved perhaps)?

This was a slow burn being a side project of a side project - started with chats with @jayhinton.bsky.social about itaconate in Salmonella and then picked up a my PhD students & undergraduate project students working together to finish a cool story - what a team!

Delighted with our new paper on a novel itaconate transporter in the human pathogen Pseudomonas aeruginosa, led by Javeria and Reyme. @ybri-uoy.bsky.social @javeriamehboob.bsky.social @bethkw.bsky.social A duplicated transporter on its way to itaconate selectivity
portlandpress.com/biochemj/art...

Very cool, congrats! #microsky

A novel two-component system controls vancomycin resistance in epidemic Clostridioides difficile The glycopeptide antibiotic vancomycin is the frontline treatment for C. difficile infection in the UK. There have been only sporadic reports of resistance in the clinic but testing is rare so the tru...

New preprint from us! The latest part of our C. difficile vancomycin resistance story. We identified a new two-component system (VnrRS) that can control expression of the vanG pathway - just needs one amino acid change

@buddlejess.bsky.social @brockhurstlab.bsky.social @claireyt.bsky.social

Great work from @kdc509.bsky.social that we had a sneak peak of at the Staph GRC. Coming from a Gram -ve background, its funny that Staph don't use polyamines at all, in fact have to evolve resistance mechanisms to host produced ones....

So much stuff in this paper about gene structure and function. Will need a few hours to digest this...

Honestly, this is just one example of where we can radically discover/unify membrane protein families across biology. Too much for us to do alone...anybody interesting in trying to do/fund a comprehensive study?

Honestly, this is just one example of where we can radically discover/unify membrane protein families across biology. Too much for us to do alone...anybody interesting in trying to do/fund a comprehensive study?

Structural unification of diverse transmembrane acyltransferases reveals a conserved fold for the Transmembrane Acyl Transferase (TmAT) superfamily The movement of acyl groups across biological membranes is essential for many cellular processes. One major family of proteins catalysing this reaction are the acyl transferase family 3 (AT3) proteins...

A cool use of DALI/FoldSeek building on new human HG-SNAT protein enabled Bethan Kinniment-Williams & co., to structural unify the TmAT superfamily of membrane-bound acyltransferases first proposed by Milton Saier Jnr in TCDB. @jnb-lab.bsky.social
www.jbc.org/article/S002...

Comparative genomics of Clostridium butyricum reveals a conserved genome architecture and novel virulence-related gene clusters Bacteria from the species Clostridium butyricum encompass a diverse range of phenotypes. While some strains are used as probiotics, others have been isolated from cases of botulism and necrotizing ent...

First paper from Orlagh Anderson PhD project is out. She found a chromid is a distinct & unique feature of Clostridium butyricum. More to come on the virulence related genes.. @yorkshirebiodtp.bsky.social @ybri-uoy.bsky.social
www.microbiologyresearch.org/content/jour...