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Reposted by Gavin Thomas (he/him)

Andy Edwards @bugsinblood.bsky.social · 9d

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

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

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Reposted by Gavin Thomas (he/him)

Jan-Willem Veening @veeninglab.com · 4d

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

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 ...

www.cell.com

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Reposted by Gavin Thomas (he/him)

Zamin Iqbal @zaminiqbal.bsky.social · 13d

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

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Reposted by Gavin Thomas (he/him)

Zeynep Baharoglu @zeynepbaharoglu.bsky.social · 12d

Synthetic lethal TN-seq! #microsky 🦠

Sarah Svensson @campy-bara.bsky.social · 13d

Dual transposon sequencing profiles the genetic interaction landscape in bacteria | Science www.science.org/doi/10.1126/...

Dual transposon sequencing profiles the genetic interaction landscape in bacteria

Gene redundancy complicates systematic characterization of gene function as single-gene deletions may not produce discernible phenotypes. We report dual transposon sequencing (dual Tn-seq), a platform...

www.science.org

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Gavin Thomas (he/him) @gavinhthomas.bsky.social · 14d

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

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Reposted by Gavin Thomas (he/him)

Nature Microbiology @natmicrobiol.nature.com · 16d

#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...

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.

www.nature.com

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Reposted by Gavin Thomas (he/him)

Emmanuele Severi @emmseveri.bsky.social · 23d

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 :-)

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

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Reposted by Gavin Thomas (he/him)

Dr Katherine Duncan @kateduncan.bsky.social · 28d

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...

Antibiotics from the Abyss | Yorkshire Philosophical Society

promoting the understanding of science since 1822

www.ypsyork.org

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Reposted by Gavin Thomas (he/him)

ASM @asm.org · 28d

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

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Reposted by Gavin Thomas (he/him)

Willem van Schaik @wvschaik.bsky.social · 28d

Important work by @robfagan.bsky.social

Wiep Klaas Smits (ExpBac/CMAT) @smitslab.bsky.social · 28d

A novel two-component system controls vancomycin resistance in epidemic Clostridioides difficile www.biorxiv.org/content/10.1...

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...

www.biorxiv.org

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Reposted by Gavin Thomas (he/him)

Zamin Iqbal @zaminiqbal.bsky.social · 28d

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...

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.

www.nature.com

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Reposted by Gavin Thomas (he/him)

Emmanuele Severi @emmseveri.bsky.social · Sep 6

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

#microsky #microbiome #glycotime

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

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Reposted by Gavin Thomas (he/him)

Rebecca Keogh @rebecca-keogh.bsky.social · Sep 3

✨ 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!

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Gavin Thomas (he/him) @gavinhthomas.bsky.social · Sep 2

The phage or the flowers :-)

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Reposted by Gavin Thomas (he/him)

javeriamehboob.bsky.social @javeriamehboob.bsky.social · Sep 2

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

Gavin Thomas (he/him) @gavinhthomas.bsky.social · Sep 2

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...

Itaconate utilisation by the human pathogen Pseudomonas aeruginosa requires uptake via the IctPQM TRAP transporter

Pseudomonas aeruginosa PA01 is one of the major causes of disease persistence and mortality in patients with lung pathologies, relying on various host metabolites as carbon and energy sources for grow...

portlandpress.com

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Gavin Thomas (he/him) @gavinhthomas.bsky.social · Sep 2

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)?

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Gavin Thomas (he/him) @gavinhthomas.bsky.social · Sep 2

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!

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Gavin Thomas (he/him) @gavinhthomas.bsky.social · Sep 2

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...

Itaconate utilisation by the human pathogen Pseudomonas aeruginosa requires uptake via the IctPQM TRAP transporter

Pseudomonas aeruginosa PA01 is one of the major causes of disease persistence and mortality in patients with lung pathologies, relying on various host metabolites as carbon and energy sources for grow...

portlandpress.com

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Reposted by Gavin Thomas (he/him)

Prof Paula Salgado @pssalgado.bsky.social · Aug 22

Very cool, congrats! #microsky

Henrik Strahl @henrikstrahl.bsky.social · Aug 22

A new methods paper from us, this time with a focus on reliable monitoring membrane potential and cell lysis at different growth stages and cell densities. Also, note the surprisingly high level of background lysis in seemingly healthy B. subtilis cultures.
www.biorxiv.org/content/10.1...

Monitoring single cell bioenergetic status and cell lysis in dense and differentiating Bacillus subtilis cultures

Bacillus subtilis is a major model organism for studying population heterogeneity in clonal bacterial cultures due to its high genetic tractability and ability to differentiate into subpopulations wit...

www.biorxiv.org

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Reposted by Gavin Thomas (he/him)

Rob Fagan @robfagan.bsky.social · Aug 22

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

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...

www.biorxiv.org

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Gavin Thomas (he/him) @gavinhthomas.bsky.social · Aug 20

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....

Ákos T Kovács @evolvedbiofilm.bsky.social · Aug 19

Evolution of polyamine resistance in Staphylococcus aureus through modulation of potassium transport

#mSphere from @biobarber.bsky.social

journals.asm.org/doi/10.1128/...

Evolution of polyamine resistance in Staphylococcus aureus through modulation of potassium transport | mSphere

Staphylococcus aureus is a leading cause of infectious disease-related deaths globally. Understanding factors that govern adaptation and survival of S. aureus and other pathogens in the host environme...

journals.asm.org

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Gavin Thomas (he/him) @gavinhthomas.bsky.social · Aug 17

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

Olivier Borkowski @oborkowski.bsky.social · Aug 16

Quantitative essentiality in a reduced genome: a functional, regulatory and structural fitness map
doi.org/10.1038/s443...

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Reposted by Gavin Thomas (he/him)

Gavin Thomas (he/him) @gavinhthomas.bsky.social · Aug 12

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?

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Gavin Thomas (he/him) @gavinhthomas.bsky.social · Aug 12

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?

1

Gavin Thomas (he/him) @gavinhthomas.bsky.social · Aug 12

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...

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...

www.jbc.org

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