Duncan Sussfeld

Epistasis and co-adaptation in bacterial genome evolution Nature Reviews Genetics - Bacterial genome evolution is shaped by epistasis, which can constrain or promote specific evolutionary paths. The authors review how integrating the effects of epistatic...

I’ve spent a lot of time over the past two years thinking about genome evolution and how recent research revealing complex gene-gene interactions has complicated traditional ‘gene-centric’ genomic approaches to evolution. So here is a review that consolidates these thoughts!

rdcu.be/e6pHY

THANKYOU to our amazing #PAG33 OneHealth Hologenomics speakers @keyfm.bsky.social @dsussfeld.bsky.social @annakovalenko.bsky.social @akang3705.bsky.social Kristina Kordova & Anders Götherström! Ancient plague & parvovirus! AMR genes! Bat ectoparasite microbiomes! & the clap is thriving in the USA! 🎉

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📣 Keynote speaker announced

Prof David Kelly @sheffielduni.bsky.social will join us at #CampyUK2025 to discuss "Campylobacter and Oxygen: A Double-Edged Sword."

24/25th Sep, register now!

campyuk.web.ox.ac.uk/speakers#col...

@biology.ox.ac.uk @microbiologysociety.org @ineosoxford.bsky.social

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📣 The deadline for abstract submission and early bird registration has been extended to 7th August. Registration fees will increase after this date! Visit campyuk.web.ox.ac.uk/home to secure your place! #microsky @biology.ox.ac.uk @microbiologysociety.org @ineosoxford.bsky.social

Genome co-adaptation and the evolution of methicillin resistant Staphylococcus aureus (MRSA) Background: Antimicrobial resistance (AMR) in bacterial pathogens is a major threat to global health, rendering standard treatments ineffective and increasing the risk of severe infection or death. Re...

🚨New pre-print 🚨
We introduce our new tool GOLD-GWAS and demonstrate its use by digging into the evolution of MRSA facilitated by SCCmec

This work was led by talented PhD student @seungwonko.bsky.social who did most of the computational heavylifting 1/n

www.biorxiv.org/content/10.1...

Our results show that even the most conserved genes have significant variants in natural biomes. These could be indicative of novel taxonomic groups and divergent biologies at play in the global ocean.

We hope that these results can guide future targeted searches into microbial dark matter! 🕵️🔬

We then highlight intriguing oceanic variants in three gene families. One of these is the SMC family, which binds DNA by opening up its "hinge" domain.

Interestingly, we detected an abundant marine clade of hinge-less SMCs in Actinobacteria, hinting at marked functional novelty in this family! ⤵️

Our first observation was that div. variants of these old, conserved genes are... everywhere. Every oceanic location hosts some of these sequences - 20% of their entire seq. content on avg. Depth had some influence locally, but on a global scale, even shallow waters are rife with such variants! ⤵️

We present an iterative model to detect increasingly distant homologues in a target dataset.

Simulations show that our method can find distant variants missed by direct searches, without increased risk of false positives.

We then looked for div. variants of 53 core genes in marine microbiomes ⤵️

New groups of highly divergent proteins in families as old as cellular life with important biological functions in the ocean - Environmental Microbiome Background Metagenomics has considerably broadened our knowledge of microbial diversity, unravelling fascinating adaptations and characterising multiple novel major taxonomic groups, e.g. CPR bacteria...

📣 So excited to share the latest paper from my PhD with @aire-team.bsky.social, out now in Environmental Microbiome! 🥳

We mined a large ocean microbiome for remote homologues of core gene families in uncultured lineages.

Key points below ⤵️
environmentalmicrobiome.biomedcentral.com/articles/10....