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Reposted by Will Smith

Cameron Thrash @jcamthrash.bsky.social · 21h

Metabolic interplay drives population cycles in a cross-feeding microbial community www.nature.com/articles/s41... #jcampubs

Metabolic interplay drives population cycles in a cross-feeding microbial community - Nature Communications

Here the authors leverage a crossfeeding, engineered microbial community to demonstrate that strain abundance cycles are robust across environmental conditions. They pair this with a nonlinear dynamic model to elucidate population cycles.

www.nature.com

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Will Smith @willpjsmith.bsky.social · 20d

LOL wet! I don't think it's stopped raining for the last 24h ^^

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Will Smith @willpjsmith.bsky.social · 22d

YES! Amazing news, big congrats Rachel! 🎉

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Reposted by Will Smith

Sorek Lab @soreklab.bsky.social · 27d

Phage "satellites" that produce capsids but have no genes to produce tails have puzzled scientists for a long time. These are abundant as prophages in bacteria, but it was unclear how they can infect without tails

Now, Penadés & co show that they hijack tails from other phages. Incredible!

José R Penadés @jrpenades.bsky.social · 28d

Thrilled to share our two latest papers with the @tcostalab.bsky.social
lab! In the first, we uncover a new mechanism of satellite transfer: cf-PICIs hijack tails from diverse phages to spread across species.
@imperialcollegeldn.bsky.social
www.cell.com/cell/fulltex...

Chimeric infective particles expand species boundaries in phage-inducible chromosomal island mobilization

Capsid-forming PICIs (cf-PICIs) produce their own capsids and exploit phage tails from unrelated species to transfer their DNA across bacterial hosts. This tail piracy enables broad dissemination and ...

www.cell.com

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Reposted by Will Smith

Joshua Weitz @joshuasweitz.bsky.social · 28d

New preprint bubbling up in our group for a while:

"Phase separation and coexistence in spatial coordination games between microbes"

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

Generalizes findings of phase separation in microbes using T6SSs to a broad range of interaction mechanisms.

Li + Steinbach et al.

$FIG. 3: Time lapse visualizations of a two player coordination game with payo matrix A = [10 5; 510]. The images show the spatial con guration (lattice size L = 256) at t = 0246810 with dt = 005. White corresponds to player 1 and black is player 2. Starting from well mixed initial condition, initial fraction of player 1 is 05, the two players separate into domains whose characteristic length scales (patch size) grow over time.$

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Will Smith @willpjsmith.bsky.social · Aug 31

Thanks for reading this thread! We hope the paper is interesting and useful Huge thanks to my coauthor @prokaryota.bsky.social for a really cool and enjoyable collab, Elisa is the best :-)

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Will Smith @willpjsmith.bsky.social · Aug 31

If your lab does competition assays where microbial antagonism is (or may be!) involved, it might be worth doing a ground-truth check for biases like these. Also, some assays won't be affected e.g. if you use colorimetric killing assays that don't rely on a selection step or c.f.u. counting.

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Will Smith @willpjsmith.bsky.social · Aug 31

What's our take-away? Competitive interactions are very common (see e.g. www.science.org/doi/10.1126/...) and we've shown they can be hard to quench in a killing assay. This can lead to over-estimation of strong competitive interactions.

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Bacterial species rarely work together

Competition is prevalent and could be harnessed as an alternative to antibiotics

www.science.org

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Will Smith @willpjsmith.bsky.social · Aug 31

Conversely, when Susceptible cells are rare (e.g. if they *didn't* do well in the competition assay), few dilutions are required to count Susceptible c.f.u.s. and there will be proportionally more contact with T6SS-armed Attackers. More T6SS contact, more residual killing, fewer c.f.u.s.

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Will Smith @willpjsmith.bsky.social · Aug 31

When Susceptible cells are abundant (e.g. if they did pretty well in the competition assay), large dilutions are necessary to count c.f.u.s. These dilutions will tend to separate Attackers and Susceptibles and minimise residual killing on the selective media.

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Will Smith @willpjsmith.bsky.social · Aug 31

Why does this bias results most where the Attacker : Susceptible ratio is high?

Here's a little cartoon explainer:

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Will Smith @willpjsmith.bsky.social · Aug 31

We also found that, if cell mixtures are pre-incubated in a liquid antibiotic that selects against T6SS attackers, this reduces the bias, especially for longer pre-incubation times.

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Will Smith @willpjsmith.bsky.social · Aug 31

We found that there was a strong, T6SS-dependent reduction in the number of E. coli c.f.u.s recovered, compared with the “”ground truth” densities we knew we should be getting (plotted here as a pink zone). The deviation tended to increase with increasing Attacker / Susceptible ratio.

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Will Smith @willpjsmith.bsky.social · Aug 31

We wondered how this would bias the results of a killing assay. We devised a "ground-truth" experiment where we mixed E. coli and A. baylyi in known ratios, before diluting and plating on selective media as per a regular killing assay, to see what c.f.u. counts we'd get back.

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Will Smith @willpjsmith.bsky.social · Aug 31

In other words, Kanamycin really isn’t quenching T6SS antagonism effectively in the aftermath of a killing assay, and so you’d predict that you’d get fewer E. coli CFUs as a result.

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Will Smith @willpjsmith.bsky.social · Aug 31

We found that T6SS-armed A. baylyi ADP1 bacteria (often used to study T6SSs), will transiently still fire their T6SS harpoons under lethal selective conditions. Here we see ADP1 killing some green E. coli when ADP1 is supposed to be dead!

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Will Smith @willpjsmith.bsky.social · Aug 31

Thinking about this in our own studies, we did some tests. Turns out that some antagonistic interactions, like those via harpoon-like Type 6 Secretion Systems (T6SSs), DON’T STOP just because cells are being selected against by lethal concentrations of antibiotic.

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Will Smith @willpjsmith.bsky.social · Aug 31

The problem is this: if one population is antagonising another, how do you STOP that antagonism happening when you plate cells on selective media? After all, biology doesn’t stop for our convenience!

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Will Smith @willpjsmith.bsky.social · Aug 31

Survival is then a read-out of competitive interactions: the lower the survival when populations are mixed c.f. control, the stronger the antagonism between them. Survival is often measured using c.f.u. counts on selective media.

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Will Smith @willpjsmith.bsky.social · Aug 31

Some background: competition assays are common in microbiology. You mix different populations of microbes (normally 2 types for simplicity), allow them to compete, and then measure how many cells survive from each population, compared with some control where the populations don’t interact.

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Will Smith @willpjsmith.bsky.social · Aug 31

Does your lab perform killing assays?
TL;DR: we’ve identified a problem that can bias the outcome of killing assays, making antagonism look stronger than it really is.
Adding a simple extra step can mitigate this bias!

Out now at #MicrobioJ www.microbiologyresearch.org/content/jour...

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Type VI secretion system activity at lethal antibiotic concentrations leads to overestimation of weapon potency

Competition assays are a mainstay of modern microbiology, offering a simple and cost-effective means to quantify microbe–microbe interactions in vitro. Here, we demonstrate a key weakness of this meth...

www.microbiologyresearch.org

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Reposted by Will Smith

The Royal Society @royalsociety.org · Aug 30

The Royal Society David Attenborough Award and Lecture 2025 is awarded to Dr Roger Highfield for a vast contribution to public engagement, reaching audiences of millions through journalism, broadcast, books and museum-led initiatives. https://royalsociety.org/medals-and-prizes/attenborough-prize/

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Reposted by Will Smith

Tracy Palmer @proftracypalmer.bsky.social · Jun 1

Check out our latest preprint! We show that the same antibacterial toxin requires different immunity proteins depending whether it’s intra or extracellular

bioRxiv Microbiology @biorxiv-microbiol.bsky.social · Jun 1

Distinct immunity protein families mediate compartment-specificneutralisation of a bacterial toxin https://www.biorxiv.org/content/10.1101/2025.05.31.657152v1

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Will Smith @willpjsmith.bsky.social · Jul 2

‪Well done @magdalenakurteu.bsky.social,
@matthewjshepherd.bsky.social,
@bexlowrypalms.bsky.social,
@flanagella.bsky.social‬,
Eric Chapman, Joy Hawley, Hannah Jones, Jeremy DeJardin and Logan Sauers!

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Will Smith @willpjsmith.bsky.social · Jul 2

Go Team! Deeply honoured that the MERMan lab reps won an @manchester.ac.uk‬ "FMBH heroes" award - thanks ‪@fbmh-uom.bsky.social‬ and @mermanchester.bsky.social for nominating us ❤️❤️❤️

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