I am glad to see this work in print & on the cover! Read more at academic.oup.com/genetics/article/228/3/iyae145/7747749

Really cool and clever study! We saw extensive core genome recombination in gut bacteria in recent work, and I’ve always wondered about the underlying mechanism -- phage-like elements seem like the best candidate. Your examples of LT and GTA are particularly striking.

Thanks for the kind words☺️

PS: after a long revision process, this paper has gotten much better but admittedly a bit long (with 41 SI figures 🙂). So don't hesitate to reach out if you have any questions!

See also Ben's thread on twitter when we first posted on biorxiv
x.com/benjaminhgoo...

(n/n)

and 2) global spread of particular sequences. (btw @rwolff.bsky.social and @nanditagarud.bsky.social recently found more evidence of global selective sweeps in these gut bacteria. www.biorxiv.org/content/10.1...)

We also found some evidence that many recombined segments are strongly selected, leading to 1) within-host sweeps

What might cause all these fine-scale variations? Many factors are commonly thought to impact realized recombination rate. Here we were able to rule out the effect of sequence divergence, which plays very little role in almost all gut species (Fig 4 & W in SI are probably my favorite figures)

We found extensive heterogeneity in the rates and lengths of recombination, both between species and within species.

However, that was only a coarse summary of recombination at the species level. Using closely related strains found in the dataset, we were able to directly identify individual recombination events.

Here are some highlights of what we found. First and foremost, gut bacterial species recombine quite a lot -- certainly closer to H pylori than to M tuberculosis, the two extremes in the microbial world when it comes to recombination

For example, do gut bacteria recombine on human-relevant timescales?
Do recombination events even matter for evolution (i.e. get selected), since it's only mixing existing genes?
What are the mechanisms responsible for this recombination?

So, there is a ton of work about HGT between species and how mobile elements hop around in this ecosystem. But genetic exchange also mixes up the core genome within a species, enabling bacteria to *recombine* like sexual organisms. Much less is known about recombination in gut bacteria: