Jesse Shapiro
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bjesseshapiro.bsky.social
Jesse Shapiro
@bjesseshapiro.bsky.social
1.8K followers 770 following 490 posts
Macrobe qui aime les microbes

http://www.shapirolab.ca/
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bjesseshapiro.bsky.social
Log bike
Photo of a bike with a bunch of firewood on the front rack and paniers on the back rack.
February 10, 2026 at 1:11 AM
bjesseshapiro.bsky.social
Why the link between HGT and co-occurrence?
1) Co-occurrence (physical proximity) drives HGT.
2) HGT drives co-occurrence?

Answer #1 is the classic, but I think #2 deserves attention: HGT of habitat-specific genes allows species sharing those genes to thrive in a habitat, and thus to co-occur.
5/n
There are at least two biological mechanisms that could underlie the general observation of an association between HGT and co-occurrence. First, taxa that are physically closer could simply have more opportunities for HGT, which must be true to some extent. For instance, taxa in completely isolated environments, with no gene flow or possibility of DNA transfer, cannot undergo HGT. In regions of the ocean stratified by geography, depth, and environmental factors, it is reasonable to expect that taxa would undergo HGT more frequently with other taxa sharing the same local environment. Second, an alternative causal explanation is that HGT of habitat-specific genes allows species sharing those genes to thrive in that habitat, and thus to co-occur. In this alternative explanation, co-occurrence is a proxy for unmeasured environmental variables that define cryptic microbial habitats. Distinguishing between these explanations for the observed associations is an avenue for future research, potentially harnessing time-series sampling to infer causal relationships. Although we cannot formally distinguish between these explanations, our results are consistent with both physical proximity driving HGT and, potentially, HGT contributing to shared niche preferences. We consistently found evidence for increased HGT among genomes in larger particle-associated filter fractions. This suggests that physical proximity on particles, in contrast to reduced encounter rates among planktonic prokaryotes enriched on the small filter fractions, could drive HGT. The larger filter fraction could also share common selective pressures, associated with a particle-attached lifestyle, which may also explain the association with HGT independently of physical proximity.
February 9, 2026 at 8:50 PM
bjesseshapiro.bsky.social
You can really see the tendency for HGT among genomes sampled from particle-associated fractions in this subset of Tara Oceans samples.

(4/n)
Breakdown of HGT and related feature prevalence across 43 Tara Oceans samples. The same biological samples are matched based on whether they were enriched for small or large particles based on the fraction filter (i.e. to enrich for free-living or particle-attached prokaryotes). The y-axis for all panels is the proportion of genomes in a sample with at least one instance of that category (e.g. the proportion of genomes in a sample with at least one gene identified to be either acquired or transferred through HGT). Asterisks indicate significant comparisons (adjusted P values <0.05) based on paired Wilcoxon tests.
February 9, 2026 at 8:45 PM
bjesseshapiro.bsky.social
Co-occurrence is the most important predictor of HGT, followed by phylogenetic distance. Genomes from particle-associated fractions of the water columns tend to share more genes, as do genomes sampled at similar depths, temperatures, salinity, etc. (3/n)
Coefficients in logistic regression model based on all pairwise genome comparisons. The response is whether those genomes have at least one called horizontal gene transfer event (based on the cluster-based approach) between them or not. Co-occurrence (based on the hypergeometric approach) is a binary variable indicating whether those genomes significantly co-occur. “Free-living” and “Free-living and particle-attached” indicate whether the genomes being compared are both enriched in samples filtered to enrich for small particles, or those with little or no size filters. The other variables are ordered quantile normalized continuous values. Variables with “diff.” represent the median inter-sample difference in each environmental variable for all samples encoding the two genomes being compared. Coefficient values less than 0 indicate that decreases in those variables are associated with increases in horizontal gene transfer, whereas a positive value represents the opposite. The intercept for this model was −14.35. Error bars represent 95% confidence intervals (1.96 × standard error). All variables were significant (P values <0.05) except for “small particle enriched”.
February 9, 2026 at 8:42 PM
bjesseshapiro.bsky.social
Reminder that it’s sometimes worth clicking the link in a cryptic email from Workday because maybe you have been promoted to Professor and didn’t realize till a week later…
Email from workday with subject: A task awaits you: review documents - update academic appointment… (what does it mean?!) Official letter from the Provost confirming my promotion to full professor. Fun detail: it is addressed to the lab where I did my undergrad honours project >20 years ago. McGill admin never forgets ;)
February 9, 2026 at 5:58 PM
bjesseshapiro.bsky.social
Olympic hockey on the big screen and soup simmering in the kitchen.
Photo of a projector screen showing a hockey faceoff between Swiss and Canadian women.
February 7, 2026 at 8:13 PM
bjesseshapiro.bsky.social
Montreal in February: we eat so much poutine that our dumpsters are overflowing with 180L vats of poutine sauce.

This message brought to you by Tourisme Montréal
A photo of a dumpster in a snowy alleyway with several large white buckets labelled “poutine Québecoise traditional sauce” strewn over the ground
February 5, 2026 at 2:32 PM
bjesseshapiro.bsky.social
Tonight’s film selection
Still shot of Catherine O’Hara and Eugene Levy in Best in Show
January 31, 2026 at 2:27 AM
bjesseshapiro.bsky.social
My neighbour is flying the Danish flag on our street. In Montreal, we know what’s up.
Danish flag flying from a flagpole on a red brick house facade.
January 17, 2026 at 8:56 PM
bjesseshapiro.bsky.social
First lab lunch of 2026! There’s not a lot to love about the year so far but getting to hang out with this cool gang on a daily basis keeps me going.
A selfie of a group of smiling people around a table
January 14, 2026 at 11:33 PM
bjesseshapiro.bsky.social
Anyone interested in discussing this opportunity to eat, drink, be merry and ski with me, my DMs are open!

(Oh yeah, and do some science to the tune of $1M/year x 8 years + $500k x 4 years)
Selfie of a bearded man in sunglasses and tuque grinning. He is in skis (not shown) with a snow-covered park in the background.
December 18, 2025 at 10:11 PM
bjesseshapiro.bsky.social
Allow me to introduce Dr. Sana Naderi !

Her thesis brilliantly followed SARS-CoV-2 evolution (1) within hosts, (2) across animal species, and (3) into wastewater (not necessarily in that order...)

1) doi.org/10.1093/ve/v...
2) elifesciences.org/articles/83685
3) doi.org/10.1101/2025...
Two people smiling and holding up golden goblets A newly minted PhD smiling and opening a bottle of sparkling wine.
December 18, 2025 at 8:43 PM
bjesseshapiro.bsky.social
Cleared bike path beside groomed ski path is the best of winter in Montreal
Photo of a winter scene with a groomed Nordic ski path running alongside.
December 13, 2025 at 4:27 PM
bjesseshapiro.bsky.social
How it’s going.
December 10, 2025 at 6:03 PM
bjesseshapiro.bsky.social
Perfect day for a winter BIXI!
Photo of a bixi bike share station covered in fluffy fresh snow
December 10, 2025 at 6:01 PM
bjesseshapiro.bsky.social
One of the highlights of #ASTMH2025: Introducing colleagues from around the world to Canadian bill-splitting technology. We are a world leader on this if nothing else.
A group of smiling people around a restaurant table.
November 11, 2025 at 3:32 PM
bjesseshapiro.bsky.social
If you’re at @astmh.bsky.social #ASTMH2025 check out our session today on Enteric Pathogen Genomics & Evolution (room 717, 16:30) featuring @ksbakes.bsky.social on Shigella, plus 2 other great talks on V. cholerae phages, and Salmonella!
November 10, 2025 at 2:04 PM
bjesseshapiro.bsky.social
Great view of the first snow of the season on the train from Montreal to Toronto for @astmh.bsky.social #ASTMH2025. Maybe in my lifetime this trip will take 3 hours instead of 5…
November 9, 2025 at 7:09 PM
bjesseshapiro.bsky.social
We heard the Kassen lab’s sequencer was being badly neglected so we have adopted it.

It’s being fed a healthy diet of high molecular weight DNA.

Will return it when your computer is fixed @reeskassen.bsky.social ;)
Two Oxford nanopore promethion sequencers sitting on a lab bench, each sequencing two flow cells each. One is labelled “Kassen” with red lab tape.
November 7, 2025 at 10:31 PM
bjesseshapiro.bsky.social
circular AI shrimp are decidedly cursed
Window of a takeout restaurant advertising pad thai with an AI-generated image of noodles with circular shrimp. It’s been defaced with the text “FUCK AI” in red marker.
October 26, 2025 at 5:11 PM
bjesseshapiro.bsky.social
Montreal scene
A mural of road cycling racers and the inclined tower of the Olympic stadium are illuminated by the golden light of the setting sun. In the foreground, orange cones casually delimit an intersection under construction.
October 14, 2025 at 10:26 PM
bjesseshapiro.bsky.social
Sabbatical planning: step 1.
A photo of a cycling map of France on a table beside a glass of beer on a table in a bar.
October 7, 2025 at 8:24 PM
bjesseshapiro.bsky.social
Hello October!
A corner grocery store with a plethora of pumpkins spilling out on the sidewalk, draped with fake cobwebs and other Halloween decorations.
October 1, 2025 at 12:29 AM
bjesseshapiro.bsky.social
Leaky pipes, happy trees!

www.montrealgazette.com/news/article...
September 25, 2025 at 11:46 PM
bjesseshapiro.bsky.social
The New Vic project @mcgill.ca is entering an exciting, noisy and rather smashy phase. Cool to watch but I’m glad my lab isn’t right across the street…
Photo of construction (and notably demolition of 1960s era wings) of the old Royal Victoria hospital
September 5, 2025 at 12:54 AM