Jesse M. Shapiro | Lightnews

Jesse Shapiro

@bjesseshapiro.bsky.social

1.8K followers 760 following 490 posts

Macrobe qui aime les microbes

http://www.shapirolab.ca/

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Jesse M. Shapiro is an American economist who has served as the George Gund Professor of Economics and Business Administration at Harvard University since 2022. He was previously the George S. and Nancy B. Parker Professor of Economics at Brown University from 2015 to 2019, and the Eastman Professor of Political Economy at Brown from 2019 to 2021. He received a MacArthur Fellowship in 2021. .. more

Economics 40%

Political science 16%

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Jesse Shapiro @bjesseshapiro.bsky.social · Jul 1

One of my favourite serendipitous results from the lab came about because we were long-read sequencing bacterial:

Vibrio cholerae, which is "supposed to" have TWO circular chromosomes (3 + 1 million base pairs) often has just ONE fused chromosome (4 Mbp).

www.nature.com/articles/s41...

(1/n)

Prevalent chromosome fusion in Vibrio cholerae O1 - Nature Communications

The pathogenic bacterium Vibrio cholerae typically has two circular chromosomes. Here, Cuénod et al. analyse 467 clinical isolates and identify several independent chromosome fusion events that are li...

www.nature.com

Reposted by Jesse M. Shapiro

Leducq Lab @leducq-lab.bsky.social · 8h

Our article on the dark matter in the #phyllosphere in Systematic and applied Microbiology!

#methylobacterium #lichenibacterium #lichenifustis #lichenihabitans and even more to discover in #Hyphomicrobiales (former Rhizobiales) inhabiting leave surfaces!

www.sciencedirect.com/science/arti...

A phylogenomic and metagenomic meta-analysis of bacterial diversity in the phyllosphere lifts a veil on hyphomicrobiales dark matter

The phyllosphere, or above-ground part of plants, hosts diverse bacterial communities that play critical ecological roles and provide beneficial funct…

www.sciencedirect.com

Jesse Shapiro @bjesseshapiro.bsky.social · 8h

Thanks Jason!

Jesse Shapiro @bjesseshapiro.bsky.social · 8h

Log bike

Photo of a bike with a bunch of firewood on the front rack and paniers on the back rack.

Jesse Shapiro @bjesseshapiro.bsky.social · 13h

Thanks Zam!

Jesse Shapiro @bjesseshapiro.bsky.social · 13h

Thanks Dor!

Jesse Shapiro @bjesseshapiro.bsky.social · 13h

Thanks!

Jesse Shapiro @bjesseshapiro.bsky.social · 13h

Merci mon ami!

Jesse Shapiro @bjesseshapiro.bsky.social · 13h

For anyone who has written a paper with all PIs and no trainee steering the ship... it's a fun and unique experience 😅

Thanks to @gmdouglas.bsky.social & @cyanophage.bsky.social for herding the cats and doing most of the work!

/fin

Jesse Shapiro @bjesseshapiro.bsky.social · 13h

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

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

Jesse Shapiro @bjesseshapiro.bsky.social · 13h

You can really see the tendency for HGT among genomes sampled from particle-associated fractions in this subset of Tara Oceans samples.

(4/n)

$Breakdown of HGT and related feature prevalence across 43 Tara Oceans samples. The same biological samples are matched based on whether they were enriched for small or large particles based on the fraction filter (i.e. to enrich for free-living or particle-attached prokaryotes). The y-axis for all panels is the proportion of genomes in a sample with at least one instance of that category (e.g. the proportion of genomes in a sample with at least one gene identified to be either acquired or transferred through HGT). Asterisks indicate significant comparisons (adjusted P values <0.05) based on paired Wilcoxon tests.$

Jesse Shapiro @bjesseshapiro.bsky.social · 13h

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”.

Jesse Shapiro @bjesseshapiro.bsky.social · 13h

The title kinda says it all: genomes that co-occur in the same ocean water samples tend to exchange more genes even after controlling for phylogeny (close relatives also tend to exchange more). This supports earlier work from @luispedrocoelho.bsky.social & co:
www.nature.com/articles/s41...

(2/n)

A global survey of prokaryotic genomes reveals the eco-evolutionary pressures driving horizontal gene transfer - Nature Ecology & Evolution

The authors analyse 8,790 prokaryotic pangenomes to identify the ecological variables associated with recent versus old horizontal gene transfer events, finding that gene transfers are more common amo...

www.nature.com

Jesse Shapiro @bjesseshapiro.bsky.social · 13h

Now out & nicely formatted in @isme-microbes.bsky.social

A big analysis of ocean genomes & metagenomes co-led by former postdocs, now PIs, @gmdouglas.bsky.social & @cyanophage.bsky.social along with co-PIs @lbobay.bsky.social & Samuel Chaffron.

A few highlights... 🧵 (1/n)

doi.org/10.1093/isme...

Co-occurrence is associated with horizontal gene transfer across marine bacteria independent of phylogeny

Abstract. Understanding the drivers and consequences of horizontal gene transfer (HGT) is a key goal of microbial evolution research. Although co-occurring

doi.org

Jesse Shapiro @bjesseshapiro.bsky.social · 14h

Thank you :)

Jesse Shapiro @bjesseshapiro.bsky.social · 15h

Thank you Rich!

Jesse Shapiro @bjesseshapiro.bsky.social · 15h

Thanks Willem!

Jesse Shapiro @bjesseshapiro.bsky.social · 15h

Thanks Aldert!

Jesse Shapiro @bjesseshapiro.bsky.social · 15h

Thanks Tami!

Reposted by Jesse M. Shapiro

Toula Drimonis @mtltoula.bsky.social · 15h

“In a historic first, Canada’s hockey delegation won’t have anyone from Quebec, where the game was born, where kids are raised to bask in the memory of Les Glorieux, & where the legacy of 24 Stanley Cups acts as a unifying force, transcending language & politics.”
thewalrus.ca/quebecs-olym...

End of an Era: Quebec Has No Hockey Players at the Olympics | The Walrus

It’s a moment of collective mourning

thewalrus.ca

Jesse Shapiro @bjesseshapiro.bsky.social · 15h

Thanks Ellinor!

Jesse Shapiro @bjesseshapiro.bsky.social · 15h

Thanks Dave!

Jesse Shapiro @bjesseshapiro.bsky.social · 15h

Doing my best to age gracefully... (mostly by keeping the profile pic updated to show the beard getting grey in real time)

Jesse Shapiro @bjesseshapiro.bsky.social · 15h

Thanks Melanie!

Jesse Shapiro @bjesseshapiro.bsky.social · 16h

Cryptic and universal indeed! Worth clicking 1 in 10 ;)

Jesse Shapiro @bjesseshapiro.bsky.social · 16h

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 ;)

Reposted by Jesse M. Shapiro, Simon Roux

Jay T Lennon @jaytlennon.bsky.social · 16h

www.growkudos.com/publications...

New work with @ckarakoc.bsky.social and @shoestrapped.bsky.social in @pnas.org

The hidden energy cost of cellular dormancy

Many organisms survive harsh environments by switching into special survival modes. Some bacteria do this by forming spores—dormant, highly resilient cells that can persist for years or even centuries...

www.growkudos.com

Reposted by Jesse M. Shapiro

André Picard @picardonhealth @picardonhealth.bsky.social · 17h

Most of the world doesn’t require a prescription for oral contraceptives. Why do Canadians still need one? Newer pills are safer — but Canada's health system still requires doctors to sign off. www.cbc.ca/news/health/... via @cbcnews.ca

Why do Canadians need a prescription for birth control when most of the world doesn't? | CBC News

Some Canadian doctors say patients on birth control need monitoring. But medical authorities in other countries increasingly disagree.

www.cbc.ca

Reposted by Jonathan A. Eisen, Jesse M. Shapiro

Zamin Iqbal @zaminiqbal.bsky.social · 18h

A long time ago in a galaxy far away, there was a SARS-CoV-2 pandemic. Our paper, led by @martibartfast.bsky.social
a) correcting errors in 4.5 million genomes & their phylogeny
b) improving representation of the Global South in public data
www.nature.com/articles/s41...
(thread 1/n)

Addressing pandemic-wide systematic errors in the SARS-CoV-2 phylogeny - Nature Methods

This Resource paper presents a global SARS-CoV-2 phylogenetic tree of 4,471,579 high-quality genomes consistently constructed by Viridian, an efficient amplicon-aware assembler.

www.nature.com

Reposted by Jonathan A. Eisen, Jesse M. Shapiro, Alan McNally

John Lees @johnlees.bacpop.org · 23h

How do bacterial pangenomes evolve, what controls their dynamics, why do they exist?
Fitting a mechanistic model to 450 species from allthebacteria.org suggesting fast vs slow gene exchange (i.e. amount of MGEs) is a major differentiating factor, correlated with phylogeny rather than lifestyle

Proportion of fast genes, as a trait mapped on the bacteria-wide phylogeny

Jesse Shapiro @bjesseshapiro.bsky.social · 2d

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.

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