Jesse Shapiro
@bjesseshapiro.bsky.social
📤 1832
📥 807
📝 563
Macrobe qui aime les microbes
http://www.shapirolab.ca/
pinned post!
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...
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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
https://doi.org/10.1093/ismejo/wraf275
4 months ago
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McGill University
1 day ago
Convocation season is officially ON 🎓✨ Big smiles, proud moments, and the start of something new! Congratulations to all
#McGillGrads
of the Class of 2026! 🎉
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Jonathan Eisen
3 days ago
A very important preprint to check out: The holobiont is not a useful model for most host-microbiome interactions By Gavin M Douglas an S. Andrew Inkpen
ecoevorxiv.org/repository/v...
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The holobiont is not a useful model for most host-microbiome interactions
https://ecoevorxiv.org/repository/view/13115/
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Sara Mitri
6 days ago
Check out our pre-print led by the fantastic Massimo Amicone, collaborating with the Bollenbach lab!
tinyurl.com/4h9p8mfb
We build a simple intuition on how ecological interactions affect resistance evolution by expanding evolutionary rescue theory and testing it with two large sets of experiments
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https://tinyurl.com/4h9p8mfb
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Lab retreat: dumplings, hike, camp fire. My gang are the best!
5 days ago
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Britt Koskella
8 days ago
Please share widely! Abstract submissions open for the 2026 Jacques Monod conference: Ecology and evolution of host-parasite interactions in a changing world! Held in beautiful Roscoff France from November 2- 6, 2026. Abstracts submission deadline : June 6
cjm.sb-roscoff.fr/en/conferenc...
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Ecology and evolution of host-parasite interactions in a changing world | CNRS - Conférences Jacques Monod (CJM)
https://cjm.sb-roscoff.fr/en/conference/ecology-and-evolution-host-parasite-interactions-changing-world
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Ponto
9 days ago
La ville est hockey! 💙🤍❤️ The city is hockey!
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And a good afternoon too!
add a skeleton here at some point
12 days ago
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/r/Habs
13 days ago
Good morning to Habs fans and Habs fans only 🌞
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Zach LaTurner
13 days ago
The paper on my Ph.D. work is fully online! We used a ribozyme that barcodes 16S rRNA to track the transduction range of phage P1 in a synthetic community and real wastewater communities, while diving deeper into the unique range conferred by P1s two tail fibers.
www.nature.com/articles/s41...
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Cross-order detection of bacteriophage transduction in microbial communities using RNA barcoding - Nature Communications
Bacteriophages are the most abundant life form on earth and can be applied to eliminate or engineer bacteria. Here, authors demonstrate RNA barcoding as a high throughput tool to measure bacteriophage...
https://www.nature.com/articles/s41467-026-70995-y
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Salvador Almagro-Moreno
13 days ago
Delighted to see our work recently published in
@natcomms.nature.com
! In our article we describe a small RNA with a unique modular structure that shapes the evolution of toxigenic Vibrio cholerae.
www.nature.com/articles/s41...
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Modular small RNA drives the emergence of virulence traits and environmental trade-offs in Vibrio cholerae - Nature Communications
In this work, authors describe a modular small RNA that drives the emergence of virulence traits in the cholera pathogen. It controls key colonization phenotypes, acting as the functional surrogate of...
https://www.nature.com/articles/s41467-026-73137-6
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Jesse Shapiro
Aidan McGlynn
14 days ago
Never forget:
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Will Ratcliff
15 days ago
1/23 New preprint! Been thinking about the origin of cellular life. Specifically, how protocells (or *any* compartments) just aren't enough to support the evolution of increasingly complex cells. You gotta de-Darwinize the parts! The ribosome/genome do this.
www.biorxiv.org/content/10.6...
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https://www.biorxiv.org/content/10.64898/2026.05.06.723269v2.full.pdf
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Ellinor Alseth
14 days ago
When is an antiphage mechanism an evolved defence adaptation? This question has been on my mind for so long, because despite the field’s rapid progress there is currently no widely agreed framework in place to answer it. So
@brownlab.bsky.social
and I wrote this, and I'm happy to share the preprint!
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The bacterial immune system: identifying evolved defense adaptations
https://ecoevorxiv.org/repository/view/12974/
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Naturally the poster session at the *Canadian* Society for Ecology and Evolution takes place on a hockey rink…
@csee-sceemtgs.bsky.social
#CSEE
14 days ago
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Jesse Shapiro
Type VI Sophia System
14 days ago
News & views piece just dropped from
@indragon.bsky.social
and
@billhanage.bsky.social
discussing some of the coolest work I've read all year! Phages shaping cholera epidemiology AND experimental evolution mirroring the real-world evolution is 🔥 (Kim Seed also gives an amazing talk!)
rdcu.be/fihkG
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Luís M. Silva
15 days ago
Into transmission? Super spreaders? Super shedders? Which traits actually predict disease spread or secondary hosts’ infection outcomes? 🦠 🤧 Come check out my talk at
#CSEE
tomorrow (Wednesday 13th) at 4pm in Room BA-2165 👀
@csee-sceemtgs.bsky.social
@csee-scee.bsky.social
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Rebecca Shapiro
16 days ago
It's been a long time coming to finally see this in print! While not the first paper from my lab, it is one of the very first projects we started working on from day 1
links.springernature.com/f/a/1IP7gCfA...
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Pooled CRISPRi screening reveals fungal-specific drug target candidates - Nature Microbiology
This study presents a pooled CRISPRi screening approach in Candida albicans to investigate essential genes at scale, revealing environment- and strain-dependent gene sensitivities and conserved vulner...
https://links.springernature.com/f/a/1IP7gCfAK_4IvrBY6WGd-A~~/AABE5hA~/sDloX8m24Rtgm_hufqkkRfVugnI34K3sy7oh2G9IuewMYtUYxNWcLeRmgd4AG02LecFE-2w9xs8qLhmuasqUxHLkPUtg_-Cdf1UV7ALemHxg1OtkgYwkVXObelo-H0uwm1kQPK5EDKvYrYYdHCPFTBk86XP8SZhpy2EHxW60NoucP0OBjxq8lb4X62-W9VGn7pNsQASF89W4jISls6WaKP734B2Zp-lDO5rbLV3x5AFJ2rvLb8DK66KPSIZeEBsnDgVQWVrrphGQFNkzRMAIO8ms4BtHUadiGaHHzVKYqZQ~
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#SCEECSEE20
here I come!
16 days ago
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ArtButMakeItSports
17 days ago
La République, Honoré Daumier, 1848
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2022
350
#GoHabsGo
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17 days ago
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And they said I didn’t need a front rack for my bike
18 days ago
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Grant writing. You can tell which paragraphs were harder to write by measuring the cappuccino rings.
19 days ago
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Sarah Dorner
21 days ago
Our latest paper: "Automated β-D-glucuronidase activity monitoring for identification of combined sewer overflows driving microbial water quality degradation". Félicitations Luan!
doi.org/10.1016/j.wr...
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Jesse Shapiro
Youssef El Mouali
21 days ago
New paper out in
@cp-cellhostmicrobe.bsky.social
! Microbes evolving with modern lifestyles 🧬🦠 S. copri uses PerR to manage oxygen stress, but some strains acquired OxyR via HGT, boosting oxygen tolerance. These strains are enriched in industrialized populations.
www.cell.com/cell-host-mi...
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Biogeography-associated emergence of enhanced oxygen tolerance in the abundant human gut commensal Segatella copri
El Mouali and Tawk et al. characterize the oxygen-tolerance response in the human gut-residing bacterium Segatella copri. They identified a subset of strains that acquired an additional oxygen regulat...
https://www.cell.com/cell-host-microbe/fulltext/S1931-3128%2826%2900162-9
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Martin Polz
21 days ago
Very excited to share our new paper out in Nature. Congrats to Xiaoqian (Annie) Yu and all the coauthors.
www.nature.com/articles/s41...
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Genome-wide sweeps create ecological units in the human gut microbiome - Nature
Genome-wide selective sweeps commonly occur in the human gut microbiome and can spread across the world within decades to produce epidemic-like population structures.
https://www.nature.com/articles/s41586-026-10476-w
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Noah Fierer
21 days ago
New pre-print out - we sought to determine if Antarctic soil bacteria are really endemic to the continent. Would love feedback.
www.biorxiv.org/content/10.6...
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Evidence for endemism and local adaptation in Antarctic soil bacteria
Antarctic soils represent one of the more extreme environments for microbial life on Earth, yet they harbor heterogeneous and diverse microbial communities. Biologists have long hypothesized that Antarctic microorganisms are unique from those found on other continents due to the extreme geographic isolation and the cold, dry, and challenging conditions typical of Antarctica. To test this hypothesis, we focused on a cosmopolitan bacterial genus, Arthrobacter, that is widely distributed across global soils. We first profiled a global metagenomic dataset from both Antarctic and non-Antarctic surface soils to quantify the distributions of Arthrobacter strains. Despite high strain-level diversity, 90% of the strains found in the Antarctic soils were only found on the continent. We then used cultivation-based phenotypic analyses and strain-level genomic comparisons to assess how Antarctic strains and non-Antarctic strains differ in their traits and environmental preferences. Not only did we find evidence of endemism, but Antarctic Arthrobacter also have genomic characteristics and environmental tolerances that suggest they are uniquely adapted to Antarctic conditions. ### Competing Interest Statement The authors have declared no competing interest. U.S. National Science Foundation, NSF 21-567, EAR 1950681 Australian Research Council, FT240100502, DE250101210
https://www.biorxiv.org/content/10.64898/2026.05.01.722257v1
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Andrew Roger
21 days ago
IQ-TREE 3: Phylogenomic Inference Software using Complex Evolutionary Models
academic.oup.com/mbe/article/...
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IQ-TREE 3: Phylogenomic Inference Software using Complex Evolutionary Models
Abstract. IQ-TREE (https://iqtree.github.io/) is a widely used open-source software tool for efficiently inferring phylogenetic trees under maximum likelih
https://academic.oup.com/mbe/article/doi/10.1093/molbev/msag117/8669857
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Nandita Garud
21 days ago
Our paper entitled "The persistence and loss of hard selective sweeps amid admixture in ancient Eurasians" is now out in PNAS!
www.pnas.org/doi/abs/10.1...
. A really fun and informative collaboration with
@mharris.bsky.social
, Ziyi Mo and Adam Siepel. (1/n)
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The persistence and loss of hard selective sweeps amid admixture in ancient Eurasians | PNAS
The extent to which human adaptations have persisted throughout history despite strong eroding demographic events such as admixture, genetic drift,...
https://www.pnas.org/doi/abs/10.1073/pnas.2528672123
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Jesse Shapiro
Kristian G. Andersen
21 days ago
Since there's taboo around this, suggesting that cases of Andes virus may be caused by human-to-human transmission on a cruise ship is entirely uncontroversial: 1️⃣ We already know it's able to. 2️⃣ Conditions are "optimal". 3️⃣ This doesn't change the fact that a larger outbreak is extremely unlikely.
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Tom Flood
22 days ago
so sorry.
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John Lees
22 days ago
New work on using transformers (using gene order) for tasks in genomic epidemiology:
www.biorxiv.org/content/10.6...
We trained BART models (w/ extended context windows) on E.coli and S.pneumo from AllTheBacteria and tested if the model could find new strains, insertions (blaCTX-M) and co-selection
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Jesse Shapiro
Lucas Eckert
22 days ago
How useful can
#herbarium
collections be for genetic monitoring? 🌿 We show that Earth’s currently digitized herbarium specimens can be clustered into HUNDREDS OF THOUSANDS of historical “populations” suitable for population genetic studies 🔗
doi.org/10.1093/bios...
🧵
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The utility of herbarium collections for genetic monitoring
Abstract. Despite growing evidence of widespread genetic responses to anthropogenic activity, data shortfalls constrain genetic monitoring efforts and prec
https://doi.org/10.1093/biosci/biag048
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Jesse Shapiro
Montreal Gazette
22 days ago
Lack of bike lane contributed to cyclist’s death on Parc Ave., Quebec coroner says
montrealgazette.com/news/lack-of...
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Jesse Shapiro
Marie-Eve VAL
24 days ago
This one means a lot. Our paper, “Large extrachromosomal replicons are widespread across bacterial lineages and show coordinated replication termination and spatial coupling with the chromosome,” is out!
doi.org/10.1038/s414...
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Large extrachromosomal replicons are widespread across bacterial lineages and show coordinated replication termination and spatial coupling with the chromosome - Nature Communications
Bacterial genomes often include extrachromosomal replicons, ranging from small plasmids to chromosome-scale replicons. Here, Czarnecki et al. analyse more than 40,000 complete bacterial genomes and sh...
https://doi.org/10.1038/s41467-026-72671-7
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Jesse Shapiro
Stephen Turner
25 days ago
Free and open-source images, icons, and tools for creating scientific illustrations
doi.org/10.59350/5zt...
🧪
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Free and open-source images, icons, and tools for creating scientific illustrations
Phylopic, NIH Bioart, Bioicons, Scidraw, Open Science Art, Health Icons, Servier Medical Art, Biodiversity Heritage Library, the Noun Project, Segment Anything, Excalidraw, draw.io, Biographics
https://doi.org/10.59350/5zttj-fay97
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Lucas Eckert
24 days ago
Second preprint from my PhD! Using our whole lake transplant experiment in Alaska 🏔️ we test for assortative mating following secondary contact among divergent stickleback populations 🐟 and found the opposite of what we expected… 🔗
www.biorxiv.org/content/10.6...
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Simon Fisher
25 days ago
Been training for this moment my whole life.
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Tera Levin
25 days ago
Bacterial immune proteins have repeatedly evolved to become parts of eukaryotic immunity. But how? Our new preprint uncovers a recent horizontal transfer event & shows how eukaryotes co-opted a toxic bacterial immune protein 🦠🧪🧵 1/
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Lifelong Habs fan here and I’m loving the ongoing Habs Friendship Tour. Impeccable vibes. 100%, no notes.
#GoHabsGo
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26 days ago
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Michael Brockhurst
27 days ago
Why does antibiotic resistance evolution vary between patients? Come to
@officialuom.bsky.social
@mermanchester.bsky.social
to help us find out! 2.5 year
@wellcometrust.bsky.social
postdoc position in experimental evolution Closing 15 May. Apply here:
www.jobs.manchester.ac.uk/Job/JobDetai...
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Research Associate in Microbial Evolution:Oxford Road
https://www.jobs.manchester.ac.uk/Job/JobDetail?JobId=34868
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Richard Lenski
27 days ago
The Barrick & Lenski Labs in Dept of Microbiology, Genetics, & Immunology at Michigan State Univ seek a Research Assistant II to manage their research operations and participate in projects related to microbial evolution and synthetic biology. See details below.
careers.msu.edu/jobs/researc...
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Research Assistant II - East Lansing, Michigan, United States
Position Summary The Barrick and Lenski Labs in the Department of Microbiology, Genetics, & Immunology at Michigan State University are seeking a Research Assistant II to manage their research ope...
https://careers.msu.edu/jobs/research-assistant-ii-east-lansing-michigan-united-states-8725dfd6-64b7-402d-b34a-daac3a7d968d
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because they are part of our cultural heritage? Someone call UNESCO
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27 days ago
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Vaughn Cooper
27 days ago
Delighted this significant microbial ecology study related to climate change appears in the
@asm.org
flagship journal mBio
@mbio.bsky.social
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Christian Landry
27 days ago
This is how serious we are about our national sport and the best professional sport franchise ever!
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Teppo Hiltunen
28 days ago
New results from our synthetic communities, antibiotics & resilience project: Eco-evolutionary dynamics and environmental detoxification jointly shape bacterial community response to antibiotic perturbation
www.biorxiv.org/content/10.6...
Work led by
@jcairns.bsky.social
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https://www.biorxiv.org/content/10.64898/2026.04.27.721019v1
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McGill School of Population and Global Health
28 days ago
We are pleased to announce that Professor Mona Nemer (
@chiefscican.bsky.social
), Chief Science Advisor of Canada, will deliver the 2026 Dzau Lecture, titled: "Evidence, Trust, and Collaboration: Science Advice for Global Health". Join us on May 11! Learn more & RSVP at
www.mcgill.ca/spgh/channel...
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Turning on Seinfeld to wind down. Phew.
#GoHabsGo
28 days ago
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Asher Leeks
30 days ago
We're recruiting! We're looking for two graduate students to join us at UBC in Vancouver. Fully funded and open to global applicants, with flexible start-date. Topics include theory, bioinformatics, and microbiology. More details:
asherleeks.com/apply
#socialviruses
#evosky
#virosky
🧪
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Yan Shao
30 days ago
Great to see TRACS out in press - a new metagenomic strain transmission tool, led by
@gerrythill.bsky.social
. With improved precision and sensitivity, and unique support for custom reference and minor-strain detection, TRACS enables more rigorous and comprehensive strain-level metagenomics analysis.
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