Jesse Shapiro
@bjesseshapiro.bsky.social
📤 1769
📥 761
📝 485
Macrobe qui aime les microbes
http://www.shapirolab.ca/
pinned post!
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)
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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...
https://www.nature.com/articles/s41467-025-60699-0
7 months ago
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Leducq Lab
about 6 hours ago
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...
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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…
https://www.sciencedirect.com/science/article/pii/S0723202026000056?via%3Dihub
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Log bike
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about 7 hours ago
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André Picard @picardonhealth
about 15 hours ago
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
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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.
https://www.cbc.ca/news/health/canada-prescription-birth-control-9.7074160
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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
about 12 hours ago
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Les Perreaux
about 13 hours ago
Too add one more layer of cause to this fine piece, every time I tell my friends in the rest of the country that the total fees for my three kids playing minor hockey in Montreal came to less than $1,500, they fall out of their chairs. +
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Jay T Lennon
about 14 hours ago
www.growkudos.com/publications...
New work with
@ckarakoc.bsky.social
and
@shoestrapped.bsky.social
in
@pnas.org
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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...
https://www.growkudos.com/publications/10.1073%25252Fpnas.2524274123/reader
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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…
about 14 hours ago
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Zamin Iqbal
about 17 hours ago
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)
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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.
https://www.nature.com/articles/s41592-025-02947-1
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John Lees
about 21 hours ago
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
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Olympic hockey on the big screen and soup simmering in the kitchen.
2 days ago
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Jesse Shapiro
Daniel Bolnick
4 days ago
New preprint from our big collaborative evolution experiment in 9 whole lakes in Alaska, written by McGill grad student
@lucaseckert.bsky.social
www.biorxiv.org/content/10.6...
What happens if you put a mixture of multiple source populations together to complete & evolve in multiple new lakes?
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Stephen Heard
3 days ago
Excellent classification.
xkcd.com/3204/
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Dinosaurs And Non-Dinosaurs
https://xkcd.com/3204/
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BF Francis Ouellette
4 days ago
This is the final week to submit your abstract to the Canadian Bioinformatics Hub Conference 2026 |
#ActNow
#Bioinformatics
#OpenScience
#Toronto
#Canada
#GreatScience
🧬 🖥️ 🧪 🔓 ⬇️
www.iscb.org/cbhc2026/
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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
5 days ago
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Paul Turner Lab
5 days ago
How does population density affect evolutionary trajectory? Microbes construct their own niche which in turn reshapes their evolution. Preprint drop from grad student
@noahhoupt.bsky.social
whose evolution experiments featured blue/white colonies, 1000 generations, a lab move, and much more!
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Dave Baltrus 🦦
6 days ago
Hey y’all, New paper out from the lab in Microbial Genomics, starting down the rabbit hole of IS elements in Paeudomonas syringae
www.microbiologyresearch.org/content/jour...
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Independent, ongoing clade-specific expansions of IS5 elements in Pseudomonas syringae
Insertion sequence (IS) elements are transposable regions of DNA present in a majority of bacterial genomes. It is hypothesized that differences in distributions of IS elements across bacterial strain...
https://www.microbiologyresearch.org/content/journal/mgen/10.1099/mgen.0.001613
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How your email finds me today
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7 days ago
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Jonathan Eisen
8 days ago
Rereading these two papers: Holes in the hologenome: why host-microbe symbioses are not holobionts.
journals.asm.org/doi/10.1128/...
The Hologenome Concept: Helpful or Hollow?
journals.plos.org/plosbiology/...
And I still find myself in general agreement with most of the points in them
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Holes in the Hologenome: Why Host-Microbe Symbioses Are Not Holobionts | mBio
ABSTRACT The advent of relatively inexpensive tools for characterizing microbial communities has led to an explosion of research exploring the diversity, ecology, and evolution of microbe-host systems...
https://journals.asm.org/doi/10.1128/mbio.02099-15
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Montreal Gazette
9 days ago
Anti-ICE demonstration being held in downtown Montreal Sunday
montrealgazette.com/news/local-n...
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Isabel
10 days ago
People always say, “oh, but what if ‘zero tolerance for sex pests’ gets earth’s rare geniuses fired?!?” as though many of these manipulative creeps haven’t also manipulated their way into professional positions far above their skill level…
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Tonight’s film selection
10 days ago
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Jesse Shapiro
Oliver Moore
11 days ago
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Laurie Belcher
12 days ago
Calling all OrthoFinder users! We’ve just released GLADE, a tool to infer gene gains, losses, duplications, and ancestral genomes across a phylogeny. GLADE runs directly on OrthoFinder results.
www.biorxiv.org/content/10.6...
github.com/lauriebelch/...
(1/10)
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https://www.biorxiv.org/content/10.64898/2026.01.27.702036v1
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Keith Robison
15 days ago
ONT Axes P2 Solo, Roiling Community 🧬🖥️
omicsomics.blogspot.com/2026/01/ont-...
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ONT Axes P2 Solo, Roiling Community
Oxford Nanopore has a serious case of user community unrest, triggered by the announcement that the P2 Solo (aka P2s) will be phased out sta...
https://omicsomics.blogspot.com/2026/01/ont-axes-p2-solo-roiling-community.html?m=1
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Jesse Shapiro
Bruce Springsteen
13 days ago
I wrote this song on Saturday, recorded it yesterday and released it to you today in response to the state terror being visited on the city of Minneapolis. It’s dedicated to the people of Minneapolis, our innocent immigrant neighbors and in memory of Alex Pretti and Renee Good. Stay free
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Bruce Springsteen - Streets Of Minneapolis (Official Audio)
YouTube video by Bruce Springsteen
https://youtu.be/wWKSoxG1K7w?si=7ciYwNLv34RrdD1p
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Nonia Pariente
13 days ago
The names of 72 female scientists will be added to the Eiffel Tower, to accompany those of 72 male scientists that are already engraved there
tinyurl.com/e2satnyp
👏👩🔬 🧪
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Locutus Tips
13 days ago
Locutus movie pick: The Breakfast Club. Five unique individuals discover that they are essentially the same and can be used as interchangeable components of a collective.
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Michael Hendricks 🇨🇦
14 days ago
I was maybe 2.5 years into my position as an Assistant Professor when my phone rang, and it was Kirsty Duncan, the new federal science minister, calling out of the blue. I had never met her. She asked me what she could do for early career investigators. /1
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Pleuni Pennings
20 days ago
Made a drawing to explain what a soft sweep is (and a hard sweep) in the context of drug resistance evolution in a viral population within a person's body. Anyone teaching about selective sweeps? Feel free to use.
#populationgenetics
#HIV
#drugresistance
#evolution
#PopulationGenomics
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Jesse Shapiro
MSU MGI
18 days ago
Vaughn Cooper’s new Scientific American article offers a clear look at the potential threats posed by mirror‑life. He trained with MGI's Rich Lenski
@relenski.bsky.social
, whose contributions to the field are referenced in the piece. Important context for a complex topic.
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Jesse Shapiro
Zamin Iqbal
18 days ago
Thread!
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Jesse Shapiro
Paul Carini
19 days ago
Excited to see this published! A big part of why SAR11 is so tricky to grow like "normal" microbes.
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Cool study showing in exquisite details what every parent of kids in daycare already knows...
add a skeleton here at some point
19 days ago
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Jesse Shapiro
Alex Crits-Christoph
20 days ago
Sad to hear that Oxford Nanopore wants to discontinue the P2Solo later this year in favor of the P2i (the very pricey P2Solo that comes with a GPU to do the basecalling in it) It feels like such a big step in the wrong direction. They are a great sequencing company, not a great GPU upseller...
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nanoporetech-customers - Sign In
https://community.nanoporetech.com/posts/product-update-p2
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Jesse Shapiro
A. Murat Eren (Meren)
21 days ago
We just released
#anvio
v9, "eunice" 🎉 This version represents over 2,000 changes in the codebase since v8, increasing the total number of programs in the anvi'o ecosystem to 176. Read the release notes:
github.com/merenlab/anv...
Visit our up-to-date web page:
anvio.org
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unraveled
22 days ago
God bless the United States of Minnesota
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Jesse Shapiro
Christian Landry
21 days ago
Another way in which Denmark is helping the US!
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Jesse Shapiro
Luís M. Silva
23 days ago
Call for abstracts ENDS MONDAY!! details below :)
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Jesse Shapiro
Oh The Urbanity!
23 days ago
Montreal’s snow removal operation — snow is trucked away from streets to snow dumps — is really effective. But also *expensive*. Each centimetre collected across the city costs $1 million. An operation collecting 15 cm of snow costs $15 million. The city does it about half a dozen times a year.
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Steven Salzberg
25 days ago
very sad news. Peer Bork was one of the leaders of our field, a wonderful scientist, and he's much too young to be gone.
www.embl.org/news/embl-an...
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In remembrance of Peer Bork | EMBL
EMBL and its community are deeply saddened by the death of Peer Bork, the organisation’s Interim Director General.
https://www.embl.org/news/embl-announcements/in-remembrance-of-peer-bork/
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Rachel M. Wheatley
26 days ago
🚨4-year fully funded PhD in the lab of
@magicmicrobe.bsky.social
(& collaborating with me!): How does iron availability shape the ability of pathogens to invade the gut microbiome? Apply by Jan 26th Advert:
research.reading.ac.uk/foodbiosyste...
How to apply:
research.reading.ac.uk/foodbiosyste...
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https://research.reading.ac.uk/foodbiosystems/wp-content/uploads/sites/145/2025/12/FBS2026-69-Sharp-rq-AD.pdf
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Trying to keep these vibes in my heart and mind as I digest (yet another!) rejected grant.
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25 days ago
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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.
26 days ago
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Chris MacQuarrie
27 days ago
Peer Review is broken because a generation of Editors were trained that peer review is sacrosanct. Thus we have Editors who are clerks, sending and re-sending manuscripts to reviewers until they are happy. That's not the job. Be an Editor, not a clerk. Use your skill and judgement. Make decisions.
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Guillaume Larocque
28 days ago
Our new paper on BON in a Box is out! 📦 This project has high ambitions: linking biodiversity science to meaningful policy, transforming messy data into useful metrics. 🐝 🌳 📊 💡 Our vision is to make biodiversity science more user friendly, powerful and accessible!
academic.oup.com/bioscience/a...
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BON in a Box: An Open and Collaborative Platform for Biodiversity Monitoring, Indicator Calculation, and Reporting
Abstract. The Convention on Biological Diversity’s Kunming–Montreal Global Biodiversity Framework (GBF) sets ambitious goals to protect and restore biodive
https://academic.oup.com/bioscience/advance-article/doi/10.1093/biosci/biaf189/8424339?utm_source=authortollfreelink&utm_campaign=bioscience&utm_medium=email&login=true
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Joshua Weitz
29 days ago
Viruses transform microbes, populations, & ecosystems. In new work jointly led w/@tn-marine-micro.bsky.social + more, we find a link between enhanced viral infection and productivity 50 meters below the surface in the otherwise nutrient limited Sargasso Sea. a 🧵
www.nature.com/articles/s41...
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Locutus Tips
2 months ago
Locutus safety tip: To prevent identity theft, avoid having your own identity.
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Very cool paper, and I look forward to the fight with the copy editor about whether it should be "deletion-born fusions" or "deletion-borne fusions"! (I think both could work?!)
add a skeleton here at some point
about 1 month ago
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Jesse Shapiro
/r/Habs
about 1 month ago
There’s no place in the NHL like the Bell Centre in Montreal. Just listen to the Habs crowd on Alexandre Texier’s hat trick goal 🔥
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Vaughn Cooper
about 1 month ago
🚨Call for papers🚨 Microbial Evolution: Impacts on Human Health in the society journal Evolution, Medicine, and Public Health Guest Editors: Bob Woods, Silvie Huijben & Camilo Barbosa EIC: me This will be great, please submit and share!
academic.oup.com/emph/pages/m...
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