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Jesse Shapiro

@bjesseshapiro.bsky.social
1.9K followers 865 following 672 posts

Macrobe qui aime les microbes www.shapirolab.ca

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Reposted by Jesse Shapiro
Paul Hoskisson 🧫 🦠🐸 @paulhoskisson.bsky.social · 4h
this is such a cool paper - Microbial community dynamics in a traditional Swiss mountain cheese over 142 years of cheesemaking www.cell.com/current-biol...
cell.com
Microbial community dynamics in a traditional Swiss mountain cheese over 142 years of cheesemaking
How did modernizing cheesemaking change the microbes inside the cheese? By sequencing preserved traditional Alpine cheese wheels spanning 142 years from a single Alpine dairy, Somerville et al. trace ...
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Richard Sever @richardsever.bsky.social · 03/10/2026
As AI increases both productivity & ease of creating slop, there's a big challenge for those of us disseminating science. This from @pracheeac.bsky.social is an essential read. [disclaimer: she & I've spent 10+ years a̶r̶g̶u̶i̶n̶g̶ ̶a̶b̶o̶u̶t̶ discussing this stuff] 1/n pracheeac.substack.com/p/arxiv-is-k...
pracheeac.substack.com
arXiv Is Killing Itself So AI Doesn't Have To
Disclosure: I ranted to Claude with a bunch of my grievances and ideas, and had it organize them into this blog post.
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Reposted by Jesse Shapiro
Alexander Harms @aharms485.bsky.social · 19h
Cover image alert 🎨🚨👇🏼 - check out the amazing drawing of Sophia Zimmermann from our group in Nature Microbiology @natmicrobiol.nature.com ! Fun fact: Sophia initially drew it as a present to Dorentina @humollidorentina.bsky.social when we celebrated her recent paper on TnSeq with phages 🥂😊.
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Jesse Shapiro @bjesseshapiro.bsky.social · 06/10/2026
Minimoy, the cat we are cat-sitting for the year, is my sabbatical spirit animal
Photo of a sleeping black and brown cat curled up on a sofa cushion
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Reposted by Jesse Shapiro
Toulouse-Lautrec @toulouselautrec.bsky.social · 22/09/2026
At Montrouge ( Rosa la Rouge)
"At Montrouge (Rosa la Rouge)" by Henri de Toulouse-Lautrec portrays a solitary woman in a vibrant but earthy palette, capturing a sense of introspection and complexity. The artist, known for his intimate and candid depictions of Parisian life, uses soft brushwork and expressive color to convey mood and character.
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Danna Gifford @dannagifford.bsky.social · 06/10/2026
📣 New preprint: We looked at population survival and recovery of the thermophilic archaeon Sulfolobus acidocaldarius at near-boiling temperatures—conditions that occur in its environmental niche. www.biorxiv.org/content/10.6...
biorxiv.org
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Jesse Shapiro @bjesseshapiro.bsky.social · 06/10/2026
Our village is celebrating the rainy season
Photo of a old stone building decorated with bright pink umbrellas strung across the square in front
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Reposted by Jesse Shapiro
Saria McKeithen-Mead, PhD @sciria.bsky.social · 05/10/2026
Pleased to share my first preprint from my postdoc, where I ask what drives mobile DNA movement between bacterial cells in complex communities like the gut microbiome. To answer this, we built a way to capture mobile DNA in the act of moving between cells, using short-read metagenomics. 🧵
doi.org
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Reposted by Jesse Shapiro
Vincent Burrus 🇨🇦💙💛 @vincentburrus.bsky.social · 05/10/2026
#plasmidbiology #plasmid Just out! 🚀 Thrilled by our discovery: the function of the C-terminal domain of MOBH1 relaxases! We uncovered this thanks to a fertility inhibitor encoded by a parasitic mobile genetic element. Congrats to Florence on a great piece of work! 👏 academic.oup.com/nar/article/...
academic.oup.com
Conjugative transfer inhibition of IncA and IncC plasmids by SGI1-like elements via relaxosome assembly interference
Abstract. Broad-host-range IncA and IncC (A/C) conjugative plasmids propagate multidrug resistance in bacteria and mobilize chromosomal resistance islands,
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Jesse Shapiro @bjesseshapiro.bsky.social · 03/10/2026
Perfection!
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Reposted by Jesse Shapiro
Will Ratcliff @wcratcliff.bsky.social · 30/09/2026
Application review for the GRC in Microbial Population Biology will start October 15th! Please apply before then if you are keen on coming. www.grc.org/microbial-po...
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Reposted by Jesse Shapiro
Julia Van Etten @couchmicroscopy.bsky.social · 29/09/2026
Spread the word! I’m looking to recruit a PhD student to grow the Paulinella project. Some details can be found here: www.vanettenlab.org/join
vanettenlab.org
Join! — Van Etten lab at UMD
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Jesse Shapiro @bjesseshapiro.bsky.social · 30/09/2026
Glyphosate-based herbicide exposure triggers genetic adaptation but not diversity collapse within bacterioplankton species (reposting with the article title and a gratuitous glam shot of the lake these bugs called home until we rudely plopped them into experimental ponds...)
Screenshot of the article title: Glyphosate-based herbicide exposure triggers genetic adaptation but not diversity collapse within bacterioplankton speciesPhoto of a beautiful blue sky with some clouds reflected in a lake. The surrounding hills are dappled with red and gold fall foliage.

Photo credit: Akhil Kholwadwala
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Nikolai Slavov @slavov-n.bsky.social · 30/09/2026
bioRxiv has a dedicated section for negative results. Use it. Share negative results. Your colleagues will appreciate it.
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c0nc0rdance @c0nc0rdance.bsky.social · 30/09/2026
Omigod, this is the most heartwarming story possible! Backpack (bear 89) is the son of the 2019 winner of Fat Bear Week, Holly (bear 435). In 2007, he injured his foot & a practice of riding on momma's Holly's back had a new meaning: he was mobility-restricted while it healed. So Holly moved him.
From DISCVR blog's Facebook page, a momma bear & a yearling cub on her back in the shallow water.  I think the background has been swapped out, and I can't rule out some AI use there?  God, Facebook has become the social media for AI slop : (

The title of the article, which I link below, is "How Bear 89 earned the name Backpack"
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Reposted by Jesse Shapiro
Craig MacLean @craigmaclean.bsky.social · 30/09/2026
Postdoc position available in my group to work on ERC funded project on evolutionary biology of antibiotic resistance. Looking for someone with expertise in bacterial genetics, AMR, and evolutionary biology. www.jobs.ac.uk/job/DSZ416/p...
jobs.ac.uk
Postdoctoral Research Associate at University of Oxford
Explore an exciting academic career as a Postdoctoral Research Associate. Don't miss out on other academic jobs. Click to apply and explore more opportunities.
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Jesse Shapiro @bjesseshapiro.bsky.social · 30/09/2026
Thanks!
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Jesse Shapiro @bjesseshapiro.bsky.social · 29/09/2026
Thanks Sean!
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Reposted by Jesse Shapiro
Prasad Jallepalli, MD, PhD @prasad.bsky.social · 29/09/2026
5 potatoes cubed is still 5 potatoes because potatoes are root vegetables
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Jesse Shapiro @bjesseshapiro.bsky.social · 29/09/2026
(This is me applying for a job in your lab if you cant tell)
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Jesse Shapiro @bjesseshapiro.bsky.social · 29/09/2026
So truue
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Reposted by Jesse Shapiro
Pleuni Pennings @pleunipennings.bsky.social · 29/09/2026
I am hiring a postdoc! Are you interested to work on population genetics/ drug resistance/ data? Want to work in Montpellier, France? Fastq files don't scare you? PhD required, start date hopefully Nov 1! (end date Sep 30 2028) Please share! abetterscientist.wordpress.com/2026/09/29/p...
abetterscientist.wordpress.com
Postdoc position on drug resistance evolution in Montpellier, France
I have some exciting news (again!). I got money from the region (Occitanie) to hire a postdoc (and later an engineer / technician) to work on drug resistance evolution in malaria (P. faciparum) and…
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Reposted by Jesse Shapiro
Dave Jorgenson @davejorgenson.bsky.social · 26/09/2026
🎃 Pumpkin Spice GLP-1 season 🍂
Smoothie King’s new pumpkin spice GLP-1 smoothie??
And
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Jesse Shapiro @bjesseshapiro.bsky.social · 29/09/2026
Maybe something from Tim van Opijnen? www.vanopijnenlab.com
vanopijnenlab.com
van Opijnen Lab
Microbial Systems Biology, the science of bacterial pathogens and antibiotic discovery
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Reposted by Jesse Shapiro
Christian Landry @christianlandry.bsky.social · 29/09/2026
Single-cell biologists: I am trying to find examples in which people have encapsulated individual cells into droplets, let them grow and performed PCR at two loci with droplet-specific barcoded primers to link the genotypes at these loci using sequencing.
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Jesse Shapiro @bjesseshapiro.bsky.social · 29/09/2026
It's all a distant and fading memory...
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Jesse Shapiro @bjesseshapiro.bsky.social · 29/09/2026
Thanks Michael! Given the Venn diagram of conferences we attend, I know you've seen multiple iterations of this as a talk, poster, etc. Now we can move on to something new ;)
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Reposted by Jesse Shapiro
Kate Baker @ksbakes.bsky.social · 25/09/2026
We have an open Assistant/Associate Professor position in Pathogen Biology at the Department of Genetics - come and join us! 🦠 🧫 🧬https://www.cam.ac.uk/jobs/assistantassociate-professor-in-pathogen-genetics-pc51175
cam.ac.uk
Assistant/Associate Professor in Pathogen Genetics
Applications are invited for an Assistant or Associate Professorship in Pathogen Genetics to be held in the Department of Genetics. We are searching for a talented individual with a track record of fu...
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Jesse Shapiro @bjesseshapiro.bsky.social · 29/09/2026
2021: @emderrick.bsky.social does the experiments. Easy right? 2022-23: Data analysis 2024: Preprint and first submission 2025: Resequenced everything to higher depth and reanalysis 2026: Published! So… I think the word *finally* is justified here! /fin academic.oup.com/ismecommun/a...
academic.oup.com
Validate User
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Jesse Shapiro @bjesseshapiro.bsky.social · 29/09/2026
20. We often qualify our posts about a new publication by saying it’s *finally* out, which speaks to the long lag between submission and acceptance. But…
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Jesse Shapiro @bjesseshapiro.bsky.social · 29/09/2026
19. Ours is one of a growing number of studies looking at evolution in the context of (semi) natural communities with known selective pressures. Still lots of open questions, but hopefully we can start to reach more general conclusions!
slide summarizing results of our work on eco-evolutionary effects of GBH selection, and listing other similar studies applying known selective pressures to semi-natural microbial commnities.
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Jesse Shapiro @bjesseshapiro.bsky.social · 29/09/2026
18. What about soft sweeps, in which targets of selection are shared by different lineages (strains)? It’s far from conclusive, but this explains many of our observations.
sketch of a soft selective sweep
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Jesse Shapiro @bjesseshapiro.bsky.social · 29/09/2026
17. So what is going on? Genome-wide sweeps are not occurring in a classic sense, because polymorphism is retained. Gene-sweeps? Maybe, but dozens of concurrent sweeps would be required to explain the many genes under selection.
Sketches of genome-wide and gene-specific selective sweeps
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Jesse Shapiro @bjesseshapiro.bsky.social · 29/09/2026
16. Across all 7 MAGs, the targets of selection are enriched in amino acid metabolism (COG category E), in and around the AroA pathway known to be inhibited by GBH. Some other metabolism genes are enriched too.
Barplot of functional gene categories enriched in SNV frequency changes during GBH treatment relative to controls.
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Jesse Shapiro @bjesseshapiro.bsky.social · 29/09/2026
15. In some MAGs, we detect thousands of genes potentially under selection, too many to explain by gene-specific sweeps and more consistent with a rare strain rising in frequency in response to GBH (because average nucleotide identify [ANI] stays pretty low). In others, gene-sweeps are plausible.
table enumerating genes inferred to be under GBH-driven selection across 7 MAGs
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Jesse Shapiro @bjesseshapiro.bsky.social · 29/09/2026
14. To identify candidate genes under selection by GBH, we looked for large changes in SNV frequency in GBH but not control ponds. We could do this in 7 MAGs with sufficient coverage at both time points.
cartoon showing criteria to identify genes with large differences in SNV frequencies between GBH treatment and control ponds
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Jesse Shapiro @bjesseshapiro.bsky.social · 29/09/2026
13. But if we look at *polymorphic* SNVs (those that remain variable in the population, not fixing during the experiment), they are unaffected by GBH treatment. This is *inconsistent* with classic genome-wide sweeps, which predicts purging of polymorphisms.
boxplot showing that GBH does not purge polymorphism within MAGs
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Jesse Shapiro @bjesseshapiro.bsky.social · 29/09/2026
12. First, we find that GBH drives fixed SNVs (those that go to 100% frequency, replacing the nucleotide present in the reference genome from time 0). There is also a smaller but detectable effect of SNVs that fix over time due to drift, not treatment.
boxplots showing an increased in fixed substitutions with GBH treatment
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Jesse Shapiro @bjesseshapiro.bsky.social · 29/09/2026
11. Consistent with our previous experiments, GBH shifts the community from Beta to Alphaproteobacteria. But we really want to zoom in and look at genetic variation (SNVs) within MAGs (rough proxy for species).
Barplots showing Alphaproteobacteria increasing in relative abundance with GBH (Roundup) treatment
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Jesse Shapiro @bjesseshapiro.bsky.social · 29/09/2026
10. So we designed a pretty simple experiment: deeply sequence microbial communities before and 28 days after exposure to a Roundup (GBH) pulse.
Cartoon of experimental design at LEAP
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Jesse Shapiro @bjesseshapiro.bsky.social · 29/09/2026
9. In previous LEAP work, we found that the glyphosate-based herbicide (GBH) Roundup selects for MAGs (metagenome-assembled genomes, a proxy for bacterial species) that encode more efflux pumps. This explains much of the community-level response, but what about the population level, within species?
Slide showing a plot of MAG success being predicted by efflux pumps in their genome
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Jesse Shapiro @bjesseshapiro.bsky.social · 29/09/2026
8. Here we took an experimental approach by applying a known selective pressure to a semi-natural community in the Large Experimental Array of Ponds (LEAP) at the @mcgill.ca Gault Nature Reserve.
Slides showing the Large Experimental Array of Ponds
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Jesse Shapiro @bjesseshapiro.bsky.social · 29/09/2026
7. There is also evidence for both genome-wide and gene-specific sweeps in human gut bacteria. But in both cases, the selection driving these sweeps must be inferred and remains uncertain. Great work by @polzlab.bsky.social @nanditagarud.bsky.social @rwolff.bsky.social & co
Screen shots of recent studies showing genome-wide and gene-specific sweeps in human gut microbiomes
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Jesse Shapiro @bjesseshapiro.bsky.social · 29/09/2026
6. Putting gene ecology aside for the moment, do we observe sweeps in nature? Yes! Here’s an example (from @quendi.bsky.social & co) of a genome-wide sweep happening in a lake bacterium over 9 years. But was it driven by selection (and if so, what selective pressure?) or drift?
Heatmap of a genome-wide sweep observed by Bendall et al.
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Jesse Shapiro @bjesseshapiro.bsky.social · 29/09/2026
5. Of course, speciation is not guaranteed. There are models that could lead to ‘gene ecology’ where genes, not species, inhabit ecological niches.
Gene ecology sketch
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Jesse Shapiro @bjesseshapiro.bsky.social · 29/09/2026
4. If recombination is stronger, we can get gene-specific selective sweeps. Diversity is only purged locally near the targets of selection, and preserved genome-wide. If recombination becomes restricted between niches over time, we can get something resembling the Biological Species Concept.
Gene-specific selective sweep sketch
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Jesse Shapiro @bjesseshapiro.bsky.social · 29/09/2026
3. If recombination is weak relative to selection, we expect genome-wide selective sweeps. Genetic diversity is purged genome-wide as linked variants hitchhike with the target of selection. If sweeps occur independently in different species, this leads to Fred Cohan’s Ecotype Species Concept.
Genome-wide selective sweep sketch
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Jesse Shapiro @bjesseshapiro.bsky.social · 29/09/2026
2. This work is motivated by big questions that have haunted me since my PhD: Do genes or genomes (species?) inhabit ecological niches? On what time scales do they respond to selection? First, some theory on selective sweeps (slides from my talk at @meehubs.bsky.social #MEEHubs2026 #MEEhubs26)
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Jesse Shapiro @bjesseshapiro.bsky.social · 29/09/2026
Our latest, spearheaded by the truly indefatigable @emderrick.bsky.social in which we search for selective sweeps in nature and genetic targets of selection within a species in the context of a diverse background community @isme-microbes.bsky.social doi.org/10.1093/isme... 🧵 1/n
doi.org
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Asaf Levy @asaflevylab.bsky.social · 29/09/2026
Our new preprint is out. www.biorxiv.org/content/10.6... We applied an XGBoost algorithm with genomic and biochemical features to detect all T6SS effectors in bacterial genomes. Next, we validated 3 novel effectors that serve as antibacterial or anti-euk toxins. One of the effectors, from
biorxiv.org
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