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Alex Crits-Christoph

@acritschristoph.bsky.social
5.2K followers 2K following 2.3K posts

Computational microbiologist I like to post about: microbial genomics, microbial ecology, evolution, micro+plant biotechnology, climate, symbiosis, virology, ag, sci publishing and policy

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Reposted by Alex Crits-Christoph
Taylor priest @taylorpriest.bsky.social · 9h
Our new preprint is out! We show that genomically discrete and ecologically cohesive subspecies are a common feature in the global ocean microbiome, and represent a fundamental level at which ecological and evolutionary forces act to shape microbial diversity www.biorxiv.org/content/10.6...
biorxiv.org
Genomically and ecologically cohesive subspecies as biologically meaningful units in the global ocean microbiome
Microbial diversity is organised into operationally defined species. However, it remains unclear whether these, or finer-scale groups represent biologically meaningful units in natural communities. He...
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Reposted by Alex Crits-Christoph
Jonathan Eisen @phylogenomics.bsky.social · 11h
Just nobly posting this phylogenetic tree I made of rhodopsins / sensory opsins / halorhodopsins / proteorhodopsins trees from the Venter 2004 Sargasso Sea paper. No reason. Just a random reference to rhodopsin diversity.
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Karl Deisseroth @deisseroth.bsky.social · 21h
Thank you to everyone sharing in this moment! I’m so grateful to all my trainees & collaborators… dlab.stanford.edu/group-members (pic: Peter and I together in 2017) Reading for all those asking: for technical details: dlab.stanford.edu for everyone: deisseroth.org/projections
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Seth Shipman @seth-shipman.bsky.social · 19h
@jihoon-han.bsky.social's new detectron technology -- out now in Nature Biotechnology. Toehold RNA sensing controls a retron-derived DNA barcode generator. Check it out!
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Alex Crits-Christoph @acritschristoph.bsky.social · 18h
How the discovery of microbial opsins led to the development of optogenetics www.cell.com/cell/fulltex... Here is a nice article on the origin of optogenetics in microbial rhodopsins, and first of all were the haloarchaea:
cell.com
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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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Kevin K. Yang 楊凱筌 @kevinkaichuang.bsky.social · 18h
Combine a chemical knowledge, generative modeling, and structure prediction into a pipeline that can design enzymes for new-to-nature chemistry. @zacharywu.bsky.social @alexechu.bsky.social @francesarnold.bsky.social @pushmeet.bsky.social @juewang.bsky.social www.biorxiv.org/content/10.6...
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Ana Gutiérrez-Preciado @anagtz.bsky.social · 04/10/2026
Where did eukaryogenesis likely happened? We studied a modern analog: microbial mats from a sulfidic, low O2, volcanic crater lake in the Afar region. Asgardarchaea thrive in the SO4-reduction zone along SO4-reducers :) @deemteam.bsky.social doi.org/10.1038/s415...
doi.org
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Tom Costello @tomcostello.bsky.social · 04/10/2026
More from our group on this! (And using the same cool format as Matt): the effect comes mostly from facts and evidence¹ and holds for conspiracies only days old². LLMs can also talk people into conspiracies³. ¹ psyarxiv.com/h7n8u ² arxiv.org/abs/2608.06151 ³ arxiv.org/abs/2601.05050
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Alex Crits-Christoph @acritschristoph.bsky.social · 03/10/2026
Ah, 2014. That was a simpler time, when all we argued about was rarefaction
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James Gurney @jamesgurney.bsky.social · 02/10/2026
www.biorxiv.org/content/10.6... New preprint from the lab. We tried to capture phage infection using scRNAseq. With admittedly mixed results. Importantly our reads weren’t random and we see predicted biological patterns. Phage gene expression along the genome for one 1/3
biorxiv.org
Robust Inference of Phage-Host Infection Dynamics from Sparse Single-Cell Transcriptomics Profiles in Pseudomonas aeruginosa
Phage therapy is providing a benefit to a limited number of people. To date those who have received phage therapy typically have done so via an IND expanded access mechanism, colloquially referred to ...
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junhyongkim.bsky.social @junhyongkim.bsky.social · 03/10/2026
There's both a misunderstanding of the problem that arXiv is addressing and the problem generated by the change in policy. First, there is no scientist who is sitting on 3 finished manuscripts, not having previously submitted at least one of them, and suddenly is stymied by the 2/month limit.
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Sean Gibbons 🦠💩 @gibbological.bsky.social · 02/10/2026
We are hosting a symposium at @isbscience.org in December on the frontiers of computational biology, with a focus on "AI, Multi-Omics, and the Future of Human Health." Join us! Virtual is free and it's $50 if you want to join in-person. isbscience.org/frontiers-in...
isbscience.org
Frontiers in Computational Biology - Institute for Systems Biology (ISB)
Symposium Schedule Learn more about our presenters below. 8:30–9 a.m. Registration, Coffee & Light Breakfast 9–9:10 a.m. Welcome & Opening Remarks by Jim Heath SESSION 1 Chair: Nitin Baliga, ISB
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Costa Samaras @costasamaras.com · 30/09/2026
Here's the topline for me on the permitting bill: we need to double or triple the grid with clean electricity if we are going to solve climate change. We need to do this in concert with communities & the environment, and do this quickly on a climate-relevant timeline. The contours of this look good.
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Archaea Biology Vienna @archaea-vienna.bsky.social · 01/10/2026
Our paper on the dynamics of Asgard archaea (Promethearchaeota) is now out in Nature! Huge thanks to the reviewers for helping make the manuscript stronger. www.nature.com/articles/s41... Two “Lokis” stained for Lokiactin (FastAct, magenta), reaching toward each other to celebrate 🎉 #archaea
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Joel Wertheimer @wertwhile.bsky.social · 30/09/2026
Everything I have heard about this bill is that it is more or less excellent and the planet would benefit a lot of it passes and I hope it does and it becomes law.
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bioRxiv Microbiology @biorxiv-microbiol.bsky.social · 30/09/2026
De novo minibinders targeting RH5 achieve nanomolar inhibition of blood-stage malaria replication www.biorxiv.org/content/10.64898/20…
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Nature Microbiology @natmicrobiol.nature.com · 30/09/2026
Out Now! Wild rice locus enables microbiome re-domestication for enhanced nitrogen-use efficiency #MicroSky
go.nature.com
Wild rice locus enables microbiome re-domestication for enhanced nitrogen-use efficiency
Nature Microbiology, Published online: 30 September 2026; doi:10.1038/s41564-026-02498-xHybridization of wild and cultivated rice plants improves nitrogen use efficiency through microbiome re-domestication.
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Sternberg Lab @sternberglab.bsky.social · 28/09/2026
1/13 — New pre-print from the Sternberg Lab in collaboration with Leifu Chang's Lab! TnpB nucleases have repeatedly given rise to TldRs, nuclease-dead RNA-guided transcription factors. Here we define the biological role of one TldR clade in its native host. Story: www.biorxiv.org/content/10.6...
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Matt Olm @mattolm.bsky.social · 29/09/2026
This is an interesting paper! Starting with a really big screen to look for GPCR activation by microbes, and ending with a convincing story by which microbes make acetylcholine in the gut to promote IgA production, ultimately leading to better colonization. www.nature.com/articles/s41...
nature.com
Commensal-derived acetylcholine enhances mucosal immune education - Nature
A diet–microbiome–host axis strengthens mucosal immune defences and reinforces host–microbiota mutualism.
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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
Validate User
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Chelsea Harvey @chelseaeharvey.bsky.social · 28/09/2026
NEW - Conservative orgs are filing records requests by the dozens at public universities, demanding documents from climate researchers. @lesleyclark.bsky.social @corbinhiar.bsky.social & I have uncovered more than 100 requests, a campaign targets/allies say is an effort to derail climate litigation
politico.com
Inside the anti-climate campaign against researchers
A POLITICO investigation reveals more than 100 open records requests demanding documents from climate scientists nationwide.
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Union of Concerned Scientists @ucs.org · 28/09/2026
Today, the Trump administration finalized a rollback of fuel economy standards for passenger cars and trucks. This move effectively kills the nation's CAFE standards, a program that has saved drivers $321 billion in fuel costs since 2010. Read UCS Statement: act.ucs.org/46NApCk
“The federal government’s decision to gut fuel economy standards is a handout to automakers and oil companies that will strap American consumers already struggling with an affordability crisis...Weakening these standards means drivers will spend more on fuel while having fewer options to choose efficient vehicles."
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Vaughn Cooper @vscooper.micropopbio.org · 27/09/2026
How do Burkholderia multivorans bacteria adaptively evolve during infections of the cystic fibrosis airway? A longtime collab and intensive study of 8 patients links bacterial adaptations to disease progression. Our findings also unite prior studies. www.biorxiv.org/content/10.6...
biorxiv.org
Convergent genetic evolution within Burkholderia multivorans chronic infections correlates with lung function decline in cystic fibrosis patients
The patterns and pathways of pathogen adaptation during chronic infections can reveal the gateways microbes must unlock to colonize and persist. In chronic lung infections of cystic fibrosis (CF) pati...
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Carl Zimmer @carlzimmer.com · 27/09/2026
Four days ago, a scientist was surprised by the news that Anthropic discovered new virus genes for making DNA. He says he’s been studying them for years—and feeding his data to Anthropic’s AI as part of his own research. Coincidence? Here’s my story. nyti.ms/3VSWayc
nyti.ms
Did Anthropic’s A.I. Really Make a Scientific Discovery on Its Own? (Gift Article)
An expert at the University of Copenhagen said his team had been sharing its research with the company’s A.I. model, Claude, and that its new finding matched their work.
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Alex Crits-Christoph @acritschristoph.bsky.social · 27/09/2026
the Folkers deadpan
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Caroline Bartman @cbartman.bsky.social · 25/09/2026
Ok what is the most death metal biology term? Cytokine storm? Programmed death 1? Executioner caspase? Other?
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Alex Crits-Christoph @acritschristoph.bsky.social · 25/09/2026
looks promising!
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Andrew Urquhart @starships-andrew.bsky.social · 24/09/2026
Another step in the #Starship story - they move via a circular intermediate. Helps explain how these elements horizontally transfer and means that we can modify them into transformation vectors (starmids). www.biorxiv.org/content/10.6...
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Alex Crits-Christoph @acritschristoph.bsky.social · 24/09/2026
Two preprints both out today identifying *different* reverse transcriptase systems associated with arrays reminiscent of CRISPR/Cas, encoded by different phage. One from Anthropic and one from Stanford. Worth pointing out that the Stanford work clearly began earlier, and has more wetlab follow-up:
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Tominaga K. (tomiken) @pacyc184.bsky.social · 23/09/2026
A phage DUF669 protein mediates post-cleavage DNA repair against host CRISPR immunity | Nature Communications
nature.com
A phage DUF669 protein mediates post-cleavage DNA repair against host CRISPR immunity - Nature Communications
Using affinity purification-mass spectrometry, these authors identified the Healer system, a phage two-protein effector that repairs CRISPR-mediated DNA breaks via homologous recombination.
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Simonetta Gribaldo @sgribaldo.bsky.social · 23/09/2026
Interested in #archaea, #methane, #cell-envelopes? New paper out @nature.com ! We discovered an enzyme that specifically cleaves the cell wall of methanogens, revealing a new chemical structure of archaeal peptidoglycan, 50 yrs after its first description www.nature.com/articles/s41... #MicroSky 🧵👇
nature.com
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Colin Carlson @colincarlson.bsky.social · 23/09/2026
1: For every hour you travel from the nearest clinic, the odds of detecting an outbreak decreases by about 1/3. 👉 For policymakers: the best thing we can do to catch and intercept spillovers before they become epidemics is build rural clinics and pay for diagnostic machines and supplies.
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Alex Crits-Christoph @acritschristoph.bsky.social · 23/09/2026
All journals should have a mascot like this guy
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Friedemann Weber @friedemann.bsky.social · 23/09/2026
"We are unaware of any evidence that Dr. Baric’s studies were conducted outside the research guidelines...his work was approved by the National Institutes of Health and the relevant institutional biosafety committees"
journals.asm.org
Protecting strength and integrity in virology | Journal of Virology
The American Society for Virology (ASV), American Society for Microbiology (ASM), and the Infectious Diseases Society of America (IDSA) are alarmed by the initiative of the U.S. Department of Health a...
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bioRxiv Bioinfo @biorxiv-bioinfo.bsky.social · 22/09/2026
baltic: the Backronymed Adaptable Lightweight Tree vIsualisation Code www.biorxiv.org/content/10.64898/20…
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H. B. Beryl Rappaport @hbrappap.bsky.social · 22/09/2026
Our description of fire amoeba, 𝘐𝘯𝘤𝘦𝘯𝘥𝘪𝘢𝘮𝘰𝘦𝘣𝘢 𝘤𝘢𝘴𝘤𝘢𝘥𝘦𝘯𝘴𝘪𝘴, is now online at Cell! Thanks @oliverio.bsky.social and amazing team for questioning the limits of eukaryotes! 🔥 www.cell.com/cell/fulltex...
cell.com
A geothermal amoeba sets a new upper temperature limit for eukaryotes
The amoeba Incendiamoeba cascadensis demonstrates that eukaryotic life can withstand temperatures beyond what was thought possible and sheds light on molecular strategies for survival in extreme heat.
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Eduardo Rocha @epcrocha.bsky.social · 22/09/2026
Great work led by @tomipou.bsky.social and @jrpenades.bsky.social with contributions of Yiqing Wang from our lab. While plasmid conduction has a very long history, there is a flood of papers coming on the combinatorics of plasmid co-integrations and excisions. Makes research fun, but not easier...
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ProPublica @propublica.org · 22/09/2026
Sen. Susan Collins helped steer millions in federal defense contracts to Navatek, whose CEO illegally funneled thousands of dollars to her campaign. The FBI sought to launch a probe and was eyeing Collins and other lawmakers. Then Trump gutted the unit in charge. THREAD 🧵
Martin Kao, CEO of defense contractor Navatek, poses next to Sen. Susan Collins for a photo. Collins is holding a model of a boat in her hands. Behind them is a large sign with the Navatek logo.
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Ben Parker @ben-parker.bsky.social · 21/09/2026
Aphids harbor a bacterium called Regiella that protects them from a major natural enemy, a 'zombie' fungus called Pandora. We show this defense depends on a small plasmid that has moved among distantly related Regiella lineages. When a strain lost the plasmid in culture, protection disappeared.
A picture of an aphid that has been infected with a fungal pathogen.
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Alex Crits-Christoph @acritschristoph.bsky.social · 21/09/2026
Speed is very exciting here because how long you run correlates pretty strongly with how promising your candidates are
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Martin Pacesa @martinpacesa.bsky.social · 21/09/2026
ʙɪɴᴅᴄʀᴀꜰᴛ2 is out, and we're not waiting for the paper. The full code drops today, free for academic and industry use. We're releasing it early so you can start designing right now, and bring its full power to the current Adaptyv competition. github.com/PacesaLab/Bi...
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David Bikard @dbikard.bsky.social · 21/09/2026
New paper from the lab, out in Nature Microbiology. We ran CRISPRi screens to ask what genes E. coli needs in order to live in a gut and what this can tell us about the gut environment itself. doi.org/10.1038/s41564-026-02471-8
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Mozammel Hoque @mozammel.bsky.social · 20/09/2026
1/ New paper out in ISME Communications now in full version. Bacteria rarely live alone in nature, so we ran a 6-month evolution experiment asking what happens when species are forced to share the same biofilm. Turns out, company changes everything. 🧵 doi.org/10.1093/isme...
doi.org
Mixed-species interactions constrain diversification and shape biofilm evolution
Abstract. Experimental evolution provides a powerful framework for dissecting how ecological interactions shape adaptive trajectories. Here, we evolved Kle
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Abdul El-Sayed @abdulelsayed.bsky.social · 20/09/2026
This is about one thing and one thing alone. Steering our research dollars for cancer, heart disease, and new infectious diseases to Trump’s political allies and friends.
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Willem van Schaik @wvschaik.bsky.social · 20/09/2026
Brilliant paper by the labs of @epcrocha.bsky.social @jrpenades.bsky.social 'Mobile genetic elements drive a plasmid fusion and deletion lifecycle shaping evolution and antimicrobial resistance' www.nature.com/articles/s41...
nature.com
Mobile genetic elements drive a plasmid fusion and deletion lifecycle shaping evolution and antimicrobial resistance - Nature Communications
Plasmids drive bacterial adaptation, but how their diversity arises has remained unclear. Here, they show that in Staphylococcus aureus, mobile genetic elements repeatedly fuse and delete plasmids, re...
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Alex Crits-Christoph @acritschristoph.bsky.social · 20/09/2026
oh this is a cool feed:
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Dave Baltrus 🦦 @surtlab.bsky.social · 20/09/2026
Ran is correct about this IMO…. There’s use and there’s abuse and there’s laziness with regard to AI and academia. And there’s no one size all answer that works for everything. I do disagree with the footnote but acknowledge old Twitter has been better for science discussions.
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Vaughn Cooper @vscooper.micropopbio.org · 20/09/2026
Now published from a fun collaboration, please see 🧵 academic.oup.com/ismecommun/a...
academic.oup.com
Mixed-species interactions constrain diversification and shape biofilm evolution
Abstract. Experimental evolution provides a powerful framework for dissecting how ecological interactions shape adaptive trajectories. Here, we evolved Kle
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Dr. Jonathan Foley @globalecoguy.bsky.social · 19/09/2026
Joe Romm was a climate hero. Most of all, he was a scientist and a fantastic bullshit slayer. He called out greenwashing nonsense better than anyone. web.sas.upenn.edu/pcssm/news/r...
web.sas.upenn.edu
Remembering Dr. Joe Romm
It is with great sadness that the Penn Center for Science, Sustainability and the Media shares news of the passing of PCSSM Senior Research Fellow Dr. Joe Romm. Please find below an obituary prepared ...
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