another example of AI as tracer dye, exposing an already existing problem (and, of course, significantly worsening it)

The final form of my 2nd postdoc paper with the Bassler Lab! Turns out our favorite quorum-sensing phage isn’t a one-off, but rather a member of a globally dispersed family of phages that sense a universal autoinducer. #phagesky #microsky journals.asm.org/doi/10.1128/...

"The changing roles of Escherichia coli" -- a short essay by yours truly. rdcu.be/eVtXT

Enjoyed reading “AI for chemistry in 2025 is like AI for images in 2010” leashbio.substack.com/p/ai-for-che...

Phosphorus stress and spatial confinement lower the threshold for quorum-sensing activation of redox-active metabolite production in Pseudomonas synxantha bioRxiv from Dianne Newman www.biorxiv.org/content/10.1...

📢 NEW exciting opportunity! Join Queen’s University as a tenure-track Assistant Professor in Cell Engineering and Biomanufacturing, with opportunities for interdisciplinary research across #ChemicalEngineering and #Biomedical and #MolecularSciences. 🔬 🔗 stemcellnetwork.ca/career-oppor...

DOE's Office of Science is making a big push into AI, and that includes our work at the @jgi.doe.gov . We want to hear your thoughts (+ and -) on AI-enabled biological data. Consider joining one of our interviews or focus groups by filling out this form! 🧪🧬🦠🖥️ #secmet jointgeno.me/PortalStorie...

It’s good to see papers start to address LLMs as structural plagiarism — provenance, more hidden than the original words or training data. www.nature.com/articles/s42...

Have you ever used a #bioinformatics #database and were frustrated by its lack of coverage? Did you ever think about starting your own resource? We just published a new strategy for community-driven #biocuration, based on our experiences with the #MIBiG database (1/8)! doi.org/10.1093/bib/...

What started out as a structure-function project for an undergraduate researcher morphed into something bigger w/ @popea.bsky.social leading the way. Check out how RhlR fine tunes its response to its autoinducer to avoid producing too much pyocyanin. www.biorxiv.org/content/10.6...

In our new paper in @natcomms.nature.com We discovered how Ruminococcus bromil organizes and regulates its enzyme complex to efficiently break down resistant starch, forming a key metabolic foundation for the human gut ecosystem. (1/12) 📄 www.nature.com/articles/s41...

Our BEHIND THE STORY. A glimpse into the role of auxiliary metabolic genes in cyanophages during infection communities.springernature.com/posts/a-glim...

Excited to share our new @natecoevo.nature.com paper. We identified microbes found across nearly all ruminants that act as the functional backbone of both the rumen ecosystem and the host, with major implications for food security and climate change mitigation. (1/8) www.nature.com/articles/s41...

Angelina Fanny Hesse: The Woman Who Brought Agar from the Kitchen to the Laboratory voxmeditantis.com/2025/10/30/a... #WomenInSTEM #STEM #Microbiology #Agarology #Bacteriology

We analyzed changes in physiology relative to menopause using two large scale studies that include millions of lab tests. Rather than align by age, we used statistical inference to align tests to final menstrual period. (1/2) arunamed.com/the-menopaus...

Amazing dataset describing the metabolic profiles of 66 E. coli transporter knockouts by @sulheim.bsky.social with Peter Doubleday and @nzamboni.bsky.social. The tool, set up by @lambdapp.bsky.social and Eric Ulrich allows you to explore for yourself. Enjoy! Pre-print here: doi.org/10.1101/2025...

Do you think transporters in E. coli contribute to metabolite release? No? Explore the effect of 66 different transporter knockout mutations on the exometabolome dynamics of ~300 metabolites yourself: keio.unil.ch Teaser: Increased proline in ΔputP #microsky #MEvoSky

This project wouldn't been possible without Peter Doubleday and @nzamboni.bsky.social at @imsb-eth.bsky.social. Peter conducted >10,000 mass spec analyses 🤯. So grateful for this opportunity to team up with the best of the best in metabolomics 😍 Read more: www.biorxiv.org/content/10.1... #microsky

Poster deadline for the Keystone Microbiome Meeting in Banff is December 30th www.keystonesymposia.org/conferences/... Will be a great meeting focused on human microbiomes, spanning basic, mechanistic, and applied. Organized by myself, @amibhatt.bsky.social , and Harry Sokol. Join us!

PanBGC: A pangenome-inspired framework for comparative analysis of biosynthetic gene clusters #ISMEComms from @nadineziemert.bsky.social academic.oup.com/ismecommun/a...

Optimized k-mer search across millions of bacterial genomes on laptops https://www.biorxiv.org/content/10.1101/2025.11.23.690050v1

Boris Shraiman points a physicist’s eye on biological quandaries news.ucsb.edu/2025/022264/... 🧪

Excited to share our latest research in @natmicrobiol.nature.com . We uncover hundreds of inhibitory interactions between common chemical pollutants and human gut bacteria. A thread🧵 (1/10) #microbiomesky #microsky @kiranrpatil.bsky.social lab @mrc-tu.bsky.social www.nature.com/articles/s41...

Models and co-culture experiments assess four mechanisms of phytoplankton–bacteria interactions www.nature.com/articles/s41... #jcampubs

Every biologist knows the story of Fleming's chance discovery of penicillin. But is it true? Here, with @asimovpress.bsky.social, I write about inconsistencies in the canonical story, and explore a few alternative theories about what really happened in that St. Mary's lab in the summer of 1928.

Strain matters: host responses reflect symbiont origin in the squid-vibrio symbiosis in #mSystems from Margaret McFall-Ngai journals.asm.org/doi/10.1128/...

Thrilled to share our new work uncovering how membrane transporters determine resource-size preferences in gut bacteria, and showing that deleting a single protein domain can shift a transporter’s preference from long to short fructans. www.biorxiv.org/content/10.1...

Incredibly cool work by @smorenogamez.bsky.social et al, from the ecology to the mechanism and back again. This is Darwin's finches at the microbial scale- how do niches emerge based on resource size in the gut? #MicroSky #microbiome #microbiomesky

Happy to share our new AMR resource which has phenotypic AMR (usually MIC data) collected from publications and databases. This is paired with assemblies and annotations We're excited for users who might train new models, find phenotype/genotype mismatches, or any other use

The University at Albany Biomedical Sciences Department is hiring at the Assistant Professor level. We are looking for researchers at the intersection of infectious disease and artificial intelligence: albany.interviewexchange.com/jobofferdeta... #infectiousdisease #artificialintelligence

We've updated our recent @biorxivpreprint.bsky.social on 'Hidden but discoverable diversity in the global microbiome', led by @vishnuprasoodanan.bsky.social & @omaistrenko.bsky.social www.biorxiv.org/content/10.1...

On #LGBTQSTEMDay, Bruno Francesco Rodrigues de Oliveira, a founding member of the Pride in Microbiology Network, reveals how it has developed since it was launched three years ago - and what needs to happen next. www.the-microbiologist.com/opinion/prid...

The @crick.ac.uk is recruiting Early Career Group Leaders - Lab set-up, research costs, salaries for up to 5 researchers - Support for up to 12 years - Access to our core facilities - Competitive salary - Fantastic colleagues - All areas of biology Deadline 27 Nov www.crick.ac.uk/careers-stud...

Diving through the purple sulfur bacteria layer of Fayetteville Green Lake with our ROV last month. This is the most intense density of PSB that I've seen in many years!

Starting this week, I set aside one hour each week to meet ECRs outside my group who want to discuss career development, mentorship, or any non-technical professional questions. Here is a blog that explains my motivation for this and how to schedule a meeting: merenlab.org/2025/11/16/E...

NEW pub in @science.org 🥳 Is it sponges (panels A & B) or comb jellies (C & D) that root the animal tree of life? For over 15 years, #phylogenomic studies have been divided. We provide new evidence suggesting that... 🔗: www.science.org/doi/10.1126/...

Nearly ten years in the making and finally out in print! www.nature.com/articles/s41... Entotheonella are insanely biosynthetically rich bacteria, but few genomes were available. Working with far-flung collaborators, we obtained genomes for 14 candidate species from 8 sponges.

With much gratitude to everyone who supported the wonderful #STAMPS summer course at the MBL, I share that STAMPS will not be offered in 2026. 💔😿

Bluetorial-Jim Watson I met Jim Watson a few times but did not know him well. However, I was greatly influenced by his book “The Double Helix”. He was a complicated human being with some very, very bad features, but some good contributions. What follows is my personal perspective. 1/41

On the event of James Watson's death, I highly recommend this 2023 commentary from @matthewcobb.bsky.social and Nathaniel Comfort with crucial new insights into the discovery of the double helix. (And also check out Cobb's brand new biography of Francis Crick) www.nature.com/articles/d41...

Can we leverage bacterial competition for targeted replacement of harmful strains? Maybe! Our recent piece in @natmicrobiol.nature.com provides a theoretical framework and a set of experiments to show what it might take: www.nature.com/articles/s41...

Preprint: Bacteria sense virus-induced genome degradation via methylated mononucleotides tinyurl.com/ch3damp We show how molecular byproducts released during virus-induced cell exploitation are used as signals to trigger host immunity Revealed by the amazing Ilya Osterman. See his thread below👇

The ocean’s got rhythm — and so do its viruses. With the Bermuda Atlantic Time-Series (BATS), we dove deep — every 4 to 12 hours — to see how viral populations swing through day and night.

We are recruiting new faculty in IMES at MIT! IMES (Institute for Medical Engineering and Science) is the MIT home of the famous HST program. As faculty are also appointed in a department at MIT, we have diverse research programs, all focused on human health. faculty-searches.mit.edu/imes-search/

The ocean plays an important role in locking away carbon from the atmosphere. A new imaging system developed by @cadurkin.bsky.social and team provides real-time observations of the tiny particles of marine snow that drive carbon storage in the deep sea. Learn more: www.mbari.org/news/new-mba...

Whatever strategy you’re about to suggest, we’ve thought about it. docs.google.com/document/d/1...

Do you want to do a Masters in Evolutionary Biology? The call for applying to the MEME program is now open! MEME is a fantastic 2-year MSc between four European Universities on all areas of Evolutionary Biology. Apply and study in Sweden/France/the Netherlands/Germany/USA/Switzerland! www.evobio.eu

PhD project available on Marine Microbe Interactions During Macromolecule Degradation available via NERC-TREES-DTP. Applicants will go through a selection/interview process within the program. Apps due Dec. 17th. Please feel free to contact me if interested! www.trees-dla.ac.uk/projects/mar...

Let's talk -80 freezers: Recommendations? Dis-recommendations? What do you suggest prioritising and why? Bonus points if you have input on buying one in Europe. * photo of Muffin for cat tax