This is your cue to try Claude if you’ve been holding out still…

We're looking to sponsor applications to the new NSF PRFB who are interested in using AI to tackle microbiology's "Great Plate Count Anomaly" Details below. Please share. #microsky #postdoc #AI #microbiology open.substack.com/pub/carinila...

CARB-X is opening a new funding round soon—sign up for their newsletter (link in replies) to get the announcement. CARB-X is one of few organizations making meaningful progress ensuring access to new antimicrobial drugs and supporting preventatives/diagnostics.

Looks interesting

My parking spot today

Tried Edison Analysis (not Kosmos) on two tasks and was blown away: 1. Uploaded 96 high-res NMR spectra of bacterial supernatants and asked for metabolite ID and quantification 2. Uploaded a bacterial genome and asked it to identify mobile genetic elements (more complex, but this is the gist)

Old news by now, but this is a fantastic short course—feels like Andrew Ng’s early coursera neural networks class. If you have not tried Claude Code, I recommend just skimming the videos to see what the chatter is about. www.deeplearning.ai/short-course...

Antimicrobial resistance (AMR) is one of the greatest threats to public health, with the potential to undo decades of medical progress. This #WAAW2025, head to our LinkedIn to hear from world-leading experts on how we can tackle AMR and protect the future of medicine: t.ly/3Oxk1

Registration is now open for @keystonesymposia.bsky.social "Beyond #Antibiotics: Emerging Strategies Combating #BacterialInfection." Deadline for scholarships and abstract selected short talks is Jan 7! Join us this May for an amazing meeting! keysym.us/KSBeyondAntibiotics26 #KSBeyondAntibiotics26

I'll be speaking at Beyond Antibiotics: Emerging Strategies for Combating Bacterial Infection @keystonesymposia.bsky.social May 4-7, 2026. Abstract and scholarship submissions are open through Jan 7. Please encourage those in your network working on novel infection prevention/treatment to submit!

Incredibly powerful story from endocrinologist Dr. Caroline Fox candidly sharing her experience w an acute mental health crisis & her long, difficult, maddening, deeply inspiring journey towards recovery - & return to work as a senior biopharma R&D leader. www.youtube.com/watch?v=YVWS...

Largely agree with this—clinical validation of drugs is an extremely small N universe, and it’s not feasible to validate human- vs AI-generated hypothesis prob of success. AI is much better suited to solving the sub-problems in drug dev (which vanilla machine learning was already pretty good at).

Amazing resource—hope it gets used broadly and we see TnSeq datasets become more common for Bacteroidales.

Things I love about London: BOLLARDS

🚨 Microbiologists! We are recruiting Assistant / Associate Professors in 3 collaborative areas of our U. Pittsburgh School of Medicine. 1) MMG (my dept): fundamental research in med micro 2) Peds ID / I4Kids institute 3) Center for Vaccine Research 🔗 to all 3 w/info: www.linkedin.com/posts/vaughn...

Report: You To Be Fired For Reading This Headline About Charlie Kirk

Such a delight to share our work on the evolution of a cheese rind fungus in @currentbiology.bsky.social. This is the fantastic PhD work of @nicolasleonlouw.bsky.social and resulted from amazing collaborations, a wedding proposal(!), an undergrad course, & more! 🧵 www.cell.com/current-biol...

Preprint out for myloasm, our new nanopore / HiFi metagenome assembler! Nanopore's getting accurate, but 1. Can this lead to better metagenome assemblies? 2. How, algorithmically, to leverage them? with co-author Max Marin @mgmarin.bsky.social, supervised by Heng Li @lh3lh3.bsky.social 1 / N

We published a new lane of research today on human gut fungi. Shout out to 1st author @emilyvansyoc.bsky.social sky.social & @erdavenport.bsky.social For 20 years, bacteria received the lion's share of interest in the human gut. Yet we know little about the gut mycobiome. doi.org/10.1371/jour...

Optimizing storage, high-molecular weight DNA extraction and genome reconstructions from human faecal samples. https://www.biorxiv.org/content/10.1101/2025.08.27.672560v1

Cryptosporidium parvum multidrug resistance protein confers resistance to toxic gut microbial metabolite Wonder how frequent this variability in bile acid sensitivity is across bacterial pathogens! www.cell.com/cell-host-mi...

Very neat, looking forward to exploring this hypothesis with gut microbes. Nice work @sulheim.bsky.social

This work is finally published! 🥳🧬 Plasmids are associated with very variable fitness costs in their different bacterial hosts. But, what is the contribution of each of the plasmid-genes in these host-specific effects? Study led by @jorgesastred.bsky.social, @sanmillan.bsky.social and myself! 1/14

Vedanta has an opening for a contract QC analyst. Please share with your network! The ideal candidate will have both micro and molecular biology experience. job-boards.greenhouse.io/vedantabiosc...

Breaking: The Gates Foundation said it would commit $2.5 billion through 2030 to support women’s health initiatives, its largest funding commitment ever to the issue. www.statnews.com/2025/08/04/b...

Excited to share this collaborative study with @ritatamayo.bsky.social showing that E. faecalis influences C. diff morphology through the phase variable CmrRST system! This work was co-led by the amazing team of @ashleyweiss.bsky.social and Jilarie Santos-Santiago!

📖

Enterococcus faecalis modulates phase variation in Clostridioides difficile https://www.biorxiv.org/content/10.1101/2025.07.24.666506v1

New paper is out from our lab showing that some probiotics can accelerate and prolong the return of colonization resistance to C. difficile after antibiotics. news.ncsu.edu/2025/07/prob...

8ft tube light, no gas needed

Finally online! Our latest research is out @nature.com: We show that non-antibiotic drugs can disrupt colonization resistance, raising the risk of enteric infections. rdcu.be/ewwrG

After many months of waiting, there is one fewer gas appliance in the world! This battery-powered range from Copper (copperhome.com) helped us switch without needing a large electrical supply upgrade to our condo building.

Systematic pairwise co-cultures uncover predominant negative interactions among human gut bacteria -in BMC Microbiome microbiomejournal.biomedcentral.com/articles/10....

The annual PACCARB meeting l, hosted by HHS, is essential for disseminating research on AMR and developing the US national action plan, but was cancelled during the presidential administration transition. Several stakeholders issued this plea to reschedule. asm.org/articles/pol...

What’s everyone’s favorite “modern” textbook on bacterial metabolism? Gottschalk’s Bacterial Metabolism is great but now nearly 40 years since last edition. #microsky

Love the science being done on creatine right now… but it’s very quickly affecting the supply-demand equation. alz-journals.onlinelibrary.wiley.com/doi/10.1002/...

MINN: A METABOLIC-INFORMED NEURAL NETWORK FOR INTEGRATING OMICS DATA INTO GENOME-SCALE METABOLIC MODELING https://www.biorxiv.org/content/10.1101/2025.05.14.653943v1

Hot off the press in @nature.com the global evolution of #IBD across epidemiological stages www.nature.com/articles/s41... So nice to see the real-world data supporting theory in this @natrevgastrohep.nature.com Perspective www.nature.com/articles/s41... #gastrosky #IBDsky

A lot of what looks like microbial engraftment after FMT might actually be noise. Using placebo sequencing and culture-enriched metagenomics, we sort signal from noise. Our latest from the Surette lab: www.nature.com/articles/s41... @surettem.bsky.social @mcmasteruniversity.bsky.social

Dynamic coexistence driven by physiological transitions in microbial communities www.pnas.org/doi/abs/10.1... #jcampubs

New paper: long-term trends in antibiotic resistance show signs of stabilisation (thread). journals.plos.org/plospathogen...

Ah, the “I have small children” mouse model!

Peter Marks, FDA’s top vaccine regulator, forced out ‘It has become clear that truth and transparency are not desired,’ his resignation letter said. RFK Jr "wishes subservient confirmation of his misinformation and lies.” www.statnews.com/2025/03/28/f...

Looking forward to meeting folks in Brussels next week for the Microbiome Times partnering forum.

Introduce a new antibiotic (fidaxomicin), develop resistance to the new antibiotic (fidaxomicin). 😔 #AMR #IDSky #ClinMicro @cidjournal.bsky.social academic.oup.com/cid/advance-...

Disease tolerant mice shelter a pathogenic intestinal microbiota able to trigger lethal disease in low tolerant hosts -- this will be a fun read! www.biorxiv.org/content/10.1...

In two weeks I am headed to Brussels for the Microbiome Times partnering forum. Please reach out if you are interested in learning more about Vedanta or connecting at the event! www.microbiomeforum.com/speakers-pro...

Looking for either/both of: - service where I can paste some random text from an email containing a description of an event and its date and time, and have it parsed by AI and a nice event created in my Google calendar - that but achieved by forwarding an email to a special address

Already living RFK Jr’s ideal reality. Happy January, parents of small kids. This is the bad place: Norovirus 4x Ear infection 2x, perforation Flu Ear infection Ear infection, new perforation

Alternative drug modalities/approaches are desperately needed to supplement the pipeline of antibiotics.