Last week I took one of my favorite Chicago photos of all time. This city is LONG

Our latest is out today in @plosbiology.org: "Metabolic modeling reveals determinants of prebiotic and probiotic treatment efficacy across multiple human intervention trials" @isbscience.org @uwbioe.bsky.social @uwgenome.bsky.social doi.org/10.1371/jour...

Yes, they can hallucinate papers that don't exist, discuss results that seem to be imaginary, and can be confusing and inconsistent. But talking to tenured professors may still be helpful

Terrible. Still need to see a bit more of the timeline, but based on this trend I don't see how the NIH will fund even 10,000 new awards this fiscal year. Maybe closer to 8000

In 1800 (not that long ago!) the average life expectancy was ~30 years.

I've been hearing from more and more people who received peer reviews that were clearly written by AI. It's frustrating, and no one knows what to do. I have some thoughts. blekhman.substack.com/p/so-your-pa...

Good morning from Chicago

I am seeking a postdoc to join my group at UCLA -- ideally the candidate would have some experience in either population genetics or microbes/microbiome (computational background needed). We have a range of projects and are happy to tailer to your interests. Please dm/email me if interested.

We should talk more about the graduate admissions crisis that's taking shape in the US. Talking to colleagues across universities, many graduate programs are slashing admission numbers and reducing class sizes substantially for the upcoming academic year. This is shortsighted

if you're in line to sack drake maye, STAY IN LINE

Our new paper, where we use metabolic modeling to show Fusobacterium grows faster in colorectal tumor vs normal tissue microenvironments, and use computational + experimental approach to find specific metabolic pathways driving host-microbiome interactions in cancer www.biorxiv.org/content/10.6...

This is not heartbreaking. Keep in mind that the authors perspective: they probably disagree that their paper "needs a lot of work". Instead they find another journal (and another set of reviewers) that agree with them, and save months of expensive, time consuming, unnecessary work.

Breast milk isn't just nutrition – it delivers live bacterial strains that colonize the infant gut and persist for months. Happy to share our new paper, where we used metagenomics to track bacterial strains between 195 mother-infant pairs over the first 6 months of life: doi.org/10.1038/s414...

I just signed up and read the first of Ran's posts. Excellent stuff, highly recommended.

I'm usually skeptical about AI research tools. But Google's new tool for literature search is fantastic - because it does less, not more. New post: substack.com/home/post/p-...

My favorite Chicago photos of 2025

another one bites the dust

Review: Genomics of host–microbiome interactions in humans by @pamferretti.bsky.social ocial, Kelsey Johnson, @sambhawa.bsky.social & @blekhman.bsky.social rdcu.be/etIRy

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...

One month later

Due to the shutdown, NIH cancelled >370 study sections, impacting >24,000 applications Rescheduled meetings will only discuss 30-35% of applications, have simplified summary statements (no narrative paragraph), and a new category - "competitive but not discussed" grants.nih.gov/grants/guide...

Great example of what I call a "grift bag"

I wrote about the recent autism-microbiome paper, why I think it's the most important microbiome paper this year, and what it says about the field open.substack.com/pub/blekhman...

Amazing journal cover for the new Trends In Microbiology special issue on geographic diversity in microbiology www.cell.com/trends/micro...

🧬 🦠 🏙️ Urban vs rural lifestyles create dramatically different gut microbiomes. But how do these different gut microbiomes affect the host? Excited to share our new paper: www.biorxiv.org/content/10.1...

Indiana Dunes National Park, yesterday

Never seen our campus like this before. Like every single tree decided to turn red at the same moment

So funny that this is still the top search term for biorxiv. Like asking what is the impact factor of pubmed. Or your local library.

UChicago Microbiology is searching for tenured or tenure-track faculty working in host-pathogens interactions, viral and bacterial pathogenesis, and emerging infectious diseases. Come join our vibrant Department! microbiology.uchicago.edu Apply here apply.interfolio.com/174404

Night heron, spotted at the Garden of the Phoenix

Unrelated to anything, just a cool recent paper jamanetwork.com/journals/jam...

Garden of the Phoenix in Hyde Park is a gem

I'm hiring a computational biologist interested in complex trait genetics using deep learning approaches. Reach out to me, if interested.

Excellent journal club discussion today of a new paper finding human genetic variants associated with fungi in the gut - interesting results! journals.plos.org/plosbiology/...

Update from Chicago. The situation is dire. Complete anarchy. Please send the national guard asap to put an end to this lawlessness

More foundations should do this: "Funding is exclusively available to applicants who have already received federal funding (e.g., from the NIH, CDC, NSF) for their health equity research, but have since had their funding rescinded due to federal administrative actions" www.rwjf.org/en/grants/ac...

"It's people who will get cancer in 10, 20 or 30 years who will really pay the price." We're literally defunding our future survival.

Cool application of microbiome in food science Using metagenomics on Colombian cacao, they mapped how microbes influence chocolate flavors. Then they built a defined microbial consortium that replicates premium chocolate flavors -- validated by trained tasters! www.nature.com/articles/s41...

The second BME UNITE Future Faculty Seminar will be on Monday, August 25th, at 1 pm EST. Come hear from Drs. Mattea Allert, Taj Yeruva, and Said Arévalo Alquichire, PhD to learn more about their science and future research programs! Register here: tinyurl.com/bmeunite25

Chicago ✈️

200 days in, checking in on HHMI funding opportunities: Freeman Hrabowski Scholars Program - not accepting applications Gilliam Fellows Program - not accepting applications Hanna H. Gray Fellows Program - not accepting applications Investigator Program - not accepting applications

Fascinating new paper reveals a new gut microbiome connection to heart disease. Microbes produce imidazole propionate (ImP), which directly triggers atherosclerosis through immune activation - even without high cholesterol. www.nature.com/articles/s41...

Good night from Chicago

New paper in @nature.com! With @kiseokmicro.bsky.social , Siqi Liu, Kyle Crocker, Jojo Wang, Mikhail Tikhonov & Madhav Mani — a massive dataset and simple model reveal a few conserved regimes that capture how soil microbiome metabolism responds to perturbations. www.nature.com/articles/s41...

New paper showing that gut bacteria absorb "forever chemicals" (PFAS) at high levels. This bacterial "sponge effect" could influence PFAS levels in our bodies and explain individual differences in PFAS exposure. www.nature.com/articles/s41...

Our article on the challenges and opportunities in studying host-microbe symbioses is now published in Cell Host & Microbe! @cp-cellhostmicrobe.bsky.social www.sciencedirect.com/science/arti...

Some personal news: I was recently promoted to Full Professor at the University of Chicago. This milestone is deeply meaningful, and also feels quite surreal. When I started as a graduate student at UChicago in 2005 I never imagined my journey would lead me here 20 years later as a professor.

New paper that looked at 15 million biomedical abstracts and found specific words that abruptly increased in frequency in 2024, likely due to the authors using LLMs. Take home message: don't use the word "Delve" www.science.org/doi/10.1126/...