Tami Lieberman

Don't miss out on our free virtual symposium (Dec. 12th) focused on microbial metabolites and their effects on the host.

Sponsors: @amiposts.bsky.social, Pendulum, & Liv (@zymoresearch.bsky.social)

Registrants will receive free memberships to Applied Microbiology International.

Details below 👇

Sentinel Awarded $100 Million to Prevent Pandemics

Thrilled to see this finally announced - and glad to see good things still happening to good people!

Congratulations to Pardis, Christian, and the rest of the Sentinel team! 👏🥳

www.macfound.org/press/press-...

people are actually very susceptible to just-so stories about human origins because listening to bullshit helped us survive on the savanna

Fecal exfoliome sequencing captures immune dynamics of the healthy and inflamed gut - Nature Biotechnology Profiling host RNA shed in feces reveals disease states in the gut.

Introducing Foli-seq in @natbiotech.nature.com today. Foli-seq can be used to measure gut-derived RNA from fecal matter (signals of immune, secretory & epithelial cells). We used this to map gut inflammation, drug response, and host-microbe interactions. 💩🧬💊🦠
www.nature.com/articles/s41...

Quantitative modeling of multi-signal quorum-sensing maps environment to bacterial regulatory responses Bacterial quorum sensing is often assumed to follow a strict hierarchy, limiting understanding of how multiple signals interact. This study finds that Pseudomonas aeruginosa uses a reciprocal, coopera...

Quantitative modelling of multi-signal quorum sensing in Pseudomonas aeruginosa reveals that its las and rhl signalling systems engage in reciprocal, non-linear and synergistic interactions rather than a simple hierarchy.

I had been elated to attend a scientific talk from a legend. It was fucking weird to see him objectifying these women. No mention of their scientific contributions, only their role as romantic interests. He even joked about how they knew not to work late nights in the lab because he might show up. 🤮

📢 Our Dept. of Systems Biology at Columbia University has an open tenure-track Assistant Professor position in the broad area of quantitative biology. Come join our awesome department in NYC! Please circulate.
apply.interfolio.com/177622
Suggested deadline: 12/15/2025.
@columbiasysbio.bsky.social

Very cool print demonstrating how variation in at TonB-dependent transporter repertoires shapes the ability of Bacteroides and Phocaeicola species to utilize fructooligosaccharides (FOS) of different chain lengths

Metagenomic editing of commensal bacteria in vivo using CRISPR-associated transposases Although metagenomic sequencing has revealed a rich microbial biodiversity in the mammalian gut, methods to genetically alter specific species in the microbiome are highly limited. Here, we introduce ...

Very excited to share our latest work in Science on metagenomic editing (MetaEdit) of the gut microbiome in vivo & directly modifying unculturable immune-modulatory SFB bug in the small intestine. 🦠🧬🛠️
www.science.org/doi/10.1126/...

Introgression impacts the evolution of bacteria, but species borders are rarely fuzzy - Nature Communications It is commonly thought that bacterial species borders tend to be fuzzy, due to frequent exchange of DNA. Here, Diop et al. quantify the patterns of gene flow between core genomes across 50 major bacte...

Introgression impacts the evolution of bacteria, but species borders are rarely fuzzy www.nature.com/articles/s41... #jcampubs

Yay Zam! Very happy to see your work recognized like this.

First page of Opinion piece: "Conceptual and methodological flaws undermine claims of a link between the gut microbiome and autism"

The link between the gut #microbiome and autism is not backed by science, researchers say.

Read the full opinion piece in @cp-neuron.bsky.social: spkl.io/63322AbxpA

@wiringthebrain.bsky.social, @statsepi.bsky.social, & @deevybee.bsky.social

2025 ISB Virtual Microbiome Symposium - Institute for Systems Biology (ISB) Symposium Schedule All presentation times are shown in Pacific Daylight Time (GMT -07:00 / UTC -07:00) Time Talk / Session 9:00 Welcoming remarks by Sid Venkatesh Session One: Neural Effects

📣 Join us for the 2025 @isbscience.org Virtual Microbiome Symposium, focused on "Gut Microbial Metabolites and Their Impact on Host Systems".

co-director - @flash-point.bsky.social 🦠💥

It's free, & we have an amazing line-up of speakers!

Dec. 12th. Please share!

isbscience.org/2025-isb-vir...

Are there good challengers yet?

Northern lights once again visible from my Cambridge MA rooftop. 🤯

An empirical approach to evaluating the prevalence of long-lived balancing selection in humans--and important limitations. Work by @hannahmm.bsky.social

Massively parallel interrogation of the fitness of natural variants in ancient signaling pathways reveals pervasive local adaptation The nature of standing genetic variation remains a central debate in population genetics, with differing perspectives on whether common variants are almost always neutral as suggested by neutral and n...

One of the most exciting works of my career, years in the making. We used high-throughput precision genome editing to test the fitness effects of thousands of natural variants. Our findings challenge the long-held assumption that common variants are inconsequential.

www.biorxiv.org/content/10.1...

Frequency-dependent fitness effects are ubiquitous In simple microbial populations, the fitness effects of most selected mutations are generally taken to be constant, independent of genotype frequency. This assumption underpins predictions about evolutionary dynamics, epistatic interactions, and the maintenance of genetic diversity in populations. Here, we systematically test this assumption using beneficial mutations from early generations of the Escherichia coli Long-Term Evolution Experiment (LTEE). Using flow cytometry-based competition assays, we find that frequency-dependent fitness effects are the norm rather than the exception, occurring in approximately 80\% of strain pairs tested. Most competitions exhibit negative frequency-dependence, where fitness advantages decline as mutant frequency increases. Furthermore, we demonstrate that the strength of frequency-dependence is predictable from invasion fitness measurements, with invasion fitness explaining approximately half of the biological variation in frequency-dependent slopes. Additionally, we observe violations of fitness transitivity in several strain combinations, indicating that competitive relationships cannot always be predicted from fitness relative to a single reference strain alone. Through high-resolution measurements of within-growth cycle dynamics, we show that simple resource competition explains a substantial portion of the frequency-dependence: when faster-growing genotypes dominate populations, they deplete shared resources more rapidly, reducing the time available for fitness differences to accumulate. Our results demonstrate that even in a simple model system designed to minimize ecological complexity, subtle ecological interactions between closely related genotypes create frequency-dependent selection that can fundamentally alter evolutionary dynamics. ### Competing Interest Statement The authors have declared no competing interest.

How common are frequency dependent fitness effects?

New preprint out today 👇
doi.org/10.1101/2025...

Super excited that the bulk of my PhD work is now preprinted! Here we used whole-community competition, or coalescence, experiments to quantify selection acting on genetically diverged strains within larger communities. (1/n)
www.biorxiv.org/content/10.1...

High-throughput conjugation reveals strain specific recombination patterns enabling precise trait mapping in Escherichia coli Author summary Escherichia coli demonstrates a remarkable ability to adapt to diverse environments. This adaptability is in part connected to its ability to recombine incoming DNA in its chromosome, a...

#microsky 😮

journals.plos.org/plosgenetics...

"The world's richest man continually manipulates his company's AI to lie about science and promote white supremacism" sounds like some hack sci-fi writing, but it's just our current reality

Registration here ai4id.eventbrite.com

Woops registration link here ai4id.eventbrite.com

Excited for the 'AI4ID Symposium: Bridging Infection and Artificial Intelligence' on January 28th at the Broad Institute.

The symposium will unite infectious disease researchers, clinicians, and AI experts to discuss how AI can help address the most pressing challenges in infectious diseases.

Next Gen Pregnancy Initiative - Burroughs Wellcome Fund by

The Next Gen Pregnancy Initiative is now accepting applications. Up to $500,000 over 4 years to support bold research into pregnancy duration, fetal growth, and pregnancy complications. Deadline: Dec 4, 2025.
Apply now buff.ly/rNhJKMW #bwfrepro

Open position at the Swiss Institute of Bioinformatics:
We are looking for a Director of the Center of Pathogen Bioinformatics
apply.refline.ch/499599/0346/...
I am in the Center's steering board together with fantastic colleagues (Emma Hodcroft @firefoxx66.bsky.social, Richard Neher @neher.io, and

Fantastic. Every school should have this!

www.nsf.gov/statistics/2...

Only 48% of US high schools offer calculus.

This seems like a huge problem and an easy place where high schools embracing online courses (+/- AI) could easily benefit students.