New review article with @mmdesai.bsky.social is out today! Grateful for the opportunity to contribute something we hope will serve the community well

Our paper in @science.org 👉🏽 www.science.org/doi/10.1126/... is accompanied by an especially thoughtful perspective by Carey Nadell and Chris Marx 👉🏽 www.science.org/doi/10.1126/...

Our work on the facial skin microbiome of non-human primates is out in mSystems! We show there is no close relative of Cutibacterium on the faces of gorillas and chimps at the Lincoln Park Zoo, furthering the mysterious origin of the dominant human skin colonizer. journals.asm.org/doi/10.1128/...

How does metabolic dependency evolve at the single cell level? 🔄 In our new preprint, Divvya Ramesh combines microfluidics, microscopy and modelling to show that the benefits of gene loss are highly context dependent. Check it out here: www.biorxiv.org/content/10.1...

1/ In our new paper, we explored whether obligate mutualisms can survive abrupt stress via evolutionary rescue. We found that evolutionary rescue is possible—but it comes at the cost of mutualism. @jfriedman.bsky.social #microsky #evosky #mevosky

A new preprint from the lab. Might be of interest to people who use barcode lineage tracking to catch de novo adaptive mutations. #popgen #evolbiol

In our new paper we discuss how modern coexistence theory can help microbial ecologists tackle fundamental & applied questions, and how microbial systems can help to push coexistence theory forward! With Andrew Letten and Dave Armitage (@darmitage.bsky.social). doi.org/10.1111/1462...

Community stability is usually assessed by invading single species from rare and measuring relative fitness. However does this hold up when multiple species invade from rare? We test this using our super stable microbial community 👇🏻

Universal bacterial clade dynamics dominate under predation despite altered phenotypes and mutation targets www.biorxiv.org/content/10.1...

Hey folks, microbial evolution (and I interpret this super broadly- bacteria, archaea, viruses, theory, Alife, field, lab, biophys, etc) now has a feed thanks to @atinygreencell.bsky.social. I hope this will be my ye olde Science Twitter v2. Come join us! 🧪 #MEvoSky Link: bsky.app/profile/did:...

New paper from my group and the group of @kiranrpatil.bsky.social: Obligate cross-feeding of metabolites is common in soil microbial communities By Ghada Yousif @metagenomez.bsky.social with @swagatika.bsky.social @isamirgiri.bsky.social Sharvari Harshe et al. www.biorxiv.org/content/10.1... 🧵👇

Pre-exposure of abundant species to disturbance improves resilience in microbial metacommunities www.nature.com/articles/s41...

What do bacterial cells do when they run out of nutrients? Although most bacterial studies focus on cells in exponentially growing states, in the wild bacteria likely spend most of their time slowly starving to death. 1/n www.biorxiv.org/content/10.1...

What does it really mean to be in nutrient colimitation? We demonstrate a distinct growth phenotype and that (co)limitation can (and should!) be quantified. The result of many late afternoon chats with @michaelmanhart.bsky.social. Let us know what you think! www.pnas.org/doi/10.1073/pnas.2400304121

Excited to share a sparkly new paper from our lab! We show how spatial refuges can facilitate evolutionary rescue using experimental evolution with P. fluorescens doi.org/10.1098/rspb...

Is it “winner-takes all” when the simplest living things compete? Check out my fresh publication on phage coexistence in Science and a thread below🧵 www.science.org/doi/10.1126/...

Final version of our article testing previous evolutionary forecasts in two Pseudomonas species is now out in Proceedings B royalsocietypublishing.org/doi/10.1098/... . Work led by @jtpentz.bsky.social, with Aparna Biswas and Bassel Alsaed.

Do mutations that drive evolution improve many traits or few? Does this change over the course of evolution? Excited to share our work in PLOS Biology exploring these questions in the first 2 adaptive steps w/ Yuping Li, @gsherloc.bsky.social, @petrovadmitri.bsky.social 🧵 doi.org/10.1371/jour...

Outstanding work on distributed metabolism in microbiomes in @naturemicrobiol.bsky.social by PharmaBiome's great Matthias Hülsmann from his time at @micsysecolab.bsky.social. I'm super excited to work together on our next consortium LBPs. www.nature.com/articles/s41...

Agents of change: a partnership between mobile genetic elements facilitates rapid bacterial adaptation #TrendsMicrobiol Spotlight by Elizabeth Duan, @oliviakosterlitz.bsky.social and Benjamin Kerr on the Nat Eco Evo paper from @sanmillan.bsky.social group www.cell.com/trends/micro...

This is a really important perspective on microbial ecology/evolution (Balakrishnan & Cremer). Quantitative physiology shows that microbes do not optimize growth, but instead express unutilized proteins that confer distinct dynamics when environments change. www.sciencedirect.com/science/arti...

📢 New preprint: Mutator strains of E. coli accelerate nitrofurantoin resistance by enabling both faster evolution and "better" resistance mutations. We also find evidence for defects in DNA replication fidelity and repair in clinically-resistant isolates. Read more: www.biorxiv.org/content/10.1...

Several years of work with several great collaborators, that combined computational biology, molecular microbiology, biochemistry, structural biology and mycology assay culminated in today's publication on discovery of novel bacterial toxins: www.nature.com/articles/s41...

Great to see our paper published! We show that the presence of another species doesn't necessarily influence evolution. @jfriedman.bsky.social authors.elsevier.com/c/1jxht8YyDf... Thanks to the anonymous reviewers for their constructive comments!

Very happy to see the “optoscillator” - a synthetic optogenetic oscillator - published! By applying light pulses on growing E. coli colonies and analysing the ring patterns, we observed synchronisation, (subharmonic) resonance, period doubling and chaos! www.nature.com/articles/s41...

Our article on microbial interactions is out! We discuss what are microbial interactions, what are they useful for, and how to quantify them. For more, see lead author @nittaym.bsky.social 's 🧵: x.com/NittayMeroz/... or read the full article here (free access until Sep 1st): shorturl.at/ONiNS

Happy to share our latest manuscript we we study evolutionary rescue in a bacterial mutualism: Reversion to metabolic autonomy underpins evolutionary rescue of a bacterial obligate mutualism shorturl.at/tFNTw

Brilliant paper. A great example of how principles of quantitative physiology can inform our understanding of microbial evolution. "Proteome partitioning constraints in long-term laboratory evolution" www.nature.com/articles/s41...

Sharing the preprint for my first foray into experimental evolution: adaptation of Pseudomonas aeruginosa to repeated invasion into a commensal competitor 🦠🧬 www.biorxiv.org/content/10.1...

Almost a decade after proposing this experiment in a grant application, we have a preprint! A huge experiment by Philippe Piccardi with many helping hands to generate and analyze the data especially genomic & transcriptomic analysis by Eric Ulrich! www.biorxiv.org/content/10.1...

We have a new preprint testing our previous evolutionary forecasts in two Pseudomonas species. Some successes & some surprises. Work mainly by Jennifer Pentz, with Aparna Biswas and Bassel Alsaed. www.biorxiv.org/content/10.1...

New collaborative work from our lab on the transmission of AMR in a community context. www.biorxiv.org/content/10.1... We find that Gram positive bacteria, particularly enterocci, increase the conjugation efficiency of uropathogenic E.coli.

1/5 Can random sequences encode meaningful functions and allow de novo gene birth? To explore this, Michael Laub and I screened 100 million random genes, without sequence similarity to natural genes, for their ability to rescue growth arrest of E. coli cells producing the ribonuclease toxin MazF.

Excited to share our new preprint! w @jfriedman.bsky.social #Microsky#evosky We tackle a simple question - How much of species evolution depends on the presence of other species? Bottom line: Most evolutionary changes were robust across strains that evolved with different biotic partners 1/