Evolution induced state shifts in a long-term microbial community experiment Biological communities are complex, dynamic systems that underpin ecosystem functionality, yet their long-term dynamics and predictability remain poorly understood. Understanding how Darwinian evoluti...

Evolution induced state shifts in a long-term microbial community experiment www.biorxiv.org/content/10.1...

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/...

The microbiome of the human facial skin is unique compared to that of other hominids | mSystems Understanding how and why human skin bacteria differ from our closest animal relatives provides crucial insights into human evolution and health. While we have known that human facial skin hosts disti...

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...

Mutualism breakdown underpins evolutionary rescue in an obligate cross-feeding bacterial consortium - Nature Communications Rapid genetic adaptation to environmental change, or evolutionary rescue, can be constrained by a less adaptable mutualistic partner. Here, the authors explore evolutionary rescue in an obligate mutua...

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

Coexistence Theory for Microbial Ecology, and Vice Versa Classical models from theoretical ecology are seeing increasing uptake in microbial ecology, but there remains rich potential for closer cross-pollination. Here we explore opportunities for stronger ....

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 Recent studies have revealed bacterial genome-wide evolution to be complex and dynamic even in a constant environment. The evolution is characterized by the emergence of new clades competing or tempor...

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:...

Obligate cross-feeding of metabolites is common in soil microbial communities Many microorganisms are refractory to laboratory cultivation. One possible explanation, known as the great plate count anomaly, is metabolic dependencies among community members. However, systematic s...

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 Nature Ecology & Evolution - Community resilience to stress is affected by factors such as pre-exposure to the same stress and intercommunity dispersal. The authors show that pre-exposing the...

Pre-exposure of abundant species to disturbance improves resilience in microbial metacommunities

www.nature.com/articles/s41...

E. coli prepares for starvation by dramatically remodeling its proteome in the first hours after loss of nutrients It is widely believed that due to nutrient limitations in natural environments, bacteria spend most of their life in non-growing states. However, very little is known about how bacteria change their p...

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

Nutrient-rich spatial refuges buffer against extinction and promote evolutionary rescue in evolving microbial populations | Proceedings of the Royal Society B: Biological Sciences Microbial populations are often exposed to long-term abiotic disturbances, which can reduce population viability and cause local extinction. Eco-evolutionary theory suggests that spatial refuges can f...

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...

Diverse phage communities are maintained stably on a clonal bacterial host Bacteriophages are the most abundant and phylogenetically diverse biological entities on Earth, yet the ecological mechanisms that sustain this extraordinary diversity remain unclear. In this study, w...

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/...

Extending evolutionary forecasts across bacterial species | Proceedings of the Royal Society B: Biological Sciences Improving evolutionary forecasting requires progressing from studying repeated evolution of a single genotype under identical conditions to formulating broad principles. These principles should enable...

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.

A high-resolution two-step evolution experiment in yeast reveals a shift from pleiotropic to modular adaptation Evolution is expected to involve mutations that are small and modular in effect, but recent findings suggest that mutations early in an adaptive process can have strong and pleiotropic effects. This s...

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...

A framework for understanding collective microbiome metabolism - Nature Microbiology This Perspective explores why microbiome members perform partial metabolism of substrates and suggests that proteome efficiency is a driver of collective microbiome metabolism.

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 While the evolutionary interests of mobile genetic elements may differ from those of their bacterial hosts, these elements can be beneficial for their hosts by delivering, disrupting, or activating ge...

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...

Conditionally unutilized proteins and their profound effects on growth and adaptation across microbial species Protein synthesis is an important determinant of microbial growth and response that demands a high amount of metabolic and biosynthetic resources. Des…

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...

Evolutionary risk analysis of mutators for the development of nitrofurantoin resistance The rising prevalence of antimicrobial resistance is a significant global health crisis. However, nitrofurantoin remains an outlier, with low resistance rates despite prolonged and sustained use. This...

📢 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...

Systematic discovery of antibacterial and antifungal bacterial toxins - Nature Microbiology Genome sequence mining and computational analyses lead to the discovery and functional characterization of conserved bacterial toxins with activity against bacteria and fungi.

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!

From resonance to chaos by modulating spatiotemporal patterns through a synthetic optogenetic oscillator - Nature Communications Oscillations are a recurrent phenomenon in biological systems across scales, but deciphering their fundamental principles is very challenging. Here the authors construct a synthetic oscillator in bact...

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

Reversion to metabolic autonomy underpins evolutionary rescue of a bacterial obligate mutualism bioRxiv - the preprint server for biology, operated by Cold Spring Harbor Laboratory, a research and educational institution

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...

Adaptation of Pseudomonas aeruginosa to repeated invasion into a commensal competitor bioRxiv - the preprint server for biology, operated by Cold Spring Harbor Laboratory, a research and educational institution

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...