Nittay Meroz
@nittaym.bsky.social
Studying microbial evolution & ecology. Postdoc @the Microbial Systems Ecology group, Eawag/ETH Zürich
Thrilled that our paper "Eco-evolutionary dynamics of massive, parallel bacteriophage outbreaks in compost communities" is out! 🎉🦠🧬 www.science.org/doi/10.1126/... w/ @paulbrainey.bsky.social, Petros Skiadas, Paulien Hogeweg, @bedutilh.bsky.social
Eco-evolutionary dynamics of massive, parallel bacteriophage outbreaks in compost communities
A single bacteriophage can dominate microbial communities yet only evolves when migration changes its ecological context.
science.org
Evolution induced state shifts in a long-term microbial community experiment www.biorxiv.org/content/10.1...
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...
biorxiv.org
New review article with @mmdesai.bsky.social is out today! Grateful for the opportunity to contribute something we hope will serve the community well
Nature Reviews Genetics@natrevgenet.nature.com · last yr.New online! Experimental evolution in an era of molecular manipulation
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/...
Antagonism as a foraging strategy in microbial communities
In natural habitats, nutrient availability limits bacterial growth. We discovered that bacteria can overcome this limitation by acquiring nutrients by lysing neighboring cells through contact-dependen...
science.org
Glen Dsouza@nonresidentdesi.bsky.social · last yr.This story started when we put two Vibrio species commonly found in the coastal oceans under the microscope. V. anguillarum cannot grow on alginate, an algal polysaccharide, but V. cyclitrophicus can. So how does the former species grow? The answer: By killing the ones that can #Microsky #T6SS
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/...
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...
journals.asm.org
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...
biorxiv.org
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
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...
nature.com
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
bioRxiv Evolutionary Biology@biorxiv-evobio.bsky.social · last yr.A Bayesian filtering method for estimating the fitness effects of nascent adaptive mutations https://www.biorxiv.org/content/10.1101/2025.03.29.646120v1
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...
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 ....
doi.org
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 👇🏻
Ákos T Kovács@evolvedbiofilm.bsky.social · last yr.Estimates of microbial community stability using relative invader growth rates are robust across levels of invader species richness #ISMEComms by @mcastd.bsky.social, @padpadpadpad.bsky.social and Angus Buckling academic.oup.com/ismecommun/a...
Universal bacterial clade dynamics dominate under predation despite altered phenotypes and mutation targets www.biorxiv.org/content/10.1...
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...
biorxiv.org
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... 🧵👇
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...
biorxiv.org
Pre-exposure of abundant species to disturbance improves resilience in microbial metacommunities www.nature.com/articles/s41...
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...
nature.com
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...
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...
biorxiv.org
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
pnas.org
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...
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...
doi.org
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/...
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...
science.org
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.
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...
royalsocietypublishing.org
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 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...
doi.org
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...
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.
nature.com
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...
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...
cell.com
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...
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…
sciencedirect.com
📢 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...
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...
biorxiv.org
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...
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.
nature.com
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!
authors.elsevier.com
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...
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...
nature.com
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
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
shorturl.at
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...
