Alvaro Sanchez Lab

Plasmids promote bacterial evolution through a copy number-driven increase in mutation rate Plasmids are autonomously replicating DNA molecules that stably coexist with chromosomes in bacterial cells. These genetic elements drive horizontal gene transfer and play a fundamental role in bacter...

New paper alert! 🚨

Plasmids promote bacterial evolution through a copy number-driven increase in mutation rate.

We combine theory, simulations, experimental evolution, and bioinformatics to demonstrate that mutation rates scale with plasmid copy number.

Let's dive in! 🧵👇

Do plasmids evolve faster 🐇, slower 🐢, or just like chromosomes 🧬?

In our new paper, we tackled this question using theory, simulations, bioinformatics, and experiments!

👇 Check out all the details in Paula’s thread!

Hint: 🐇 (most of the time)

Check out my first PhD paper on between-species genetic interactions (intergenomic epistasis) with @cbank.bsky.social 🌿↔️🦠✨ We define intergenomic epistasis mathematically and highlight its potential in understanding co-evolution :)

Non-antibiotics disrupt colonization resistance against enteropathogens - Nature Non-antibiotic drugs from a wide range of therapeutic classes can alter the ability of gut commensals to resist invasion by enteropathogens, a previously underappreciated side effect of such drugs.

Seeing this published is even better than eating sweets! I am so happy and proud of whole @lisamaierlab.bsky.social, especially Lisa and @jdlcz.bsky.social who walked the funny/exciting/rocky road with me until the very end. Check it out!
#science #microbiome #health

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

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...

This paper by Belda et al makes the case for wine fermentation as a model system in microbial ecology and evolution, one which hits a sweet spot between experimental tractability and rich ecological and evolutionary dynamics.
enviromicro-journals.onlinelibrary.wiley.com/doi/full/10....

This paper by Shraddha Karve discusses how evolutionary novelties emerge in microorganisms, focusing on the different types of novel traits and the role played by the environment.
enviromicro-journals.onlinelibrary.wiley.com/doi/10.1111/...

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 ...

This piece by Orr, Armitage & Letten provides a nice & clear introduction to modern coexistence theory for microbiologists, discussing how it can be applied to microbial communities & highlighting its promise, limitations & opportunities.
enviromicro-journals.onlinelibrary.wiley.com/doi/10.1111/...

Assembly Graph as the Rosetta Stone of Ecological Assembly This paper introduces the assembly graph as an integrative lens to unify ecological assembly theories across dynamical, informational, and probabilistic approaches. In addition to theory, it also pre....

This excellent article by @clsong.bsky.social‬ synthesizes research on the Assembly Graph, a useful conceptual & methodological tool to understand the dynamic assembly of microbial communities and multispecies coexistence.
enviromicro-journals.onlinelibrary.wiley.com/doi/abs/10.1...

This paper by Belda et al makes the case for wine fermentation as a model system in microbial ecology and evolution, one which hits a sweet spot between experimental tractability and rich ecological and evolutionary dynamics.
enviromicro-journals.onlinelibrary.wiley.com/doi/full/10....

This paper by Shraddha Karve discusses how evolutionary novelties emerge in microorganisms, focusing on the different types of novel traits and the role played by the environment.
enviromicro-journals.onlinelibrary.wiley.com/doi/10.1111/...

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 ...

This piece by Orr, Armitage & Letten provides a nice & clear introduction to modern coexistence theory for microbiologists, discussing how it can be applied to microbial communities & highlighting its promise, limitations & opportunities.
enviromicro-journals.onlinelibrary.wiley.com/doi/10.1111/...

Assembly Graph as the Rosetta Stone of Ecological Assembly This paper introduces the assembly graph as an integrative lens to unify ecological assembly theories across dynamical, informational, and probabilistic approaches. In addition to theory, it also pre....

This excellent article by @clsong.bsky.social‬ synthesizes research on the Assembly Graph, a useful conceptual & methodological tool to understand the dynamic assembly of microbial communities and multispecies coexistence.
enviromicro-journals.onlinelibrary.wiley.com/doi/abs/10.1...

How may theoretical ecology & evolutionary theory push microbiology forward?
At Environmental Microbiology, I am commissioning a series of Perspectives exploring that question. Excited to share them in the 🧵 below
The series is open, so do get in touch if you'd like to propose a new contribution!

Chromosomal capture of beneficial genes drives plasmids toward ecological redundancy Abstract. Plasmids are a ubiquitous feature of bacterial genomes, but the forces driving genes and phenotypes to become associated with plasmids are poorly

New paper with @rwheatley8.bsky.social and Cedric Lood

Actual title: Chromosomal capture of beneficial genes drives plasmids towards ecological redundancy.

Sensationalist title: Plasmids carry useless genes

academic.oup.com/ismej/articl...

Felipe VI, king of Spain, greeting my grandma

Felipe VI and Jero

A selfie of some of the Prize Recipients

It was an honor and a joy to receive the National Research Prize for Young (!) Researchers. The highlight? My grandma greeting the King of Spain.

What a day!

www.youtube.com/watch?v=oSQP...

Universal rules govern plasmid copy number - Nature Communications Plasmids exhibit a broad range of sizes and copies per cell, and these two parameters appear to be negatively correlated. Here, Ramiro-Martínez et al. analyse the copy number of thousands of diverse b...

🚨🚨New paper out in @natcomms.nature.com!!

Come for the first large-scale analysis of plasmid copy number across species,
stay for one of the most intriguing results of my lab: universal scaling laws in plasmid biology! 📈🧬

👉 www.nature.com/articles/s41...

Happy to have this out! Thanks to @asanchezlab.bsky.social and @jacrickets.bsky.social for their mentorship on this project. Below is the thread I previously posted on then-Twitter

Macroecological patterns in experimental microbial communities Author summary Determining whether an empirical pattern can be manipulated is a crucial step towards building a predictive theory. Our study aimed to determine the extent that experimental manipulatio...

Macroecological patterns in experimental microbial communities, led by Will Shoemaker & Jacopo Grilli
journals.plos.org/ploscompbiol...

Microbial communities can harbor many species that do not coexist in pairs, yet can coexist in the full community. Here we provide the mathematical foundations of emergent coexistence, and explain why it can't be predicted from pairwise tests www.biorxiv.org/content/10.1...

How can we understand ecosystem dynamics using information theory? Using Shannon's entropy, this paper by Chuliang Song gives a clever introduction to IT within the context of assembly graphs. @longcy.bsky.social @guimaguade.bsky.social @blaividiella.bsky.social
www.clsong.com/assets/pdf/s...

Mobile integrons encode phage defense systems Integrons are bacterial genetic elements that capture, stockpile, and modulate the expression of genes encoded in integron cassettes. Mobile integrons (MIs) are borne on plasmids, acting as a vehicle ...

🧪
Finally out after peer review, our work showing that "Mobile #Integrons carry Phage Defense Systems" is now published in Science 🎉

Short 🧵
www.science.org/doi/10.1126/...

Very neat application of the community-function landscape! Congrats @seppekuehnlab.bsky.social and rest of coauthors!

Genome duplication in a long-term multicellularity evolution experiment - Nature In the Multicellularity Long Term Evolution Experiment, diploid yeast evolve to be tetraploid under selection for larger multicellular size, revealing how whole-genome duplication can arise due to its...

1/46 Hey folks, we have a new paper out on the MuLTEE. Strap in and I’ll tell you the story of how this “little paper on polyploidy” turned into the most data rich paper our lab has produced, largely thanks to the leadership and work ethic of @kaitong25.bsky.social.

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

Experimental evolution of evolvability Evolvability—the capacity to generate adaptive variation—is a trait that can itself evolve through natural selection. However, the idea that mutation can become biased toward adaptive outcomes remains...

Lovely paper. The bug we work on, Neisseria gonorrhoeae, has *hundreds* of genes that can phase-vary (stochastically switch on and off), to allow immune evasion and adaptation to different niches within and between hosts. 1/

Plant domestication does not reduce diversity in root microbiomes Domestication has profoundly shaped human civilization and the genetic makeup of numerous plant and animal species. While the effects of plant domestication at the genetic and phenotypic levels are well-documented, its impact on plant microbiome remains less understood. Root microbiomes play crucial roles in nutrient acquisition, pathogen defense, and biotic stress tolerance, yet the influence of domestication on their diversity and assembly is still debated. Two primary hypotheses have been proposed: 1) the reduction in microbial diversity resulting from the domestication process, and 2) the diminished ability of host plants to control their microbiomes. To evaluate these hypotheses, we conducted a meta-analysis of multiple crops, comparing the root microbiomes of domesticated plants and their wild relatives. Our results indicate that the effects of domestication are species-specific and context-dependent, with most domesticated plants exhibiting increased microbial diversity and more structured communities, while others show no significant change. Overall, this study provides evidence that plant domestication does not lead to a uniform reduction in microbial diversity or a consistently diminished ability of plants to influence their microbiomes. Based on these findings, we discuss new perspectives and the need for future studies incorporating native soils and host genetic variation in such experiments, analyzing not only diversity but also microbiome function, and considering how root morphology might affect microbiome recruitment. Finally, we highlight the need for research on the potential adaptive or maladaptive consequences that introgression between wild and domesticated plants could have from a microbiome perspective. ### Competing Interest Statement The authors have declared no competing interest.

In the literature of domestication and microbiomes there seems to be the expectation that: domestication should lead to the loss of microbiome diversity and host-control. Alejandra Hernandez-Teran and I were both skeptical of both, so we decided to see what we know so far (1/6)
shorturl.at/FHY9H

⚠️ Job(s) alert! ⚠️

We are launching a new postdoctoral program in Systems Biology at IBFG. Join us!

👉 Several positions available with competitive work conditions for up to 4 years

📄 More info: jdiazc9.github.io/files/jobs/2...

A plasmid-chromosome crosstalk in multidrug resistant enterobacteria - Nature Communications The authors describe a new crosstalk between a globally disseminated carbapenem resistance plasmid and clinical enterobacteria clones. This crosstalk provides a fitness advantage to the plasmid-carryi...

www.nature.com/articles/s41...
New paper out!!

Global epistasis and the emergence of function in microbial consortia Global epistasis, traditionally applied in genetics research, can be used to model complex microbial communities and predict the effects of a species on community-level functions.

If interactions may instead refer to functional effects (funct effect of B is different when A is also present) this is one of my favorite questions!
www.cell.com/cell/fulltex...

Learning beyond-pairwise interactions enables the bottom–up prediction of microbial community structure | PNAS Understanding the assembly of multispecies microbial communities represents a significant challenge in ecology and has wide applications in agricul...

If you are interested in pairwise interactions defined as the effect two species have on each other’s population size, this paper comes to mind:
www.pnas.org/doi/10.1073/...
@kostchristian.bsky.social