Interesting new preprint from Giulia Ghedini's lab comparing trait-based and population-based predictability in phytoplankton communities:
Fant et al, Ecological predictability emerges at the population level in phytoplankton communities www.biorxiv.org/content/10.6...
Moran et al. in Science
Emergent predictability in microbial ecosystems
www.science.org/doi/10.1126/...
It looks like there will be an open postdoc position in my lab soon. I'll be looking for someone with substantial wet-lab experience in microbiology / microbial ecology / evolution / physiology. If everything goes well, an ad will be coming. But if you know someone, ask them to reach out already.
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 journals.plos.org/ploscompbiol...
New preprint alert!!! 🚀🤓 We are very happy to finally share this with the world — the result of seven years of work and a new tool to study integrons and discover new functions encoded in these bacterial platforms.
If you want to know more, here is a thread 🧵
www.biorxiv.org/content/10.6...
This paper started as an idea @albertomarina.bsky.social had many years ago… which of course means he was right all along 😄. Some of us just needed a few years (and a lot of experiments) to catch up.
Grateful (and slightly humbled) to be part of this. Thanks Alberto!
www.cell.com/cell/fulltex...
We are pleased to share our last article rdcu.be/fabhM. It offers the most comprehensive analysis so far of Ab+non-Ab resistance genes in human gut microbiome, using an Indigenous population (low industrialization, chronic Hg exposure from gold mining) 6/6👇
Glad to see our latest work out in Nature Microbiology!!
Extremely grateful to everyone involved in the project.
Check it out!! 👇🏻👇🏻
From genes to collective modes: biological constraints shape metabolic evolution www.biorxiv.org/content/10.64898/2026.03...
📢¡Atención! El #IRNASA-CSIC busca incorporar un/a Técnico/a de Internacionalización y Gestión de Proyectos Europeos.
🗓️Hasta el 23 de marzo.
🔗Más info: www.irnasa.csic.es/nuevo-puesto...
Excited to share our latest work! 📝
We measured the fitness effect of 136 AMR genes and found that many are neutral or even beneficial without selection. 🤯🧬
Oxygen availability can flip their fitness and our stochastic model indicates that oxygen fluctuations help maintain them.
Learn more 👇🏼
Thank you Itzik!!
This! 👇
That being said, we do find that the strength of interactions that CAN be resolved over noise does decline for higher-order interactions. Above third order they cannot be reliably discriminated from empirical noise.
Even if higher-order interactions exist biologically and are strong, they will tend to contribute little to the total variance in small landscapes, simply because there are few of them.
Noise amplification and structural constraints severely limit our ability to detect them.
Importantly, all previously studied fully sampled landscapes are smaller than ours (Typically N=8 or smaller). In practice, combinatorial explosion means that fully sampled experimental landscapes become extremely difficult to measure once we reach ~10 species.
Note that these two factors are purely statistical and do not speak of the underlying biology. As the number of species increases, the relative contribution of higher-order interactions to the total variance will eventually grow, simply because there are many more of them.
Part of this pattern is structural. Two factors shape the variance spectrum: how many interactions exist at each order, & a geometric factor that suppresses higher orders as the number of measurements needed to estimate them grows. Together they naturally bias landscapes toward low-order structure.
To analyze the global structure of the landscape, we decomposed the total functional variance by interaction order. Consistent with previous work, first- and second-order interactions explain most of the variance, while higher orders contribute very little.
To explore this empirically, we built one of the largest, factorially complete microbial community-function landscapes we are aware of, containing all 1023 communities one may form with 10 species, each in 5 biological replicates. Function was optical density, a metric of productivity.
Estimating higher-order interactions quickly becomes difficult. A k-species interaction requires combining measurements from 2^k different community configurations.
Because each measurement contains experimental noise, uncertainty grows exponentially with interaction order.
In this framework, interactions appear as epistasis. If the effect of adding one species depends on whether another species is present, we have an interaction. Higher-order interactions involve three or more species simultaneously.
We study community-function landscapes, where each species may be either present or absent, and each community composition maps to a measurable function (e.g. total biomass).
This defines a high-dimensional map from composition → ecosystem function, inspired by fitness landscapes in genetics.
New preprint on the limits of detecting higher-order interactions in microbial communities.
www.biorxiv.org/content/10.6...
We find that the dominance of additive and pairwise interactions on community function may not reflect biological simplicity, but fundamental limits of statistical detection.
New #BehindThePaper for our latest paper in @natcomms.nature.com (rdcu.be/e2qMK)
Secret Invasion: Strain Fate Across Microbiomes
Cover illustration by Helena Klein (@illuzation.bsky.social).
communities.springernature.com/posts/secret...
How does population density affect evolutionary trajectory?
Microbes construct their own niche which in turn reshapes their evolution.
Preprint drop from grad student @noahhoupt.bsky.social whose evolution experiments featured blue/white colonies, 1000 generations, a lab move, and much more!
Registration is open for the inaugural GRC conference in the Function of Evolving Systems. Aug 9-14, 2026, Waterville Valley. Truly stellar speaker lineup. Student/postdoc fellowships are available! Please come join us! www.grc.org/function-of-... @joybergelson.bsky.social
New paper out in @pnas.org, and it made the cover! 👁️
We represent plasmids as circles and mutations as dots, resembling an eye, because in this paper we literally 𝑤𝑎𝑡𝑐ℎ plasmids evolve.
‼️Check Paula’s 🧵 and the paper👇
𝗣𝗹𝗮𝘀𝗺𝗶𝗱 𝗺𝘂𝘁𝗮𝘁𝗶𝗼𝗻 𝗿𝗮𝘁𝗲𝘀 𝘀𝗰𝗮𝗹𝗲 𝘄𝗶𝘁𝗵 𝗰𝗼𝗽𝘆 𝗻𝘂𝗺𝗯𝗲𝗿
www.pnas.org/doi/10.1073/...
