Alvaro Sanchez

Alvaro Sanchez

@asanchezlab.bsky.social

CSIC Professor and Principal Investigator of the Quantitative Biology group at IBFG in Salamanca. Previously at Yale EEB, CNB-CSIC. Our group works on building predictive models of biological teams. More information at www.sanchezlaboratory.weebly.com

1.1K followers1.1K following114 posts

Alvaro Sanchez reposted

Alvaro Sanchez reposted

This looks promising! "...free to read and free to publish, with no subscription barriers for readers and no article processing charges for authors. The journal is run by researchers, for researchers, with the goal of advancing ecology through systems thinking."

Systems Ecology@systems-ecology.bsky.social

We're pleased to share that Systems Ecology has now received its eISSN (3143-5769) and is a Crossref member with DOI prefix 10.67837. These are important steps as we prepare for our public launch in September. Free to read. Free to publish. systems-ecology.org

Alvaro Sanchez reposted

1/ Our new paper is out in PRX Life. Physicists' often treat microbiomes as disordered systems with coexistence in very high-dimensional niche spaces. We asked whether empirical data supports this picture, and found the data point somewhere else: journals.aps.org/prxlife/abst...

journals.aps.orgLow-Dimensional Coexistence in Complex Microbial EcosystemsAnalysis of nearly 200 human gut microbiome datasets shows that microbial coexistence is governed by a few effective ecological dimensions, rather than the high-dimensional niches assumed by prevailing theory.

Alvaro Sanchez reposted

It’s out! 🥹🎉 We’re so incredibly happy and proud to see this work out in the world. And once again, a huge thank you to the great mastermind @jaescudero.bsky.social and all the co-authors; this wouldn’t have been possible without you! doi.org/10.1038/s415... @natmicrobiol.nature.com

doi.orgHigh-throughput recovery of integron cassettes for gene discovery screens - Nature MicrobiologyIntegron insertion sites engineered into counterselection markers allow large-scale and high-throughput capture of integron-encoded genes from genetically tractable bacteria or DNA samples.
Filipa Trigo da Roza@filipatr.bsky.social

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...

Alvaro Sanchez reposted

Replying to @asanchezlab.bsky.social

We thus find that community function is predictable not because interactions are absent or weak, but because interactions at different orders are not independent, they're linked by simple linear relationships. What looks like significant intxn complexity can hide a strikingly simple organization.

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We thus find that community function is predictable not because interactions are absent or weak, but because interactions at different orders are not independent, they're linked by simple linear relationships. What looks like significant intxn complexity can hide a strikingly simple organization.

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This leads to a final hypothesis: if the dominant biomass mode is set by species yield, it should remain stable as species abundances change. We tested this over 10 days of serial passaging. Despite large shifts in abundance, the dominant mode barely moved and stayed aligned with yield.

The most surprising consequence is that presence/absence remained highly predictive of community function even after 10days of population dynamics. Communities moved far from their initial abundances, yet knowing which species were present at the start predicts community biomass at equilibrium!

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Importantly, this collapse is not just descriptive. Once the leading mode (u_1) is known, together with its eigenvalue and the additive effects, we can actually calculate the one-dimensional curve that organizes the landscape. With two modes, the same idea gives the full two-dimensional surface.

This is of course the classic "non-linear transformation of a latent, additive variable" that is the hallmark of global epistasis in genetics, only now demonstrated for ecological communities, and calculated explicitly from independently measurable parameters.

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Consumer-Resource models gave us a clear prediction: the dominant collective mode that makes community-function landscapes approximately 1-dimensional should be approx. the same as a vector of species traits, formed by the metabolic efficiencies, or yields, of each species.

This prediction also holds in the experiments. Across all 31 resource environments, the leading biomass mode closely aligned with species yields measured in monoculture. In other words, the dominant organization of community function could be traced back to a simple, measurable species trait.

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This simple organization has a major consequence: species’ effects on community function do not vary independently across backgrounds. Instead, they rise and fall together. As a result, the full community-function landscape becomes a function of just one or two ecological collective modes.

This is interesting but provides little ecological insight. What do these collective modes actually represent biologically? For biomass, we turned to consumer-resource models, where species compete for shared resources and their underlying traits are explicitly defined.

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To test this prediction, we built complete community-function landscapes containing every combination of five bacterial species, measuring both biomass and pyoverdine production. We then repeated the entire experiment across 31 different resource environments.

Indeed, across all species, higher-order interaction coefficients were strongly related to the corresponding lower-order ones, with slopes predicted by the FEEs. The same pattern held across different functions (e.g. biomass, pyoverdine) and all 31 resource environments.

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A clue comes from the previous observation of Functional Effect Equations (FEEs): the effect of adding a species often depends linearly on the function of the community it joins. But that effect itself emerges from interactions at all orders. What does a strong FEE tell us about those interactions?

The answer is remarkably simple: if a species follows a good FEE, its pairwise interactions scale with its additive effect, its three-way interactions with the corresponding pairwise ones, and so on across all orders.

We explore an apparent paradox: As communities grow in size, the number of possible interactions between their members grows exponentially. In principle, predicting community function should quickly become intractable. And yet, in experiments, this often isn't the case at all. What gives?