Uncategorized

First up, Snorre Sulheim led a study probing the capacity of our 4-species synthetic community (species originally isolated from industrial fluids) to coexist on different minimal media in the lab. The answer: pretty much all of those we tested. We then explore all the different possible explanations we could think of and settle on metabolite cross-feeding as the main driver of this robust coexistence. A simple model shows that if species release enough different metabolites and others have different affinities for these metabolites and are somewhat specialized, it is not difficult to achieve such coexistence. It remains to be seen whether this will hold in other synthetic communities! Congratulations to all co-authors: Eric Ulrich, Alisson Gillon, Samuele Testa, Prajwal Padmanabha, and Miguel Teixeira and Daniel Machado our collaborators in Norway!

Second, Eric Ulrich published the main pre-print of his PhD! Our first venture into chemostat world. It turns out they are more complicated than I thought. We work through the theory and how to think about chemostats and then explore why two species from our 4-species SynCom (see above) again stubbornly coexist in a chemostat on a single carbon source. The answer is again cross-feeding, but this time, Eric shows how only micromolar concentrations of metabolites can be sufficient to support the coexistence of a species that would otherwise go extinct. Eric also shows that these metabolites don’t necessarily have to come from cross-feeding but can also be explained if the minimal medium contains trace contaminants, which we honestly expect to always be the case. Another important message from the paper: the effects that explain coexistence in chemostats are likely to be missed in batch culture competition experiments. So beware how you interpret those.

After several years as a pre-print, Björn, Pablo and Flora’s paper is now published in PLoS Computational Biology. I think it has much improved compared to the original version of the pre-print and I hope this clarity makes it more useful! Read it here.

I recently gave a talk about our work at the Microbiome Virtual International Forum. You can watch it here.

Led by Maggie Vogel and former lab member Oliver Meacock, also with Julien Luneau and Prajwal Padmanabha (not Sara ;)), check out this beautiful review (preprint) summarizing how concepts from classic ecology map to microbial ecology. It is a thought-provoking read that is also a great introduction to ecology and microbial ecology. Happy reading!

Check out the work by Alessia Del Panta, in collaboration with Alyssa Henderson, Olga Schubert and Simon van Vliet thinking about how to make sense of emergent spatial patterns in microbial communities: how does the feedback between the growth of organisms, their environment and the way the organisms’ growth changes the environment shape spatial patterns?

Second, Afra Salazar has just put our her first published work: an opinion piece discussing to what extent microbial communities can be seen as evolutionary individuals and how we can increase their similarity to evolutionary individuals with the goal of subjecting them to artificial selection in the lab.

What a day! 😀

I’m really excited that Flora’s paper is finally out at Nature Communications. The paper shows how one can apply artificial community selection, an approach inspired by genetic algorithms, to “breed” communities and find species combinations that are able to degrade pollutants. Huge thanks to all other co-authors: Björn Vessman, Alice Haym and Géraldine Alberti who played no small part in getting this project done. It would not have been possible without them!

Flora also wrote a “behind the paper” blog post, revealing the ups and downs we went through to get to the final result. A recommended read for all those feeling that their projects are too complicated and tedious:.

We are looking to recruit an experimentalist PhD student to join our lab to work on one of two projects: (1) controlling species coexistence in microbial communities, and (2) studying division of labour in denitrifying communities. Applicants are also welcome to suggest other topics that are in line with the interests of the lab, and whichever project is agreed upon will be adapted based on discussions.

Project 1: Natural microbial communities are often composed of many different species that stably coexist together over long timescales, exhibiting impressive emergent properties, such as the production of valuable nutrients in the gut or the regulation of the global carbon cycle. Taking inspiration from these and building similar, simpler communities from scratch, would enable and enhance many key technologies, including the degradation of pollutants, the sequestration of greenhouse gases or the production of valuable chemicals. Yet artificially combining environmental isolates to stably coexist in the long term is far from being a predictive science. This project aims to address this challenge: given a set of species, which ones should one combine in what chemical and physical environment to guarantee their long-term coexistence? The student will build a collection of species and characterize their growth and interactions in different chemical environments. Based on these measurements, a mathematical model will predict which species to combine in which environment to achieve stable coexistence. The student will then test these predictions through growth-and-dilution experiments. To deepen our understanding and ability to control these communities, these experiments will be repeated in altered chemical environments to break coexisting communities and fix ones that do not.

Project 2: Nitrous oxide is a potent greenhouse gas that is emitted in high concentrations from wastewater treatment plants and agricultural soil. Nitrous oxide is produced as the last step part of the denitrification pathway, which involves the conversion of oxidized nitrogen compounds to nitrogen gas. Individual steps of this pathway can be performed by many different bacteria in the environment. Such division of labour requires a delicate balance between all involved species, without which the populations of species that perform the last step in the pathway – the removal of nitrous oxide – may collapse, leading to a burst of nitrous oxide production. The goal of this project then is to understand and control this balance, such that the different denitrifying species can coexist together in a way that minimizes nitrous oxide production. The student will begin by constructing a collection of natural isolates that can perform different steps of the pathway. Each will be characterized according to its growth preferences. Using this information coupled with mathematical models developed in the lab, we will predict the conditions that balance the abundances of the different species to minimize nitrous oxide production. These predictions will then be tested in the lab.

You can find more details about the position and apply here before August 31st, 2024 (only applications via the link will be considered)!

Very much overdue: we have added some sections to the Research page. Check them out!

We have been having a great few months since several people joined the lab:

Prajwal Padmanabha joined as a postdoc in February!

Federica Sibilla (officially in Simon van Vliet’s lab) and Aitana Ralda Colfas have joined us as Master students.

Alisson Gillon is working with us over the summer as a research assistant.

Chiara Vischioni is visiting us through from Gianni Liti’s lab on a fellowship from the NCCR Microbiomes (our first time to work with yeast!)

And Théodora Steiner has just started as a research assistant in the lab for one year!

Welcome everyone!

I have been a bit slow updating our publication list, but it’s finally there! This year, in addition to a short highlight piece by Snorre, we have posted four papers on bioRxiv: two on artificial community selection (a theoretical model led by Björn and Pablo and a monster of an experiment led by Flora), one on how interactions can change to facilitation when the environment becomes toxic (experiment by Rita and model by Aurore) and a theoretical framework that can be used to predict how interactions can change as a function of the environment (by Oli)!

We have also published one paper where we built a simple model of the gut with two compartments and explore how this compartmentalization can affect the stability of the community (by Shota), and a review/opinion paper (by Shota, Aurore and Oli) discussing when one should use which model (Lotka-Volterra versus consumer-resource models) depending on the experimental system.

It’s been a productive year (go team!) and we’re excited to see what 2024 brings, with lots of exciting work in the pipeline 🙂