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Prajwal Padmanabha

@lambdapp.bsky.social
165 followers 178 following 29 posts

Ecology of microbes with statistical physics lens - theory and experiments 📝🔬🦠 Postdoc at UNIL 🇨🇭 | Previously at UniPD 🇮🇹, IISER Kolkata 🇮🇳

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Reposted by Prajwal Padmanabha
Systems Ecology @systems-ecology.bsky.social · 21/09/2026
🌱 Systems Ecology is now live! A new independent, researcher-run, diamond OA journal for ecological research through systems science. Free to read. Free to publish. No APCs. We are now open for submissions: systems-ecology.org Please help spread the word!
systems-ecology.org
Systems Ecology
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Snorre Sulheim @sulheim.bsky.social · 18/09/2026
Finally online! Cross-feeding enables robust coexistence between four bacterial species | PNAS www.pnas.org/doi/10.1073/... #microsky
pnas.org
Cross-feeding enables robust coexistence between four bacterial species | PNAS
Resource supply is generally considered a dominant driver of microbial diversity. Here, using a four-species bacterial consortium, we asked whether...
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Purushottam Dixit @pdixit.bsky.social · 15/09/2026
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.org
Low-Dimensional Coexistence in Complex Microbial Ecosystems
Analysis 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.
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Anna S. Weiss @annasophieweiss.bsky.social · 08/09/2026
Over the past year, I’ve been thinking a lot about functional redundancy. A concept that seems so intuitive it almost feels boring, until you really start thinking it through. So excited to see the results of this brain-twisting thought process now out 🥳 authors.elsevier.com/sd/article/S...
authors.elsevier.com
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SeppeKuehnLab @seppekuehnlab.bsky.social · 07/08/2026
New preprint! A monumental four year effort by Vaibhhav Sinha: when a bacterium eats organic carbon, how much becomes biomass and how much comes back out as CO₂? The answer is structured hierarchically by substrate and taxonomy. 🧵 www.biorxiv.org/content/10.6...
biorxiv.org
Hierarchical control of bacterial growth efficiency by substrate and taxonomy
Heterotrophic bacteria utilize organic carbon as a source of energy and material for growth. The balanced allocation of carbon between these two processes, termed growth efficiency, is a key physiolog...
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Prajwal Padmanabha @lambdapp.bsky.social · 07/08/2026
I agree!! An essay on what theoretical ecologists might consider significant progress by LLMs would be great. Data is an interesting point I didn't think about before. I don't know how much of the methodology impact on data collection will affect these questions
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Prajwal Padmanabha @lambdapp.bsky.social · 06/08/2026
There's also a little bit of a meta question. The recent discoveries in math are quite specific. The problems are stated in exact detail. Whereas my first thought when I read your original post was to think of conceptual advances in theoretical ecology. These might be quite different for LLMs/LRMs
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Prajwal Padmanabha @lambdapp.bsky.social · 06/08/2026
But the existence of LEAN is also something that I see is different. There's a set of axioms that are universally agreed and these are foundational. I don't know if anything as universal exists in theoretical ecology.
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Prajwal Padmanabha @lambdapp.bsky.social · 06/08/2026
Yes. As far as I understand, the LLM discoveries relied significantly on checking each step through LEAN. From the LLM discovery perspective, there is somewhat of an automated step to say if the outcome is correct or not, which would require manual oversight in theoretical ecology.
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Prajwal Padmanabha @lambdapp.bsky.social · 06/08/2026
Do you think it has something to do with the existence of something like LEAN?
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Sara Mitri @saramitri.bsky.social · 04/08/2026
@massimoamicone.bsky.social giving a fantastic talk on evolutionary rescue in simple microbial communities at MEEHubs 2026 @meehubs.bsky.social #meehubs2026
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Prajwal Padmanabha @lambdapp.bsky.social · 16/07/2026
Thanks a lot to @saramitri.bsky.social's support in this fun journey of a project! Also to @snsf.ch for funding and Mitri lab in general for a great work environment! Reach out if you want to chat about the work! 17/17
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Prajwal Padmanabha @lambdapp.bsky.social · 16/07/2026
Why are we seeing these consistent distribution shapes across ecological scales despite different mechanisms? Interaction dimensionality is much smaller than expected. What does this mean for who determines what the community does? Can we operationalize this better to predict communities in lab? 16/
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Prajwal Padmanabha @lambdapp.bsky.social · 16/07/2026
Overall, we've tried to bridge what the field has understood about processes that impact microbial community assembly with what ecological theory has considered the default for decades. We've just opened many new fundamental and exciting questions during this venture! 15/
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Prajwal Padmanabha @lambdapp.bsky.social · 16/07/2026
Two datasets had community assembly experiments independent from interaction measurements. We then simulated Gaussian and lognormal LVs to predict drop-one-out Shannon diversities and it confirmed what we see from models - that lognormal is better at prediction, especially in larger communities! 14/
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Prajwal Padmanabha @lambdapp.bsky.social · 16/07/2026
lognormal better captures exactly the "many weak, few strong" structure we observed consistently. We constructed and simulated different "informed" Lotka-Volterra communities. We found that the lognormal captures richness better while also having more stable simulations. What about in data? 13/
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Prajwal Padmanabha @lambdapp.bsky.social · 16/07/2026
..explanation for the origin of distribution shape for microbes. Does this matter? Lotka-Volterra theory routinely uses Gaussian because we didn't know a mechanistic alternative. Our consumer-resource derived interaction distribution showed that a heavy-tailed distribution like 12/
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Prajwal Padmanabha @lambdapp.bsky.social · 16/07/2026
Using analytics and simulations, we found that competition and crossfeeding are sufficient to mechanistically explain what creates this shape - less niche overlap / more growth rate heterogeneity could increase skew, but so does increasing leakage of metabolites. This provided an alternative.. 11/
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Prajwal Padmanabha @lambdapp.bsky.social · 16/07/2026
Food web theory explains this shape using body size differences and energy constraints in predator-prey relationships. But these don't really apply to microbes. Interactions are mostly driven by metabolite-mediated processes. So we turned back to our model and looked at the two processes in it. 10/
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Prajwal Padmanabha @lambdapp.bsky.social · 16/07/2026
So now, what about the shape itself? This shape is not new -- food web theory has long identified "many weak, few strong" interaction structure but we didn't know so far that this shape extends to microbes too. Is it expected that this extends to microbes? Actually no! 9/
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Prajwal Padmanabha @lambdapp.bsky.social · 16/07/2026
The skewness and kurtosis were tightly correlated. We fit this correlation and it turns out this model fit predicts the datasets with R2=0.78! Note once again that these communities have different interactions, origins, and methods of measurements, but share a common higher order relationships! 8/
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Prajwal Padmanabha @lambdapp.bsky.social · 16/07/2026
uses statistics like skewness (third order) and kurtosis (fourth order), which for us will quantify a) how many weak values there are, and b) what is the proportion of strong outliers. Second big surprise was that the many communities we simulated in the model ALL showed a scaling relationship!! 7/
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Prajwal Padmanabha @lambdapp.bsky.social · 16/07/2026
..with a wide variety of community origins. Turns out all 9 were significantly skewed, with nearly 78% of interactions being weak!! How do we quantify this observation? We turned to non-dimensional distributional statistics (think like coefficient of variation). Probability theory routinely ... 6/
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Prajwal Padmanabha @lambdapp.bsky.social · 16/07/2026
Turns out most distributions are skewed - quite a lot of values near zero, but, simultaneously, there are some pairs of species that interact much stronger than a Gaussian null expectation. We turned to different datasets to ask is this really true. We took 9 published interaction datasets... 5/
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Prajwal Padmanabha @lambdapp.bsky.social · 16/07/2026
...and crossfeeding, both impact community assembly in microbes. We simulated many model communities and computed the interactions at steady state (see @olimeacock.bsky.social 's work for details on the computation). We were surprised - more than 98% of communities showed a consistent shape!! 4/
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Prajwal Padmanabha @lambdapp.bsky.social · 16/07/2026
But we don't understand these distributions well in microbes -- how they are shaped, what drives the shape, does it matter for community properties in line with theory, etc. We set out to answer these question. We started from consumer-resource models which combine competition... 3/
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Prajwal Padmanabha @lambdapp.bsky.social · 16/07/2026
There has been a lot of discussions on how microbes interact and whether the interactions are negative or positive. BUT interaction strength also matters significantly! From ecological theory we know that the distribution of strengths changes MANY things - from stability to composition. 2/
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Prajwal Padmanabha @lambdapp.bsky.social · 16/07/2026
Very happy to share that the work I've been doing with @saramitri.bsky.social is now out on biorxiv! www.biorxiv.org/content/10.6... We broadly ask how are microbial interactions distributed, is there a common shape across datasets, what drives it, and why it matters. Summary thread below 🧵 1/17
biorxiv.org
Metabolic processes shape microbial interaction distributions
Microbial communities are largely driven by metabolic interactions, whereby species compete for shared resources and exchange byproducts. Such interactions are commonly classified by their sign alone....
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fbm-unil.bsky.social @fbm-unil.bsky.social · 23/06/2026
🎉 Félicitations aux professeures 𝗦𝗮𝗿𝗮 𝗠𝗶𝘁𝗿𝗶 @saramitri.bsky.social @dmf-unil.bsky.social et 𝗧𝗮𝗻𝗷𝗮 𝗦𝗰𝗵𝘄𝗮𝗻𝗱𝗲𝗿 au Département d’écologie et évolution @fbm-unil.bsky.social @unil.bsky.social qui reçoivent chacune un ERC Advanced Grant @erc.europa.eu 👉 www.unil.ch/news/fr/1781...
unil.ch
Deux ERC Advanced Grants pour la FBM
Les professeures Sara Mitri, au Département de microbiologie fondamentale, et Tanja Schwander, au Département d’écologie et évolution de l’Unil, reçoivent chacune un ERC Advanced Grant de l’European R...
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Massimo Amicone @massimoamicone.bsky.social · 23/06/2026
From a Workshop to a Perspective piece (on modelling AMR within microbiomes 🦠), glad to have been part of this! Big thanks to Lisa Pagani and @rleonsampedro.bsky.social for carrying it through, and to the Collegium Helveticum for hosting the kickoff meeting 👋
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Prajwal Padmanabha @lambdapp.bsky.social · 25/05/2026
It was a great pleasure to be a part of this and I learnt so much during the process as well! Check it out when you get some time and thanks to all the co-authors for great work! 🙌
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Sara Mitri @saramitri.bsky.social · 22/05/2026
Check out our pre-print led by the fantastic Massimo Amicone, collaborating with the Bollenbach lab! tinyurl.com/4h9p8mfb We build a simple intuition on how ecological interactions affect resistance evolution by expanding evolutionary rescue theory and testing it with two large sets of experiments
tinyurl.com
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Charles Mullon @charlesmullon.bsky.social · 09/05/2026
1 week left to apply for scholarships ! If you are based at an institution in an ODA recipient country (e.g. Brazil, South Africa, India, Mexico; full list: tinyurl.com/5dv7vvs8), you can get all expenses covered to attend the summer school in Lausanne for a week.
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Sara Mitri @saramitri.bsky.social · 05/05/2026
The first preprint on chemostats from our lab! What a ride it's been with Eric Ulrich doi.org/10.64898/202... Congratulations on what was a challenging project that taught us so much about cross-feeding, chemostat theory and how minimal media are impossible to keep minimal ;) Enjoy the read!
doi.org
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Snorre Sulheim @sulheim.bsky.social · 22/04/2026
Happy to finally share these results: Cross-feeding enables robust coexistence between four bacterial species www.biorxiv.org/content/10.6... With @saramitri.bsky.social @lambdapp.bsky.social @dan1elmachado.bsky.social @lhtxra.bsky.social Eric Ulrich, Alisson Gillon & Sam Testa #microsky
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Prajwal Padmanabha @lambdapp.bsky.social · 20/04/2026
Congratulations Will! Great news!!
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Sonja Lehtinen @sonjalehtinen.bsky.social · 14/04/2026
Interested in predicting the dynamics of antibiotic resistance? Come work with us! We're looking for two postdocs to develop predictive models of resistance. We're interested in a range of approaches (mathematical & statistical modelling, causal inference, machine learning). tinyurl.com/6c4y3jke
tinyurl.com
Career Opportunities: Postdoctoral positions in predictive modelling of antibiotic resistance spread (22755)
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Yolanda Schaerli @yschaerli.bsky.social · 12/04/2026
Interested in synthetic biology & microbiomes? 🧬🧫 We are recruiting a PhD student to develop biosensors to study microbe–microbe & microbe–host interactions. In beautiful Lausanne, Switzerland🏔️⛵ @dmf-unil.bsky.social @fbm-unil.bsky.social Apply by 24.05.2026 👇 shorturl.at/6X7M4 Boosts appreciated!
shorturl.at
Career Opportunities: PhD position in microbial synthetic biology (22753)
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Thomas Lesaffre 🌱 @thomaslesaffre.bsky.social · 16/03/2026
🚨 PhD position available ! 🚨 I am hiring a PhD student to work with me on the evolution of plant sexual systems 🌺 at @unifrbiology.bsky.social ! The position is funded for 4 years by @snsf.ch as part of my Ambizione fellowship. More info here: tinyurl.com/monoecy 🌱 Please RP and share widely ! 🌱
View of the old city of Fribourg from the "Pont du Milieu". 
© Ville de Fribourg
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Charles Mullon @charlesmullon.bsky.social · 09/03/2026
With @saramitri.bsky.social, @sonjalehtinen.bsky.social and L. Lehmann we’ve launched the UNIL Center for Theory in Ecology and Evolution @unil.bsky.social🇨🇭 To kick things off, we’re offering short visiting fellowships for theorists in ecology & evolution. Apply & pls RP 😀 tinyurl.com/2wem36zz
unil.ch
Unil center for theory in ecology and evolution (UCTEE) - FBM Unil
Page Unil Center for Theory in Ecology and Evolution of site Faculty of Biology and Medicine hosted by the University of Lausanne
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Will Shoemaker @shoestrapped.bsky.social · 08/03/2026
A personal honor to have the work of myself and my collaborators covered in Il Piccolo, the Trieste newspaper that published James Joyce when he lived here.
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Simon van Vliet @simonvanvliet.bsky.social · 11/02/2026
Excited to share first preprint from our lab! @giubotti.bsky.social found that antibiotic tolerance in multispecies biofilms follows a surprising spatial pattern: cells survive only at intermediate distances from a partner species. 🦠 Preprint: doi.org/10.64898/202...
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Oliver Meacock @olimeacock.bsky.social · 07/01/2026
Do you have an interest in quantitative microbiology and interdisciplinary research? I'm recruiting a UK PhD student to develop high-throughput ecological screens to help us understand how chemical inputs impact microbial ecosystems: www.findaphd.com/phds/project...
findaphd.com
Identifying how chemicals shape microbial diversity through high-throughput ecological screens at University of Sheffield on FindAPhD.com
PhD Project - Identifying how chemicals shape microbial diversity through high-throughput ecological screens at University of Sheffield, listed on FindAPhD.com
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Snorre Sulheim @sulheim.bsky.social · 03/12/2025
Do you think transporters in E. coli contribute to metabolite release? No? Explore the effect of 66 different transporter knockout mutations on the exometabolome dynamics of ~300 metabolites yourself: keio.unil.ch Teaser: Increased proline in ΔputP #microsky #MEvoSky
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Sara Mitri @saramitri.bsky.social · 02/12/2025
New preprint from our lab www.biorxiv.org/content/10.1...! Andrea Dos Santos and Clément Vulin combine experiments and models showing how adding glucose can strengthen negative interactions between microbial species. This can be used in tandem with antibiotic treatment to inhibit pathogens!
Diagram illustrating "feed the enemy's enemy": ampicillin inhibits Pseudomonas aeruginosa. Citrobacter freundii acidifies the environment, further inhibiting P. aeruginosa.
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Oliver Meacock @olimeacock.bsky.social · 30/10/2025
I am excited to announce two PhD opportunities! Come and join our interdisciplinary team in Sheffield, UK. - Destroying forever chemicals with microbes and cold plasma: tinyurl.com/mth8ymx5 - Learning how motile bacteria make decisions: tinyurl.com/2hmc9a8u UK and overseas students welcome to apply!
tinyurl.com
ECOSOLUTIONS DFA - Harnessing microbes and cold plasma to concentrate and destroy ‘forever chemicals’ in food associated ecosystems at University of Sheffield on FindAPhD.com
PhD Project - ECOSOLUTIONS DFA - Harnessing microbes and cold plasma to concentrate and destroy ‘forever chemicals’ in food associated ecosystems at University of Sheffield, listed on Find...
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Oliver Meacock @olimeacock.bsky.social · 17/10/2025
I'm delighted to announce that the Interdisciplinary Challenges (IntCha) meeting is returning in April 2026! Abstract submission is now open. We encourage young scientists working at the interface between biology and physics to join us at the IESC in Corsica. Website here: intcha26.sciencesconf.org
The Institut d'Études Scientifiques (IESC), on the coast of Corsica.
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Snorre Sulheim @sulheim.bsky.social · 20/08/2025
Excited to share the first results from my postdoc at @dmf-unil.bsky.social with @saramitri.bsky.social www.biorxiv.org/content/10.1...
biorxiv.org
Microbes release lower-value metabolites at higher rates
Microbes release a wide range of metabolites into their environment, yet the reasons for this release and the factors that influence release rates are not well understood. Here, using a combination of...
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Jacopo Grilli @jacrickets.bsky.social · 28/07/2025
Three postdoctoral positions open (almost equally longitudinally spaced: one at @yale.edu with @martinadalbello.bsky.social , one at ELSI Tokyo with Shawn McGlynn, one with myself at ICTP in Trieste) to work collaboratively on www.dalbellolab.com/hfsp-project funded by @hfspo.bsky.social
dalbellolab.com
HFSP project — dal bello lab
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Sara Mitri @saramitri.bsky.social · 01/07/2025
Beautiful new review paper in preprint bridging microbial ecology and classic ecology led by Maggie Vogel, @olimeacock.bsky.social and @annasophieweiss.bsky.social, also by @juliensluneau.bsky.social and @lambdapp.bsky.social from our lab (not me :)) ecoevorxiv.org/repository/v...
ecoevorxiv.org
Bridging the scales: what can microbial ecologists learn from classic ecology?
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