Snorre Sulheim
@sulheim.bsky.social
SNSF postdoc fellow in Mitri lab @UNIL
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
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
What a resource!
Statistical Physics of Cells and Genomes@spcggroup.bsky.social · 4mo agoOur Hands On Growth Laws Theory Cookbook is out today! journals.aps.org/prxlife/abst... It covers cell growth models through step-by-step recipes, bridging theory and practical applications, from basic to complex settings. Happy cooking! With @micalilab.bsky.social and @lciandrini.bsky.social
Another example showing how common it is for microbes to release metabolites way beyond what's thought of as waste products Characterization of phytoplankton-excreted metabolites mediating carbon flux through the surface ocean | PNAS www.pnas.org/doi/10.1073/...
PNAS
Proceedings of the National Academy of Sciences (PNAS), a peer reviewed journal of the National Academy of Sciences (NAS) - an authoritative source of high-impact, original research that broadly spans...
pnas.org
One of the biggest challenges in microbial biotechnology? Unlocking the potential of non-model microbes and synthetic communities! Glad to share our review @sonjablasche.bsky.social @simonemozzachiodi.bsky.social @kiranrpatil.bsky.social @cambridgebiosci.bsky.social🧵(1/7) doi.org/10.1016/j.co...
Cells maintain low metabolite pools to: - enable substrate level regulation - prevent competitive inhibition - avoid side reactions #microsky www.cell.com/cell-systems...
The metabolome of an E. coli CRISPRi library identifies benefits of minimal metabolite levels and targets for engineering
Rapp et al. combine genome-scale CRISPRi and metabolomics in E. coli. CRISPRi of enzymes enforces metabolite accumulation, which leads to regulatory crosstalk and side reactions. This suggests that ma...
cell.com
Imbalance in gut microbial interactions as a marker of health and disease www.science.org/doi/10.1126/...
Imbalance in gut microbial interactions as a marker of health and disease
Imbalances in the human gut microbiome, or dysbioses, are associated with multiple diseases but remain poorly understood. Existing biomarkers of dysbiosis fail to capture the ecological mechanisms tha...
science.org
Nice thread on the importance of spatial structure in microbial communities
Bram van Dijk 🏳️🌈@bramvandijk.bsky.social · 5mo agoIn case you missed it: our review titled "Spatial structure: shaping the ecology and evolution of microbial communities" is out! 🚨 Let me hit you with some highlights on why spatial structure matters. (and why you should care!) Sharing is appreciated 🙏 🧵👇 doi.org/10.1093/fems...
Really elegant work showing how spatial distance can determine the net effect of two interaction mechanisms
Simon van Vliet@simonvanvliet.bsky.social · 6mo agoExcited 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...
Metabolic blueprints of monocultures enable prediction and design of synthetic microbial consortia A nice demonstration of how cross-feeding shapes small microbial community compositions From Segré lab @dsegre.bsky.social www.biorxiv.org/content/10.6...
biorxiv.org
Intra-species crossfeeding in K. pneumonia supports growth of co-cultivated partners. I think such commensal interactions are very common journals.plos.org/plosbiology/...
A metabolic atlas of the Klebsiella pneumoniae species complex reveals lineage-specific metabolism and capacity for intra-species co-operation
Why are there so many co-circulating Klebsiella pneumoniae clones? Using genomics and large-scale metabolic modelling of >7000 isolates, this study identifies structured, clone-specific metabolic spec...
journals.plos.org
Metabolic control of porin permeability www.nature.com/articles/s41...
Metabolic control of porin permeability influences antibiotic resistance in Escherichia coli - Nature Microbiology
The permeability of bacterial porins is dynamically regulated by periplasmic proton and potassium concentrations, altering antibiotic resistance.
nature.com
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!
This project wouldn't been possible without Peter Doubleday and @nzamboni.bsky.social at @imsb-eth.bsky.social. Peter conducted >10,000 mass spec analyses 🤯. So grateful for this opportunity to team up with the best of the best in metabolomics 😍 Read more: www.biorxiv.org/content/10.1... #microsky
Snorre Sulheim@sulheim.bsky.social · 8mo agoDo 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
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
After two rounds of "peer review" at Scientific reports 😵💫
Erik Angner@erikangner.com · 8mo ago"Runctitiononal features"? "Medical fymblal"? "1 Tol Line storee"? This gets worse the longer you look at it. But it's got to be good, because it was published in Nature Scientific Reports last week: www.nature.com/articles/s41... h/t @asa.tsbalans.se
Great to see the increased use of genome-scale models in microbial ecology. Here is another recent example: www.nature.com/articles/s41... But why is no one questioning the often implicit assumption that growth-optimization at the community level is the driving force of cross-feeding?
Substrate utilization and cross-feeding synergistically determine microbiome resistance to pathogen invasion - Nature Ecology & Evolution
Combining genome-scale metabolic modelling with in vitro and in planta experiments, the authors show that cross-feeding metabolites and substrate utilization synergistically determine microbial commun...
nature.com
Great opportunity with a very nice PI👇
Oliver Meacock@olimeacock.bsky.social · 9mo agoI 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!
Nice review of metabolic exchanges in microbiomes across environments www.cell.com/trends/micro...
An updated view of metabolic handoffs in microbiomes
From the human gut to the deep ocean, diverse microbial communities underpin essential ecosystem processes. Limited understanding of the dynamics and interactions that shape these communities, however...
cell.com
Excited to share the first results from my postdoc at @dmf-unil.bsky.social with @saramitri.bsky.social www.biorxiv.org/content/10.1...
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...
biorxiv.org
