NCCR Microbiomes

𝗠𝗶𝗰𝗿𝗼𝗯𝗶𝗼𝗺𝗲𝘀 𝗶𝗻 𝗺𝗼𝘁𝗶𝗼𝗻: 𝘀𝗰𝗶𝗲𝗻𝗰𝗲, 𝗱𝗮𝘁𝗮, 𝗮𝗻𝗱 𝗰𝗼𝗹𝗹𝗮𝗯𝗼𝗿𝗮𝘁𝗶𝗼𝗻 𝗮𝘁 𝘁𝗵𝗲 𝗦𝘄𝗶𝘀𝘀 𝗠𝗶𝗰𝗿𝗼𝗯𝗶𝗼𝗺𝗲𝘀 𝗙𝗼𝗿𝘂𝗺 𝟮𝟬𝟮𝟲 The NCCR Microbiomes proudly presents the third edition of the Swiss Microbiomes Forum, a flagship event advancing science, technology, and collaboration across this rapidly evolving field. 🗓️ Thursday, Feb 5th 2026 📍 EPFL Rolex Learning Center, Lausanne This Forum spotlights Switzerland’s microbiome technology ecosystem, bringing together researchers, innovators, and industry leaders to explore how microbiomes can help solve real-world challenges. Two sessions will explore: 🌍 Microbiomes in Action – How can we mobilise microbial communities to solve challenges in health, nutrition, and sustainability? 💻 The Data Side of the Microbiome – What tools and methods are driving breakthroughs in diagnostics, monitoring, and research? 🎤 The speaker lineup features experts from industry, startups, and academia who will share cutting-edge insights and join roundtable discussions. 💡 Expect: • A dynamic, cross-sector exchange of ideas • Networking with peers shaping the future of microbiome science • Exhibits featuring the latest technologies and innovations. Whether you’re working in research, biotech, or policy, this is the place to connect with the full community driving microbial innovation. 🎟️ Free to attend, but registration is required. Spaces are limited! 📢 Join us to connect, collaborate, and catalyse the next wave of microbiome innovation. 👉 https://lnkd.in/eVi8wDr4 #Microbiome #SwissMicrobiomesForum #NCCRMicrobiomes #Bioinformatics #OneHealth #LifeSciences #Innovation #ScienceEvents #Networking Mickaël Bouvet-Gueguen, PhD, MBA, Christophe Dessimoz, Rita Di Martino, Camille Goemans, Benoit Guery, Marco Meola - DATABIOMIX, Petar Scepanovic, Hanne Tytgat, FBM UNIL - Faculté de biologie et de médecine de l'Université de Lausanne, University of Lausanne, ETH Zürich, Swiss National Science Foundation SNSF

🌍 𝗢𝗻𝗲 𝗛𝗲𝗮𝗹𝘁𝗵, 𝗢𝗻𝗲 𝗠𝗶𝗰𝗿𝗼𝗯𝗶𝗼𝗺𝗲: 𝗮 𝗳𝗿𝗮𝗺𝗲𝘄𝗼𝗿𝗸 𝗳𝗼𝗿 𝗰𝗼𝗻𝗻𝗲𝗰𝘁𝗶𝗻𝗴 𝗵𝘂𝗺𝗮𝗻, 𝗮𝗻𝗶𝗺𝗮𝗹 𝗮𝗻𝗱 𝗲𝗻𝘃𝗶𝗿𝗼𝗻𝗺𝗲𝗻𝘁𝗮𝗹 𝗵𝗲𝗮𝗹𝘁𝗵 𝘁𝗵𝗿𝗼𝘂𝗴𝗵 𝗺𝗶𝗰𝗿𝗼𝗯𝗲𝘀 Microbes are the invisible threads that knit together people, livestock, wildlife, plants and ecosystems. This new NCCR Microbiomes review from the lab of Pascale Vonaesch and colleagues explores the “One Health Microbiome” concept, a planetary‑scale network of shared bacterial strains, genes and resistance traits, reframing how we understand shared microbial life across domains. 🔬 For the first time, this review synthesises ecological theory (dispersal + environmental filtering) with concrete evidence of strain‑sharing across domains, and links this network to climate‑change resilience and antimicrobial‑resistance (AMR) dynamics. 🔑 Key insights ➤ Interconnected microbiomes: Human, animal, and environmental microbial communities form a continuous “One Health Microbiome” with extensive cross-domain strain sharing. ➤ Two sides of sharing: Microbial exchange can yield benefits such as stress resilience and climate buffering, but also risks like pathogen spread and AMR transfer. ➤ Ecological rules apply: Strain‑sharing obeys dispersal and host‑filtering; only certain taxa (generalists vs. specialists) succeed in new habitats. ➤ Dysbiosis breaks the balance: Disturbances in gut, soil or marine microbiomes (e.g., antibiotics, pollutants, climate stress) erode colonisation resistance and favour invasive, often resistant, microbes.  ➤ AMR as a global microbiome challenge: Resistance genes circulate through shared microbial networks spanning livestock, pets, food, soils, and water, demanding integrated surveillance and intervention. ➤ Climate change intensifies the link: Rising temperatures, pollution and biodiversity loss reshape microbial networks, altering disease transmission, ecosystem function and even greenhouse‑gas cycling. 🌱 Implication: Health and sustainability are microbiome-dependent. Tackling AMR, emerging diseases, and climate impacts requires uniting microbiome science with the One Health approach; studying microbes not in isolation but as shared ecological systems. 💬 What concrete One Health‑integrated policies or interventions could preserve beneficial strain‑sharing while curbing AMR spread and climate‑driven disruption? 👉 Read the open-access review here: https://lnkd.in/eHk5Zzku 🎉 Congratulations to authors Abdifatah Muktar Muhummed, Kayla C. Lanker, Simon Yersin, Jakob Zinsstag & Pascale Vonaesch. FBM UNIL - Faculté de biologie et de médecine de l'Université de Lausanne, University of Lausanne - UNIL, Jigjiga University, Swiss Tropical and Public Health Institute, University of Basel, ETH Zürich, Swiss National Science Foundation SNSF #OneHealth #Microbiome #MicrobialEcology #AntimicrobialResistance #ClimateChange #PlanetaryHealth #SystemsBiology #NCCRMicrobiomes

🌱 𝗪𝗵𝗲𝗿𝗲 𝗶𝘁 𝗮𝗹𝗹 𝗯𝗲𝗴𝗮𝗻... A few weeks ago, citizen scientists across Switzerland opened a special soil sample and mixed it into their own, kicking off a 6-week NCCR Microbiomes experiment. We’re now about halfway through, and while participants wait for the date to collect their samples, we’re looking back at the energy, curiosity, and care they brought to day zero. 💡 What’s next? Keep tending your soil as normal and stay curious! Your samples will soon return to the lab, and we can’t wait to explore what’s beneath the surface. 🙏 Thank you to everyone participating for helping grow our understanding of the hidden dynamics of soil microbes. #SoilMicrobiome #CitizenScience #SoilScience #EnvironmentalMicrobiology #SoilStories #NCCRMicrobiomes FBM UNIL - Faculté de biologie et de médecine de l'Université de Lausanne, University of Lausanne, ETH Zürich, Swiss National Science Foundation SNSF

Fantastic to see the full story brought together! From Switzerland to Japan, “INVISIBLES: The Hidden Life of Microbes” continues its journey, now with a citizen science twist: The Garden Experiment, engaging communities in both countries to explore how we can rebuild microbial life in our soils. 🌱🦠 We’re proud to see this project take root globally, connecting science, art, and society. 📅 Looking forward to the special talk on October 25! More info 👉 https://lnkd.in/gmMq4S-Y Huge thanks to the Science & Technology Office Tokyo for making this possible! 🇨🇭🤝🇯🇵 Musée de la main UNIL-CHUV, FBM UNIL - Faculté de biologie et de médecine de l'Université de Lausanne, University of Lausanne, ETH Zürich, Swiss National Science Foundation SNSF #SciArt #CitizenScience #SoilHealth #Microbiology #ScienceDiplomacy #MISAF2025 #NCCRMicrobiomes

📢 𝗡𝗲𝘄𝗹𝘆 𝗼𝗽𝗲𝗻𝗲𝗱: 𝗣𝗼𝘀𝘁𝗱𝗼𝗰𝘁𝗼𝗿𝗮𝗹 𝗽𝗼𝘀𝗶𝘁𝗶𝗼𝗻 𝗶𝗻 𝗰𝗼𝗺𝗽𝘂𝘁𝗮𝘁𝗶𝗼𝗻𝗮𝗹 𝗺𝗼𝗱𝗲𝗹𝗶𝗻𝗴 𝗼𝗳 𝗺𝗲𝘁𝗮𝗯𝗼𝗹𝗶𝗰 𝗶𝗻𝘁𝗲𝗿𝗮𝗰𝘁𝗶𝗼𝗻𝘀! Our NCCR Microbiomes partner Prof. Alan Pacheco at the University of Lausanne is recruiting a postdoctoral researcher to investigate how metabolic mechanisms shape microbial interactions and community ecology through computational modeling. 🗓 Expected start date: flexible, earliest 01 January 2026 This is a unique opportunity to join a new dynamic, interdisciplinary lab, contribute to cutting-edge research on microbial interactions, and be part of a vibrant scientific community in the heart of Europe. More info about NCCR Microbiomes, the position, and how to apply 👇 https://lnkd.in/eeg7zc7N More about the Pacheco lab: https://lnkd.in/ePzvbpmQ #Microbiome #Postdoc #ComputationalBiology #MicrobialEcology #CommunityEcology #NCCRMicrobiomes

📢 Two PhD positions are open in the lab of our NCCR Microbiomes colleague, Prof. Rizlan Bernier-Latmani in EPFL. 1. PhD project in geomicrobiology: To study microbial uranium reduction and the attendant isotopic fractionation. 2. PhD project in geochemistry: To study abiotic uranium reduction and the attendant isotopic fractionation. Share this with / tag interested parties. All application details below 👇

🐝 𝗛𝗼𝘄 𝘀𝘁𝗮𝗯𝗹𝗲 𝗮𝗿𝗲 𝗴𝘂𝘁 𝗺𝗶𝗰𝗿𝗼𝗯𝗶𝗼𝘁𝗮 𝗮𝗰𝗿𝗼𝘀𝘀 𝗰𝗹𝗼𝘀𝗲𝗹𝘆 𝗿𝗲𝗹𝗮𝘁𝗲𝗱 𝗮𝗻𝗶𝗺𝗮𝗹 𝘀𝗽𝗲𝗰𝗶𝗲𝘀? 𝗡𝗼𝘁 𝗮𝘀 𝘀𝘁𝗮𝗯𝗹𝗲 𝗮𝘀 𝘄𝗲 𝘁𝗵𝗼𝘂𝗴𝗵𝘁. Honeybees have long been seen as a prime example of co-evolved gut bacteria and their hosts, but this newly published NCCR Microbiomes study challenges that view. 🔬 Using shotgun metagenomics, a technique that sequences all DNA in a sample, on 200 individual bees from five Apis species, the authors reconstructed thousands of microbial genomes. This expanded the known diversity of bee gut bacteria and uncovered new species, host switches at the strain level, and surprising variation in how specific bacteria are to their hosts, even among closely related bacterial groups. 🔑 Key findings ➤ Most gut bacterial communities were specific to each host species, but strict co-evolution between microbes and hosts was weak. ➤ Both specialist bacteria (found in few hosts) and generalists (found across multiple hosts) coexist, sometimes even within the same bacterial genus. ➤ Functional differences, like the ability to break down pollen-derived pectin, are linked to gains or losses of specific bacterial partners. ➤ Ecological factors, such as host body size, migration behavior, and gut environment filtering, play key roles in determining which microbes colonize and persist. 🌍 Implication: Honeybee gut microbiomes evolve dynamically through symbiont turnover and host switching, rather than stable, parallel evolution. This leads to functionally distinct microbiomes even among closely related species. 🧬 This study reframes host–microbe co-evolution and offers a genomic foundation for comparative symbiosis research across animals. 💬 𝗪𝗵𝗲𝗿𝗲 𝗲𝗹𝘀𝗲 𝗵𝗮𝘃𝗲 𝘆𝗼𝘂 𝘀𝗲𝗲𝗻 𝗲𝗰𝗼𝗹𝗼𝗴𝘆 𝗼𝘃𝗲𝗿𝗿𝗶𝗱𝗲 𝗲𝘃𝗼𝗹𝘂𝘁𝗶𝗼𝗻𝗮𝗿𝘆 𝗵𝗶𝘀𝘁𝗼𝗿𝘆 𝗶𝗻 𝘀𝗵𝗮𝗽𝗶𝗻𝗴 𝗵𝗼𝘀𝘁-𝗺𝗶𝗰𝗿𝗼𝗯𝗲 𝗮𝘀𝘀𝗼𝗰𝗶𝗮𝘁𝗶𝗼𝗻𝘀? 👉 Read the open-access paper here: https://lnkd.in/eCYKp7W9 🎉 Congrats to the authors: Aiswarya P., Asha Pallujam, Rajath Siddaganga, Ashwin Suryanarayanan, Florent Mazel, Axel Brockmann, Sze Huei Yek, Philipp Engel. FBM UNIL - Faculté de biologie et de médecine de l'Université de Lausanne, Monash University Malaysia, National Centre for Biological Sciences (NCBS), University of Lausanne, ETH Zürich, Swiss National Science Foundation SNSF #Microbiome #Honeybees #Metagenomics #HostMicrobeInteractions #EvolutionaryBiology #ComparativeGenomics #OpenAccess #NCCRMicrobiomes

🌟 Editor's Choice! We’re thrilled to see this important work carried out by Senka Causevic, PhD et al., as part of the NCCR Microbiomes, selected as an Editor’s Choice by ISME | International Society for Microbial Ecology. 🧪 This recognition underscores the role of microbiome engineering as a promising approach to address the global soil health crisis. 🌱 Although synthetic microbiomes with targeted functions may not always establish long-term, the research shows that their temporary presence can influence the development of resident microbial communities. This effect depends on key factors such as habitat filtering, functional redundancy, and microbial interactions. 🔬 By demonstrating that habitat filtering is the dominant force shaping microbial assembly and merger outcomes, the study provides a practical framework for designing and guiding soil microbiomes to support ecosystem recovery. 👏 Congratulations to the authors and the team behind this impactful research! #EditorsChoice #SoilHealth #MicrobiomeResearch #MicrobiomeEngineering #EcosystemRestoration #NCCRMicrobiomes With Jan Roelof van der Meer, Senka Causevic, PhD, Berg Gabriele, Joana Falcão Salles, Lukas Malfertheiner, Vladimir Sentchilo, Raquel Peixoto, Philip Hugenholtz, Lisa Y. Stein, Jillian Petersen, FBM UNIL - Faculté de biologie et de médecine de l'Université de Lausanne, University of Lausanne, ETH Zürich, Swiss National Science Foundation SNSF

𝗪𝗵𝗲𝗻 𝗮 𝗴𝘂𝘁 𝗺𝗶𝗰𝗿𝗼𝗯𝗶𝗮𝗹 𝗰𝗼𝗺𝗺𝘂𝗻𝗶𝘁𝘆 𝗴𝗲𝘁𝘀 𝗱𝗶𝘀𝘁𝘂𝗿𝗯𝗲𝗱, 𝘄𝗵𝘆 𝗱𝗼𝗲𝘀 𝗶𝘁 𝗼𝗳𝘁𝗲𝗻 𝗳𝗮𝗶𝗹 𝘁𝗼 𝗴𝗼 𝗯𝗮𝗰𝗸? Join us at the next NCCR Microbiomes online seminar for a talk by Prof. Karoline Faust on new experimental and modeling work exploring the gut microbiota's surprising capacity for multiple stable states, and what drives them. 🗣️ Alternative Stable States in a Synthetic Human Gut Community 🧑🔬 Prof. Karoline Faust, KU Leuven 🗓 Tuesday November 4th, 12:00 to 13:00 CET 💻 Zoom link https://lnkd.in/eDC8UCNX Karoline Faust is Associate Professor at KU Leuven, where she leads research in microbial systems biology, at the interface of microbial ecology, systems biology and bioinformatics. Her lab aims to understand the dynamics and resilience of microbial communities, supported by her European Research Council (ERC)-funded project EcoBox. In this seminar, she’ll present new experimental and modeling work showing how gut microbiota can shift into stable, long-lasting states - even in controlled synthetic systems of just three species. 💡 A must-attend for anyone interested in microbiome dynamics, microbial ecology, or modeling complex systems! #Microbiome #GutHealth #Microbiology #SystemsBiology #MicrobialEcology #ResearchSeminar #NCCRMicrobiomes FBM UNIL - Faculté de biologie et de médecine de l'Université de Lausanne, University of Lausanne, ETH Zürich Banner micrograph courtesy of Estelle Pignon, Unil.

🚨 Happening today! Join us at 12:00 CEST for Sarah Lebeer's talk 𝗧𝗼𝗴𝗲𝘁𝗵𝗲𝗿 𝗶𝗻 𝗦𝗰𝗶𝗲𝗻𝗰𝗲: 𝗪𝗼𝗺𝗲𝗻'𝘀 𝗵𝗲𝗮𝗹𝘁𝗵 𝗮𝗻𝗱 𝘁𝗵𝗲 𝘃𝗮𝗴𝗶𝗻𝗮𝗹 𝗺𝗶𝗰𝗿𝗼𝗯𝗶𝗼𝗺𝗲 𝘄𝗶𝘁𝗵 𝗜𝘀𝗮𝗹𝗮 as part of the NCCR Microbiomes online seminar series. Don’t miss it! 👉 https://lnkd.in/eDC8UCNX #Webinar #OnlineTalk #SciComm #WomensHealth #Microbiome #CitizenScience #Isala #TogetherInScience #NCCRMicrobiomes