NOMIS-ETH fellow at Institute of Microbiology and Center of Origin and Prevalence of Life, ETH Zurich | microbial ecologist interested in diversification, evolution and mobile genetic elements | Parent of a beautiful Briard | food and fitness enthusiast
Microbial anaerobic digestion communities converge on metabolic functions and metabolite profiles despite variability in taxonomic composition - academic.oup.com/ismej/articl...
Environmental selection constrains metabolic network architecture despite taxonomic turnover in anaerobic digestion communitiesAbstract. Microbial ecosystems often sustain stable metabolic functions despite pronounced taxonomic turnover, yet the mechanisms underlying such reproduciacademic.oup.comMobile genetic elements shape microbial diversity and functions in thawing permafrost soils www.nature.com/articles/s41...
Mobile genetic elements shape microbial diversity and functions in thawing permafrost soils - Nature MicrobiologyAn 8-year soil meta-omic time series shows how mobile genetic elements shape permafrost microbial diversity and impact a range of functions, including carbon and nutrient cycling.www.nature.comIn marine microbial studies, we typically filter seawater through a 0.22 micron filter...have you ever wondered how many cells and of what taxa pass through these filters ? This study provides some new insights on this - onlinelibrary.wiley.com/doi/full/10....
onlinelibrary.wiley.comVery nice study integrated metagenomics, metatranscriptomics and geochemistry to gain insights into microbial communities and methane production in a temperate wetland ecosystem - journals.asm.org/doi/10.1128/... #MicroSky #MicroEco #EcoEvo
Mapping the soil microbiome functions shaping wetland methane emissions | mSystemsSoil microbial ecology is increasingly recognized as essential to climate mitigation, but realizing its full potential requires shifting from static genome inventories to dynamic assessments of microbial activity. This study shows that methane-cycling microbes exhibit stable, depth-stratified expression patterns, even in response to major redox and flooding shifts, undermining assumptions that water-table manipulations common in wetland management can alone reduce methanogenesis. Instead, methane cycling is shaped by spatially organized, transcriptionally active networks involving not only methanogens but also methanotrophs, fermenters, and iron reducers. These findings expose the limitations of genome-only models and highlight the need for soil diagnostics that capture in situ activity. Together, we provide a foundation for developing activity-based microbiome tools, embedding microbial functions into Earth system models, and designing interventions that move beyond “single-lever” strategies and instead work with the structure and dynamics of microbial communities as complex, layered systems.journals.asm.orgHow is the diversity of microbes structured across the global oceans ? Check out our latest paper, spearheaded by @jonas-bio.bsky.social and Dominic Eriksson, that addresses this - www.cell.com/cell-host-mi...
Variations in the latitudinal diversity gradients of the ocean microbiomeEriksson et al. conduct a global marine microbiome diversity analysis and demonstrate
how the surface ocean latitudinal diversity gradient is disproportionately shaped
by a few species-rich taxa. Mask...www.cell.comVery happy to have been given the opportunity to contribute to this great study on the spatial structuring of microbial biodiversity in the oceans #MicroSky #Microecoevo www.cell.com/cell-host-mi...
Variations in the latitudinal diversity gradients of the ocean microbiomeEriksson et al. conduct a global marine microbiome diversity analysis and demonstrate
how the surface ocean latitudinal diversity gradient is disproportionately shaped
by a few species-rich taxa. Mask...www.cell.comA survey of 2600 early-career researchers provides insights into good and bad practices of supervision - www.biorxiv.org/content/10.6... So valuable! I think supervision is, unfortunately, largely an after thought in scientific research...🧵
www.biorxiv.orgVery interesting read and great study - Genome wide sweeps creat ecological units in the human gut microbiome #MicroSky #Microevo #Microbiome www.nature.com/articles/s41...
Genome-wide sweeps create ecological units in the human gut microbiome - NatureGenome-wide selective sweeps commonly occur in the human gut microbiome and can spread across the world within decades to produce epidemic-like population structures.www.nature.comA new method for inference and tracking the transmission of strains in metagenomes #MicroSky #MicroEco www.nature.com/articles/s41...
Strain-level transmission inference across multi-kingdom metagenomic data using TRACS - Nature MicrobiologyThe TRACS algorithm tracks bacteria, viruses and parasites in metagenomic or population sequencing data, detecting microbial transmission even when multiple strains coexist within a host.www.nature.com#MicroSky #MicrobiomeSky
Microbiome Research Lab, ETH ZürichHow diverse are E. coli capsules? In collaboration with @mucosalimmunology.bsky.social we mapped this uncharted diversity in >66k genomes with a new tool, kTYPr, paving the way to capsule-targeted therapies and vaccines www.nature.com/articles/s41... @eth-microbiology.bsky.social
Seasonality drives temporal niche partitioning of pelagic prokaryotes academic.oup.com/ismej/articl...
Seasonality drives temporal niche partitioning of pelagic prokaryotesAbstract. Prokaryote seasonality is well documented in lakes, coastal areas, and inland seas, yet microbial annual periodicity in diverse open ocean settinacademic.oup.comDoes anybody have access to this article and could share a PDF with me ? www.pnas.org/doi/abs/10.1...
Check out our latest preprint that showcases a connection between complex polysaccharide degradation and methanogenesis in an anoxic lake sediment - www.biorxiv.org/content/10.6...
www.biorxiv.orgA new study exploring the diversity of microbial life encapsulated in global metagenomic contigs reveals there could be at least 250,000 bacterial species and potentially up to 750,000, with only a fraction that have genomic representatives www.nature.com/articles/s41...
Unbinned contigs expand known diversity in the global microbiome - Nature MicrobiologyRe-analysis of over 92,000 metagenomes reveals hundreds of thousands of previously undescribed Bacterial and Archaeal clades hidden in plain sight.www.nature.comUsing river biofilm microbiomes as sentinels of national-scale freshwater ecosystems Very impressive coverage of England's river system with 700 sites included! onlinelibrary.wiley.com/doi/10.1111/...
River Microbiomes as Sentinels of National‐Scale Freshwater EcosystemsRiver biofilms are complex microbial assemblages that underpin aquatic food webs and play a central role in biogeochemical cycling. By responding to environmental signals over space and time, biofilm...onlinelibrary.wiley.comDecoupled timescales of organic carbon and phosphorus recycling in the global ocean | PNAS www.pnas.org/doi/10.1073/...
Decoupled timescales of organic carbon and phosphorus recycling in the global ocean | PNASThe ocean’s biological carbon pump exports atmospheric CO2 to the deep ocean, where
it can remain sequestered for decades to centuries, and attempt...www.pnas.orgQuantifying the effects of response diversity dynamics on ecosystem stability A nice study showing the use of empirical dynamic modeling to quantify time-varying species responses to biotic and biotic factors simultaneously www.nature.com/articles/s41...
Quantifying the effects of response diversity dynamics on ecosystem stability - Nature CommunicationsSpecies’ varied responses to environmental change help stabilize ecosystems, yet quantifying these dynamics remains challenging. This study reveals that plankton in Lake Geneva exhibit time-varying re...www.nature.comA new study showcasing how the Southern ocean is filled with novel genetic content that is partially shared with the Arctic but largely endemic. Thd study also provides the Antarctic circumnavigation metagenomic dataset! #polar #marinemicrobes #metagenomics www.nature.com/articles/s41...
Water mass specific genes dominate the Southern Ocean microbiome - Nature CommunicationsSouthern Ocean microbial communities are less well studied. Here, the authors generate a circumpolar-scale gene catalog from 218 metagenomics samples revealing broadscale uniqueness and water-mass–spe...www.nature.comGenome modelling and design across all domains of life - Evo2 A biological foundation model trained on 9 trillion DNA base pairs to predict the functional impacts of genetic variation www.nature.com/articles/s41...
Genome modelling and design across all domains of life with Evo 2 - NatureEvo 2 is an artificial intelligence-based biological foundation model trained on 9 trillion DNA base pairs spanning all domains of life that predicts functional properties from genomic sequences and p...www.nature.com