New Shamonda virus clades (SHAV-EU1 and SHAV-EU2) emerged in Europe in summer 2026, primarily affecting cattle. We report the first human infection with SHAV-EU1: a French patient with a severely weakened immune system developed fatal encephalitis in September 2026, 1 month after their allogeneic stem cell transplantation. Metatranscriptomics detected SHAV-EU1 in cerebrospinal fluid, confirmed by RT-PCR. Biopsies from central nervous system showed high viral loads. Investigations revealed SHAV-EU1 in serum, respiratory and stool samples at least for 2 months before encephalitis onset.

Wastewater contains a complex mixture of nucleic acids derived from human cells, microorganisms, diets, and agricultural or industrial inputs. Metatranscriptomics has the potential to broaden the unde...

How can genomics and AI help us understand—and prevent—the next pandemic? Join this research-focused online seminar for PhD students and professional researchers to explore how metatranscriptomics is revealing hidden viral diversity and how AI is helping scientists detect viruses, investigate their evolution, and assess the risk of animal-to-human transmission. Drawing on surveys of RNA viruses in mammalian systems, including natural and farmed/market animal environments in China, the seminar examines emerging coronaviruses, species jumps, and SARS-CoV-2 as a case study. You’ll deepen your understanding of genomic surveillance, phylogenetic inference, and the ecological drivers of emergence while exploring pandemic prevention strategies, including a global pandemic radar and libraries of potential vaccines. Relevant to researchers in virology, evolution, One Health, and infectious disease epidemiology, this seminar connects scientific insights with rigorous research practice. Attend live via Zoom, with recordings, materials, and an expert-monitored Q&A forum available for 30 days afterward. An official Instats certificate of completion is included. #Virology #Ecology #PublicHealth #Epidemiology #ComputationalBiology #Bioinformatics #Genomics #Biology #Medicine #Research #ResearchTraining #Instats

This study uses metagenomics and in situ metatranscriptomics to explore microbial ecology from deep sea hadal trenches. They find that viruses and magnetotactic bacteria possibly help distant phyla sh...

This study uses metagenomics and in situ metatranscriptomics to explore microbial ecology from deep sea hadal trenches. They find that viruses and magnetotactic bacteria possibly help distant phyla share functional genes to survive extreme pressure and starvation.

Join us for an online seminar exploring how genomic science, metatranscriptomics, and AI are reshaping our understanding of viral diversity, zoonotic spillover, and pandemic prevention. Designed for PhD students and professional researchers, this seminar will examine how total RNA shotgun sequencing can reveal the viral composition of diverse samples, how viruses move across the human-animal interface, and how evolutionary, ecological, phylogenetic, and epidemiological evidence can be integrated to assess emergence risk. With examples including RNA virus diversity in mammalian systems, coronaviruses in natural and farmed/market animal environments, and SARS-CoV-2 as a key case study, participants will gain insight into host shifts, recombination, selection, genomic surveillance, and the role of AI in improving zoonotic risk assessment. The seminar also considers practical steps toward pandemic prevention, including global surveillance systems and libraries of potential vaccines. Livestream access is via Zoom, with recordings, materials, and a monitored Q&A forum available for 30 days after the seminar, plus an official certificate of completion. #Virology #Ecology #PublicHealth #Epidemiology #ComputationalBiology #Bioinformatics #Genomics #Biology #Medicine #Research #ResearchTraining #Instats

Hot springs are employed as model systems for understanding how environmental stress structures microbial communities, yet the mechanisms by which geothermal stress reorganizes community metabolism remain poorly understood. Here we combined genome-resolved metagenomics, metatranscriptomics, aqueous geochemistry, and community metabolic modelling to investigate photosynthetic biofilms across the geothermal gradient of a hot spring in Singapore. We reconstructed community taxonomic and functional composition via metagenome-assembled genomes and identified three transcriptionally coordinated ecological guilds defined by convergent metabolic strategies rather than phylogeny. Community metabolic models revealed that increasing geothermal stress reorganized nutrient exchange networks, progressively reducing metabolic redundancy and increasing dependence on reciprocal interactions among thermophilic guilds. Increasing geothermal stress redirected relative modelled elemental demand from carbon-associated metabolism towards nitrogen and sulfur metabolism, highlighting nitrogen limitation and sulfur-linked bioenergetics as defining features of stress adaptation. Electron allocation modelling further demonstrated a systems-level transition from growth-oriented biosynthesis toward catabolic energy conservation, respiratory metabolism, and oxidative stress management under geothermal stress. These coordinated metabolic shifts indicate that hot spring communities become increasingly specialized and energetically constrained near their upper geothermal limits. Overall, the findings demonstrate how environmental stress restructures microbial ecosystems through guild-level metabolic partitioning and cooperative resource exchange and establishes an integrative systems biology framework for predicting microbial ecosystem function in extreme environments. ### Competing Interest Statement The authors have declared no competing interest. Singapore Ministry of Education, MOE-T2EP30123-0007 City University of Hong Kong, Project 9678175

The language of cheese science has undergone a revolution—and if you’ve tried to read a recent paper on rind biofilms, metatranscriptomics, or the *Lacto...

Abstract. The soil microbiome drives soil organic carbon (SOC) transformation, shaped and impacted by plant growth stage and soil management such as tillag

Multi‑omics technologies increasingly provide insight into microbiome function across environmental, engineered, and host‑associated systems. Integrating metagenomics, metatranscriptomics, metaproteomics, and metabolomics links microbial composition to activity and ecological interactions1,2. These approaches extend functional interpretation beyond marker‑gene surveys, enabling the identification of novel taxa, biosynthetic pathways, and biochemical functions, offering a route to unravel previously inaccessible mechanisms and propose new hypotheses for causal relationships between microbiome shifts and host or environmental phenotypes. These multi‑layered datasets underpin emerging applications in precision therapeutics, sustainable agriculture, and ecosystem stewardship, reinforcing a “One Health” perspective that connects microbiome function across human, animal, and environmental domains3. Despite major advances in standardized profiling of taxa and genomic potential, robust and scalable integration frameworks are still needed to bridge genotype with phenotype and resolve microbe–microbe and host–microbe interactions in complex communities. Several recent reviews summarize the current state-of-the-art, opportunities and challenges of multi-omics microbiome research from different perspectives including methodological developments and analytical principles, host–microbiome integration, and applications in specific biological or clinical contexts1,4,5,6,7. Yet as the field embraces multi‑omics integration, a proliferation of analytical strategies has produced heterogeneous, non‑standardized outputs that are difficult to compare or synthesize across studies. Consequently, the central bottleneck is shifting from reproducible data...

Join us for an online seminar designed for PhD students and professional researchers exploring how genomic surveillance, metatranscriptomics, and AI are transforming our understanding of virus diversity, zoonotic spillover, and pandemic prevention. The seminar examines how RNA viruses diversify, adapt, and cross species barriers, with attention to coronaviruses, mammalian viral diversity, host jumps, SARS-CoV-2 as a case study, and emerging AI-based approaches for assessing zoonotic risk. Participants will gain a deeper understanding of viral evolution, phylogenetic and ecological inference, genomic surveillance, selection and recombination, outbreak uncertainty, and the translation of research evidence into public health preparedness, including concepts such as a global pandemic radar and vaccine libraries. Delivered via Zoom, the seminar includes access to recordings, slides, materials, and an expert-moderated Q&A forum for 30 days after the live sessions, making it suitable for both live and asynchronous participation. An official Instats certificate of completion is provided, with ECTS Equivalent points available where indicated. #Virology #Ecology #PublicHealth #Epidemiology #ComputationalBiology #Bioinformatics #Genomics #Biology #Research #ResearchTraining #Instats

In this study, using estuary metagenomics and metatranscriptomics data the authors show that ecological niche partitioning constrains DNA virus diversification at the genus level, and that DNA viruses...