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  • In this Perspective, the authors discuss the importance and current challenges of using genomic data to predict the emergence of infectious disease outbreaks, and propose the next steps to integrate genomics and modelling for infectious diseases forecasting.

    • Jessica E. Stockdale
    • Pengyu Liu
    • Caroline Colijn
  • Efforts to futureproof global microbial biodiversity are proposed, in particular in managed landscapes, to monitor, manage and restore the soil fungal microbiome.

    • Colin Averill
    • Mark A. Anthony
    • Tom W. Crowther
  • Careful and responsible microbiome management is a critical strategy to counter biodiversity loss, but practical and regulatory hurdles must be addressed to maximize its utility.

    • Raquel S. Peixoto
    • Christian R. Voolstra
    • Gabriele Berg
  • Studying the ocean microbiome can inform international policies related to ocean governance, tackling climate change, ocean acidification and pollution, and can help promote achievement of multiple Sustainable Development Goals.

    • Andre Abreu
    • Etienne Bourgois
    • Jan Vanaverbeke
  • Metagenomics-based surveillance could transform global efforts to detect risks to human health within a One Health framework.

    • Karrie K. K. Ko
    • Kern Rei Chng
    • Niranjan Nagarajan
  • Gut microbiome development in full-term infants has important implications for health and disease, but less is known for preterm infants. Here the authors summarize current knowledge in preterm infants, compare this to what is known for full-term babies, and discuss potential diagnostics and interventions to improve outcomes for preterm infants.

    • David B. Healy
    • C. Anthony Ryan
    • Eugene M. Dempsey
  • A network science framework for understanding and predicting human and animal susceptibility to viral infections is proposed.

    • Gregory F. Albery
    • Daniel J. Becker
    • Colin J. Carlson
  • This Perspective discusses current knowledge of the complex crosstalk between the microbiota and γδ T cells and future outlooks.

    • Pedro H. Papotto
    • Bahtiyar Yilmaz
    • Bruno Silva-Santos
  • This Perspective discusses fungal taxonomy and provides guidance for the naming of fungal taxa known only from sequences.

    • Robert Lücking
    • M. Catherine Aime
    • Conrad L. Schoch
  • Urban informal settlements, more commonly known as slums, are hotspots for the environmental transmission of antimicrobial resistance (AMR). Here, the authors discuss the behavioural, environmental and structural reasons for this and propose that improvements in water and waste infrastructure, as well as legal and economic incentives, could limit environmental AMR dissemination.

    • Maya L. Nadimpalli
    • Sara J. Marks
    • Amy J. Pickering
  • In this Perspective, Lopez-Garcia and Moreira update the Syntrophy hypothesis for the origin of eukaryotes, considering recent advances in the archaeal field about the physiology, metabolism, ecology and evolution of these microbes. They also compare and contrast their model with alternative ones, such as the classical Searcy’s and Hydrogen hypotheses and the more recent Reverse Flow and Entangle–Engulf–Endogenize models, and discuss model predictions and ways to test these.

    • Purificación López-García
    • David Moreira
  • This Perspective argues that microbiome research needs to consider the different philosophical definitions of function to avoid confusion in the field, and uses the hologenome concept as an example.

    • Jonathan L. Klassen
  • The colonization resistance paradigm is explored, with a focus on the benefits and limitations of current murine models used to assess the role of the microbiota in enteric infection.

    • Caroline Mullineaux-Sanders
    • Jotham Suez
    • Gad Frankel