898 results found
    1. Computational and Systems Biology

    Calibration and analysis of genome-based models for microbial ecology

    Stilianos Louca, Michael Doebeli
    A novel computation tool for microbial community modeling predicts the evolution and diversification of E. coli in laboratory evolution experiments and gives insight into the underlying metabolic processes.
    1. Genetics and Genomics
    2. Microbiology and Infectious Disease

    Pyphe, a python toolbox for assessing microbial growth and cell viability in high-throughput colony screens

    Stephan Kamrad et al.
    An open-source python package for phenotype analyses provides a versatile, modular and user-friendly solution to determine complementary fitness-related traits from large-scale assays of microbial colonies.
    1. Cell Biology
    2. Ecology

    Quantitative 3D-imaging for cell biology and ecology of environmental microbial eukaryotes

    Sebastien Colin et al.
    Three-dimensional fluorescence imaging of microbial eukaryotes in environmental samples allows accurate automated taxonomic profiling and quantitative data about ultrastructures and interactions of organisms.
    1. Physics of Living Systems

    A multiphase theory for spreading microbial swarms and films

    Siddarth Srinivasan et al.
    A multiphase hydrodynamic theory reveals that the dynamics of colony expansion in microbial swarms and biofilms are limited by the constraints of water and nutrient availability.
    1. Ecology
    2. Microbiology and Infectious Disease

    Transparent soil microcosms for live-cell imaging and non-destructive stable isotope probing of soil microorganisms

    Kriti Sharma et al.
    Two optically transparent substrates enable the exploration of the ecophysiology and spatiotemporal organization and activities of bacteria and fungi within heterogeneous soil-like environments.
    1. Ecology
    2. Microbiology and Infectious Disease

    A microbial clock provides an accurate estimate of the postmortem interval in a mouse model system

    Jessica L Metcalf et al.
    High-throughput sequencing has been used to analyze the microbiome of mouse corpses over a period of 48 days, and to provide an accurate estimate of the time since death.
    1. Ecology
    2. Physics of Living Systems

    Microbial consortia at steady supply

    Thibaud Taillefumier et al.
    In a consumer-resource model obeying the physical requirement of flux conservation, metabolic competition between microbes yields consortia of cell types that collectively resist invasion via optimal use of resources.
    1. Computational and Systems Biology
    2. Ecology

    Lotka-Volterra pairwise modeling fails to capture diverse pairwise microbial interactions

    Babak Momeni et al.
    With mathematical modeling being an important source of insight for microbial communities, we may need to move beyond commonly-used pairwise models that do not capture microbial interactions.
    1. Microbiology and Infectious Disease

    A comparative transcriptomic analysis of replicating and dormant liver stages of the relapsing malaria parasite Plasmodium cynomolgi

    Annemarie Voorberg-van der Wel et al.
    This comprehensive transcriptomic resource of dormant and replicating malaria liver parasites highlights the dearth of pathways that operate in the hypnozoites and the need to investigate druggability (i.e. selectivity and safety) of core pathways in malaria parasites.
    1. Ecology
    2. Evolutionary Biology

    Effects of domestication on the gut microbiota parallel those of human industrialization

    Aspen T Reese et al.
    Gut microbial signatures of domestication parallel those of industrialization, implicating shared ecological drivers.

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