883 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. Cell Biology
    2. Ecology

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

    Sebastien Colin, Luis Pedro Coelho ... Colomban de Vargas
    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. 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, María Rodríguez-López ... Jürg Bähler
    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. Ecology
    2. Physics of Living Systems

    Investigating macroecological patterns in coarse-grained microbial communities using the stochastic logistic model of growth

    William R Shoemaker, Jacopo Grilli
    Microbial macroecological patterns under coarse-graining are captured by a null model of ecology, a result which was leveraged to successfully predict the relationship between fine and coarse-grained diversity.
    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, Márton Palatinszky ... Elizabeth A Shank
    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. Physics of Living Systems

    A multiphase theory for spreading microbial swarms and films

    Siddarth Srinivasan, C Nadir Kaplan, L Mahadevan
    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. Epidemiology and Global Health
    2. Microbiology and Infectious Disease

    Resistome diversity in cattle and the environment decreases during beef production

    Noelle R Noyes, Xiang Yang ... Keith E Belk
    Interventions in feedlots and abattoirs place selective pressure on the beef cattle resistome, which differentially impacts the public health risk of antimicrobial resistance from beef production sources.
    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, Laura Wegener Parfrey ... Rob Knight
    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. Computational and Systems Biology
    2. Ecology

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

    Babak Momeni, Li Xie, Wenying Shou
    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. Ecology
    2. Evolutionary Biology

    Spatiotemporal ecological chaos enables gradual evolutionary diversification without niches or tradeoffs

    Aditya Mahadevan, Michael T Pearce, Daniel S Fisher
    Evolution of multiple closely related strains with host-pathogen-like interactions but only one niche and no tradeoffs, can give rise to a spatiotemporally chaotic ecological state that continually diversifies even with generalist mutations that slow the evolution.

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