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computational biology

  • Open Access
    Coevolutionary Analysis Reveals a Conserved Dual Binding Interface between Extracytoplasmic Function σ Factors and Class I Anti-σ Factors
    Research Article | Molecular Biology and Physiology
    Coevolutionary Analysis Reveals a Conserved Dual Binding Interface between Extracytoplasmic Function σ Factors and Class I Anti-σ Factors

    In the bacterial world, extracytoplasmic function σ factors (ECFs) are the most widespread family of alternative σ factors, mediating many cellular responses to environmental cues, such as stress. This work uses a computational approach to investigate how these σ factors interact with class I anti-σ factors—the most abundant regulators of ECF activity. By comprehensively classifying the anti-σs into phylogenetic groups and by comparing...

    Delia Casas-Pastor, Angelika Diehl, Georg Fritz
  • Open Access
    A Comprehensive Coexpression Network Analysis in <span class="named-content genus-species" id="named-content-1">Vibrio cholerae</span>
    Resource Report | Molecular Biology and Physiology
    A Comprehensive Coexpression Network Analysis in Vibrio cholerae

    Cholera is a devastating illness that kills tens of thousands of people annually. Vibrio cholerae, the causative agent of cholera, is an important model organism to investigate both bacterial pathogenesis and the impact of horizontal gene transfer on the emergence and dissemination of new virulent strains. Despite the importance of this pathogen, roughly one-third of...

    Cory D. DuPai, Claus O. Wilke, Bryan W. Davies
  • Open Access
    Biofilm Structure Promotes Coexistence of Phage-Resistant and Phage-Susceptible Bacteria
    Research Article | Ecological and Evolutionary Science
    Biofilm Structure Promotes Coexistence of Phage-Resistant and Phage-Susceptible Bacteria

    In the natural environment, bacteria most often live in communities bound to one another by secreted adhesives. These communities, or biofilms, play a central role in biogeochemical cycling, microbiome functioning, wastewater treatment, and disease. Wherever there are bacteria, there are also viruses that attack them, called phages. Interactions between bacteria and phages are likely to occur ubiquitously in biofilms. We show here,...

    Emilia L. Simmons, Matthew C. Bond, Britt Koskella, Knut Drescher, Vanni Bucci, Carey D. Nadell
  • Open Access
    A Novel Sparse Compositional Technique Reveals Microbial Perturbations
    Research Article | Ecological and Evolutionary Science
    A Novel Sparse Compositional Technique Reveals Microbial Perturbations

    By accounting for the sparse compositional nature of microbiome data sets, robust Aitchison PCA can yield high discriminatory power and salient feature ranking between microbial niches. The software to perform this analysis is available under an open-source license and can be obtained at https://github.com/biocore/DEICODE; additionally, a QIIME 2 plugin is provided to perform this...

    Cameron Martino, James T. Morton, Clarisse A. Marotz, Luke R. Thompson, Anupriya Tripathi, Rob Knight, Karsten Zengler
  • Open Access
    On the Road to Strain-Resolved Comparative Metagenomics
    Special Issue Perspective | Novel Systems Biology Techniques
    On the Road to Strain-Resolved Comparative Metagenomics

    Metagenomics has transformed microbiology, but its potential has not been fully expressed yet. From computational methods for digging deeper into metagenomes to study designs for addressing specific hypotheses, the Segata Lab is pursuing an integrative metagenomic approach to describe and model human-associated microbial communities as collections of strains.

    Nicola Segata
  • Open Access
    Prevalence and Source of Fecal and Oral Bacteria on Infant, Child, and Adult Hands
    Research Article | Host-Microbe Biology
    Prevalence and Source of Fecal and Oral Bacteria on Infant, Child, and Adult Hands

    Bacteria live all around us, and we are constantly exposed to them during our everyday lives. Modern standards of hygiene aim to limit exposure to fecal bacteria, and yet bacteria rapidly colonize the gut in early life and following antibacterial treatment. Exposures to fecal and oral microbes provide risk of disease, but are also necessary since commensal microbes play important roles in health. This work establishes that bacteria of...

    Michael Shaffer, Catherine Lozupone
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