computational biology
Research Article | Molecular Biology and PhysiologyCoevolutionary Analysis Reveals a Conserved Dual Binding Interface between Extracytoplasmic Function σ Factors and Class I Anti-σ FactorsIn 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...
Resource Report | Molecular Biology and PhysiologyA Comprehensive Coexpression Network Analysis in Vibrio choleraeCholera 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...
Research Article | Ecological and Evolutionary ScienceBiofilm Structure Promotes Coexistence of Phage-Resistant and Phage-Susceptible BacteriaIn 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,...
Research Article | Ecological and Evolutionary ScienceA Novel Sparse Compositional Technique Reveals Microbial PerturbationsBy 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...
Special Issue Perspective | Novel Systems Biology TechniquesOn the Road to Strain-Resolved Comparative MetagenomicsMetagenomics 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.
Research Article | Host-Microbe BiologyPrevalence and Source of Fecal and Oral Bacteria on Infant, Child, and Adult HandsBacteria 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...