microbial ecology
Methods and Protocols | Novel Systems Biology Techniquesmanta: a Clustering Algorithm for Weighted Ecological Networksmanta comes with unique strengths, such as the abilities to identify nodes that represent an intermediate between clusters, to exploit negative edges, and to assess the robustness of cluster membership. manta does not require parameter tuning, is straightforward to install and run, and can be easily combined with existing microbial network inference tools.
Editor's Pick Research Article | Applied and Environmental ScienceValidating the Cyc2 Neutrophilic Iron Oxidation Pathway Using Meta-omics of Zetaproteobacteria Iron Mats at Marine Hydrothermal VentsIron oxides are important components of our soil, water supplies, and ecosystems, as they sequester nutrients, carbon, and metals. Microorganisms can form iron oxides, but it is unclear whether this is a significant mechanism in the environment. Unlike other major microbial energy metabolisms, there is no marker gene for iron oxidation, hindering our ability to track these microbes. Here, we investigate a promising possible iron...
Research Article | Ecological and Evolutionary ScienceQuantitative Models of Phage-Antibiotic Combination TherapyThis work develops and analyzes a novel model of phage-antibiotic combination therapy, specifically adapted to an in vivo context. The objective is to explore the underlying basis for clinical application of combination therapy utilizing bacteriophage that target antibiotic efflux pumps in Pseudomonas aeruginosa. In doing so, the paper addresses three key...
Observation | Novel Systems Biology TechniquesNetwork-Based Prediction of Novel CRISPR-Associated Genes in MetagenomesEvery branch on the tree of life, including microbial life, faces the threat of viral pathogens. Over the course of billions of years of coevolution, prokaryotes have evolved a great diversity of strategies to defend against viral infections. One of these is the CRISPR adaptive immune system, which allows microbes to “remember” past infections in order to better fight them in the future. There has been much interest among molecular...
Editor's Pick Methods and Protocols | Applied and Environmental ScienceMarine Metabolomics: a Method for Nontargeted Measurement of Metabolites in Seawater by Gas Chromatography–Mass SpectrometryNontargeted approaches using metabolomics to analyze metabolites that occur in the oceans is less developed than those for terrestrial and limnic ecosystems. One of the challenges in marine metabolomics is that salt limits metabolite analysis in seawater to methods requiring salt removal. Building on previous sample preparation methods for metabolomics, we developed SeaMet, which overcomes the limitations of salt on metabolite detection...
Editor's Pick Research Article | Host-Microbe BiologyInteractions between the Gut Microbiome and Mucosal Immunoglobulins A, M, and G in the Developing Infant GutAntibodies are secreted into the gut and attach to roughly half of the trillions of bacterial cells present. When babies are born, the breastmilk supplies these antibodies until the baby’s own immune system takes over this task after a few weeks. The vast majority of these antibodies are IgA, but two other types, IgG and IgM, are also present in the gut. Here, we ask if these three different antibody types target different types of...
Editor's Pick Research Article | Ecological and Evolutionary ScienceRegime Shifts in a Phage-Bacterium Ecosystem and Strategies for Its ControlPhage-microbe communities play an important role in human health as well as natural and industrial environments. Here we show that these communities can assume several alternative species compositions separated by abrupt regime shifts. Our model predicts these regime shifts in the competition between bacterial strains protected by two different phage defense mechanisms: abortive infection/CRISPR and partial resistance. The history...
Editor's Pick Methods and Protocols | Applied and Environmental ScienceIntroducing SPeDE: High-Throughput Dereplication and Accurate Determination of Microbial Diversity from Matrix-Assisted Laser Desorption–Ionization Time of Flight Mass Spectrometry DataEstimation of the operational isolation units present in a MALDI-TOF mass spectral data set involves an essential dereplication step to identify redundant spectra in a rapid manner and without sacrificing biological resolution. We describe SPeDE, a new algorithm which facilitates culture-dependent clinical or environmental studies. SPeDE enables the rapid analysis and dereplication of isolates, a critical feature when long-term storage...
Methods and Protocols | Host-Microbe BiologyHighly Reproducible 16S Sequencing Facilitates Measurement of Host Genetic Influences on the Stickleback Gut MicrobiomeOur findings demonstrate the importance of appropriately quantifying biological and technical variance components when attempting to understand major influences on high-throughput microbiome data. Our focus was on understanding among-host (biological) variance in community metrics and its magnitude in relation to within-host (technical) variance, because meaningful comparisons among individuals are necessary in addressing major...
