Latest Articles
Research Article | Host-Microbe BiologySequential Changes in the Mesenteric Lymph Node Microbiome and Immune Response during Cirrhosis Induction in RatsCirrhosis severity in patients was previously shown to be associated with progressive changes in the fecal microbiome in a longitudinal setting. Recent evidence shows that bacterial translocation from the gut to the extraintestinal sites could play a major role in poor disease outcome and patient survival. However, the underlying mechanisms involving the microbiota in the disease progression are not well understood. Here, using an...
Research Article | Host-Microbe BiologyDifferential Gene Expression Patterns of Yersinia pestis and Yersinia pseudotuberculosis during Infection and Biofilm Formation in the Flea Digestive TractY. pestis emerged as a highly virulent, arthropod-transmitted pathogen on the basis of relatively few and discrete genetic changes from Y. pseudotuberculosis. Parallel comparisons of the in vitro and in vivo transcriptomes of...
Editor's Pick Perspective | Host-Microbe BiologyThe Dimension of Time in Host-Microbiome InteractionsThe intestinal microbiota contains trillions of commensal microorganisms that shape multiple aspects of host physiology and disease. In contrast to the host’s genome, the microbiome is amenable to change over the course of an organism’s lifetime, providing an opportunity to therapeutically modulate the microbiome’s impact on human pathophysiology.
Editor's Pick Research Article | Novel Systems Biology TechniquesPerformance of Microbiome Sequence Inference Methods in Environments with Varying BiomassMicrobial communities have important ramifications for human health, but determining their impact requires accurate characterization. Current technology makes microbiome sequence data more accessible than ever. However, popular software methods for analyzing these data are based on algorithms developed alongside older sequencing technology and smaller data sets and thus may not be adequate for modern, high-throughput data sets....
Research Article | Therapeutics and PreventionHelminth-Based Product and the Microbiome of Mice with LupusRecently, several papers referred to the association of different bacteria with lupus in mice and humans. This is the first report to demonstrate the effect of a compound derived from helminths on the induction of remission in mice with lupus and its association with a bacterial change. We show that several genera, including Akkermansia, are associated with clinical and serological parameters of lupus, while other genera,...
Research Article | Applied and Environmental ScienceUltrahigh-Throughput Multiplexing and Sequencing of >500-Base-Pair Amplicon Regions on the Illumina HiSeq 2500 PlatformAmplicon sequencing has become a popular and widespread tool for surveying microbial communities. Lower overall costs associated with high-throughput sequencing have made it a widely adopted approach, especially for projects that necessitate sample multiplexing to eliminate batch effect and reduced time to acquire data. The method for amplicon sequencing on the Illumina HiSeq 2500 platform described here provides improved multiplexing...
Research Article | Host-Microbe BiologyEvaluating Metagenomic Prediction of the Metaproteome in a 4.5-Year Study of a Patient with Crohn's DiseaseA majority of current microbiome research relies heavily on DNA analysis. However, as the field moves toward understanding the microbial functions related to healthy and disease states, it is critical to evaluate how changes in DNA relate to changes in proteins, which are functional units of the genome. This study tracked the abundance of genes and proteins as they fluctuated during various inflammatory states in a 4.5-year study of a...
Research Article | Ecological and Evolutionary ScienceOrphan Genes Shared by Pathogenic Genomes Are More Associated with Bacterial PathogenicityRecent pangenome analyses of numerous bacterial species have suggested that each genome of a single species may have a significant fraction of its gene content unique or shared by a very few genomes (i.e., ORFans). We selected nine bacterial genera, each containing at least five pathogenic and five nonpathogenic genomes, to compare their ORFans in relation to pathogenicity-related genes. Pathogens in these genera are known to cause a...
Research Article | Molecular Biology and PhysiologySystems-Level Analysis of Oxygen Exposure in Zymomonas mobilis: Implications for Isoprenoid ProductionMicrobially generated biofuels and bioproducts have the potential to provide a more environmentally sustainable alternative to fossil-fuel-derived products. In particular, isoprenoids, a diverse class of natural products, are chemically suitable for use as high-grade transport fuels and other commodity molecules. However, metabolic engineering for increased production of isoprenoids and other bioproducts is limited by an incomplete...
Research Article | Ecological and Evolutionary ScienceSalinity Is a Key Determinant for Soil Microbial Communities in a Desert EcosystemBelowground microorganisms are indispensable components for nutrient cycling in desert ecosystems, and understanding how they respond to increased salinity is essential for managing and ameliorating salinization. Our sequence-based data revealed that microbial diversity decreased with increasing salinity, and certain salt-tolerant phylotypes and phenotypes showed a positive relationship with salinity. Using a null modeling approach to...
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mSystems®, an open access journal from the American Society for Microbiology, publishes the best research in single-cell and community microbial systems biology, new computational and laboratory approaches, and synthetic biology.
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