metagenomics
Research Article | Ecological and Evolutionary ScienceVirus Genomes from Deep Sea Sediments Expand the Ocean Megavirome and Support Independent Origins of Viral GigantismGenomics and evolution of giant viruses are two of the most vigorously developing areas of virus research. Lately, metagenomics has become the main source of new virus genomes. Here we describe a metagenomic analysis of the genomes of large and giant viruses from deep sea sediments. The assembled new virus genomes substantially expand the known diversity of the nucleocytoplasmic large DNA viruses of eukaryotes. The results support the...
Research Article | Ecological and Evolutionary ScienceCRISPR Spacers Indicate Preferential Matching of Specific Virioplankton GenesThe CRISPR-Cas system is one means by which bacterial and archaeal populations defend against viral infection which causes 20 to 50% of cell mortality in the ocean. We tested the hypothesis that certain viral genes are preferentially targeted for the initial attack of the CRISPR-Cas system on a viral genome. Using CASC, a pipeline for CRISPR spacer discovery, and metagenome data from oceanic microbes and viruses, we found a clear subset...
Research Article | Clinical Science and EpidemiologyGenomic Analyses of Acute Flaccid Myelitis Cases among a Cluster in Arizona Provide Further Evidence of Enterovirus D68 RoleEnteroviruses frequently result in respiratory and gastrointestinal illness; however, multiple subtypes, including poliovirus, can cause severe neurologic disease. Recent biennial increases (i.e., 2014, 2016, and 2018) in cases of non-polio acute flaccid paralysis have led to speculations that other enteroviruses, specifically enterovirus D68 (EV-D68), are emerging to fill the niche that was left from poliovirus eradication. A cluster...
Research Article | Host-Microbe BiologySupragingival Plaque Microbiome Ecology and Functional Potential in the Context of Health and DiseaseOral health has substantial economic importance, with over $100 billion spent on dental care in the United States annually. The microbiome plays a critical role in oral health, yet remains poorly classified. To address the question of how microbial diversity and function in the oral cavities of children relate to caries diagnosis, we surveyed the supragingival plaque biofilm microbiome in 44 juvenile twin pairs. Using shotgun sequencing...
Research Article | Host-Microbe BiologyGut Microbial and Metabolic Responses to Salmonella enterica Serovar Typhimurium and Candida albicansThe gut microbiota is increasingly recognized for playing a critical role in human health and disease, especially in conferring resistance to both virulent pathogens such as Salmonella, which infects 1.2 million people in the United States every year (E. Scallan, R. M. Hoekstra, F. J. Angulo, R. V. Tauxe, et al., Emerg Infect Dis 17:7–15, 2011, https://doi.org/10.3201/eid1701....
Research Article | Applied and Environmental ScienceMembers of the Genus Methylobacter Are Inferred To Account for the Majority of Aerobic Methane Oxidation in Oxic Soils from a Freshwater WetlandHere we used soil metagenomics and metatranscriptomics to uncover novel members within the genus Methylobacter. We denote these closely related genomes as members of the lineage OWC Methylobacter. Despite the incredibly high microbial diversity in soils, here we present findings that unexpectedly showed that methane cycling was primarily mediated by a single genus for both methane production (“Candidatus...