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DNA sequencing

  • Open Access
    Theoretical and Simulation-Based Investigation of the Relationship between Sequencing Effort, Microbial Community Richness, and Diversity in Binning Metagenome-Assembled Genomes
    Research Article | Novel Systems Biology Techniques
    Theoretical and Simulation-Based Investigation of the Relationship between Sequencing Effort, Microbial Community Richness, and Diversity in Binning Metagenome-Assembled Genomes

    Short-read sequencing with Illumina sequencing technology provides an accurate, high-throughput method for characterizing the metabolic potential of microbial communities. Short-read sequences can be assembled and binned into metagenome-assembled genomes, thus shedding light on the function of microbial ecosystems that are important for health, agriculture, and Earth system processes. The work presented here provides an analytical...

    Taylor M. Royalty, Andrew D. Steen
  • Open Access
    Taxon Disappearance from Microbiome Analysis Reinforces the Value of Mock Communities as a Standard in Every Sequencing Run
    Research Article | Applied and Environmental Science
    Taxon Disappearance from Microbiome Analysis Reinforces the Value of Mock Communities as a Standard in Every Sequencing Run

    Despite the routine use of standards and blanks in virtually all chemical or physical assays and most biological studies (a kind of “control”), microbiome analysis has traditionally lacked such standards. Here we show that unexpected problems of unknown origin can occur in such sequencing runs and yield completely incorrect results that would not necessarily be detected without the use of standards. Assuming that the microbiome...

    Yi-Chun Yeh, David M. Needham, Ella T. Sieradzki, Jed A. Fuhrman
  • Open Access
    Deblur Rapidly Resolves Single-Nucleotide Community Sequence Patterns
    Editor's Pick Observation | Novel Systems Biology Techniques
    Deblur Rapidly Resolves Single-Nucleotide Community Sequence Patterns

    Deblur provides a rapid and sensitive means to assess ecological patterns driven by differentiation of closely related taxa. This algorithm provides a solution to the problem of identifying real ecological differences between taxa whose amplicons differ by a single base pair, is applicable in an automated fashion to large-scale sequencing data sets, and can integrate sequencing runs collected over time.

    Amnon Amir, Daniel McDonald, Jose A. Navas-Molina, Evguenia Kopylova, James T. Morton, Zhenjiang Zech Xu, Eric P. Kightley, Luke R. Thompson, Embriette R. Hyde, Antonio Gonzalez, Rob Knight
  • Open Access
    Correcting for Microbial Blooms in Fecal Samples during Room-Temperature Shipping
    Observation | Host-Microbe Biology
    Correcting for Microbial Blooms in Fecal Samples during Room-Temperature Shipping

    In many microbiome studies, the necessity to store samples at room temperature (i.e., remote fieldwork) and the ability to ship samples without hazardous materials that require special handling training, such as ethanol (i.e., citizen science efforts), is paramount. However, although room-temperature storage for a few days has been shown not to obscure physiologically relevant microbiome differences between comparison groups, there are...

    Amnon Amir, Daniel McDonald, Jose A. Navas-Molina, Justine Debelius, James T. Morton, Embriette Hyde, Adam Robbins-Pianka, Rob Knight
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