Daniel McDonald

TL;DR: A ‘taxonomy to tree’ approach for transferring group names from an existing taxonomy to a tree topology is developed and used to apply the Greengenes, National Center for Biotechnology Information (NCBI) and cyanoDB (Cyanobacteria only) taxonomies to a de novo tree comprising 408 315 sequences.

TL;DR: Comparing the microbial signatures between the ileum, the rectum, and fecal samples indicates that at this early stage of disease, assessing the rectal mucosal-associated microbiome offers unique potential for convenient and early diagnosis of CD.

TL;DR: The Human Microbiome Project (HMP) Consortium has established a population-scale framework which catalyzed significant development of metagenomic protocols resulting in a broad range of quality-controlled resources and data including standardized methods for creating, processing and interpreting distinct types of high-throughput metagenomics data available to the scientific community as mentioned in this paper.

TL;DR: A meta-analysis of microbial community samples collected by hundreds of researchers for the Earth Microbiome Project is presented, creating both a reference database giving global context to DNA sequence data and a framework for incorporating data from future studies, fostering increasingly complete characterization of Earth’s microbial diversity.

TL;DR: A novel sub-operational-taxonomic-unit (sOTU) approach that uses error profiles to obtain putative error-free sequences from Illumina MiSeq and HiSeq sequencing platforms, Deblur, which substantially reduces computational demands relative to similar sOTU methods and does so with similar or better sensitivity and specificity.