Studies of inflammatory bowel disease (IBD) have been inconclusive in relating microbiota
with distribution of inflammation. We report microbiota, host transcriptomics, epigenomics�…

We have created a Shiny-based Web application, called Shiny-phyloseq, for dynamic
interaction with microbiome data that runs on any modern Web browser and requires no�…

Background An increasing body of evidence implicates the resident gut microbiota as
playing a critical role in type 2 diabetes (T2D) pathogenesis. We previously reported�…

Objective Colorectal cancer (CRC) is the second leading cause of cancer-associated
mortality in the USA. The faecal microbiome may provide non-invasive biomarkers of CRC�…

We investigated the distribution and activity of chloroethene-degrading microorganisms and
associated functional genes during reductive dehalogenation of tetrachloroethene to ethene�…

Background Vinyl chloride is a widespread groundwater pollutant and Group 1 carcinogen.
A previous comparative genomic analysis revealed that the vinyl chloride reductase operon�…

Microbial communities are commonly characterized by amplifying and sequencing target
genes, but errors limit the precision of amplicon sequencing. We present DADA2, a software�…

This article compares different methods for combining abundance data, phylogenetic trees
and clinical covariates in a nonparametric setting. In particular we study the output from the�…

Hydrogen (H2) release from photosynthetic microbial mats has contributed to the chemical
evolution of Earth and could potentially be a source of renewable H2 in the future. However�…

Normalization is a term that is often used but rarely defined and poorly understood. The
number of choices of normalization procedure is large—some are inappropriate or�…