J. Gregory Caporaso

Optimizing taxonomic classification of marker-gene amplicon sequences with QIIME 2’s q2-feature-classifier plugin

Taxonomic classification of marker-gene sequences is an important step in microbiome analysis. We present q2-feature-classifier (https://github.com/qiime2/q2-feature-classifier)...

QIIME allows analysis of high-throughput community sequencing data

Stability of operational taxonomic units: an important but neglected property for analyzing microbial diversity

As a compromise to the factors listed above, we propose using an open-reference method to enhance OTU stability. This type of method clusters sequences against a database and in...

Predictive functional profiling of microbial communities using 16S rRNA marker gene sequences

Global patterns of 16S rRNA diversity at a depth of millions of sequences per sample

The ongoing revolution in high-throughput sequencing continues to democratize the ability of small groups of investigators to map the microbial component of the biosphere. In pa...

Cross-biome metagenomic analyses of soil microbial communities and their functional attributes

For centuries ecologists have studied how the diversity and functional traits of plant and animal communities vary across biomes. In contrast, we have only just begun exploring ...

Phylogenetic stratigraphy in the Guerrero Negro hypersaline microbial mat

Abstract The microbial mats of Guerrero Negro (GN), Baja California Sur, Mexico historically were considered a simple environment, dominated by cyanobacteria and sulfate-reducin...

Ultra-high-throughput microbial community analysis on the Illumina HiSeq and MiSeq platforms

Abstract DNA sequencing continues to decrease in cost with the Illumina HiSeq2000 generating up to 600 Gb of paired-end 100 base reads in a ten-day run. Here we present a protoc...