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QIIME allows analysis of high-throughput community sequencing data
Supplementary Figure 1 Overview of the analysis pipeline. Supplementary Table 1 Details of conventionally raised and conventionalized mouse samples. Supplementary Discussion Expanded discussion ofExpand
UCHIME improves sensitivity and speed of chimera detection
We describe UCHIME, a new program that detects chimeric sequences with two or more segments. Expand
UniFrac: a New Phylogenetic Method for Comparing Microbial Communities
ABSTRACT We introduce here a new method for computing differences between microbial communities based on phylogenetic information. This method, UniFrac, measures the phylogenetic distance betweenExpand
Predictive functional profiling of microbial communities using 16S rRNA marker gene sequences
Profiling phylogenetic marker genes, such as the 16S rRNA gene, is a key tool for studies of microbial communities but does not provide direct evidence of a community's functional capabilities. HereExpand
PyNAST: a flexible tool for aligning sequences to a template alignment
Python Nearest Alignment Space Termination (PyNAST) is a complete reimplementation of NAST, which includes three convenient interfaces: a Mac OS X GUI, a command-line interface and a simple application programming interface (API). Expand
Quality-filtering vastly improves diversity estimates from Illumina amplicon sequencing
High-throughput sequencing has revolutionized microbial ecology, but read quality remains a considerable barrier to accurate taxonomy assignment and α-diversity assessment for microbial communities.Expand
A core gut microbiome in obese and lean twins
The human distal gut harbours a vast ensemble of microbes (the microbiota) that provide important metabolic capabilities, including the ability to extract energy from otherwise indigestible dietaryExpand
An improved Greengenes taxonomy with explicit ranks for ecological and evolutionary analyses of bacteria and archaea
Reference phylogenies are crucial for providing a taxonomic framework for interpretation of marker gene and metagenomic surveys, which continue to reveal novel species at a remarkable rate.Expand
Human gut microbiome viewed across age and geography
Gut microbial communities represent one source of human genetic and metabolic diversity. To examine how gut microbiomes differ among human populations, here we characterize bacterial species in fecalExpand
Ultra-high-throughput microbial community analysis on the Illumina HiSeq and MiSeq platforms
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 protocol for community ampliconExpand