Share This Author
QIIME allows analysis of high-throughput community sequencing data
An overview of the analysis pipeline and links to raw data and processed output from the runs with and without denoising are provided.
UCHIME improves sensitivity and speed of chimera detection
UCHIME has better sensitivity than ChimeraSlayer (previously the most sensitive database method), especially with short, noisy sequences, and in testing on artificial bacterial communities with known composition, UCHIME de novo sensitivity is shown to be comparable to Perseus.
UniFrac: a New Phylogenetic Method for Comparing Microbial Communities
The results illustrate that UniFrac provides a new way of characterizing microbial communities, using the wealth of environmental rRNA sequences, and allows quantitative insight into the factors that underlie the distribution of lineages among environments.
Predictive functional profiling of microbial communities using 16S rRNA marker gene sequences
The results demonstrate that phylogeny and function are sufficiently linked that this 'predictive metagenomic' approach should provide useful insights into the thousands of uncultivated microbial communities for which only marker gene surveys are currently available.
PyNAST: a flexible tool for aligning sequences to a template alignment
- J. Caporaso, K. Bittinger, F. Bushman, T. DeSantis, G. Andersen, R. Knight
- Computer ScienceBioinform.
- 13 November 2009
Motivation: The Nearest Alignment Space Termination (NAST) tool is commonly used in sequence-based microbial ecology community analysis, but due to the limited portability of the original…
Reproducible, interactive, scalable and extensible microbiome data science using QIIME 2
QIIME 2 development was primarily funded by NSF Awards 1565100 to J.G.C. and R.K.P. and partial support was also provided by the following: grants NIH U54CA143925 and U54MD012388.
A core gut microbiome in obese and lean twins
The faecal microbial communities of adult female monozygotic and dizygotic twin pairs concordant for leanness or obesity, and their mothers are characterized to address how host genotype, environmental exposure and host adiposity influence the gut microbiome.
Human gut microbiome viewed across age and geography
The need to consider the microbiome when evaluating human development, nutritional needs, physiological variations and the impact of westernization is underscored, as distinctive features of the functional maturation of the gut microbiome are evident in early infancy as well as adulthood.
Ultra-high-throughput microbial community analysis on the Illumina HiSeq and MiSeq platforms
It is shown that the protocol developed for these instruments successfully recaptures known biological results, and additionally that biological conclusions are consistent across sequencing platforms (the HiSeq2000 versus the MiSeq) and across the sequenced regions of amplicons.
Linking Long-Term Dietary Patterns with Gut Microbial Enterotypes
Alternative enterotype states are associated with long-term diet, particularly protein and animal fat (Bacteroides) versus carbohydrates (Prevotella) and other enterotypes distinguished primarily by levels of Bacteroide and Prevotella.