Fast UniFrac: Facilitating high-throughput phylogenetic analyses of microbial communities including analysis of pyrosequencing and PhyloChip data

By Micah Hamady, Catherine A. Lozupone, Rob Knight. The ISME Journal, 2009

1,106 citations recorded by the source corpus.

Next-generation sequencing techniques, and PhyloChip, have made simultaneous phylogenetic analyses of hundreds of microbial communities possible. Insight into community structure has been limited by the inability to integrate and visualize such vast datasets. Fast UniFrac overcomes these issues, allowing integration of larger numbers of sequences and samples into a single analysis. Its new array-based implementation offers orders of magnitude improvements over the original version. New 3D visualization of principal coordinates analysis results, with the option to view multiple coordinate axes simultaneously, provides a powerful way to quickly identify patterns that relate vast numbers of microbial communities. We show the potential of Fast UniFrac using examples from three data types: Sanger-sequencing studies of diverse free-living and animal-associated bacterial assemblages and from the gut of obese humans as they diet, pyrosequencing data integrated from studies of the human hand and gut, and PhyloChip data from a study of citrus pathogens. We show that a Fast UniFrac analysis using a reference tree recaptures patterns that could not be detected without considering phylogenetic relationships and that Fast UniFrac, coupled with BLAST-based sequence assignment, can be used to quickly analyze pyrosequencing runs containing hundreds of thousands of sequences, showing patterns relating human and gut samples. Finally, we show that the application of Fast UniFrac to PhyloChip data could identify well-defined subcategories associated with infection. Together, these case studies point the way toward a broad range of applications and show some of the new features of Fast UniFrac.

Subfields: Ecology, Molecular Biology

View Paper: https://www.semanticscholar.org/paper/ac9f04999666b73eba7eea627f65b9ee10fff163

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Citations in the corpus

EFFECTS OF PLANT-BASED DIETS ON THE DISTAL GUT MICROBIOME OF RAINBOW TROUT (Oncorhynchus mykiss). (2012, methodology): “Intestinal microbial profiles from the various experimental and control groups were compared using cluster analysis and principal coordinate analysis (PCoA) based on the distance metric in Fast UniFrac, incorporating sequence frequencies (weighted UniFrac) (Hamady et al., 2010).”
Composition, variability, and temporal stability of the intestinal microbiota of the elderly (2010, methodology): “Hamady M, Lozupone C, Knight R (2010) Fast UniFrac: Facilitating high-throughput phylogenetic analyses of microbial communities including analysis of pyrosequencing and PhyloChip data.”
Fungal community analysis by high-throughput sequencing of amplified markers – a user's guide (2013, methodology): “The need to employ the most stringent discipline during preparation of samples for community sequencing cannot be emphasized enough.”
Chapter 12: Human Microbiome Analysis (2012, methodology): “The assignment of sequences to OTUs is referred to as binning, and it can be performed by A) unsupervised clustering of similar sequences [19], B) phylogenetic models incorporating mutation rates and evolutionary relationships [20], or C) supervised methods that directly assign sequences to taxonomi”
Responses of soil bacterial and fungal communities to extreme desiccation and rewetting (2013, methodology): “Phylogenetic pairwise dissimilarity matrices were calculated using FastUniFrac (Hamady et al., 2010), based on sequence abundance, without normalizing for differing mutation rates.”
Structural segregation of gut microbiota between colorectal cancer patients and healthy volunteers (2011, methodology): “The tree, together with sequence abundance data, was then used for online Fast UniFrac analysis based on weighted metric (Hamady et al., 2010).”
UniFrac: an effective distance metric for microbial community comparison (2011, methodology): “UniFrac’s widespread application is facilitated by its user-friendly web interface that handles large data sets from next-generation sequencing technologies (Hamady et al., 2010).”
454 Pyrosequencing reveals bacterial diversity of activated sludge from 14 sewage treatment plants (2011, methodology): “For the first two approaches, taxa or OTUs are regarded as equally related, whereas UniFrac incorporates the degree of divergence in the phylogenetic tree of OTUs into PCoA (Hamady et al., 2010; Qian et al., 2010).”
Relative impacts of tillage, residue management and crop-rotation on soil bacterial communities in a semi-arid agroecosystem (2013, methodology): “The phylogenetic community analysis was done using Fast UniFrac (Hamady et al., 2010) within the QIIME pipeline (Caporaso et al.”
Bacterial Communities of Diverse Drosophila Species: Ecological Context of a Host–Microbe Model System (2011, methodology): “These sequences were aligned and trimmed as above and a full PCA analysis was performed using the Fast UniFrac Interface [62].”
Global patterns of 16S rRNA diversity at a depth of millions of sequences per sample (2010, methodology): “We have previously shown, however, that patterns that were observed with de novo tree-making methods could be captured equally well using a “BLAST to reference tree” protocol (21) and then calculating community differences with UniFrac.”