Fast UniFrac: Facilitating high-throughput phylogenetic analyses of microbial communities including analysis of pyrosequencing and PhyloChip data
Identifieur interne : 000C11 ( Main/Merge ); précédent : 000C10; suivant : 000C12Fast UniFrac: Facilitating high-throughput phylogenetic analyses of microbial communities including analysis of pyrosequencing and PhyloChip data
Auteurs : Micah Hamady [États-Unis] ; Catherine Lozupone [États-Unis] ; Rob Knight [États-Unis]Source :
- The ISME journal [ 1751-7362 ] ; 2009.
Abstract
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 (PCoA) 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 demonstrate 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, revealing 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 towards a broad range of applications and demonstrate some of the new features of Fast UniFrac.
Url:
DOI: 10.1038/ismej.2009.97
PubMed: 19710709
PubMed Central: 2797552
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uniqKey="Lozupone C" first="Catherine" last="Lozupone">Catherine Lozupone</name><affiliation wicri:level="2"><nlm:aff id="A2">Department of Chemistry and Biochemistry, University of Colorado, Boulder, CO 80309, USA</nlm:aff><country xml:lang="fr">États-Unis</country><wicri:regionArea>Department of Chemistry and Biochemistry, University of Colorado, Boulder, CO 80309</wicri:regionArea><placeName><region type="state">Colorado</region></placeName></affiliation><affiliation wicri:level="4"><nlm:aff id="A3">Center for Genome Sciences, Washington University School of Medicine, St. Louis, MO 63108, USA</nlm:aff><country xml:lang="fr">États-Unis</country><wicri:regionArea>Center for Genome Sciences, Washington University School of Medicine, St. Louis, MO 63108</wicri:regionArea><placeName><region type="state">Missouri (État)</region><settlement type="city">Saint-Louis (Missouri)</settlement></placeName><orgName type="university">École de médecine (Université Washington de Saint-Louis)</orgName></affiliation></author><author><name sortKey="Knight, Rob" sort="Knight, Rob" uniqKey="Knight R" first="Rob" last="Knight">Rob Knight</name><affiliation wicri:level="2"><nlm:aff id="A2">Department of Chemistry and Biochemistry, University of Colorado, Boulder, CO 80309, USA</nlm:aff><country xml:lang="fr">États-Unis</country><wicri:regionArea>Department of Chemistry and Biochemistry, University of Colorado, Boulder, CO 80309</wicri:regionArea><placeName><region type="state">Colorado</region></placeName></affiliation><affiliation><nlm:aff id="A4">Howard Hughes Medical Institute</nlm:aff></affiliation></author></analytic><series><title level="j">The ISME journal</title><idno type="ISSN">1751-7362</idno><idno type="eISSN">1751-7370</idno><imprint><date when="2009">2009</date></imprint></series></biblStruct></sourceDesc></fileDesc><profileDesc><textClass></textClass></profileDesc></teiHeader><front><div type="abstract" xml:lang="en"><p id="P1">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 (PCoA) 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 demonstrate 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, revealing 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 towards a broad range of applications and demonstrate some of the new features of Fast UniFrac.</p></div></front><back><div1 type="bibliography"><listBibl><biblStruct><analytic><author><name sortKey="Alexander, E" uniqKey="Alexander E">E Alexander</name></author><author><name sortKey="Stock, A" uniqKey="Stock A">A Stock</name></author><author><name sortKey="Breiner, Hw" uniqKey="Breiner H">HW Breiner</name></author><author><name sortKey="Behnke, A" uniqKey="Behnke A">A Behnke</name></author><author><name sortKey="Bunge, J" uniqKey="Bunge J">J Bunge</name></author><author><name sortKey="Yakimov, Mm" uniqKey="Yakimov M">MM Yakimov</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Altschul, Sf" uniqKey="Altschul S">SF Altschul</name></author><author><name sortKey="Gish, W" uniqKey="Gish W">W Gish</name></author><author><name sortKey="Miller, W" uniqKey="Miller W">W Miller</name></author><author><name 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Ley</name></author><author><name sortKey="Mahowald, Ma" uniqKey="Mahowald M">MA Mahowald</name></author><author><name sortKey="Magrini, V" uniqKey="Magrini V">V Magrini</name></author><author><name sortKey="Mardis, Er" uniqKey="Mardis E">ER Mardis</name></author><author><name sortKey="Gordon, Ji" uniqKey="Gordon J">JI Gordon</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Wen, L" uniqKey="Wen L">L Wen</name></author><author><name sortKey="Ley, Re" uniqKey="Ley R">RE Ley</name></author><author><name sortKey="Volchkov, Py" uniqKey="Volchkov P">PY Volchkov</name></author><author><name sortKey="Stranges, Pb" uniqKey="Stranges P">PB Stranges</name></author><author><name sortKey="Avanesyan, L" uniqKey="Avanesyan L">L Avanesyan</name></author><author><name sortKey="Stonebraker, Ac" uniqKey="Stonebraker A">AC Stonebraker</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Widmann, J" uniqKey="Widmann J">J 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