Piphillin: Improved Prediction of Metagenomic Content by Direct Inference from Human Microbiomes
Publication Date
November 07, 2016
Authors
Shoko Iwai, Thomas Weinmaier, Brian L. Schmidt, Donna G. Albertson, et al
Volume
11
Issue
11
Pages
e0166104
DOI
https://dx.plos.org/10.1371/journal.pone.0166104
Publisher URL
http://journals.plos.org/plosone/article?id=10.1371%2Fjournal.pone.0166104
Scopus
84994638542
Mendeley
http://www.mendeley.com/research/piphillin-improved-prediction-metagenomic-content-direct-inference-human-microbiomes
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Mendeley | Further Information

{"title"=>"Piphillin: Improved prediction of metagenomic content by direct inference from human microbiomes", "type"=>"journal", "authors"=>[{"first_name"=>"Shoko", "last_name"=>"Iwai", "scopus_author_id"=>"57198320512"}, {"first_name"=>"Thomas", "last_name"=>"Weinmaier", "scopus_author_id"=>"35747438400"}, {"first_name"=>"Brian L.", "last_name"=>"Schmidt", "scopus_author_id"=>"7402828720"}, {"first_name"=>"Donna G.", "last_name"=>"Albertson", "scopus_author_id"=>"7101804288"}, {"first_name"=>"Neil J.", "last_name"=>"Poloso", "scopus_author_id"=>"6506935152"}, {"first_name"=>"Karim", "last_name"=>"Dabbagh", "scopus_author_id"=>"56503676500"}, {"first_name"=>"Todd Z.", "last_name"=>"DeSantis", "scopus_author_id"=>"6602743913"}], "year"=>2016, "source"=>"PLoS ONE", "identifiers"=>{"pmid"=>"27820856", "doi"=>"10.1371/journal.pone.0166104", "sgr"=>"84994638542", "isbn"=>"1932-6203 (Electronic) 1932-6203 (Linking)", "scopus"=>"2-s2.0-84994638542", "issn"=>"19326203", "pui"=>"613101160"}, "id"=>"af06f0a4-4b24-31db-a7db-ee084c977fc6", "abstract"=>"Functional analysis of a clinical microbiome facilitates the elucidation of mechanisms by which microbiome perturbation can cause a phenotypic change in the patient. The direct approach for the analysis of the functional capacity of the microbiome is via shotgun meta- genomics. An inexpensive method to estimate the functional capacity of a microbial com- munity is through collecting 16S rRNA gene profiles then indirectly inferring the abundance of functional genes. This inference approach has been implemented in the PICRUSt and Tax4Fun software tools. However, those tools have important limitations since they rely on outdated functional databases and uncertain phylogenetic trees and require very specific data pre-processing protocols. Here we introduce Piphillin, a straightforward algorithm independent of any proposed phylogenetic tree, leveraging contemporary functional data- bases and not obliged to any singular data pre-processing protocol. When all three infer- ence tools were evaluated against actual shotgun metagenomics, Piphillin was superior in predicting gene composition in human clinical samples compared to both PICRUSt and Tax4Fun (p<0.01 and p<0.001, respectively) and Piphillin’s ability to predict disease asso- ciations with specific gene orthologs exhibited a 15% increase in balanced accuracy com- pared to PICRUSt. From laboratory animal samples, no performance advantage was observed for any one of the tools over the others and for environmental samples all pro- duced unsatisfactory predictions. Our results demonstrate that functional inference using the direct method implemented in Piphillin is preferable for clinical biospecimens. Piphillin is publicly available for academic use at http://secondgenome.com/Piphillin.", "link"=>"http://www.mendeley.com/research/piphillin-improved-prediction-metagenomic-content-direct-inference-human-microbiomes", "reader_count"=>80, "reader_count_by_academic_status"=>{"Unspecified"=>3, "Professor > Associate Professor"=>4, "Student > Doctoral Student"=>6, "Researcher"=>21, "Student > Ph. D. Student"=>22, "Student > Postgraduate"=>7, "Student > Master"=>9, "Other"=>2, "Student > Bachelor"=>6}, "reader_count_by_user_role"=>{"Unspecified"=>3, "Professor > Associate Professor"=>4, "Student > Doctoral Student"=>6, "Researcher"=>21, "Student > Ph. D. Student"=>22, "Student > Postgraduate"=>7, "Student > Master"=>9, "Other"=>2, "Student > Bachelor"=>6}, "reader_count_by_subject_area"=>{"Engineering"=>4, "Unspecified"=>7, "Environmental Science"=>3, "Biochemistry, Genetics and Molecular Biology"=>8, "Agricultural and Biological Sciences"=>44, "Medicine and Dentistry"=>2, "Pharmacology, Toxicology and Pharmaceutical Science"=>1, "Computer Science"=>4, "Immunology and Microbiology"=>6, "Earth and Planetary Sciences"=>1}, "reader_count_by_subdiscipline"=>{"Engineering"=>{"Engineering"=>4}, "Medicine and Dentistry"=>{"Medicine and Dentistry"=>2}, "Immunology and Microbiology"=>{"Immunology and Microbiology"=>6}, "Earth and Planetary Sciences"=>{"Earth and Planetary Sciences"=>1}, "Agricultural and Biological Sciences"=>{"Agricultural and Biological Sciences"=>44}, "Computer Science"=>{"Computer Science"=>4}, "Biochemistry, Genetics and Molecular Biology"=>{"Biochemistry, Genetics and Molecular Biology"=>8}, "Unspecified"=>{"Unspecified"=>7}, "Environmental Science"=>{"Environmental Science"=>3}, "Pharmacology, Toxicology and Pharmaceutical Science"=>{"Pharmacology, Toxicology and Pharmaceutical Science"=>1}}, "reader_count_by_country"=>{"Netherlands"=>1, "United States"=>1, "China"=>1, "Japan"=>1, "Brazil"=>2}, "group_count"=>1}

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Scopus | Further Information

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