MetaPhlAn2 for enhanced metagenomic taxonomic profiling

By Duy Tin Truong, Eric A. Franzosa, Timothy L. Tickle, Matthias Scholz, George Weingart, Edoardo Pasolli, Adrian Tett, Curtis Huttenhower, Nicola Segata. Nature Methods, 2015

1,895 citations recorded by the source corpus.

Subfields: Ecology, Molecular Biology

View Paper: https://www.semanticscholar.org/paper/ac38daf0b6943ed59eebc396587f03c60c500459

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Citations in the corpus

Tracking microbial colonization in fecal microbiota transplantation experiments via genome-resolved metagenomics (2017, methodology): “We also annotated our metagenomes and HMP gut metagenomes using MetaPhlAn2 [51].”
Multivariable association discovery in population-scale meta-omics studies (2021, methodology): “Metagenomes and metatranscriptomes were functionally profiled using HUMAnN 2 [40] to quantify MetaCyc pathways [41], and taxonomic profiles from metagenomes were determined using MetaPhlAn 2 [42] (S3 Text).”
Species-level functional profiling of metagenomes and metatranscriptomes (2018, neutral): “(An earlier version of ChocoPhlAn was published as MetaRef 46 ; the version of ChocoPhlAn incorporated in HUMAnN2 is identical to that underlying MetaPhlAn2 and its marker database 22 .)”
QIIME 2 Enables Comprehensive End‐to‐End Analysis of Diverse Microbiome Data and Comparative Studies with Publicly Available Data (2020, background): “Two plugins that are dedicated to shotgun metagenomics are currently available for QI-IME 2: q2-shogun (Hillmann et al., 2018) and q2-metaphlan2 (Truong et al., 2015).”
Integrating taxonomic, functional, and strain-level profiling of diverse microbial communities with bioBakery 3 (2020, methodology): “To assess the performance of MetaPhlAn 3, we compared it with its previous version, MetaPhlAn 2 (Truong et al., 2015) , alongside mOTUs2 (Milanese et al., 2019) and Bracken (Lu et al., 2017; Wood et al., 2019) .”
Machine Learning Meta-analysis of Large Metagenomic Datasets: Tools and Biological Insights (2016, methodology): “Before applying MetaPhlAn2 the samples were subject to standard pre-processing as described in the SOP of the Human Microbiome Project [1] without however the step of human DNA removal as these publicly available metagenomes were deposited free from human DNA contamination.”
Enterotypes of the human gut mycobiome (2022, methodology): “Quantitative profiling of the taxonomic composition of the microbial communities was performed via MetaPhlAn2 [69].”
Extensive Unexplored Human Microbiome Diversity Revealed by Over 150,000 Genomes from Metagenomes Spanning Age, Geography, and Lifestyle (2019, methodology): “…are available in Table S1 and are included in the curatedMetagenomicData package (Pa-solli et al., 2017) together with all the taxonomic (Segata et al., 2012b; Truong et al., 2015) and functional potential proﬁles (Franzosa et al., 2018) of the microbial species with available reference genomes.”