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Integrating taxonomic, functional, and strain-level profiling of diverse microbial communities with bioBakery 3.
Beghini, Francesco; McIver, Lauren J; Blanco-Míguez, Aitor; Dubois, Leonard; Asnicar, Francesco; Maharjan, Sagun; Mailyan, Ana; Manghi, Paolo; Scholz, Matthias; Thomas, Andrew Maltez; Valles-Colomer, Mireia; Weingart, George; Zhang, Yancong; Zolfo, Moreno; Huttenhower, Curtis; Franzosa, Eric A; Segata, Nicola.
Afiliação
  • Beghini F; Department CIBIO, University of Trento, Trento, Italy.
  • McIver LJ; Harvard T.H. Chan School of Public Health, Boston, United States.
  • Blanco-Míguez A; Department CIBIO, University of Trento, Trento, Italy.
  • Dubois L; Department CIBIO, University of Trento, Trento, Italy.
  • Asnicar F; Department CIBIO, University of Trento, Trento, Italy.
  • Maharjan S; Harvard T.H. Chan School of Public Health, Boston, United States.
  • Mailyan A; The Broad Institute of MIT and Harvard, Cambridge, United States.
  • Manghi P; Harvard T.H. Chan School of Public Health, Boston, United States.
  • Scholz M; The Broad Institute of MIT and Harvard, Cambridge, United States.
  • Thomas AM; Department CIBIO, University of Trento, Trento, Italy.
  • Valles-Colomer M; Department of Food Quality and Nutrition, Research and Innovation Center, Edmund Mach Foundation, San Michele all'Adige, Italy.
  • Weingart G; Department CIBIO, University of Trento, Trento, Italy.
  • Zhang Y; Department CIBIO, University of Trento, Trento, Italy.
  • Zolfo M; Harvard T.H. Chan School of Public Health, Boston, United States.
  • Huttenhower C; The Broad Institute of MIT and Harvard, Cambridge, United States.
  • Franzosa EA; Harvard T.H. Chan School of Public Health, Boston, United States.
  • Segata N; The Broad Institute of MIT and Harvard, Cambridge, United States.
Elife ; 102021 05 04.
Article em En | MEDLINE | ID: mdl-33944776
Culture-independent analyses of microbial communities have progressed dramatically in the last decade, particularly due to advances in methods for biological profiling via shotgun metagenomics. Opportunities for improvement continue to accelerate, with greater access to multi-omics, microbial reference genomes, and strain-level diversity. To leverage these, we present bioBakery 3, a set of integrated, improved methods for taxonomic, strain-level, functional, and phylogenetic profiling of metagenomes newly developed to build on the largest set of reference sequences now available. Compared to current alternatives, MetaPhlAn 3 increases the accuracy of taxonomic profiling, and HUMAnN 3 improves that of functional potential and activity. These methods detected novel disease-microbiome links in applications to CRC (1262 metagenomes) and IBD (1635 metagenomes and 817 metatranscriptomes). Strain-level profiling of an additional 4077 metagenomes with StrainPhlAn 3 and PanPhlAn 3 unraveled the phylogenetic and functional structure of the common gut microbe Ruminococcus bromii, previously described by only 15 isolate genomes. With open-source implementations and cloud-deployable reproducible workflows, the bioBakery 3 platform can help researchers deepen the resolution, scale, and accuracy of multi-omic profiling for microbial community studies.
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Texto completo: 1 Bases de dados: MEDLINE Assunto principal: Filogenia / Bactérias / Biologia Computacional / Metagenoma / Microbiota Limite: Humans Idioma: En Revista: Elife Ano de publicação: 2021 Tipo de documento: Article País de afiliação: Itália

Texto completo: 1 Bases de dados: MEDLINE Assunto principal: Filogenia / Bactérias / Biologia Computacional / Metagenoma / Microbiota Limite: Humans Idioma: En Revista: Elife Ano de publicação: 2021 Tipo de documento: Article País de afiliação: Itália