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Integrating taxonomic, functional, and strain-level profiling of diverse microbial communities with bioBakery 3

View ORCID ProfileFrancesco Beghini, View ORCID ProfileLauren J. McIver, View ORCID ProfileAitor Blanco-Míguez, Leonard Dubois, View ORCID ProfileFrancesco Asnicar, Sagun Maharjan, Ana Mailyan, Andrew Maltez Thomas, Paolo Manghi, View ORCID ProfileMireia Valles-Colomer, George Weingart, Yancong Zhang, View ORCID ProfileMoreno Zolfo, View ORCID ProfileCurtis Huttenhower, View ORCID ProfileEric A. Franzosa, View ORCID ProfileNicola Segata
doi: https://doi.org/10.1101/2020.11.19.388223
Francesco Beghini
1Department CIBIO, University of Trento, Italy
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Lauren J. McIver
2Harvard T.H. Chan School of Public Health, Boston, MA, USA
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  • ORCID record for Lauren J. McIver
Aitor Blanco-Míguez
1Department CIBIO, University of Trento, Italy
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Leonard Dubois
1Department CIBIO, University of Trento, Italy
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Francesco Asnicar
1Department CIBIO, University of Trento, Italy
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  • ORCID record for Francesco Asnicar
Sagun Maharjan
2Harvard T.H. Chan School of Public Health, Boston, MA, USA
3The Broad Institute of MIT and Harvard, Cambridge, MA, USA
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Ana Mailyan
2Harvard T.H. Chan School of Public Health, Boston, MA, USA
3The Broad Institute of MIT and Harvard, Cambridge, MA, USA
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Andrew Maltez Thomas
1Department CIBIO, University of Trento, Italy
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Paolo Manghi
1Department CIBIO, University of Trento, Italy
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Mireia Valles-Colomer
1Department CIBIO, University of Trento, Italy
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  • ORCID record for Mireia Valles-Colomer
George Weingart
2Harvard T.H. Chan School of Public Health, Boston, MA, USA
3The Broad Institute of MIT and Harvard, Cambridge, MA, USA
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Yancong Zhang
2Harvard T.H. Chan School of Public Health, Boston, MA, USA
3The Broad Institute of MIT and Harvard, Cambridge, MA, USA
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Moreno Zolfo
1Department CIBIO, University of Trento, Italy
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Curtis Huttenhower
2Harvard T.H. Chan School of Public Health, Boston, MA, USA
3The Broad Institute of MIT and Harvard, Cambridge, MA, USA
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  • For correspondence: chuttenh@hsph.harvard.edu franzosa@hsph.harvard.edu nicola.segata@unitn.it
Eric A. Franzosa
2Harvard T.H. Chan School of Public Health, Boston, MA, USA
3The Broad Institute of MIT and Harvard, Cambridge, MA, USA
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  • For correspondence: chuttenh@hsph.harvard.edu franzosa@hsph.harvard.edu nicola.segata@unitn.it
Nicola Segata
1Department CIBIO, University of Trento, Italy
4IEO, European Institute of Oncology IRCCS, Milan, Italy
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  • ORCID record for Nicola Segata
  • For correspondence: chuttenh@hsph.harvard.edu franzosa@hsph.harvard.edu nicola.segata@unitn.it
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Abstract

Culture-independent analyses of microbial communities have advanced 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 (1,262 metagenomes) and IBD (1,635 metagenomes and 817 metatranscriptomes). Strain-level profiling of an additional 4,077 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.

Competing Interest Statement

The authors have declared no competing interest.

Footnotes

  • ↵* Joint first authors

  • ↵^ Joint senior authors

Copyright 
The copyright holder for this preprint is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under a CC-BY 4.0 International license.
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Posted November 21, 2020.
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Integrating taxonomic, functional, and strain-level profiling of diverse microbial communities with bioBakery 3
Francesco Beghini, Lauren J. McIver, Aitor Blanco-Míguez, Leonard Dubois, Francesco Asnicar, Sagun Maharjan, Ana Mailyan, Andrew Maltez Thomas, Paolo Manghi, Mireia Valles-Colomer, George Weingart, Yancong Zhang, Moreno Zolfo, Curtis Huttenhower, Eric A. Franzosa, Nicola Segata
bioRxiv 2020.11.19.388223; doi: https://doi.org/10.1101/2020.11.19.388223
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Integrating taxonomic, functional, and strain-level profiling of diverse microbial communities with bioBakery 3
Francesco Beghini, Lauren J. McIver, Aitor Blanco-Míguez, Leonard Dubois, Francesco Asnicar, Sagun Maharjan, Ana Mailyan, Andrew Maltez Thomas, Paolo Manghi, Mireia Valles-Colomer, George Weingart, Yancong Zhang, Moreno Zolfo, Curtis Huttenhower, Eric A. Franzosa, Nicola Segata
bioRxiv 2020.11.19.388223; doi: https://doi.org/10.1101/2020.11.19.388223

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