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Aitor Blanco‐Míguez, Francesco Beghini, Fabio Cumbo, Lauren J. McIver, Kelsey N. Thompson, Moreno Zolfo, Paolo Manghi, Léonard Dubois, Kun D. Huang, Andrew Maltez Thomas and 16 more
Metagenomic assembly enables new organism discovery from microbial communities, but it can only capture few abundant organisms from most metagenomes. Here we present MetaPhlAn 4, which integrates information from metagenome assemblies and microbial isolate genomes for more comprehensive metagenomic taxonomic profiling. From a curated collection of 1.01 M prokaryotic reference and metagenome-assembled genomes, we define unique marker genes for 26,970 species-level genome bins, 4,992 of them taxonomically unidentified at the species level. MetaPhlAn 4 explains ~20% more reads in most international human gut microbiomes and >40% in less-characterized environments such as the rumen microbiome and proves more accurate than available alternatives on synthetic evaluations while also reliably quantifying organisms with no cultured isolates. Application of the method to >24,500 metagenomes highlights previously undetected species to be strong biomarkers for host conditions and lifestyles in human and mouse microbiomes and shows that even previously uncharacterized species can be genetically profiled at the resolution of single microbial strains.
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Blanco‐Míguez, A., Beghini, F., Cumbo, F., McIver, L. J., Thompson, K. N., Zolfo, M., Manghi, P., Dubois, L., Huang, K. D., Thomas, A. M., Nickols, W. A., Piccinno, G., Piperni, E., Punčochář, M., Valles‐Colomer, M., Tett, A., Giordano, F., Davies, R., Wolf, J., … Segata, N. (2023). Extending and improving metagenomic taxonomic profiling with uncharacterized species using MetaPhlAn 4. Nature Biotechnology, 41(11), 1633–1644. https://doi.org/10.1038/s41587-023-01688-w
Blanco‐Míguez, Aitor, et al. "Extending and improving metagenomic taxonomic profiling with uncharacterized species using MetaPhlAn 4." Nature Biotechnology, vol. 41, no. 11, 2023, pp. 1633–1644, https://doi.org/10.1038/s41587-023-01688-w.
Blanco‐Míguez, Aitor, Francesco Beghini, Fabio Cumbo, Lauren J. McIver, Kelsey N. Thompson, Moreno Zolfo, Paolo Manghi, et al. "Extending and improving metagenomic taxonomic profiling with uncharacterized species using MetaPhlAn 4." Nature Biotechnology 41, no. 11 (2023): 1633–1644. https://doi.org/10.1038/s41587-023-01688-w.
Blanco‐Míguez A., Beghini F., Cumbo F. [и др.] Extending and improving metagenomic taxonomic profiling with uncharacterized species using MetaPhlAn 4 // Nature Biotechnology. — 2023. — Vol. 41, № 11. — P. 1633–1644. — URL: https://doi.org/10.1038/s41587-023-01688-w
@article{blancomiguez2023extending,
title = {{Extending and improving metagenomic taxonomic profiling with uncharacterized species using MetaPhlAn 4}},
author = {Aitor Blanco‐Míguez and Francesco Beghini and Fabio Cumbo and Lauren J. McIver and Kelsey N. Thompson and Moreno Zolfo and Paolo Manghi and Léonard Dubois and Kun D. Huang and Andrew Maltez Thomas and William A. Nickols and Gianmarco Piccinno and Elisa Piperni and Michal Punčochář and Mireia Valles‐Colomer and Adrian Tett and Francesca Giordano and Richard Davies and Jonathan Wolf and Sarah E. Berry and Tim D. Spector and Eric A. Franzosa and Edoardo Pasolli and Francesco Asnicar and Curtis Huttenhower and Nicola Segata},
journal = {Nature Biotechnology},
year = {2023},
volume = {41},
number = {11},
pages = {1633--1644},
doi = {10.1038/s41587-023-01688-w},
url = {https://doi.org/10.1038/s41587-023-01688-w}
}TY - JOUR AU - Blanco‐Míguez, Aitor AU - Beghini, Francesco AU - Cumbo, Fabio AU - McIver, Lauren J. AU - Thompson, Kelsey N. AU - Zolfo, Moreno AU - Manghi, Paolo AU - Dubois, Léonard AU - Huang, Kun D. AU - Thomas, Andrew Maltez AU - Nickols, William A. AU - Piccinno, Gianmarco AU - Piperni, Elisa AU - Punčochář, Michal AU - Valles‐Colomer, Mireia AU - Tett, Adrian AU - Giordano, Francesca AU - Davies, Richard AU - Wolf, Jonathan AU - Berry, Sarah E. AU - Spector, Tim D. AU - Franzosa, Eric A. AU - Pasolli, Edoardo AU - Asnicar, Francesco AU - Huttenhower, Curtis AU - Segata, Nicola TI - Extending and improving metagenomic taxonomic profiling with uncharacterized species using MetaPhlAn 4 JO - Nature Biotechnology VL - 41 IS - 11 SP - 1633 EP - 1644 PY - 2023 DA - 2023/02/23 DO - 10.1038/s41587-023-01688-w UR - https://doi.org/10.1038/s41587-023-01688-w ER -
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