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11 results on '"Tett, Adrian"'

1. Extending and improving metagenomic taxonomic profiling with uncharacterized species using MetaPhlAn 4

Author

Blanco-Míguez, Aitor, Beghini, Francesco, Cumbo, Fabio, McIver, Lauren J., Thompson, Kelsey N., Zolfo, Moreno, Manghi, Paolo, Dubois, Leonard, Huang, Kun D., Thomas, Andrew Maltez, Nickols, William A., Piccinno, Gianmarco, Piperni, Elisa, Punčochář, Michal, Valles-Colomer, Mireia, Tett, Adrian, Giordano, Francesca, Davies, Richard, Wolf, Jonathan, Berry, Sarah E., Spector, Tim D., Franzosa, Eric A., Pasolli, Edoardo, Asnicar, Francesco, Huttenhower, Curtis, and Segata, Nicola

Published
2023
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2. Extension of the Segatella copri complex to 13 species with distinct large extrachromosomal elements and associations with host conditions

Author

Blanco-Míguez, Aitor, Gálvez, Eric J.C., Pasolli, Edoardo, De Filippis, Francesca, Amend, Lena, Huang, Kun D., Manghi, Paolo, Lesker, Till-Robin, Riedel, Thomas, Cova, Linda, Punčochář, Michal, Thomas, Andrew Maltez, Valles-Colomer, Mireia, Schober, Isabel, Hitch, Thomas C.A., Clavel, Thomas, Berry, Sarah E., Davies, Richard, Wolf, Jonathan, Spector, Tim D., Overmann, Jörg, Tett, Adrian, Ercolini, Danilo, Segata, Nicola, and Strowig, Till

Published
2023
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3. The person-to-person transmission landscape of the gut and oral microbiomes

Author

Valles-Colomer, Mireia, Blanco-Míguez, Aitor, Manghi, Paolo, Asnicar, Francesco, Dubois, Leonard, Golzato, Davide, Armanini, Federica, Cumbo, Fabio, Huang, Kun D., Manara, Serena, Masetti, Giulia, Pinto, Federica, Piperni, Elisa, Punčochář, Michal, Ricci, Liviana, Zolfo, Moreno, Farrant, Olivia, Goncalves, Adriana, Selma-Royo, Marta, Binetti, Ana G., Becerra, Jimmy E., Han, Bei, Lusingu, John, Amuasi, John, Amoroso, Loredana, Visconti, Alessia, Steves, Claire M., Falchi, Mario, Filosi, Michele, Tett, Adrian, Last, Anna, Xu, Qian, Qin, Nan, Qin, Huanlong, May, Jürgen, Eibach, Daniel, Corrias, Maria Valeria, Ponzoni, Mirco, Pasolli, Edoardo, Spector, Tim D., Domenici, Enrico, Collado, Maria Carmen, and Segata, Nicola

Published
2023
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7. The person-to-person transmission landscape of the gut and oral microbiomes

Author

European Commission, National Cancer Institute (US), European Research Council, Simons Foundation, EMBO, 0000-0002-1988-6054, 0000-0001-7386-5572, 0000-0003-0846-6529, 0000-0003-3732-1468, 0000-0001-6371-528X, 0000-0002-4539-4811, 0000-0001-9450-9235, 0000-0001-6661-4046, 0000-0001-5212-1101, 0000-0002-8640-2662, 0000-0003-4144-2019, 0000-0002-5646-1004, 0000-0002-3872-347X, 0000-0002-7623-217X, 0000-0002-9128-9414, 0000-0001-8438-2322, 0000-0001-7831-8420, 0000-0002-7316-0772, 0000-0002-9795-0365, 0000-0001-7436-6919, 0000-0002-1583-5794, Valles-Colomer, Mireia, Blanco-Míguez, Aitor, Manghi, Paolo, Asnicar, Francesco, Dubois, Leonard, Golzato, Davide, Armanini, Federica, Cumbo, Fabio, Huang, Kun D., Manara, Serena, Masetti, Giulia, Pinto, Federica, Piperni, Elisa, Punčochář, Michal, Ricci, Liviana, Zolfo, Moreno, Farrant, Olivia, Goncalves, Adriana, Selma-Royo, Marta, Binetti, Ana G., Becerra, Jimmy E., Han, Bei, Lusingu, John, Amuasi, John, Amoroso, Loredana, Visconti, Alessia, Steves, Claire M., Falchi, Mario, Filosi, Michele, Tett, Adrian, Last, Anna, Xu, Qian, Qin, Nan, Qin, Huanlong, May, Jürgen, Eibach, Daniel, Corrias, Maria Valeria, Ponzoni, Mirco, Pasolli, Edoardo, Spector, Tim D., Domenici, Enrico, Collado, María Carmen, Segata, Nicola, European Commission, National Cancer Institute (US), European Research Council, Simons Foundation, EMBO, 0000-0002-1988-6054, 0000-0001-7386-5572, 0000-0003-0846-6529, 0000-0003-3732-1468, 0000-0001-6371-528X, 0000-0002-4539-4811, 0000-0001-9450-9235, 0000-0001-6661-4046, 0000-0001-5212-1101, 0000-0002-8640-2662, 0000-0003-4144-2019, 0000-0002-5646-1004, 0000-0002-3872-347X, 0000-0002-7623-217X, 0000-0002-9128-9414, 0000-0001-8438-2322, 0000-0001-7831-8420, 0000-0002-7316-0772, 0000-0002-9795-0365, 0000-0001-7436-6919, 0000-0002-1583-5794, Valles-Colomer, Mireia, Blanco-Míguez, Aitor, Manghi, Paolo, Asnicar, Francesco, Dubois, Leonard, Golzato, Davide, Armanini, Federica, Cumbo, Fabio, Huang, Kun D., Manara, Serena, Masetti, Giulia, Pinto, Federica, Piperni, Elisa, Punčochář, Michal, Ricci, Liviana, Zolfo, Moreno, Farrant, Olivia, Goncalves, Adriana, Selma-Royo, Marta, Binetti, Ana G., Becerra, Jimmy E., Han, Bei, Lusingu, John, Amuasi, John, Amoroso, Loredana, Visconti, Alessia, Steves, Claire M., Falchi, Mario, Filosi, Michele, Tett, Adrian, Last, Anna, Xu, Qian, Qin, Nan, Qin, Huanlong, May, Jürgen, Eibach, Daniel, Corrias, Maria Valeria, Ponzoni, Mirco, Pasolli, Edoardo, Spector, Tim D., Domenici, Enrico, Collado, María Carmen, and Segata, Nicola

Abstract

The human microbiome is an integral component of the human body and a co-determinant of several health conditions1,2. However, the extent to which interpersonal relations shape the individual genetic makeup of the microbiome and its transmission within and across populations remains largely unknown3,4. Here, capitalizing on more than 9,700 human metagenomes and computational strain-level profiling, we detected extensive bacterial strain sharing across individuals (more than 10 million instances) with distinct mother-to-infant, intra-household and intra-population transmission patterns. Mother-to-infant gut microbiome transmission was considerable and stable during infancy (around 50% of the same strains among shared species (strain-sharing rate)) and remained detectable at older ages. By contrast, the transmission of the oral microbiome occurred largely horizontally and was enhanced by the duration of cohabitation. There was substantial strain sharing among cohabiting individuals, with 12% and 32% median strain-sharing rates for the gut and oral microbiomes, and time since cohabitation affected strain sharing more than age or genetics did. Bacterial strain sharing additionally recapitulated host population structures better than species-level profiles did. Finally, distinct taxa appeared as efficient spreaders across transmission modes and were associated with different predicted bacterial phenotypes linked with out-of-host survival capabilities. The extent of microorganism transmission that we describe underscores its relevance in human microbiome studies5, especially those on non-infectious, microbiome-associated diseases.

Published
2023

8. Extending and improving metagenomic taxonomic profiling with uncharacterized species with MetaPhlAn 4

Author

Blanco-Miguez, Aitor, primary, Beghini, Francesco, additional, Cumbo, Fabio, additional, McIver, Lauren J., additional, Thompson, Kelsey N., additional, Zolfo, Moreno, additional, Manghi, Paolo, additional, Dubois, Leonard, additional, Huang, Kun D., additional, Thomas, Andrew Maltez, additional, Piccinno, Gianmarco, additional, Piperni, Elisa, additional, Punčochář, Michal, additional, Valles-Colomer, Mireia, additional, Tett, Adrian, additional, Giordano, Francesca, additional, Davies, Richard, additional, Wolf, Jonathan, additional, Berry, Sarah E., additional, Spector, Tim D., additional, Franzosa, Eric A., additional, Pasolli, Edoardo, additional, Asnicar, Francesco, additional, Huttenhower, Curtis, additional, and Segata, Nicola, additional

Published
2022
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9. Hallstatt miners consumed blue cheese and beer during the Iron Age and retained a non-Westernized gut microbiome until the Baroque period

Author

Maixner, Frank, primary, Sarhan, Mohamed S., additional, Huang, Kun D., additional, Tett, Adrian, additional, Schoenafinger, Alexander, additional, Zingale, Stefania, additional, Blanco-Míguez, Aitor, additional, Manghi, Paolo, additional, Cemper-Kiesslich, Jan, additional, Rosendahl, Wilfried, additional, Kusebauch, Ulrike, additional, Morrone, Seamus R., additional, Hoopmann, Michael R., additional, Rota-Stabelli, Omar, additional, Rattei, Thomas, additional, Moritz, Robert L., additional, Oeggl, Klaus, additional, Segata, Nicola, additional, Zink, Albert, additional, Reschreiter, Hans, additional, and Kowarik, Kerstin, additional

Published
2021
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10. The person-to-person transmission landscape of the gut and oral microbiomes

Author

Mireia Valles-Colomer, Aitor Blanco-Míguez, Paolo Manghi, Francesco Asnicar, Leonard Dubois, Davide Golzato, Federica Armanini, Fabio Cumbo, Kun D. Huang, Serena Manara, Giulia Masetti, Federica Pinto, Elisa Piperni, Michal Punčochář, Liviana Ricci, Moreno Zolfo, Olivia Farrant, Adriana Goncalves, Marta Selma-Royo, Ana G. Binetti, Jimmy E. Becerra, Bei Han, John Lusingu, John Amuasi, Loredana Amoroso, Alessia Visconti, Claire M. Steves, Mario Falchi, Michele Filosi, Adrian Tett, Anna Last, Qian Xu, Nan Qin, Huanlong Qin, Jürgen May, Daniel Eibach, Maria Valeria Corrias, Mirco Ponzoni, Edoardo Pasolli, Tim D. Spector, Enrico Domenici, Maria Carmen Collado, Nicola Segata, Valles-Colomer, Mireia, Blanco-Míguez, Aitor, Manghi, Paolo, Asnicar, Francesco, Dubois, Leonard, Golzato, Davide, Armanini, Federica, Cumbo, Fabio, Huang, Kun D, Manara, Serena, Masetti, Giulia, Pinto, Federica, Piperni, Elisa, Punčochář, Michal, Ricci, Liviana, Zolfo, Moreno, Farrant, Olivia, Goncalves, Adriana, Selma-Royo, Marta, Binetti, Ana G, Becerra, Jimmy E, Han, Bei, Lusingu, John, Amuasi, John, Amoroso, Loredana, Visconti, Alessia, Steves, Claire M, Falchi, Mario, Filosi, Michele, Tett, Adrian, Last, Anna, Xu, Qian, Qin, Nan, Qin, Huanlong, May, Jürgen, Eibach, Daniel, Corrias, Maria Valeria, Ponzoni, Mirco, Pasolli, Edoardo, Spector, Tim D, Domenici, Enrico, Collado, Maria Carmen, Segata, Nicola, European Commission, National Cancer Institute (US), European Research Council, Simons Foundation, and EMBO

Subjects
Multidisciplinary, Health, Metagenomes, Transmission, Interpersonal relations, Human microbiome
Abstract

The human microbiome is an integral component of the human body and a co-determinant of several health conditions1,2. However, the extent to which interpersonal relations shape the individual genetic makeup of the microbiome and its transmission within and across populations remains largely unknown3,4. Here, capitalizing on more than 9,700 human metagenomes and computational strain-level profiling, we detected extensive bacterial strain sharing across individuals (more than 10 million instances) with distinct mother-to-infant, intra-household and intra-population transmission patterns. Mother-to-infant gut microbiome transmission was considerable and stable during infancy (around 50% of the same strains among shared species (strain-sharing rate)) and remained detectable at older ages. By contrast, the transmission of the oral microbiome occurred largely horizontally and was enhanced by the duration of cohabitation. There was substantial strain sharing among cohabiting individuals, with 12% and 32% median strain-sharing rates for the gut and oral microbiomes, and time since cohabitation affected strain sharing more than age or genetics did. Bacterial strain sharing additionally recapitulated host population structures better than species-level profiles did. Finally, distinct taxa appeared as efficient spreaders across transmission modes and were associated with different predicted bacterial phenotypes linked with out-of-host survival capabilities. The extent of microorganism transmission that we describe underscores its relevance in human microbiome studies5, especially those on non-infectious, microbiome-associated diseases., This work was supported by the European Research Council (ERC-STG project MetaPG-716575 and ERC-CoG microTOUCH-101045015) to N.S. and by EMBO ALTF 593–2020 to M.V.-C. The work was also partially supported by MIUR ‘Futuro in Ricerca’ (grant no. RBFR13EWWI_001) to N.S., by the European H2020 programme (ONCOBIOME-825410 project, MASTER-818368 project, and IHMCSA-964590) to N.S., by the National Cancer Institute of the National Institutes of Health (1U01CA230551) to N.S., by the Premio Internazionale Lombardia e Ricerca 2019 to N.S., by the Simons Foundation (award ID 648614) to E.D. and N.S., and by the European Research Council (ERC-STG project Mami-639226) to M.C.C

Published
2023

11. Extending and improving metagenomic taxonomic profiling with uncharacterized species with MetaPhlAn 4

Author

Aitor Blanco-Míguez, Francesco Beghini, Fabio Cumbo, Lauren J. McIver, Kelsey N. Thompson, Moreno Zolfo, Paolo Manghi, Leonard Dubois, Kun D. Huang, Andrew Maltez Thomas, William A. Nickols, Gianmarco Piccinno, Elisa Piperni, Michal Punčochář, Mireia Valles-Colomer, Adrian Tett, Francesca Giordano, Richard Davies, Jonathan Wolf, Sarah E. Berry, Tim D. Spector, Eric A. Franzosa, Edoardo Pasolli, Francesco Asnicar, Curtis Huttenhower, Nicola Segata, Blanco-Míguez, Aitor, Beghini, Francesco, Cumbo, Fabio, Mciver, Lauren J, Thompson, Kelsey N, Zolfo, Moreno, Manghi, Paolo, Dubois, Leonard, Huang, Kun D, Thomas, Andrew Maltez, Nickols, William A, Piccinno, Gianmarco, Piperni, Elisa, Punčochář, Michal, Valles-Colomer, Mireia, Tett, Adrian, Giordano, Francesca, Davies, Richard, Wolf, Jonathan, Berry, Sarah E, Spector, Tim D, Franzosa, Eric A, Pasolli, Edoardo, Asnicar, Francesco, Huttenhower, Curti, and Segata, Nicola

Subjects
Biomedical Engineering, Molecular Medicine, Bioengineering, Applied Microbiology and Biotechnology, Biotechnology
Abstract

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.

Published
2023
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