25 results on '"Punčochář, Michal"'
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2. Unexplored microbial diversity from 2,500 food metagenomes and links with the human microbiome
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Alvarez-Ordóñez, Avelino, Alvarez, Pablo, Antonielli, Livio, Arendt, Elke, Armanini, Federica, Aubry, Aurelie, Baelum, Jacob, Barcenilla, Coral, Belanche, Alejandro, Benavent-Gil, Yaiza, Blake, Tony, Blanco-Míguez, Aitor, Bongoni, Radhika, Boyer, Mickael, Brennan, Fiona, Breselge, Samuel, Briem, Helgi, Butler, Derek, Calvete-Torre, Inés, Carballo, Omar Cristobal, Cardinal, Mireille, Carlino, Niccolò, Chervaux, Christian, Chopin, Christine, Clotaire, Natallia, Coakley, Mairead, Cobo-Díaz, José Francisco, Codd, Jim, Conroy, Stephen, Corral-Jara, Karla Fabiola, Corral-Jara, Karla-Fabiola, Cotter, Paul D., Coyne, Gerard, Creevey, Chris, Cuevas, Patricia D., Curran, Brendan, Delgado, Susana, Derde, Liesbeth, Derrien, Muriel, Ercolini, Danilo, Exposito, Ruth Gomez, López Fernández, María Mercedes, De Filippis, Francesca, Fordham, Daniel, Galy, Hubert, Gavriilidou, Asimenia, Gunnarsson, Oddur, Hanson, Buck, Hermes, Gerben, Huang, Rongcai, Huws, Sharon, Ikoyi, Israel, Jaeger, Alice, Jeffery, Ian, Jérôme, Marc, Juan, Pierre-Alexandre, Kenny, David, Kers, Annelies, Khinouche, Karim-Franck, Kirwan, Stuart, Klaassens, Eline S., Knobloch, Stephen, Kolbeinsson, Kristinn, Kolypczuk, Laetitia, Kostic, Tanja, Ledda, Fabio, Leech, John, Lehmann, Doerte, Leroi, Françoise, Lewis, Eva, Ley, Johanna, Lucic, Eva, Lynch, Kieran, Mace, Sabrina, MacLaren-Lee, Iain, Mahler de Sanchez, Lisa, Marchart, Juergen, Margolles, Abelardo, Marteinsson, Viggó Thór, Masetti, Giulia, McGovern, Fiona, McHugh, Noirin, McLoughlin, Steven, Meehan, Dara, Mølbak, Lars, Monin, Thomas, Moreno, Javier, Morgavi, Diego, Morrison, Steven, Müench, Steffen, Ramos Neves, Ana Rute, Neylon, Emma, Nyhan, Laura, O’Kelly, Rhona, O’Neil, Dominic, O’Toole, Paul, Ortiz-Chura, Abimael, Palma, Juan Manuel, Pasolli, Edoardo, Passerini, Delphine, Pastar, Milica, Pinto, Federica, Pirovano, Walter, Plans, Olga, Policht, Marion, Pop, Aurel, Pop, Bianca, Popova, Milka, Prieto, Miguel, Quijada, Narciso M., Reiss, Antje, Romero, Pedro, Ruas-Madiedo, Patricia, Rubino, Francesco, Rubio, Raul Cabrera, Ruiz, Lorena, Ryan, Angela, Ryan, Clodagh, Sabater, Carlos, Sahin, Aylin, Salaun, Cecile, Santos, Fernanda Godoy, Schneider, Carolin, Segata, Nicola, Selberherr, Evelyne, Sessitsch, Angela, Skírnisdóttir, Sigurlaug, Smidt, Hauke, Smith, Paul, Sprenger-Haussels, Markus, Tapio, Ilma, Tap, Julien, Valentino, Vincenzo, Wagner, Martin, Walsh, Aaron, Walsh, Liam, Waters, Sinead M., Willcocks, Spike, Yáñez-Ruiz, David R., Yan, Tianhai, Yap, Min, Zannini, Emanuele, Zuliani, Véronique, Punčochář, Michal, Mengoni, Claudia, Tatti, Alessia, Manghi, Paolo, Avagliano, Michele, Cabrera-Rubio, Raul, Coakley, Mairéad, Cobo-Díaz, José F., Dey, Hrituraj, Asnicar, Francesco, Fackelmann, Gloria, Heidrich, Vitor, and Rota Stabelli, Omar
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- 2024
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3. Extending and improving metagenomic taxonomic profiling with uncharacterized species using MetaPhlAn 4
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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
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- 2023
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4. Fecal microbiota transplantation plus anti-PD-1 immunotherapy in advanced melanoma: a phase I trial
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Routy, Bertrand, Lenehan, John G., Miller, Jr, Wilson H., Jamal, Rahima, Messaoudene, Meriem, Daisley, Brendan A., Hes, Cecilia, Al, Kait F., Martinez-Gili, Laura, Punčochář, Michal, Ernst, Scott, Logan, Diane, Belanger, Karl, Esfahani, Khashayar, Richard, Corentin, Ninkov, Marina, Piccinno, Gianmarco, Armanini, Federica, Pinto, Federica, Krishnamoorthy, Mithunah, Figueredo, Rene, Thebault, Pamela, Takis, Panteleimon, Magrill, Jamie, Ramsay, LeeAnn, Derosa, Lisa, Marchesi, Julian R., Parvathy, Seema Nair, Elkrief, Arielle, Watson, Ian R., Lapointe, Rejean, Segata, Nicola, Haeryfar, S.M. Mansour, Mullish, Benjamin H., Silverman, Michael S., Burton, Jeremy P., and Maleki Vareki, Saman
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- 2023
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5. Neuroblastoma is associated with alterations in gut microbiome composition subsequent to maternal microbial seeding
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Valles-Colomer, Mireia, Manghi, Paolo, Cumbo, Fabio, Masetti, Giulia, Armanini, Federica, Asnicar, Francesco, Blanco-Miguez, Aitor, Pinto, Federica, Punčochář, Michal, Garaventa, Alberto, Amoroso, Loredana, Ponzoni, Mirco, Corrias, Maria Valeria, and Segata, Nicola
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- 2024
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6. Extension of the Segatella copri complex to 13 species with distinct large extrachromosomal elements and associations with host conditions
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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
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- 2023
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7. Author Correction: Fecal microbiota transplantation plus anti-PD-1 immunotherapy in advanced melanoma: a phase I trial
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Routy, Bertrand, Lenehan, John G., Miller, Jr, Wilson H., Jamal, Rahima, Messaoudene, Meriem, Daisley, Brendan A., Hes, Cecilia, Al, Kait F., Martinez-Gili, Laura, Punčochář, Michal, Ernst, Scott, Logan, Diane, Belanger, Karl, Esfahani, Khashayar, Richard, Corentin, Ninkov, Marina, Piccinno, Gianmarco, Armanini, Federica, Pinto, Federica, Krishnamoorthy, Mithunah, Figueredo, Rene, Thebault, Pamela, Takis, Panteleimon, Magrill, Jamie, Ramsay, LeeAnn, Derosa, Lisa, Marchesi, Julian R., Parvathy, Seema Nair, Elkrief, Arielle, Watson, Ian R., Lapointe, Rejean, Segata, Nicola, Haeryfar, S.M. Mansour, Mullish, Benjamin H., Silverman, Michael S., Burton, Jeremy P., and Maleki Vareki, Saman
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- 2024
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8. The person-to-person transmission landscape of the gut and oral microbiomes
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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
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- 2023
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9. Variability of strain engraftment and predictability of microbiome composition after fecal microbiota transplantation across different diseases
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Ianiro, Gianluca, Punčochář, Michal, Karcher, Nicolai, Porcari, Serena, Armanini, Federica, Asnicar, Francesco, Beghini, Francesco, Blanco-Míguez, Aitor, Cumbo, Fabio, Manghi, Paolo, Pinto, Federica, Masucci, Luca, Quaranta, Gianluca, De Giorgi, Silvia, Sciumè, Giusi Desirè, Bibbò, Stefano, Del Chierico, Federica, Putignani, Lorenza, Sanguinetti, Maurizio, Gasbarrini, Antonio, Valles-Colomer, Mireia, Cammarota, Giovanni, and Segata, Nicola
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- 2022
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10. Influence of microbiota-associated metabolic reprogramming on clinical outcome in patients with melanoma from the randomized adjuvant dendritic cell-based MIND-DC trial
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MS Hematologie, Alves Costa Silva, Carolina, Piccinno, Gianmarco, Suissa, Déborah, Bourgin, Mélanie, Schreibelt, Gerty, Durand, Sylvère, Birebent, Roxanne, Fidelle, Marine, Sow, Cissé, Aprahamian, Fanny, Manghi, Paolo, Punčochář, Michal, Asnicar, Francesco, Pinto, Federica, Armanini, Federica, Terrisse, Safae, Routy, Bertrand, Drubay, Damien, Eggermont, Alexander M.M., Kroemer, Guido, Segata, Nicola, Zitvogel, Laurence, Derosa, Lisa, Bol, Kalijn F., de Vries, I. Jolanda M., MS Hematologie, Alves Costa Silva, Carolina, Piccinno, Gianmarco, Suissa, Déborah, Bourgin, Mélanie, Schreibelt, Gerty, Durand, Sylvère, Birebent, Roxanne, Fidelle, Marine, Sow, Cissé, Aprahamian, Fanny, Manghi, Paolo, Punčochář, Michal, Asnicar, Francesco, Pinto, Federica, Armanini, Federica, Terrisse, Safae, Routy, Bertrand, Drubay, Damien, Eggermont, Alexander M.M., Kroemer, Guido, Segata, Nicola, Zitvogel, Laurence, Derosa, Lisa, Bol, Kalijn F., and de Vries, I. Jolanda M.
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- 2024
11. Genomic diversity and ecology of human-associated Akkermansia species in the gut microbiome revealed by extensive metagenomic assembly
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Karcher, Nicolai, Nigro, Eleonora, Punčochář, Michal, Blanco-Míguez, Aitor, Ciciani, Matteo, Manghi, Paolo, Zolfo, Moreno, Cumbo, Fabio, Manara, Serena, Golzato, Davide, Cereseto, Anna, Arumugam, Manimozhiyan, Bui, Thi Phuong Nam, Tytgat, Hanne L. P., Valles-Colomer, Mireia, de Vos, Willem M., and Segata, Nicola
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- 2021
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12. MetaPhlAn 4 profiling of unknown species-level genome bins improves the characterization of diet-associated microbiome changes in mice
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Manghi, Paolo, primary, Blanco-Míguez, Aitor, additional, Manara, Serena, additional, NabiNejad, Amir, additional, Cumbo, Fabio, additional, Beghini, Francesco, additional, Armanini, Federica, additional, Golzato, Davide, additional, Huang, Kun D., additional, Thomas, Andrew M., additional, Piccinno, Gianmarco, additional, Punčochář, Michal, additional, Zolfo, Moreno, additional, Lesker, Till R., additional, Bredon, Marius, additional, Planchais, Julien, additional, Glodt, Jeremy, additional, Valles-Colomer, Mireia, additional, Koren, Omry, additional, Pasolli, Edoardo, additional, Asnicar, Francesco, additional, Strowig, Till, additional, Sokol, Harry, additional, and Segata, Nicola, additional
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- 2023
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13. The person-to-person transmission landscape of the gut and oral microbiomes
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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.
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- 2023
14. Endurance Test on the Rowing Machine
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Leuchter, Tomáš, primary, Novotný, Viktor, additional, Novotný, Jan, additional, Zahradníček, Petr, additional, Polách, Michal, additional, Punčochář, Michal, additional, and Kellner, Petr, additional
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- 2023
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15. The reasoning behind assessing push-up tests – an in depth analysis.
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KELLNER, PETR, NEUBAUER, JIŘÍ, KELLNEROVÁ, ZDEŇKA, ZAHRADNÍČEK, PETR, NOVOTNÝ, VIKTOR, WAWRZACZ, LIBOR, and PUNČOCHÁŘ, MICHAL
- Abstract
A good exercise does not necessarily make for a good measurement tool and using such a tool may lead to wrong conclusions if used for scientific measurement and personal evaluation, yet it happens when using pushup tests which are subjective and lack reliability. This study examined the reasons behind the questionable reliability of push-up testing. Material and Methods: Fifty videorecorded 30-second push-up test performances were evaluated by 10 highly experienced raters in two separate assessment trials. The assessment involved counting the number of acceptable repetitions and identifying any technical flaws in the execution of the exercise. The collected evaluations were analyzed using quantitative and qualitative methods. Results: Statistical analysis (p ≤ 0.05) revealed significant inter-rater differences in counting in both trials. Comparable counting was only found among raters who marked the same technique as "perfect" and overall concordance on perfect execution was 79.4%. Intra-rater counting reliability ranged from r = 0.57 to r = 0.92. Three main areas of technique deterioration were identified: incomplete arm extension (10.2% of denied repetitions), inadequate arm flexion (7%), and failure to keep the body straight and rigid (6.3%), which was also the most disputed between the raters. Additionally, male raters were more lenient towards the technique imperfections of female subjects. Many miscalculations were also detected, often correlated with perfect technique execution (88% of cases). The second most common cause of miscalculating was raters' willingness to count a repetition that was interrupted mid-execution due to time constraints. Conclusions: The study findings indicate that push-up assessment is highly subjective and should be avoided in scientific or personal evaluations that require a higher level of precision. The reliability of the assessment heavily depends on the individual administering the test, and the average evaluator demonstrates only moderate reliability. To mitigate gender-based bias, considering a female evaluator for female examinees is recommended. Therefore, caution is advised when relying on push-up tests when more reliable alternatives are available. [ABSTRACT FROM AUTHOR]
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- 2023
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16. Extending and improving metagenomic taxonomic profiling with uncharacterized species with MetaPhlAn 4
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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
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- 2022
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17. Su1885 THE IMPACT OF UNNECESSARY GLUTEN-FREE DIET ON GUT MICROBIOTA
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Manza, Francesca, Lungaro, Lisa, Costanzini, Anna, Segata, Nicola, Pinto, Federica, Puncochar, Michal, Asnicar, Francesco, Armanini, Federica, Carroccio, Antonio, Seidita, Aurelio, Mansueto, Pasquale, Calabrò, Antonino S., Cavalieri, Duccio, Barbara, Giovanni, Stanghellini, Vincenzo, Volta, Umberto, De Giorgio, Roberto, and Caio, Giacomo Pietro Ismaele
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- 2024
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18. Additional file 3 of Genomic diversity and ecology of human-associated Akkermansia species in the gut microbiome revealed by extensive metagenomic assembly
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Karcher, Nicolai, Nigro, Eleonora, Punčochář, Michal, Blanco-Míguez, Aitor, Ciciani, Matteo, Manghi, Paolo, Zolfo, Moreno, Cumbo, Fabio, Manara, Serena, Golzato, Davide, Cereseto, Anna, Arumugam, Manimozhiyan, Bui, Thi Phuong Nam, Tytgat, Hanne L. P., Valles-Colomer, Mireia, de Vos, Willem M., and Segata, Nicola
- Abstract
Additional file 3. Review history.
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- 2021
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19. Additional file 2 of Genomic diversity and ecology of human-associated Akkermansia species in the gut microbiome revealed by extensive metagenomic assembly
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Karcher, Nicolai, Nigro, Eleonora, Punčochář, Michal, Blanco-Míguez, Aitor, Ciciani, Matteo, Manghi, Paolo, Zolfo, Moreno, Cumbo, Fabio, Manara, Serena, Golzato, Davide, Cereseto, Anna, Arumugam, Manimozhiyan, Bui, Thi Phuong Nam, Tytgat, Hanne L. P., Valles-Colomer, Mireia, de Vos, Willem M., and Segata, Nicola
- Abstract
Additional file 2. Supplementary Figures S1 to S11.
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- 2021
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20. Interaction between a teacher and student in comparasion group and individual skiing lessons
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Punčochář, Michal, Jindra, Matouš, and Gnad, Tomáš
- Subjects
lyžařská škola ,Individuální a skupinová výuka lyžování ,ski school ,analysis of didactic interaction ,MADI ,Individual and group skiing lessons ,analýza didaktické interakce ,ADI - Abstract
Title of the thesis: Interaction between a teacher and a student compared group and individual teaching skiing. Objectives: The aim of this work was to find, which and how big differences are in the didactic interaction in comparison of group and individual ski lessons. Methods: In this work we used the method of observation, data collection was realized using a video camera and the subsequent recording was evaluated using the MADI method (modified analysis of didactic interaction). Results: From the results we found that the greatest difference was in the expression factual purportwhich in individual lessons grow avarage by 20%. Furthermore, in the individual lesson form grow education activity above organizational by on avarage10% and in the type of attitude activity integration has increased on avrage 7%. The results also showed that in the individual form of teaching did not appear activity without direct control. Conclusion: The biggest difference between individual and group teaching was the increase in individual teaching in the expression of the subject matter, integration attitude activities above the dominant, the teaching activity increased over the organizational and the performance of the pupil's activity was constantly under direct control. Key words: Individual and group skiing...
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- 2020
21. Author Correction: Fecal microbiota transplantation plus anti-PD-1 immunotherapy in advanced melanoma: a phase I trial
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Routy, Bertrand, Lenehan, John G., Miller, Wilson H., Jamal, Rahima, Messaoudene, Meriem, Daisley, Brendan A., Hes, Cecilia, Al, Kait F., Martinez-Gili, Laura, Punčochář, Michal, Ernst, Scott, Logan, Diane, Belanger, Karl, Esfahani, Khashayar, Richard, Corentin, Ninkov, Marina, Piccinno, Gianmarco, Armanini, Federica, Pinto, Federica, Krishnamoorthy, Mithunah, Figueredo, Rene, Thebault, Pamela, Takis, Panteleimon, Magrill, Jamie, Ramsay, LeeAnn, Derosa, Lisa, Marchesi, Julian R., Parvathy, Seema Nair, Elkrief, Arielle, Watson, Ian R., Lapointe, Rejean, Segata, Nicola, Haeryfar, S.M. Mansour, Mullish, Benjamin H., Silverman, Michael S., Burton, Jeremy P., and Maleki Vareki, Saman
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- 2023
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22. Unexplored microbial diversity from 2,500 food metagenomes and links with the human microbiome.
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Carlino, Niccolò, Blanco-Míguez, Aitor, Punčochář, Michal, Mengoni, Claudia, Pinto, Federica, Tatti, Alessia, Manghi, Paolo, Armanini, Federica, Avagliano, Michele, Barcenilla, Coral, Breselge, Samuel, Cabrera-Rubio, Raul, Calvete-Torre, Inés, Coakley, Mairéad, Cobo-Díaz, José F., De Filippis, Francesca, Dey, Hrituraj, Leech, John, Klaassens, Eline S., and Knobloch, Stephen
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HUMAN microbiota , *GUT microbiome , *MICROBIAL diversity , *FOOD quality , *MICROBIAL genomics - Abstract
Complex microbiomes are part of the food we eat and influence our own microbiome, but their diversity remains largely unexplored. Here, we generated the open access curatedFoodMetagenomicData (cFMD) resource by integrating 1,950 newly sequenced and 583 public food metagenomes. We produced 10,899 metagenome-assembled genomes spanning 1,036 prokaryotic and 108 eukaryotic species-level genome bins (SGBs), including 320 previously undescribed taxa. Food SGBs displayed significant microbial diversity within and between food categories. Extension to >20,000 human metagenomes revealed that food SGBs accounted on average for 3% of the adult gut microbiome. Strain-level analysis highlighted potential instances of food-to-gut transmission and intestinal colonization (e.g., Lacticaseibacillus paracasei) as well as SGBs with divergent genomic structures in food and humans (e.g., Streptococcus gallolyticus and Limosilactobabillus mucosae). The cFMD expands our knowledge on food microbiomes, their role in shaping the human microbiome, and supports future uses of metagenomics for food quality, safety, and authentication. [Display omitted] • With curatedFoodMetagenomicData, we integrated and analyzed >2,500 food metagenomes • Over 10,000 prokaryotic and eukaryotic MAGs uncover substantial food microbial diversity • Food microbes account for up to an average of 3% of the adult gut microbiome • Strain-level analysis highlights potential instances of food-to-gut microbe transmission Despite extensive studies on nutrition and the abiotic components of food, the food microbiome remains largely uncharacterized. In this study, a systematic metagenomic sequencing of microbiomes from over 2,500 food sources, integrated with metadata and analyzed in connection with the human microbiome, showed that many members of the gut microbiome may have been recently acquired from food sources. [ABSTRACT FROM AUTHOR]
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- 2024
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23. Genomic diversity and ecology of human-associated Akkermansiaspecies in the gut microbiome revealed by extensive metagenomic assembly
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Karcher, Nicolai, Nigro, Eleonora, Punčochář, Michal, Blanco-Míguez, Aitor, Ciciani, Matteo, Manghi, Paolo, Zolfo, Moreno, Cumbo, Fabio, Manara, Serena, Golzato, Davide, Cereseto, Anna, Arumugam, Manimozhiyan, Bui, Thi Phuong Nam, Tytgat, Hanne L. P., Valles-Colomer, Mireia, de Vos, Willem M., and Segata, Nicola
- Abstract
Background: Akkermansia muciniphilais a human gut microbe with a key role in the physiology of the intestinal mucus layer and reported associations with decreased body mass and increased gut barrier function and health. Despite its biomedical relevance, the genomic diversity of A. muciniphilaremains understudied and that of closely related species, except for A. glycaniphila, unexplored. Results: We present a large-scale population genomics analysis of the Akkermansiagenus using 188 isolate genomes and 2226 genomes assembled from 18,600 metagenomes from humans and other animals. While we do not detect A. glycaniphila, the Akkermansiastrains in the human gut can be grouped into five distinct candidate species, including A. muciniphila, that show remarkable whole-genome divergence despite surprisingly similar 16S rRNA gene sequences. These candidate species are likely human-specific, as they are detected in mice and non-human primates almost exclusively when kept in captivity. In humans, Akkermansiacandidate species display ecological co-exclusion, diversified functional capabilities, and distinct patterns of associations with host body mass. Analysis of CRISPR-Cas loci reveals new variants and spacers targeting newly discovered putative bacteriophages. Remarkably, we observe an increased relative abundance of Akkermansiawhen cognate predicted bacteriophages are present, suggesting ecological interactions. A. muciniphilafurther exhibits subspecies-level genetic stratification with associated functional differences such as a putative exo/lipopolysaccharide operon. Conclusions: We uncover a large phylogenetic and functional diversity of the Akkermansiagenus in humans. This variability should be considered in the ongoing experimental and metagenomic efforts to characterize the health-associated properties of A. muciniphilaand related bacteria.
- Published
- 2021
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24. The person-to-person transmission landscape of the gut and oral microbiomes
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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
25. Evaluating metagenomic analyses for undercharacterized environments: what's needed to light up the microbial dark matter?
- Author
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Nickols WA, McIver LJ, Walsh A, Zhang Y, Nearing JT, Asnicar F, Punčochář M, Segata N, Nguyen LH, Hartmann EM, Franzosa EA, Huttenhower C, and Thompson KN
- Abstract
Non-human-associated microbial communities play important biological roles, but they remain less understood than human-associated communities. Here, we assess the impact of key environmental sample properties on a variety of state-of-the-art metagenomic analysis methods. In simulated datasets, all methods performed similarly at high taxonomic ranks, but newer marker-based methods incorporating metagenomic assembled genomes outperformed others at lower taxonomic levels. In real environmental data, taxonomic profiles assigned to the same sample by different methods showed little agreement at lower taxonomic levels, but the methods agreed better on community diversity estimates and estimates of the relationships between environmental parameters and microbial profiles.
- Published
- 2024
- Full Text
- View/download PDF
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