Integrating taxonomic, functional, and strain-level profiling of diverse microbial communities with bioBakery 3 von Beghini, Francesco, McIver, Lauren J., Blanco-Miguez, 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

Volltext

Precise phylogenetic analysis of microbial isolates and genomes from metagenomes using PhyloPhlAn 3.0 von Asnicar, Francesco, Thomas, Andrew Maltez, Beghini, Francesco, Mengoni, Claudia, Manara, Serena, Manghi, Paolo, Zhu, Qiyun, Bolzan, Mattia, Cumbo, Fabio, May, Uyen, Sanders, Jon G., Zolfo, Moreno, Kopylova, Evguenia, Pasolli, Edoardo, Knight, Rob, Mirarab, Siavash, Huttenhower, Curtis, Segata, Nicola

Volltext

Microbiome connections with host metabolism and habitual diet from 1,098 deeply phenotyped individuals von Asnicar, Francesco, Berry, Sarah E., Valdes, Ana M., Nguyen, Long H., Piccinno, Gianmarco, Drew, David A., Leeming, Emily, Gibson, Rachel, Le Roy, Caroline, Khatib, Haya Al, Francis, Lucy, Mazidi, Mohsen, Mompeo, Olatz, Valles-Colomer, Mireia, Tett, Adrian, Beghini, Francesco, Dubois, Léonard, Bazzani, Davide, Thomas, Andrew Maltez, Mirzayi, Chloe, Khleborodova, Asya, Oh, Sehyun, Hine, Rachel, Bonnett, Christopher, Capdevila, Joan, Danzanvilliers, Serge, Giordano, Francesca, Geistlinger, Ludwig, Waldron, Levi, Davies, Richard, Hadjigeorgiou, George, Wolf, Jonathan, Ordovás, José M., Gardner, Christopher, Franks, Paul W., Chan, Andrew T., Huttenhower, Curtis, Spector, Tim D., Segata, Nicola

Volltext

Metagenomic analysis of colorectal cancer datasets identifies cross-cohort microbial diagnostic signatures and a link with choline degradation von Thomas, Andrew Maltez, Manghi, Paolo, Asnicar, Francesco, Pasolli, Edoardo, Armanini, Federica, Zolfo, Moreno, Beghini, Francesco, Manara, Serena, Karcher, Nicolai, Pozzi, Chiara, Gandini, Sara, Serrano, Davide, Tarallo, Sonia, Francavilla, Antonio, Gallo, Gaetano, Trompetto, Mario, Ferrero, Giulio, Mizutani, Sayaka, Shiroma, Hirotsugu, Shiba, Satoshi, Shibata, Tatsuhiro, Yachida, Shinichi, Yamada, Takuji, Wirbel, Jakob, Schrotz-King, Petra, Ulrich, Cornelia M., Brenner, Hermann, Arumugam, Manimozhiyan, Bork, Peer, Zeller, Georg, Cordero, Francesca, Dias-Neto, Emmanuel, Setubal, João Carlos, Tett, Adrian, Pardini, Barbara, Rescigno, Maria, Waldron, Levi, Naccarati, Alessio, Segata, Nicola

Volltext

Microbial genomes from non-human primate gut metagenomes expand the primate-associated bacterial tree of life with over 1000 novel species von Manara, Serena, Asnicar, Francesco, Beghini, Francesco, Bazzani, Davide, Cumbo, Fabio, Zolfo, Moreno, Nigro, Eleonora, Karcher, Nicolai, Manghi, Paolo, Metzger, Marisa Isabell, Pasolli, Edoardo, Segata, Nicola

Volltext

How inoculation affects the development and the performances of microalgal-bacterial consortia treating real municipal wastewater von Petrini, Serena, Foladori, Paola, Beghini, Francesco, Armanini, Federica, Segata, Nicola, Andreottola, Gianni

Volltext

Unexplored diversity and strain-level structure of the skin microbiome associated with psoriasis von Tett, Adrian, Pasolli, Edoardo, Farina, Stefania, Truong, Duy Tin, Asnicar, Francesco, Zolfo, Moreno, Beghini, Francesco, Armanini, Federica, Jousson, Olivier, De Sanctis, Veronica, Bertorelli, Roberto, Girolomoni, Giampiero, Cristofolini, Mario, Segata, Nicola

Volltext

MetaPhlAn 4 profiling of unknown species-level genome bins improves the characterization of diet-associated microbiome changes in mice von Manghi, Paolo, Blanco-Míguez, Aitor, Manara, Serena, NabiNejad, Amir, Cumbo, Fabio, Beghini, Francesco, Armanini, Federica, Golzato, Davide, Huang, Kun D., Thomas, Andrew M., Piccinno, Gianmarco, Punčochář, Michal, Zolfo, Moreno, Lesker, Till R., Bredon, Marius, Planchais, Julien, Glodt, Jeremy, Valles-Colomer, Mireia, Koren, Omry, Pasolli, Edoardo, Asnicar, Francesco, Strowig, Till, Sokol, Harry, Segata, Nicola

Volltext

Thermal Therapy Modulation of the Psoriasis-Associated Skin and Gut Microbiome von Manara, Serena, Beghini, Francesco, Masetti, Giulia, Armanini, Federica, Geat, Davide, Galligioni, Giulia, Segata, Nicola, Farina, Stefania, Cristofolini, Mario

Volltext

Commensal Bifidobacterium Strains Enhance the Efficacy of Neo-Epitope Based Cancer Vaccines von Tomasi, Michele, Dalsass, Mattia, Beghini, Francesco, Zanella, Ilaria, Caproni, Elena, Fantappie, Laura, Gagliardi, Assunta, Irene, Carmela, Koenig, Enrico, Frattini, Luca, Masetti, Giulia, Isaac, Samine Jessica, Armanini, Federica, Cumbo, Fabio, Blanco-Miguez, Aitor, Grandi, Alberto, Segata, Nicola, Grandi, Guido

Volltext

Extensive Unexplored Human Microbiome Diversity Revealed by Over 150,000 Genomes from Metagenomes Spanning Age, Geography, and Lifestyle von Pasolli, Edoardo, Asnicar, Francesco, Manara, Serena, Zolfo, Moreno, Karcher, Nicolai, Armanini, Federica, Beghini, Francesco, Manghi, Paolo, Tett, Adrian, Ghensi, Paolo, Collado, Maria Carmen, Rice, Benjamin L., DuLong, Casey, Morgan, Xochitl C., Golden, Christopher D., Quince, Christopher, Huttenhower, Curtis, Segata, Nicola

Volltext

Accessible, curated metagenomic data through ExperimentHub von Pasolli, Edoardo, Schiffer, Lucas, Manghi, Paolo, Renson, Audrey, Obenchain, Valerie, Truong, Duy Tin, Beghini, Francesco, Malik, Faizan, Ramos, Marcel, Dowd, Jennifer B, Huttenhower, Curtis, Morgan, Martin, Segata, Nicola, Waldron, Levi

Volltext

Extending and improving metagenomic taxonomic profiling with uncharacterized species using MetaPhlAn 4 von 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, Segata, Nicola

Volltext

Variability of strain engraftment and predictability of microbiome composition after fecal microbiota transplantation across different diseases von 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, Segata, Nicola

Volltext

Large-scale comparative metagenomics of Blastocystis, a common member of the human gut microbiome von Beghini, Francesco, Pasolli, Edoardo, Truong, Tin Duy, Putignani, Lorenza, Cacciò, Simone M, Segata, Nicola

Volltext

Mother-to-Infant Microbial Transmission from Different Body Sites Shapes the Developing Infant Gut Microbiome von Ferretti, Pamela, Pasolli, Edoardo, Tett, Adrian, Asnicar, Francesco, Gorfer, Valentina, Fedi, Sabina, Armanini, Federica, Truong, Duy Tin, Manara, Serena, Zolfo, Moreno, Beghini, Francesco, Bertorelli, Roberto, De Sanctis, Veronica, Bariletti, Ilaria, Canto, Rosarita, Clementi, Rosanna, Cologna, Marina, Crifò, Tiziana, Cusumano, Giuseppina, Gottardi, Stefania, Innamorati, Claudia, Masè, Caterina, Postai, Daniela, Savoi, Daniela, Duranti, Sabrina, Lugli, Gabriele Andrea, Mancabelli, Leonardo, Turroni, Francesca, Ferrario, Chiara, Milani, Christian, Mangifesta, Marta, Anzalone, Rosaria, Viappiani, Alice, Yassour, Moran, Vlamakis, Hera, Xavier, Ramnik, Collado, Carmen Maria, Koren, Omry, Tateo, Saverio, Soffiati, Massimo, Pedrotti, Anna, Ventura, Marco, Huttenhower, Curtis, Bork, Peer, Segata, Nicola

Volltext

Reporting guidelines for human microbiome research: the STORMS checklist von Mirzayi, Chloe, Renson, Audrey, Zohra, Fatima, Elsafoury, Shaimaa, Geistlinger, Ludwig, Kasselman, Lora J., Eckenrode, Kelly, van de Wijgert, Janneke, Loughman, Amy, Marques, Francine Z., MacIntyre, David A., Arumugam, Manimozhiyan, Azhar, Rimsha, Beghini, Francesco, Bergstrom, Kirk, Bhatt, Ami, Bisanz, Jordan E., Braun, Jonathan, Bravo, Hector Corrada, Buck, Gregory A., Bushman, Frederic, Casero, David, Clarke, Gerard, Collado, Maria Carmen, Cotter, Paul D., Cryan, John F., Demmer, Ryan T., Devkota, Suzanne, Elinav, Eran, Escobar, Juan S., Fettweis, Jennifer, Finn, Robert D., Fodor, Anthony A., Forslund, Sofia, Franke, Andre, Furlanello, Cesare, Gilbert, Jack, Grice, Elizabeth, Haibe-Kains, Benjamin, Handley, Scott, Herd, Pamela, Holmes, Susan, Jacobs, Jonathan P., Karstens, Lisa, Knight, Rob, Knights, Dan, Koren, Omry, Kwon, Douglas S., Langille, Morgan, Lindsay, Brianna, McGovern, Dermot, McHardy, Alice C., McWeeney, Shannon, Mueller, Noel T., Nezi, Luigi, Olm, Matthew, Palm, Noah, Pasolli, Edoardo, Raes, Jeroen, Redinbo, Matthew R., Rühlemann, Malte, Balfour Sartor, R., Schloss, Patrick D., Schriml, Lynn, Segal, Eran, Shardell, Michelle, Smirnova, Ekaterina, Sokol, Harry, Sonnenburg, Justin L., Srinivasan, Sujatha, Thingholm, Louise B., Turnbaugh, Peter J., Upadhyay, Vaibhav, Walls, Ramona L., Wilmes, Paul, Yamada, Takuji, Zeller, Georg, Zhang, Mingyu, Zhao, Ni, Zhao, Liping, Bao, Wenjun, Culhane, Aedin, Devanarayan, Viswanath, Dopazo, Joaquin, Fan, Xiaohui, Fischer, Matthias, Kusko, Rebecca, Mason, Christopher E., Mercer, Tim R., Sansone, Susanna-Assunta, Scherer, Andreas, Shi, Leming, Thakkar, Shraddha, Tong, Weida, Wolfinger, Russ, Hunter, Christopher, Segata, Nicola, Dowd, Jennifer B., Jones, Heidi E., Waldron, Levi

Volltext

Gut microbiome strain-sharing within isolated village social networks von Beghini, Francesco, Pullman, Jackson, Alexander, Marcus, Shridhar, Shivkumar Vishnempet, Prinster, Drew, Singh, Adarsh, Matute Juárez, Rigoberto, Airoldi, Edoardo M, Brito, Ilana L, Christakis, Nicholas A

Volltext

Environmental, socioeconomic, and health factors associated with gut microbiome species and strains in isolated Honduras villages von Shridhar, Shivkumar Vishnempet, Beghini, Francesco, Alexander, Marcus, Singh, Adarsh, Juárez, Rigoberto Matute, Brito, Ilana L., Christakis, Nicholas A.

Volltext

Sociodemographic variation in the oral microbiome von Renson, Audrey, Jones, Heidi E., Beghini, Francesco, Segata, Nicola, Zolnik, Christine P., Usyk, Mykhaylo, Moody, Thomas U., Thorpe, Lorna, Burk, Robert, Waldron, Levi, Dowd, Jennifer B.

Volltext