Probiotics, gut microbiota, and their influence on host health and disease von Sánchez, Borja, Delgado, Susana, Blanco‐Míguez, Aitor, Lourenço, Anália, Gueimonde, Miguel, Margolles, Abelardo

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Faecal microbiota transplantation for the treatment of diarrhoea induced by tyrosine-kinase inhibitors in patients with metastatic renal cell carcinoma von Ianiro, Gianluca, Rossi, Ernesto, Thomas, Andrew M., Schinzari, Giovanni, Masucci, Luca, Quaranta, Gianluca, Settanni, Carlo Romano, Lopetuso, Loris Riccardo, Armanini, Federica, Blanco-Miguez, Aitor, Asnicar, Francesco, Consolandi, Clarissa, Iacovelli, Roberto, Sanguinetti, Maurizio, Tortora, Giampaolo, Gasbarrini, Antonio, Segata, Nicola, Cammarota, Giovanni

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Genomic diversity and ecology of human-associated Akkermansia species in the gut microbiome revealed by extensive metagenomic assembly von 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, Segata, Nicola

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BlasterJS: A novel interactive JavaScript visualisation component for BLAST alignment results von Blanco-Míguez, Aitor, Fdez-Riverola, Florentino, Sánchez, Borja, Lourenço, Anália

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Microbiota-Derived β-Amyloid-like Peptides Trigger Alzheimer’s Disease-Related Pathways in the SH-SY5Y Neural Cell Line von Blanco-Míguez, Aitor, Tamés, Hector, Ruas-Madiedo, Patricia, Sánchez, Borja

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Metabolomic and gut microbiome profiles across the spectrum of community-based COVID and non-COVID disease von Österdahl, Marc F., Whiston, Ronan, Sudre, Carole H., Asnicar, Francesco, Cheetham, Nathan J., Blanco Miguez, Aitor, Bowyer, Vicky, Antonelli, Michela, Snell, Olivia, dos Santos Canas, Liane, Hu, Christina, Wolf, Jonathan, Menni, Cristina, Malim, Michael, Hart, Deborah, Spector, Tim, Berry, Sarah, Segata, Nicola, Doores, Katie, Ourselin, Sebastien, Duncan, Emma L., Steves, Claire J.

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

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Targeted depletion of pks + bacteria from a fecal microbiota using specific antibodies von Blanco-Míguez, Aitor, Marcos-Fernández, Raquel, Guadamuro-García, Lucía, Fdez-Riverola, Florentino, Cubiella, Joaquín, Lourenço, Anália, Margolles, Abelardo, Sánchez, Borja

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

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Computational prediction of the bioactivity potential of proteomes based on expert knowledge von Blanco-Míguez, Aitor, Blanco, Guillermo, Gutierrez-Jácome, Alberto, Fdez-Riverola, Florentino, Sánchez, Borja, Lourenço, Anália

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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

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In Silico Screening of the Human Gut Metaproteome Identifies Th17-Promoting Peptides Encrypted in Proteins of Commensal Bacteria von Hidalgo-Cantabrana, Claudio, Moro-García, Marco A., Blanco-Míguez, Aitor, Fdez-Riverola, Florentino, Lourenço, Anália, Alonso-Arias, Rebeca, Sánchez, Borja

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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

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Cross-cohort gut microbiome associations with immune checkpoint inhibitor response in advanced melanoma von Lee, Karla A., Thomas, Andrew Maltez, Bolte, Laura A., Björk, Johannes R., de Ruijter, Laura Kist, Armanini, Federica, Asnicar, Francesco, Blanco-Miguez, Aitor, Board, Ruth, Calbet-Llopart, Neus, Derosa, Lisa, Dhomen, Nathalie, Brooks, Kelly, Harland, Mark, Harries, Mark, Leeming, Emily R., Lorigan, Paul, Manghi, Paolo, Marais, Richard, Newton-Bishop, Julia, Nezi, Luigi, Pinto, Federica, Potrony, Miriam, Puig, Susana, Serra-Bellver, Patricio, Shaw, Heather M., Tamburini, Sabrina, Valpione, Sara, Vijay, Amrita, Waldron, Levi, Zitvogel, Laurence, Zolfo, Moreno, de Vries, Elisabeth G. E., Nathan, Paul, Fehrmann, Rudolf S. N., Bataille, Véronique, Hospers, Geke A. P., Spector, Tim D., Weersma, Rinse K., Segata, Nicola

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The person-to-person transmission landscape of the gut and oral microbiomes von 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

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The extracellular proteins of Lactobacillus acidophilus DSM 20079T display anti-inflammatory effect in both in piglets, healthy human donors and Crohn’s Disease patients von Hidalgo-Cantabrana, Claudio, Moro-García, Marco Antonio, Blanco-Míguez, Aitor, Fdez-Riverola, Florentino, Oliván, Mamen, Royo, Luis J., Riestra, Sabino, Margolles, Abelardo, Lourenço, Anália, Alonso-Arias, Rebeca, Sánchez, Borja

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In silico and functional analyses of immunomodulatory peptides encrypted in the human gut metaproteome von Cambeiro-Pérez, Noelia, Hidalgo-Cantabrana, Claudio, Moro-García, Marco Antonio, Blanco-Míguez, Aitor, Fdez-Riverola, Florentino, Riestra, Sabino, Lourenço, Anália, Alonso-Arias, Rebeca, Margolles, Abelardo, Martínez-Carballo, Elena, Sánchez, Borja

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Improving phylogeny reconstruction at the strain level using peptidome datasets von Blanco-Míguez, Aitor, Meier-Kolthoff, Jan P., Gutiérrez-Jácome, Alberto, Göker, Markus, Fdez-Riverola, Florentino, Sánchez, Borja, Lourenço, Anália

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A distinct Fusobacterium nucleatum clade dominates the colorectal cancer niche von Zepeda-Rivera, Martha, Minot, Samuel S., Bouzek, Heather, Wu, Hanrui, Blanco-Míguez, Aitor, Manghi, Paolo, Jones, Dakota S., LaCourse, Kaitlyn D., Wu, Ying, McMahon, Elsa F., Park, Soon-Nang, Lim, Yun K., Kempchinsky, Andrew G., Willis, Amy D., Cotton, Sean L., Yost, Susan C., Sicinska, Ewa, Kook, Joong-Ki, Dewhirst, Floyd E., Segata, Nicola, Bullman, Susan, Johnston, Christopher D.

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Next generation community assessment of biomedical entity recognition web servers: metrics, performance, interoperability aspects of BeCalm von Pérez-Pérez, Martin, Pérez-Rodríguez, Gael, Blanco-Míguez, Aitor, Fdez-Riverola, Florentino, Valencia, Alfonso, Krallinger, Martin, Lourenço, Anália

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