Manghi, Paolo
Manghi, Paolo
A distinct Fusobacterium nucleatum clade dominates the colorectal cancer niche
2024-01-01 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.
Accessible, curated metagenomic data through ExperimentHub
2017-01-01 Pasolli, Edoardo; Schiffer, Lucas Michael; 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
Altered fecal small RNA profiles in colorectal cancer reflect gut microbiome composition in stool samples
2019-01-01 Tarallo, S.; Ferrero, G.; Gallo, G.; Francavilla, A.; Clerico, G.; Luc, A. R.; Manghi, P.; Thomas, A. M.; Vineis, P.; Segata, N.; Pardini, B.; Naccarati, A.; Cordero, F.
Analysis of 1321 Eubacterium rectale genomes from metagenomes uncovers complex phylogeographic population structure and subspecies functional adaptations
2020-01-01 Karcher, Nicolai; Pasolli, Edoardo; Asnicar, Francesco; Huang, Kun D.; Tett, Adrian; Manara, Serena; Armanini, Federica; Bain, Debbie; Duncan, Sylvia H.; Louis, Petra; Zolfo, Moreno; Manghi, Paolo; Valles-Colomer, Mireia; Raffaetà, Roberta; Rota-Stabelli, Omar; Collado, Maria Carmen; Zeller, Georg; Falush, Daniel; Maixner, Frank; Walker, Alan W.; Huttenhower, Curtis; Segata, Nicola
Coffee consumption is associated with intestinal Lawsonibacter asaccharolyticus abundance and prevalence across multiple cohorts
2024-01-01 Manghi, Paolo; Bhosle, Amrisha; Wang, Kai; Marconi, Roberta; Selma-Royo, Marta; Ricci, Liviana; Asnicar, Francesco; Golzato, Davide; Ma, Wenjie; Hang, Dong; Thompson, Kelsey N.; Franzosa, Eric A.; Nabinejad, Amir; Tamburini, Sabrina; Rimm, Eric B.; Garrett, Wendy S.; Sun, Qi; Chan, Andrew T.; Valles-Colomer, Mireia; Arumugam, Manimozhiyan; Bermingham, Kate M.; Giordano, Francesca; Davies, Richard; Hadjigeorgiou, George; Wolf, Jonathan; Strowig, Till; Berry, Sarah E.; Huttenhower, Curtis; Spector, Tim D.; Segata, Nicola; Song, Mingyang
Cross-cohort gut microbiome associations with immune checkpoint inhibitor response in advanced melanoma
2022-01-01 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
Detecting contamination in viromes using ViromeQC
2019-01-01 Zolfo, Moreno; Pinto, Federica; Asnicar, Francesco; Manghi, Paolo; Tett, Adrian; Bushman, Frederic D; Segata, Nicola
Extending and improving metagenomic taxonomic profiling with uncharacterized species using MetaPhlAn 4
2023-01-01 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
Extension of the Segatella copri complex to 13 species with distinct large extrachromosomal elements and associations with host conditions
2023-01-01 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; Strowig, Till
Extensive Unexplored Human Microbiome Diversity Revealed by Over 150,000 Genomes from Metagenomes Spanning Age, Geography, and Lifestyle
2019-01-01 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
Favorable subgingival plaque microbiome shifts are associated with clinical treatment for peri-implant diseases
2024-01-01 Bazzani, Davide; Heidrich, Vitor; Manghi, Paolo; Blanco-Miguez, Aitor; Asnicar, Francesco; Armanini, Federica; Cavaliere, Sara; Bertelle, Alberto; Dell'Acqua, Federico; Dellasega, Ester; Waldner, Romina; Vicentini, Daniela; Bolzan, Mattia; Tomasi, Cristiano; Segata, Nicola; Pasolli, Edoardo; Ghensi, Paolo
Genomic diversity and ecology of human-associated Akkermansia species in the gut microbiome revealed by extensive metagenomic assembly
2021-01-01 Karcher, N.; Nigro, E.; Puncochar, M.; Blanco-Miguez, A.; Ciciani, M.; Manghi, P.; Zolfo, M.; Cumbo, F.; Manara, S.; Golzato, D.; Cereseto, A.; Arumugam, M.; Bui, T. P. N.; Tytgat, H. L. P.; Valles-Colomer, M.; de Vos, W. M.; Segata, N.
Hallstatt miners consumed blue cheese and beer during the Iron Age and retained a non-Westernized gut microbiome until the Baroque period
2021-01-01 Maixner, Frank; Sarhan, Mohamed S; Huang, Kun D; Tett, Adrian; Schoenafinger, Alexander; Zingale, Stefania; Blanco-Míguez, Aitor; Manghi, Paolo; Cemper-Kiesslich, Jan; Rosendahl, Wilfried; Kusebauch, Ulrike; Morrone, Seamus R; Hoopmann, Michael R; Rota-Stabelli, Omar; Rattei, Thomas; Moritz, Robert L; Oeggl, Klaus; Segata, Nicola; Zink, Albert; Reschreiter, Hans; Kowarik, Kerstin
Integrating taxonomic, functional, and strain-level profiling of diverse microbial communities with bioBakery 3
2021-01-01 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
Intestinal Blastocystis is linked to healthier diets and more favorable cardiometabolic outcomes in 56,989 individuals from 32 countries
2024-01-01 Piperni, Elisa; Nguyen, Long H.; Manghi, Paolo; Kim, Hanseul; Pasolli, Edoardo; Andreu-Sánchez, Sergio; Arrè, Alberto; Bermingham, Kate M.; Blanco-Míguez, Aitor; Manara, Serena; Valles-Colomer, Mireia; Bakker, Elco; Busonero, Fabio; Davies, Richard; Fiorillo, Edoardo; Giordano, Francesca; Hadjigeorgiou, George; Leeming, Emily R.; Lobina, Monia; Masala, Marco; Maschio, Andrea; Mciver, Lauren J.; Pala, Mauro; Pitzalis, Maristella; Wolf, Jonathan; Fu, Jingyuan; Zhernakova, Alexandra; Cacciò, Simone M.; Cucca, Francesco; Berry, Sarah E.; Ercolini, Danilo; Chan, Andrew T.; Huttenhower, Curtis; Spector, Tim D.; Segata, Nicola; Asnicar, Francesco
Large-scale meta-analytic approaches for systematic and reproducible associations between the human microbiome and host's conditions
2022-10-13 Manghi, Paolo
Longitudinal gut microbiome changes in immune checkpoint blockade-treated advanced melanoma
2024-01-01 Björk, Johannes R.; Bolte, Laura A.; Maltez Thomas, Andrew; Lee, Karla A.; Rossi, Niccolo; Wind, Thijs T.; Smit, Lotte M.; Armanini, Federica; Asnicar, Francesco; Blanco-Miguez, Aitor; Board, Ruth; Calbet-Llopart, Neus; Derosa, Lisa; Dhomen, Nathalie; Brooks, Kelly; Harland, Mark; Harries, Mark; 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; Waldron, Levi; Zitvogel, Laurence; Zolfo, Moreno; de Vries, Elisabeth G. E.; Nathan, Paul; Fehrmann, Rudolf S. N.; Spector, Tim D.; Bataille, Véronique; Segata, Nicola; Hospers, Geke A. P.; Weersma, Rinse K.
Maternal and food microbial sources shape the infant microbiome of a rural Ethiopian population
2023-01-01 Manara, Serena; Selma-Royo, Marta; Huang, Kun D; Asnicar, Francesco; Armanini, Federica; Blanco-Miguez, Aitor; Cumbo, Fabio; Golzato, Davide; Manghi, Paolo; Pinto, Federica; Valles-Colomer, Mireia; Amoroso, Loredana; Corrias, Maria Valeria; Ponzoni, Mirco; Raffaetà, Roberta; Cabrera-Rubio, Raul; Olcina, Mari; Pasolli, Edoardo; Collado, Maria Carmen; Segata, Nicola
Meta-analysis of fecal metagenomes reveals global microbial signatures that are specific for colorectal cancer
2019-01-01 Wirbel, Jakob; Pyl, Paul Theodor; Kartal, Ece; Zych, Konrad; Kashani, Alireza; Milanese, Alessio; Fleck, Jonas S.; Voigt, Anita Y.; Palleja, Albert; Ponnudurai, Ruby; Sunagawa, Shinichi; Coelho, Luis Pedro; Schrotz-King, Petra; Vogtmann, Emily; Habermann, Nina; Niméus, Emma; Thomas, Andrew M.; Manghi, Paolo; Gandini, Sara; Serrano, Davide; Mizutani, Sayaka; Shiroma, Hirotsugu; Shiba, Satoshi; Shibata, Tatsuhiro; Yachida, Shinichi; Yamada, Takuji; Waldron, Levi; Naccarati, Alessio; Segata, Nicola; Sinha, Rashmi; Ulrich, Cornelia M.; Brenner, Hermann; Arumugam, Manimozhiyan; Bork, Peer; Zeller, Georg
Metagenomic analysis of ancient dental calculus reveals unexplored diversity of oral archaeal Methanobrevibacter
2021-01-01 Granehäll, Lena; Huang, Kun D.; Tett, Adrian; Manghi, Paolo; Paladin, Alice; O’Sullivan, Niall; Rota-Stabelli, Omar; Segata, Nicola; Zink, Albert; Maixner, Frank