MetaMLST: multi-locus strain-level bacterial typing from metagenomic samples

por Zolfo, Moreno, Tett, Adrian, Jousson, Olivier, Donati, Claudio, Segata, Nicola
Publicado 2017

Profiling microbial strains in urban environments using metagenomic sequencing data

por Zolfo, Moreno, Asnicar, Francesco, Manghi, Paolo, Pasolli, Edoardo, Tett, Adrian, Segata, Nicola
Publicado 2018

Metagenomic Sequencing with Strain-Level Resolution Implicates Uropathogenic E. coli in Necrotizing Enterocolitis and Mortality in Preterm Infants

por Ward, Doyle V., Scholz, Matthias, Zolfo, Moreno, Taft, Diana H., Schibler, Kurt R., Tett, Adrian, Segata, Nicola, Morrow, Ardythe L.
Publicado 2016

Draft Genome Sequence of the Planktic Cyanobacterium Tychonema bourrellyi, Isolated from Alpine Lentic Freshwater

por Pinto, Federica, Tett, Adrian, Armanini, Federica, Asnicar, Francesco, Boscaini, Adriano, Pasolli, Edoardo, Zolfo, Moreno, Donati, Claudio, Salmaso, Nico, Segata, Nicola
Publicado 2017

Draft Genome Sequences of Novel Pseudomonas, Flavobacterium, and Sediminibacterium Species Strains from a Freshwater Ecosystem

por Pinto, Federica, Tett, Adrian, Armanini, Federica, Asnicar, Francesco, Boscaini, Adriano, Pasolli, Edoardo, Zolfo, Moreno, Donati, Claudio, Salmaso, Nico, Segata, Nicola
Publicado 2018

Correction for Pinto et al., “Draft Genome Sequences of Novel Pseudomonas, Flavobacterium, and Sediminibacterium Strains from a Freshwater Ecosystem”

por Pinto, Federica, Tett, Adrian, Armanini, Federica, Asnicar, Francesco, Boscaini, Adriano, Pasolli, Edoardo, Zolfo, Moreno, Donati, Claudio, Salmaso, Nico, Segata, Nicola
Publicado 2018

Studying Vertical Microbiome Transmission from Mothers to Infants by Strain-Level Metagenomic Profiling

por Asnicar, Francesco, Manara, Serena, Zolfo, Moreno, Truong, Duy Tin, Scholz, Matthias, Armanini, Federica, Ferretti, Pamela, Gorfer, Valentina, Pedrotti, Anna, Tett, Adrian, Segata, Nicola
Publicado 2017

Microbial genomes from non-human primate gut metagenomes expand the primate-associated bacterial tree of life with over 1000 novel species

por 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
Publicado 2019

Automated identification of sequence-tailored Cas9 proteins using massive metagenomic data

por Ciciani, Matteo, Demozzi, Michele, Pedrazzoli, Eleonora, Visentin, Elisabetta, Pezzè, Laura, Signorini, Lorenzo Federico, Blanco-Miguez, Aitor, Zolfo, Moreno, Asnicar, Francesco, Casini, Antonio, Cereseto, Anna, Segata, Nicola
Publicado 2022

Strong oral plaque microbiome signatures for dental implant diseases identified by strain-resolution metagenomics

por Ghensi, Paolo, Manghi, Paolo, Zolfo, Moreno, Armanini, Federica, Pasolli, Edoardo, Bolzan, Mattia, Bertelle, Alberto, Dell’Acqua, Federico, Dellasega, Ester, Waldner, Romina, Tessarolo, Francesco, Tomasi, Cristiano, Segata, Nicola
Publicado 2020

Longitudinal survey of microbiome associated with particulate matter in a megacity

por Qin, Nan, Liang, Peng, Wu, Chunyan, Wang, Guanqun, Xu, Qian, Xiong, Xiao, Wang, Tingting, Zolfo, Moreno, Segata, Nicola, Qin, Huanlong, Knight, Rob, Gilbert, Jack A., Zhu, Ting F.
Publicado 2020

Unexplored diversity and strain-level structure of the skin microbiome associated with psoriasis

por 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
Publicado 2017

Precise phylogenetic analysis of microbial isolates and genomes from metagenomes using PhyloPhlAn 3.0

por 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
Publicado 2020

Extensive Unexplored Human Microbiome Diversity Revealed by Over 150,000 Genomes from Metagenomes Spanning Age, Geography, and Lifestyle

por 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
Publicado 2019

Integrating taxonomic, functional, and strain-level profiling of diverse microbial communities with bioBakery 3

por 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
Publicado 2021

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

por 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
Publicado 2021

Analysis of 1321 Eubacterium rectale genomes from metagenomes uncovers complex phylogeographic population structure and subspecies functional adaptations

por 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
Publicado 2020

MetaPhlAn 4 profiling of unknown species-level genome bins improves the characterization of diet-associated microbiome changes in mice

por 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
Publicado 2023

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

por 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
Publicado 2023

The Prevotella copri Complex Comprises Four Distinct Clades Underrepresented in Westernized Populations

por Tett, Adrian, Huang, Kun D., Asnicar, Francesco, Fehlner-Peach, Hannah, Pasolli, Edoardo, Karcher, Nicolai, Armanini, Federica, Manghi, Paolo, Bonham, Kevin, Zolfo, Moreno, De Filippis, Francesca, Magnabosco, Cara, Bonneau, Richard, Lusingu, John, Amuasi, John, Reinhard, Karl, Rattei, Thomas, Boulund, Fredrik, Engstrand, Lars, Zink, Albert, Collado, Maria Carmen, Littman, Dan R., Eibach, Daniel, Ercolini, Danilo, Rota-Stabelli, Omar, Huttenhower, Curtis, Maixner, Frank, Segata, Nicola
Publicado 2019